FAIRsharing.chmyvk; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:12 p.m.

Other names: BLAT Format

BLAT is a multiple algorithms developed for the analysis and comparison of biological sequences such as DNA, RNA and proteins.

Webpage:

http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign

Licence:

Name: Kent Informatics License - required for commercial use
URL: http://www.kentinformatics.com

Publications:

Publications
More detailed information about this field from each metasource.

BLAT--the BLAST-like alignment tool
PMID: 11932250
metasource: Fairsharing.org
version: FAIRsharing.org: BLAT Format; BLAST-like Alignment Tool Format; DOI: https://doi.org/10.25504/FAIRsharing.chmyvk; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Jan 03 2022 7:12 p.m.

BLAT--the BLAST-like alignment tool PubMed citations: 4200.

4200 articles citing: BLAT--the BLAST-like alignment tool

Complete genome sequencing and investigation on the fiber-degrading potential of Bacillus amyloliquefaciens strain TL106 from the tibetan pig. PMID:35906551
Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species. PMID:35895167
Exceptional diversity and selection pressure on coronavirus host receptors in bats compared to other mammals. PMID:35892217
Screening of Genes Related to Sex Determination and Differentiation in Mandarin Fish (Siniperca chuatsi). PMID:35887035
REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. PMID:35886794
Identification of fusions with potential clinical significance in melanoma. PMID:35871080
Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study. PMID:35865473
Phylogeographical Pattern and Population Evolution History of Indigenous Elymus sibiricus L. on Qinghai-Tibetan Plateau. PMID:35845670
Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp. PMID:35835759
Turnover in Life-Strategies Recapitulates Marine Microbial Succession Colonizing Model Particles. PMID:35814698
Chromosome-level assembly and annotation of the blue catfish Ictalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies. PMID:35809049
Retrospective Natural History Study of RPGR-Related Cone- and Cone-Rod Dystrophies While Expanding the Mutation Spectrum of the Disease. PMID:35806195
Differential Transcriptional Responses in Two Old World Bemisia tabaci Cryptic Species Post Acquisition of Old and New World Begomoviruses. PMID:35805143
Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs. PMID:35796972
Computational Methods for the Discovery and Annotation of Viral Integrations. PMID:35796971
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. PMID:35789323
Complex Feline Disease Mapping Using a Dense Genotyping Array. PMID:35782544
Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data. PMID:35765182
Along the Bos taurus genome, uncover candidate imprinting control regions. PMID:35764919
A chromosome-level genome of Brachymystax tsinlingensis provides resources and insights into salmonids evolution. PMID:35758619
A Novel miRNA Located in the HER2 Gene Shows an Inhibitory Effect on Wnt Signaling and Cell Cycle Progression. PMID:35747498
Population Scale Analysis of Centromeric Satellite DNA Reveals Highly Dynamic Evolutionary Patterns and Genomic Organization in Long-Tailed and Rhesus Macaques. PMID:35741082
The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis. PMID:35733792
Chromosomal Translocation t(5;12)(p13;q14) Leading to Fusion of High-mobility Group AT-hook 2 Gene With Intergenic Sequences From Chromosome Sub-Band 5p13.2 in Benign Myoid Neoplasms of the Breast: A Second Case. PMID:35732319
Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. PMID:35729321
Human follicular mites: Ectoparasites becoming symbionts. PMID:35724423
Expansion of a retrovirus lineage in the koala genome. PMID:35696585
Repetitive Elements, Sequence Turnover and Cyto-Nuclear Gene Transfer in Gymnosperm Mitogenomes. PMID:35692831
Taxonomy, comparative genomics and evolutionary insights of Penicillium ucsense: a novel species in series Oxalica. PMID:35678932
Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome. PMID:35676699
Deep Sequencing Analysis of Individual HIV-1 Proviruses Reveals Frequent Asymmetric Long Terminal Repeats. PMID:35674431
Genetic and genomic architecture of species-specific cuticular hydrocarbon variation in parasitoid wasps. PMID:35673870
Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry. PMID:35666193
Genome-wide specificity of plant genome editing by both CRISPR-Cas9 and TALEN. PMID:35665758
Semi-subterranean environment and soil metagenomic datasets of the Gyeongju Seokbinggo (stone ice storage) in South Korea. PMID:35664653
Intron losses and gains in the nematodes. PMID:35659725
First Chromosome-Scale Assembly and Deep Floral-Bud Transcriptome of a Male Kiwifruit. PMID:35651931
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation. PMID:35646390
Computationally designed hyperactive Cas9 enzymes. PMID:35641498
mebipred: identifying metal binding potential in protein sequence. PMID:35639953
Chromosome-level genome assembly of the black widow spider Latrodectus elegans illuminates composition and evolution of venom and silk proteins. PMID:35639632
Phyloepigenetics. PMID:35625482
Revealing diverse alternative splicing variants of the highly homologous SMN1 and SMN2 genes by targeted long-read sequencing. PMID:35612622
Chromosome-scale genome assembly of an important medicinal plant honeysuckle. PMID:35610245
Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis. PMID:35605198
The assembled and annotated genome of the masked palm civet (Paguma larvata). PMID:35583674
Genome-Based Analysis of Aspergillus niger Aggregate Species from China and Their Potential for Fumonisin B2 and Ochratoxin A Production. PMID:35579721
Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions. PMID:35557718
Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models. PMID:35538082
Nitrogen fixation and other biogeochemically important features of Atacama Desert giant horsetail plant microbiomes inferred from metagenomic contig analysis. PMID:35533355
Genes and evolutionary fates of the amanitin biosynthesis pathway in poisonous mushrooms. PMID:35533275
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species. PMID:35524165
EBV genome variations enhance clinicopathological features of nasopharyngeal carcinoma in a non-endemic region. PMID:35485636
Evolution of coastal forests based on a full set of mangrove genomes. PMID:35484219
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding. PMID:35482491
KmerKeys: a web resource for searching indexed genome assemblies and variants. PMID:35474383
A Chromosome-Level Reference Genome of Chinese Balloon Flower (Platycodon grandiflorus). PMID:35464833
Intraspecific de novo gene birth revealed by presence-absence variant genes in Caenorhabditis elegans. PMID:35464238
Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics. PMID:35456378
Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. PMID:35440598
Open reading frame dominance indicates protein-coding potential of RNAs. PMID:35438231
Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds. PMID:35437972
Assessing the Effect of Smokeless Tobacco Consumption on Oral Microbiome in Healthy and Oral Cancer Patients. PMID:35433507
A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation. PMID:35418663
Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine. PMID:35415013
Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila. PMID:35413957
Using iRNA-seq analysis to predict gene expression regulatory level and activity in Zea mays tissues. PMID:35404453
Relationship between nitrifying microorganisms and other microorganisms residing in the maize rhizosphere. PMID:35394234
The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions. PMID:35392808
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl. PMID:35383847
RNA aptamers specific for transmembrane p24 trafficking protein 6 and Clusterin for the targeted delivery of imaging reagents and RNA therapeutics to human β cells. PMID:35383192
Accurate detection of tumor-specific gene fusions reveals strongly immunogenic personal neo-antigens. PMID:35379963
A generalist-specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range. PMID:35377798
Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction. PMID:35373735
Beyond Genes: Inclusion of Alternative Splicing and Alternative Polyadenylation to Assess the Genetic Architecture of Predisposition to Voluntary Alcohol Consumption in Brain of the HXB/BXH Recombinant Inbred Rat Panel. PMID:35368676
Linking genomic and epidemiologic information to advance the study of COVID-19. PMID:35354824
Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens. PMID:35342556
The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features. PMID:35333302
Global mapping of RNA homodimers in living cells. PMID:35332098
Original Leaf Colonisers Shape Fungal Decomposer Communities of Phragmites australis in Intermittent Habitats. PMID:35330286
Host-Species Variation and Environment Influence Endophyte Symbiosis and Mycotoxin Levels in Chinese Oxytropis Species. PMID:35324678
ADARs act as potent regulators of circular transcriptome in cancer. PMID:35314703
Ethylene Response Factor109 Attunes Immunity, Photosynthesis, and Iron Homeostasis in Arabidopsis Leaves. PMID:35310669
A point mutation in HIV-1 integrase redirects proviral integration into centromeric repeats. PMID:35304442
Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing. PMID:35294336
PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2. PMID:35288589
Comprehensive RNA dataset of tissue and plasma from patients with esophageal cancer or precursor lesions. PMID:35288573
Dissection of molecular and histological subtypes of papillary thyroid cancer using alternative splicing profiles. PMID:35277656
Exome sequencing identifies variants in infants with sacral agenesis. PMID:35274497
Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis. PMID:35273169
Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron. PMID:35266513
The evolution, evolvability and engineering of gene regulatory DNA. PMID:35264797
Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. PMID:35260071
Transposon insertions regulate genome-wide allele-specific expression and underpin flower colour variations in apple (Malus spp.). PMID:35258172
Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources. PMID:35255079
ExceS-A: an exon-centric split aligner. PMID:35254744
Genome-Wide Methylation Profiling in the Thalamus of Scrapie Sheep. PMID:35252421
Landscape of adenosine-to-inosine RNA recoding across human tissues. PMID:35246538
Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs. PMID:35244721
Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma. PMID:35243413
Conservation of chromatin conformation in carnivores. PMID:35217621
Transcriptomic Analysis Suggests Auxin Regulation in Dorsal-Ventral Petal Asymmetry of Wild Progenitor Sinningia speciosa. PMID:35216188
Characterizing mobile element insertions in 5675 genomes. PMID:35212372
A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs. PMID:35211148
Comparison of Immune Checkpoint Molecules PD-1 and PD-L1 in Paired Primary and Recurrent Glioma: Increasing Trend When Recurrence. PMID:35204029
Background splicing as a predictor of aberrant splicing in genetic disease. PMID:35188075
Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution. PMID:35186789
Comparative genomics analysis of bHLH genes in cucurbits identifies a novel gene regulating cucurbitacin biosynthesis. PMID:35184192
Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells. PMID:35180378
Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat. PMID:35172813
Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. PMID:35168652
Association of Tandem Repeat Number Variabilities in Subunit S of the Type I Restriction-Modification System with Macrolide Resistance in Mycoplasma pneumoniae. PMID:35160167
High Stability of the Epigenome in Drosophila Interspecific Hybrids. PMID:35143649
Multiple phylogenetically-diverse, differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand. PMID:35143500
Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. PMID:35139817
Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. PMID:35135349
WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. PMID:35134929
Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut. PMID:35134055
A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia. PMID:35132310
A Chromosome-Level Genome Assembly of Yellowtail Kingfish (Seriola lalandi). PMID:35126476
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. PMID:35115520
Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892). PMID:35100986
Dysgu: efficient structural variant calling using short or long reads. PMID:35100420
Evolution of DNA Methylation Across Ecdysozoa. PMID:35089376
Chromosome-Level Genome Assembly of a Human Fungal Pathogen Reveals Synteny among Geographically Distinct Species. PMID:35089059
Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource. PMID:35078504
Mitochondrial DNA variation across 56,434 individuals in gnomAD. PMID:35074858
Genome sequence data of the antagonistic soil-borne yeast Cyberlindnera sargentensis (SHA 17.2). PMID:35071701
Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.). PMID:35069651
Genomically Hardwired Regulation of Gene Activity Orchestrates Cellular Iron Homeostasis in Arabidopsis. PMID:35067184
A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex. PMID:35064146
No link between population isolation and speciation rate in squamate reptiles. PMID:35058358
Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications. PMID:35052465
Trade-off between sex and growth in diatoms: Molecular mechanisms and demographic implications. PMID:35044817
The Barley and Wheat Pan-Genomes. PMID:35037204
Circulating T-Cell Repertoires Correlate With the Tumor Response in Patients With Breast Cancer Receiving Neoadjuvant Chemotherapy. PMID:35025620
De novo mutations identified by whole-genome sequencing implicate chromatin modifications in obsessive-compulsive disorder. PMID:35020433
Long-read nanopore DNA sequencing can resolve complex intragenic duplication/deletion variants, providing information to enable preimplantation genetic diagnosis. PMID:35014072
Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data. PMID:35013600
The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain. PMID:34993013
Metatranscriptome Profiling of a Specialized Microbial Consortium during the Degradation of Nixtamalized Maize Pericarp. PMID:34985337
The Dark Side of Microbial Processes: Accumulation of Nitrate During Storage of Surface Water in the Dark and the Underlying Mechanism. PMID:34985332
CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo. PMID:34980913
Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans. PMID:34969986
Genetic and Molecular Characterization of a Self-Compatible Brassica rapa Line Possessing a New Class II S Haplotype. PMID:34961286
Identification of starch candidate genes using SLAF-seq and BSA strategies and development of related SNP-CAPS markers in tetraploid potato. PMID:34932571
Genomic analysis of Elsinoë arachidis reveals its potential pathogenic mechanism and the biosynthesis pathway of elsinochrome toxin. PMID:34914789
Uncovering the Role of Gut Microbiota in Amino Acid Metabolic Disturbances in Heart Failure Through Metagenomic Analysis. PMID:34912870
Evaluation of accessible regions of Escherichia coli fimH mRNA through computational prediction and experimental investigation. PMID:34900163
Identification of Novel Regulatory Regions Induced by Intrauterine Growth Restriction in Rat Islets. PMID:34894232
Epigenetic Dysregulation of KCNK9 Imprinting and Triple-Negative Breast Cancer. PMID:34885139
Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. PMID:34875081
Medium levels of transcription and replication related chromosomal instability are associated with poor clinical outcome. PMID:34873180
Transcriptome Analysis Reveals Higher Levels of Mobile Element-Associated Abnormal Gene Transcripts in Temporal Lobe Epilepsy Patients. PMID:34868252
ChiTaH: a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data. PMID:34859212
Error-prone, stress-induced 3' flap-based Okazaki fragment maturation supports cell survival. PMID:34855483
Rare and potentially pathogenic variants in hydroxycarboxylic acid receptor genes identified in breast cancer cases. PMID:34852802
Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. PMID:34849810
MammaPrint and BluePrint comprehensively capture the cancer hallmarks in early-stage breast cancer patients. PMID:34841595
Baiting out a full length sequence from unmapped RNA-seq data. PMID:34837950
Chloranthus genome provides insights into the early diversification of angiosperms. PMID:34836973
Origins and Function of VL30 lncRNA Packaging in Small Extracellular Vesicles: Implications for Cellular Physiology and Pathology. PMID:34829970
Plastome sequencing reveals phylogenetic relationships among Comastoma and related taxa (Gentianaceae) from the Qinghai-Tibetan Plateau. PMID:34824809
Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae). PMID:34814832
Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites. PMID:34809466
InsectBase 2.0: a comprehensive gene resource for insects. PMID:34792158
The U1 snRNP component RBP45d regulates temperature-responsive flowering in Arabidopsis. PMID:34791475
A Rapid Evolving microRNA Cluster Rewires Its Target Regulatory Networks in Drosophila. PMID:34777478
Massively parallel DNA target capture using long adapter single stranded oligonucleotide (LASSO) probes assembled through a novel DNA recombinase mediated methodology. PMID:34775678
PCR Primer Design for the Rapidly Evolving SARS-CoV-2 Genome. PMID:34773624
Genome-wide survey and characterization of transcription factors in the silk gland of the silkworm, Bombyx mori. PMID:34762712
Shotgun metagenomics evaluation of soil fertilization effect on the rhizosphere viral community of maize plants. PMID:34762236
Resolving the Microalgal Gene Landscape at the Strain Level: a Novel Hybrid Transcriptome of Emiliania huxleyi CCMP3266. PMID:34757817
Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization. PMID:34754629
CSC software corrects off-target mediated gRNA depletion in CRISPR-Cas9 essentiality screens. PMID:34753924
SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA. PMID:34745213
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. PMID:34737427
Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data. PMID:34737285
Transposable elements that have recently been mobile in the human genome. PMID:34732136
Uncovering Bleomycin-Induced Genomic Alterations and Underlying Mechanisms in the Yeast Saccharomyces cerevisiae. PMID:34731050
Genome-Wide Identification of Tomato Xylem Sap Fitness Factors for Three Plant-Pathogenic Ralstonia Species. PMID:34726495
Phylogenomics of Salvia L. subgenus Calosphace (Lamiaceae). PMID:34721456
Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols. PMID:34714886
RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment. PMID:34694603
MINTIA: a metagenomic INserT integrated assembly and annotation tool. PMID:34692239
Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals. PMID:34692118
MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data. PMID:34686194
An Emiliania huxleyi pan-transcriptome reveals basal strain specificity in gene expression patterns. PMID:34675226
High-quality genome assembly of an important biodiesel plant, Euphorbia lathyris L. PMID:34664644
Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. PMID:34662416
Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae. PMID:34659355
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database. PMID:34643708
Chromosomal-Level Genome Assembly of a True Bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae). PMID:34623414
Chemical Inhibition of Apurinic-Apyrimidinic Endonuclease 1 Redox and DNA Repair Functions Affects the Inflammatory Response via Different but Overlapping Mechanisms. PMID:34616737
High-Quality de novo Chromosome-Level Genome Assembly of a Single Bombyx mori With BmNPV Resistance by a Combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing. PMID:34603381
RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis. PMID:34597582
Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish. PMID:34594040
Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq. PMID:34589103
The Euscaphis japonica genome and the evolution of malvids. PMID:34587334
The genome of the naturally evolved obesity-prone Ossabaw miniature pig. PMID:34585119
Transcriptomic profile of leg muscle during early growth and development in Haiyang yellow chicken. PMID:34584942
The genomic basis of army ant chemosensory adaptations. PMID:34582590
De Novo Genome Assembly of the Electric Fish Brachyhypopomus occidentalis (Hypopomidae, Gymnotiformes). PMID:34581791
Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness. PMID:34578455
Patterns of Coevolutionary Adaptations across Time and Space in Mouse Gammaretroviruses and Three Restrictive Host Factors. PMID:34578445
Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories. PMID:34573413
Prognostic Roles of BRAF, KIT, NRAS, IGF2R and SF3B1 Mutations in Mucosal Melanomas. PMID:34571863
Tiara: Deep learning-based classification system for eukaryotic sequences. PMID:34570171
Genome assembly of primitive cultivated potato Solanum stenotomum provides insights into potato evolution. PMID:34568923
Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics. PMID:34563039
Protein-coding repeat polymorphisms strongly shape diverse human phenotypes. PMID:34554798
Characterization of the complete chloroplast genome of Hordeum jubatum (Poaceae: Pooideae: Triticeae) and phylogenetic analysis. PMID:34553047
Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. PMID:34547909
Genome-wide detection and classification of terpene synthase genes in Aquilaria agallochum. PMID:34539112
Genomic Epidemiology and Strain Taxonomy of Corynebacterium diphtheriae. PMID:34524891
Phylogeographic analysis delimits three evolutionary significant units of least chipmunks in North America and identifies unique genetic diversity within the imperiled Peñasco population. PMID:34522364
Genome and transcriptome assemblies of the kuruma shrimp, Marsupenaeus japonicus. PMID:34515781
Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome. PMID:34512724
A near complete genome for goat genetic and genomic research. PMID:34507524
Gender-Dependent Deregulation of Linear and Circular RNA Variants of HOMER1 in the Entorhinal Cortex of Alzheimer's Disease. PMID:34502114
Genomic insights into the origin, domestication and diversification of Brassica juncea. PMID:34493868
Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing. PMID:34493830
Genomic anatomy of male-specific microchromosomes in a gynogenetic fish. PMID:34491994
A chromosome-level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating. PMID:34486812
Recombination Marks the Evolutionary Dynamics of a Recently Endogenized Retrovirus. PMID:34480565
A Bayesian approach for accurate de novo transcriptome assembly. PMID:34480063
Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome. PMID:34480029
Molecular and functional profiling identifies therapeutically targetable vulnerabilities in plasmablastic lymphoma. PMID:34465776
Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution. PMID:34465765
Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. PMID:34465761
Highly susceptible SARS-CoV-2 model in CAG promoter-driven hACE2-transgenic mice. PMID:34463644
Evidence for and localization of proposed causative variants in cattle and pig genomes. PMID:34461824
The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution. PMID:34460814
Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells. PMID:34458728
Aptamer-mediated transcriptional gene silencing of Fox p 3 inhibits regulatory T cells and potentiates antitumor response. PMID:34457999
The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing. PMID:34454585
A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD-Pass. PMID:34452438
Technology dictates algorithms: recent developments in read alignment. PMID:34446078
Transcriptional Regulation of RUNX1: An Informatics Analysis. PMID:34440349
Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case. PMID:34439964
Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes. PMID:34395586
Genome-Wide Association Study of Root and Shoot Related Traits in Spring Soybean (Glycine max L.) at Seedling Stages Using SLAF-Seq. PMID:34394134
Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles. PMID:34385515
nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over. PMID:34383887
Cancer cells are highly susceptible to accumulation of templated insertions linked to MMBIR. PMID:34379776
Nanopore sequencing of brain-derived full-length circRNAs reveals circRNA-specific exon usage, intron retention and microexons. PMID:34376658
Exome sequencing of child-parent trios with bladder exstrophy: Findings in 26 children. PMID:34355505
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. PMID:34354050
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. PMID:34353948
Evidence that toxin resistance in poison birds and frogs is not rooted in sodium channel mutations and may rely on "toxin sponge" proteins. PMID:34351379
Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae. PMID:34336405
Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L. PMID:34332553
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs (Sus-scrofa). PMID:34314293
A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.). PMID:34303361
Accurate spliced alignment of long RNA sequencing reads. PMID:34302453
Large palindromes on the primate X Chromosome are preserved by natural selection. PMID:34290043
Early-life social experience affects offspring DNA methylation and later life stress phenotype. PMID:34285226
An actin-related protein that is most highly expressed in Drosophila testes is critical for embryonic development. PMID:34282725
Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation. PMID:34281175
Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus). PMID:34270728
Large parental differences in chromatin organization in pancreatic beta cell line explaining diabetes susceptibility effects. PMID:34267199
Haplotype-resolved germline and somatic alterations in renal medullary carcinomas. PMID:34261517
Levenshtein Distance, Sequence Comparison and Biological Database Search. PMID:34257466
DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans. PMID:34257290
An epigenetic switch regulates the ontogeny of AXL-positive/EGFR-TKi-resistant cells by modulating miR-335 expression. PMID:34254585
GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. PMID:34253237
Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events. PMID:34250543
Dynamic partitioning of search patterns for approximate pattern matching using search schemes. PMID:34235407
Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. PMID:34226565
Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes. PMID:34223195
The complete mitochondrial genome of Osmanthus fragrans (Lamiales, Oleaceae) from China. PMID:34212096
High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility. PMID:34211458
Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity. PMID:34209383
The Influence of Soil Fertilization on the Distribution and Diversity of Phosphorus Cycling Genes and Microbes Community of Maize Rhizosphere Using Shotgun Metagenomics. PMID:34209356
DNA-RNA Hybrid (R-Loop): From a Unified Picture of the Mammalian Telomere to the Genome-Wide Profile. PMID:34205454
Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR. PMID:34202310
Plasmodium matutinum Causing Avian Malaria in Lovebirds (Agapornis roseicollis) Hosted in an Italian Zoo. PMID:34201448
NGS Methodologies and Computational Algorithms for the Prediction and Analysis of Plant Circular RNAs. PMID:34195961
Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. PMID:34193417
Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome. PMID:34193290
SINE jumping contributes to large-scale polymorphisms in the pig genomes. PMID:34183049
Acute Effects on the Human Peripheral Blood Transcriptome of Decompression Sickness Secondary to Scuba Diving. PMID:34177613
A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues. PMID:34172835
A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila. PMID:34161320
Mobile element insertions and associated structural variants in longitudinal breast cancer samples. PMID:34158539
Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. PMID:34156172
Gene Expression Modification by an Autosomal Inversion Associated With Three Male Mating Morphs. PMID:34149796
Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination. PMID:34146097
Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi. PMID:34146095
Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. PMID:34144992
Genome-wide analysis of European sea bass provides insights into the evolution and functions of single-exon genes. PMID:34141239
LIQA: long-read isoform quantification and analysis. PMID:34140043
The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution. PMID:34135482
Molecular classification and diagnostics of upper urinary tract urothelial carcinoma. PMID:34129823
Complete chloroplast genome of Alternanthera philoxeroides by de novo sequencing. PMID:34124357
A porcine brain-wide RNA editing landscape. PMID:34112917
SNP detection and population structure evaluation of Salix gordejevii Y. L. Chang et Skv. in Hunshandake Sandland, Inner Mongolia, China. PMID:34108824
Contiguous erosion of the inactive X in human pluripotency concludes with global DNA hypomethylation. PMID:34107261
Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia. PMID:34103329
SaQuant: a real-time PCR assay for quantitative assessment of Staphylococcus aureus. PMID:34103012
Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity. PMID:34099660
Wolfberry genomes and the evolution of Lycium (Solanaceae). PMID:34083720
Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence. PMID:34082735
High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata. PMID:34072027
Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome. PMID:34070911
Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning. PMID:34064595
Identification of A-to-I RNA editing profiles and their clinical relevance in lung adenocarcinoma. PMID:34050895
TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. PMID:34050351
Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden. PMID:34050156
Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement. PMID:34045708
Hardware Acceleration of Genomics Data Analysis: Challenges and Opportunities. PMID:34037688
Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species. PMID:34012463
Long non-coding RNAs and their targets as potential biomarkers in breast cancer. PMID:33991433
Transcriptomic Analysis of Skin Color in Anole Lizards. PMID:33988681
Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads. PMID:33987534
Tissue-specific activation of gene expression by the Synergistic Activation Mediator (SAM) CRISPRa system in mice. PMID:33986266
Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe. PMID:33986115
piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline. PMID:33985970
Comparative Analyses of Gibbon Centromeres Reveal Dynamic Genus-Specific Shifts in Repeat Composition. PMID:33983366
Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression. PMID:33978893
Impact of cropping systems on the functional diversity of rhizosphere microbial communities associated with maize plant: a shotgun approach. PMID:33973044
Pests, diseases, and aridity have shaped the genome of Corymbia citriodora. PMID:33972666
The cytochrome P450 (CYP) superfamily in cnidarians. PMID:33972594
Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. PMID:33971925
Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues. PMID:33958444
The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress. PMID:33957908
Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses. PMID:33944920
Comparative transcriptomic analysis highlights contrasting levels of resistance of Vitis vinifera and Vitis amurensis to Botrytis cinerea. PMID:33931625
Sex-Biased lncRNA Signature in Fetal Growth Restriction (FGR). PMID:33923632
Genetic Diversity and Population Structures in Chinese Miniature Pigs Revealed by SINE Retrotransposon Insertion Polymorphisms, a New Type of Genetic Markers. PMID:33921134
Targeting of the Essential acpP, ftsZ, and rne Genes in Carbapenem-Resistant Acinetobacter baumannii by Antisense PNA Precision Antibacterials. PMID:33921011
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. PMID:33920047
Identification and Characterization of Alternatively Spliced Transcript Isoforms of IRX4 in Prostate Cancer. PMID:33919200
Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase. PMID:33918244
Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere. PMID:33917127
Universal nomenclature for oxytocin-vasotocin ligand and receptor families. PMID:33911268
Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer. PMID:33910608
Single cell transcriptome sequencing on the Nanopore platform with ScNapBar. PMID:33906975
Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers. PMID:33902690
Sp1 is a substrate of Keap1 and regulates the activity of CRL4AWDR23 ubiquitin ligase toward Nrf2. PMID:33895141
Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. PMID:33893684
Increased expression of peptides from non-coding genes in cancer proteomics datasets suggests potential tumor neoantigens. PMID:33888849
The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation. PMID:33888695
Radiation-related genomic profile of papillary thyroid carcinoma after the Chernobyl accident. PMID:33888599
Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species. PMID:33883608
Complete genome sequence analysis of the peanut pathogen Ralstonia solanacearum strain Rs-P.362200. PMID:33874906
Functional and Pathological Roles of AHCY. PMID:33869213
Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms. PMID:33868290
ΔNp63 is a pioneer factor that binds inaccessible chromatin and elicits chromatin remodeling. PMID:33865440
Conserved long-range base pairings are associated with pre-mRNA processing of human genes. PMID:33863890
Effect of thermospermine on expression profiling of different gene using massive analysis of cDNA ends (MACE) and vascular maintenance in Arabidopsis. PMID:33854285
Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. PMID:33849527
A novel KCNQ4 gene variant (c.857A>G; p.Tyr286Cys) in an extended family with non‑syndromic deafness 2A. PMID:33846771
Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. PMID:33836575
A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome. PMID:33833373
Complete chloroplast genome of Zingiber mioga by de novo sequencing. PMID:33829093
Complete chloroplast genome and phylogenetic analysis of a wild grass, Hordeum roshevitzii Bowden. PMID:33829089
An EAV-HP insertion in the promoter region of SLCO1B3 has pleiotropic effects on chicken liver metabolism based on the transcriptome and proteome analysis. PMID:33828143
ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics. PMID:33827654
Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence. PMID:33824960
Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages. PMID:33822040
Characterization of Haemophilus Parasuis Serovar 2 CL120103, a Moderately Virulent Strain in China. PMID:33817086
Fast lightweight accurate xenograft sorting. PMID:33810805
Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges. PMID:33809937
Searching the Dark Genome for Alzheimer's Disease Risk Variants. PMID:33800766
The complete mitochondrial and plastid genomes of Rhododendron simsii, an important parent of widely cultivated azaleas. PMID:33796782
Plasmodium matutinum Transmitted by Culex pipiens as a Cause of Avian Malaria in Captive African Penguins (Spheniscus demersus) in Italy. PMID:33796578
The Physcomitrella patens chromatin adaptor PpMRG1 interacts with H3K36me3 and regulates light-responsive alternative splicing. PMID:33793927
Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals. PMID:33790324
Deciphering the transcriptomic regulation of heat stress responses in Nothofagus pumilio. PMID:33784314
Comprehensive identification of somatic nucleotide variants in human brain tissue. PMID:33781308
Primate innate immune responses to bacterial and viral pathogens reveals an evolutionary trade-off between strength and specificity. PMID:33771921
Long insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast. PMID:33768233
The complete mitochondrial genome of Aconitum kusnezoffii Rchb. (Ranales, Ranunculaceae). PMID:33763576
Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant. PMID:33757516
Nanopore Sequencing Indicates That Tandem Amplification of Chromosome 20q11.21 in Human Pluripotent Stem Cells Is Driven by Break-Induced Replication. PMID:33757297
High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids. PMID:33727392
Alvis: a tool for contig and read ALignment VISualisation and chimera detection. PMID:33726674
A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology. PMID:33712730
X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters. PMID:33710276
Hepatitis delta virus-like circular RNAs from diverse metazoans encode conserved hammerhead ribozymes. PMID:33708415
Revealing the active microbiome connected with the rhizosphere soil of maize plants in Ventersdorp, South Africa. PMID:33688297
Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms. PMID:33686438
riboCIRC: a comprehensive database of translatable circRNAs. PMID:33685493
Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks. PMID:33683357
Comparative analysis of chloroplast genomes of kenaf cytoplasmic male sterile line and its maintainer line. PMID:33674697
Metagenomic profiling of rhizosphere microbial community structure and diversity associated with maize plant as affected by cropping systems. PMID:33666787
A Spontaneous rapZ Mutant Impairs Infectivity of Lytic Bacteriophage vB_EcoM_JS09 against Enterotoxigenic Escherichia coli. PMID:33658278
CRISPR-SE: a brute force search engine for CRISPR design. PMID:33655210
The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids. PMID:33642574
Latent trait modeling of tau neuropathology in progressive supranuclear palsy. PMID:33635380
The complete mitochondrial genome of Glycyrrhiza uralensis Fisch. (Fabales, Leguminosae). PMID:33628894
Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika. PMID:33619328
Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7. PMID:33609314
Rare KMT2A-ELL and Novel ZNF56-KMT2A Fusion Genes in Pediatric T-cell Acute Lymphoblastic Leukemia. PMID:33608309
Optimization of scleroglucan production by Sclerotium rolfsii by lowering pH during fermentation via oxalate metabolic pathway manipulation using CRISPR/Cas9. PMID:33602329
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Improved contiguity of the threespine stickleback genome using long-read sequencing. PMID:33598708
Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees. PMID:33595436
A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes. PMID:33586292
Draft genome of the herbaceous bamboo Raddia distichophylla. PMID:33585868
Enrichment of Circular RNA Expression Deregulation at the Transition to Recurrent Spontaneous Seizures in Experimental Temporal Lobe Epilepsy. PMID:33584828
Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data. PMID:33575605
A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. PMID:33574576
Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp. PMID:33574498
A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. PMID:33568770
Flagellar Perturbations Activate Adhesion through Two Distinct Pathways in Caulobacter crescentus. PMID:33563824
Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile. PMID:33561170
Soil fertilization affects the abundance and distribution of carbon and nitrogen cycling genes in the maize rhizosphere. PMID:33555438
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. PMID:33539279
First finding of free-living representatives of Prokinetoplastina and their nuclear and mitochondrial genomes. PMID:33536456
Detecting High Scoring Local Alignments in Pangenome Graphs. PMID:33532821
Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development. PMID:33517348
Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk. PMID:33513090
A microbial gene catalog of anaerobic digestion from full-scale biogas plants. PMID:33506264
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. PMID:33505029
Identification and sequencing of 59 highly polymorphic microhaplotypes for analysis of DNA mixtures. PMID:33502549
A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed. PMID:33502491
Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera). PMID:33501983
The Compact Macronuclear Genome of the Ciliate Halteria grandinella: A Transcriptome-Like Genome with 23,000 Nanochromosomes. PMID:33500338
Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence. PMID:33493169
Unveiling the putative functional genes present in root-associated endophytic microbiome from maize plant using the shotgun approach. PMID:33486715
RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. PMID:33483506
A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape. PMID:33471161
Stenoparib, an Inhibitor of Cellular Poly(ADP-Ribose) Polymerase, Blocks Replication of the SARS-CoV-2 and HCoV-NL63 Human Coronaviruses In Vitro. PMID:33468703
InsectOR-Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes. PMID:33465132
A novel terpene synthase controls differences in anti-aphrodisiac pheromone production between closely related Heliconius butterflies. PMID:33465061
The complete chloroplast genome sequence of Red Asparagus Lettuce (Lactuca sativa var. asparagine L. red) (Asteraceae), endemic to China. PMID:33458037
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. PMID:33452249
The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample. PMID:33452027
Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements. PMID:33432714
Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences. PMID:33430943
The complete mitochondrial genome of an endangered tree: Malania oleifera. PMID:33426292
WY195, a New Inducible Promoter From the Rubber Powdery Mildew Pathogen, Can Be Used as an Excellent Tool for Genetic Engineering. PMID:33424812
Significantly improving the quality of genome assemblies through curation. PMID:33420778
Therapy-induced Deletion in 11q23 Leading to Fusion of KMT2A With ARHGEF12 and Development of B Lineage Acute Lymphoplastic Leukemia in a Child Treated for Acute Myeloid Leukemia Caused by t(9;11)(p21;q23)/KMT2A-MLLT3. PMID:33419897
A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons. PMID:33419731
Evolution of regulatory networks associated with traits under selection in cichlids. PMID:33419455
Genome-Wide Characterization of RNA Editing Sites in Primary Gastric Adenocarcinoma through RNA-seq Data Analysis. PMID:33415135
Evaluating High-Throughput Sequencing Data of Microalgae Living in Melting Snow: Improvements and Limitations1. PMID:33414851
Survey of Maize Rhizosphere Microbiome Using Shotgun Metagenomics. PMID:33414318
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias). PMID:33410870
Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. PMID:33407428
HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding. PMID:33407090
Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers. PMID:33400074
Improved metagenome binning and assembly using deep variational autoencoders. PMID:33398153
Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya. PMID:33395690
A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. PMID:33372175
Complete chloroplast genome of Physalis chenopodifolia Lam. (Solanaceae). PMID:33366468
Mutations altering acetylated residues in the CTD of HIV-1 integrase cause defects in proviral transcription at early times after integration of viral DNA. PMID:33351861
Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice. PMID:33348666
Unique k-mer sequences for validating cancer-related substitution, insertion and deletion mutations. PMID:33345188
Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. PMID:33335035
Whole-Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou (Potos flavus) and Northern Raccoon (Procyon lotor). PMID:33331895
Frameshift Variant in Novel Adenosine-A1-Receptor Homolog Associated With Bovine Spastic Syndrome/Late-Onset Bovine Spastic Paresis in Holstein Sires. PMID:33329738
A Chromosome-Level Genome Assembly of the Anglerfish Lophius litulon. PMID:33329719
The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening. PMID:33328440
High-Resolution Typing of Staphylococcus epidermidis Based on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones. PMID:33328176
AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Noncoding RNAs. PMID:33326073
C-terminal truncated HBx initiates hepatocarcinogenesis by downregulating TXNIP and reprogramming glucose metabolism. PMID:33323975
Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene. PMID:33323528
Long-read assembly of the Brassica napus reference genome Darmor-bzh. PMID:33319912
Hormonal regulation of microRNA expression dynamics in the gut of the yellow fever mosquito Aedes aegypti. PMID:33317406
Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier. PMID:33315133
The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes. PMID:33305470
Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ. PMID:33303762
Shotgun Sequencing Revealed the Microbiota of Zea mays Rhizosphere of a Former Grassland and an Intensively Cultivated Agricultural Land. PMID:33272993
Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse. PMID:33270708
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements. PMID:33267872
Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation. PMID:33253423
Major SCP/TAPS protein expansion in Lucilia cuprina is associated with novel tandem array organisation and domain architecture. PMID:33246493
Multiple wheat genomes reveal global variation in modern breeding. PMID:33239791
The barley pan-genome reveals the hidden legacy of mutation breeding. PMID:33239781
KRAB zinc finger protein diversification drives mammalian interindividual methylation variability. PMID:33239447
Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes. PMID:33228538
Genomic and Transcriptomic Analysis for Identification of Genes and Interlinked Pathways Mediating Artemisinin Resistance in Leishmania donovani. PMID:33213096
Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. PMID:33208749
Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework. PMID:33208101
A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions. PMID:33202901
Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel. PMID:33202822
A long-term study of AAV gene therapy in dogs with hemophilia A identifies clonal expansions of transduced liver cells. PMID:33199875
Conservative route to genome compaction in a miniature annelid. PMID:33199869
Development and validation of a 4-color multiplexing spinal muscular atrophy (SMA) genotyping assay on a novel integrated digital PCR instrument. PMID:33199817
BiSCoT: improving large eukaryotic genome assemblies with optical maps. PMID:33194395
Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks. PMID:33193743
The Eruca sativa Genome and Transcriptome: A Targeted Analysis of Sulfur Metabolism and Glucosinolate Biosynthesis Pre and Postharvest. PMID:33193472
Catabolic Machinery of the Human Gut Microbes Bestow Resilience Against Vanillin Antimicrobial Nature. PMID:33193247
An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites. PMID:33193242
Insertion variants missing in the human reference genome are widespread among human populations. PMID:33187521
Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines. PMID:33180766
Progressive Cactus is a multiple-genome aligner for the thousand-genome era. PMID:33177663
Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype. PMID:33175097
Comprehensive profiling of extracellular RNA in HPV-induced cancers using an improved pipeline for small RNA-seq analysis. PMID:33173155
A Persisting Nontropical Focus of Burkholderia pseudomallei with Limited Genome Evolution over Five Decades. PMID:33172968
Molecular basis of resistance to organophosphate insecticides in the New World screw-worm fly. PMID:33168079
LSH mediates gene repression through macroH2A deposition. PMID:33159050
Neoantigen prediction in human breast cancer using RNA sequencing data. PMID:33155341
Towards a better understanding of the low recall of insertion variants with short-read based variant callers. PMID:33148192
A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis. PMID:33146374
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. PMID:33139952
Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds. PMID:33124220
LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients. PMID:33112702
MDACP: A Pathogen Genome and Metagenome Analysis Cloud Platform. PMID:33110420
New methodology for repetitive sequences identification in human X and Y chromosomes. PMID:33101452
Temperate Bacteriophages (Prophages) in Pseudomonas aeruginosa Isolates Belonging to the International Cystic Fibrosis Clone (CC274). PMID:33101229
Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2. PMID:33099302
A chromosome-level genome assembly provides insights into ascorbic acid accumulation and fruit softening in guava (Psidium guajava). PMID:33098334
Dietary Phytase- and Lactic Acid-Treated Cereals Caused Greater Taxonomic Adaptations than Functional Adaptations in the Cecal Metagenome of Growing Pigs. PMID:33097516
The celery genome sequence reveals sequential paleo-polyploidizations, karyotype evolution and resistance gene reduction in apiales. PMID:33095976
Genome streamlining in a minute herbivore that manipulates its host plant. PMID:33095158
Metagenomes of Maize Rhizosphere Samples after Different Fertilization Treatments at Molelwane Farm, Located in North-West Province, South Africa. PMID:33093043
Extracellular microRNA 3' end modification across diverse body fluids. PMID:33092484
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PMID:33090996
Genome sequencing increases diagnostic yield in clinically diagnosed Alagille syndrome patients with previously negative test results. PMID:33077891
Chromosome-level genome assembly of a parent species of widely cultivated azaleas. PMID:33077749
Global RNA editome landscape discovers reduced RNA editing in glioma: loss of editing of gamma-amino butyric acid receptor alpha subunit 3 (GABRA3) favors glioma migration and invasion. PMID:33062411
Draft Genome Sequences of Two Virulent Streptococcus equi subsp. zooepidemicus Swine Isolates from Pennsylvania. PMID:33060275
Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.). PMID:33059596
A MicroRNA Expression Signature as Prognostic Marker for Oropharyngeal Squamous Cell Carcinoma. PMID:33057626
dbGuide: a database of functionally validated guide RNAs for genome editing in human and mouse cells. PMID:33051688
The mechanism of potato resistance to Globodera rostochiensis: comparison of root transcriptomes of resistant and susceptible Solanum phureja genotypes. PMID:33050888
Use of the Illumina EPIC methylation array for epigenomic research in the crab-eating macaque (Macaca fascicularis). PMID:33037870
Origin and adaptation to high altitude of Tibetan semi-wild wheat. PMID:33033250
pH-dependent transcriptional profile changes in iron-deficient Arabidopsis roots. PMID:33023472
Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode. PMID:33020495
Genomic diversity generated by a transposable element burst in a rice recombinant inbred population. PMID:33020276
An All-In-One Transcriptome-Based Assay to Identify Therapy-Guiding Genomic Aberrations in Nonsmall Cell Lung Cancer Patients. PMID:33019710
HIV-1 viremia not suppressible by antiretroviral therapy can originate from large T cell clones producing infectious virus. PMID:33016926
A Novel Microduplication Spanning Exons 8-16 of ATP2C1 That Was Undetectable by Standard Sanger Sequencing in a Japanese Patient With Hailey-Hailey Disease. PMID:33015087
Bacterial Genome Wide Association Studies (bGWAS) and Transcriptomics Identifies Cryptic Antimicrobial Resistance Mechanisms in Acinetobacter baumannii. PMID:33014966
A database resource and online analysis tools for coronaviruses on a historical and global scale. PMID:33009914
High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite. PMID:33001992
Haplotype-resolved genome analyses of a heterozygous diploid potato. PMID:32989320
Gene-Level, but Not Chromosome-Wide, Divergence between a Very Young House Fly Proto-Y Chromosome and Its Homologous Proto-X Chromosome. PMID:32986844
Interrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life. PMID:32986823
Shotgun Metagenomic Survey of Maize Soil Rhizobiome. PMID:32972943
Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera. PMID:32966557
The genome of Cleistogenes songorica provides a blueprint for functional dissection of dimorphic flower differentiation and drought adaptability. PMID:32964579
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
PacBio genome sequencing reveals new insights into the genomic organisation of the multi-copy ToxB gene of the wheat fungal pathogen Pyrenophora tritici-repentis. PMID:32957933
Viral Abundance and Diversity of Production Fluids in Oil Reservoirs. PMID:32957569
Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging. PMID:32943091
Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). PMID:32938378
A Novel Recurrent COL5A1 Genetic Variant Is Associated With a Dysplasia-Associated Arterial Disease Exhibiting Dissections and Fibromuscular Dysplasia. PMID:32938213
Identification of the SUT Gene Family in Pomegranate (Punica granatum L.) and Functional Analysis of PgL0145810.1. PMID:32927615
The Phoebe genome sheds light on the evolution of magnoliids. PMID:32922818
Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences. PMID:32916947
The UCSC SARS-CoV-2 Genome Browser. PMID:32908258
Cytogenetically visible inversions are formed by multiple molecular mechanisms. PMID:32906200
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. PMID:32887943
Background-suppressed live visualization of genomic loci with an improved CRISPR system based on a split fluorophore. PMID:32887690
An integrative proteogenomics approach reveals peptides encoded by annotated lincRNA in the mouse kidney inner medulla. PMID:32866085
Construction of a High-Density Genetic Map Based on SLAF Markers and QTL Analysis of Leaf Size in Rice. PMID:32849702
New Plasmodium vivax Genomes From the China-Myanmar Border. PMID:32849480
Clusters of polymorphic transmembrane genes control resistance to schistosomes in snail vectors. PMID:32845238
Genomic content of chemosensory receptors in two sister blister beetles facilitates characterization of chemosensory evolution. PMID:32842954
In Silico Analysis of HSP70 Gene Family in Bovine Genome. PMID:32840700
Positive autoregulation of lag-1 in response to LIN-12 activation in cell fate decisions during C. elegans reproductive system development. PMID:32839181
Sequencing and assembly of the Egyptian buffalo genome. PMID:32813723
Metagenomic profiling of the community structure, diversity, and nutrient pathways of bacterial endophytes in maize plant. PMID:32803452
Genomic characterization of malignant progression in neoplastic pancreatic cysts. PMID:32796935
Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model. PMID:32793490
Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. PMID:32792560
An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life. PMID:32781465
An evolutionary driver of interspersed segmental duplications in primates. PMID:32778141
Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica). PMID:32775052
The Acer truncatum genome provides insights into nervonic acid biosynthesis. PMID:32772482
Fusion transcript detection using spatial transcriptomics. PMID:32753032
smsMap: mapping single molecule sequencing reads by locating the alignment starting positions. PMID:32753028
Whole-genome de novo assemblies reveal extensive structural variations and dynamic organelle-to-nucleus DNA transfers in African and Asian rice. PMID:32748498
Ancestral regulatory mechanisms specify conserved midbrain circuitry in arthropods and vertebrates. PMID:32747566
In Vivo Gene Therapy for Canine SCID-X1 Using Cocal-Pseudotyped Lentiviral Vector. PMID:32741228
Mapping and Quantification of Non-Coding RNA Originating from the rDNA in Human Glioma Cells. PMID:32731436
Analysis of conserved miRNAs in cynomolgus macaque genome using small RNA sequencing and homology searching. PMID:32728489
Contributions of de novo variants to systemic lupus erythematosus. PMID:32724065
Accurate Detection of HPV Integration Sites in Cervical Cancer Samples Using the Nanopore MinION Sequencer Without Error Correction. PMID:32714374
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. PMID:32706331
Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps. PMID:32703219
Six reference-quality genomes reveal evolution of bat adaptations. PMID:32699395
SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. PMID:32699345
Privately computing set-maximal matches in genomic data. PMID:32693838
DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions. PMID:32692349
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. PMID:32683045
The genetic factors of bilaterian evolution. PMID:32672535
HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains. PMID:32665593
Intestinal Virome in Patients With Alcoholic Hepatitis. PMID:32654263
Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms. PMID:32651448
Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers. PMID:32645884
Shotgun metagenomic data of root endophytic microbiome of maize (Zea mays L.). PMID:32637499
High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum (Chrysanthemum × morifolium Ramat.). PMID:32637136
Termite Societies Promote the Taxonomic and Functional Diversity of Archaeal Communities in Mound Soils. PMID:32630446
Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences. PMID:32627830
A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals. PMID:32614390
Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. PMID:32605573
Ultraconserved Non-coding DNA Within Diptera and Hymenoptera. PMID:32601058
Suppression of adenosine-to-inosine (A-to-I) RNA editome by death associated protein 3 (DAP3) promotes cancer progression. PMID:32596459
High-Quality Genome Assembly of Chrysaora quinquecirrha Provides Insights Into the Adaptive Evolution of Jellyfish. PMID:32582283
Genetic Variants of the DSF Quorum Sensing System in Stenotrophomonas maltophilia Influence Virulence and Resistance Phenotypes Among Genotypically Diverse Clinical Isolates. PMID:32582100
Inducible aging in Hydra oligactis implicates sexual reproduction, loss of stem cells, and genome maintenance as major pathways. PMID:32578072
Shotgun metagenomic sequencing data of sunflower rhizosphere microbial community in South Africa. PMID:32577457
Differentially evolved drought stress indices determine the genetic variation of Brassica napus at seedling traits by genome-wide association mapping. PMID:32577311
Genome Report: Whole Genome Sequence and Annotation of the Parasitoid Jewel Wasp Nasonia giraulti Laboratory Strain RV2X[u]. PMID:32571804
CandiMeth: Powerful yet simple visualization and quantification of DNA methylation at candidate genes. PMID:32568373
Draft genome of the famous ornamental plant Paeonia suffruticosa. PMID:32551041
Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method. PMID:32547543
The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica). PMID:32545897
Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis. PMID:32545790
Dissecting the genome of star fruit (Averrhoa carambola L.). PMID:32528706
DNA markers based on retrotransposon insertion polymorphisms can detect short DNA fragments for strawberry cultivar identification. PMID:32523405
Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs. PMID:32523001
The genetic basis of sex determination in grapes. PMID:32518223
Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium. PMID:32511326
Efficient Nuclease-Directed Integration of Lentivirus Vectors into the Human Ribosomal DNA Locus. PMID:32504545
Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa. PMID:32493782
Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. PMID:32488117
Insight into the Possible Formation Mechanism of the Intersex Phenotype of Lanzhou Fat-Tailed Sheep Using Whole-Genome Resequencing. PMID:32486017
AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies. PMID:32484858
The third generation sequencing: the advanced approach to genetic diseases. PMID:32477917
Synergistic CRISPRa-Regulated Chondrogenic Extracellular Matrix Deposition Without Exogenous Growth Factors. PMID:32460686
Personalized and graph genomes reveal missing signal in epigenomic data. PMID:32450900
Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. PMID:32442304
Gapless assembly of maize chromosomes using long-read technologies. PMID:32434565
A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PMID:32433666
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. PMID:32432329
Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. PMID:32427850
The Evolution of Human Cancer Gene Duplications across Mammals. PMID:32421773
A Fast and Memory-Efficient Spectral Library Search Algorithm Using Locality-Sensitive Hashing. PMID:32415809
Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal. PMID:32415101
Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium. PMID:32401998
TGFam-Finder: a novel solution for target-gene family annotation in plants. PMID:32392385
Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution. PMID:32385269
A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle. PMID:32382536
Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels. PMID:32374870
Bioinformatic prediction of potential T cell epitopes for SARS-Cov-2. PMID:32372051
The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer. PMID:32365858
Genotyping by multiplexed sequencing (GMS): A customizable platform for genomic selection. PMID:32357171
DNA Barcoding in Nonhuman Primates Reveals Important Limitations in Retrovirus Integration Site Analysis. PMID:32355868
Independent Whole-Genome Duplications Define the Architecture of the Genomes of the Devastating West African Cacao Black Pod Pathogen Phytophthora megakarya and Its Close Relative Phytophthora palmivora. PMID:32354704
Tissue memory CD4+ T cells expressing IL-7 receptor-alpha (CD127) preferentially support latent HIV-1 infection. PMID:32353080
The gene-rich genome of the scallop Pecten maximus. PMID:32352532
Aging-regulated anti-apoptotic long non-coding RNA Sarrah augments recovery from acute myocardial infarction. PMID:32341350
Comprehensive Analysis of HERV Transcriptome in HIV+ Cells: Absence of HML2 Activation and General Downregulation of Individual HERV Loci. PMID:32340287
ASFVdb: an integrative resource for genomic and proteomic analyses of African swine fever virus. PMID:32294195
Exploring the success of Brazilian endemic clone Pseudomonas aeruginosa ST277 and its association with the CRISPR-Cas system type I-C. PMID:32293244
A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome. PMID:32292419
Expansion and Conservation of Biosynthetic Gene Clusters in Pathogenic Pyrenophora spp. PMID:32283749
First Genome Sequence of the Gunnison's Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague. PMID:32277812
Mutational landscape and genetic signatures of cell-free DNA in tumour-induced osteomalacia. PMID:32277576
Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans. PMID:32269217
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. PMID:32266012
Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut. PMID:32265983
Draft genomes of two Atlantic bay scallop subspecies Argopecten irradians irradians and A. i. concentricus. PMID:32251283
De novo Assembly of Transcriptomes From a B73 Maize Line Introgressed With a QTL for Resistance to Gray Leaf Spot Disease Reveals a Candidate Allele of a Lectin Receptor-Like Kinase. PMID:32231673
Modified nucleotides may have enhanced early RNA catalysis. PMID:32229566
Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms. PMID:32224843
Evidence of constraint in the 3D genome for trans-splicing in human cells. PMID:32221814
Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata. PMID:32211845
Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types. PMID:32209592
Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing. PMID:32208422
Genomic characterization of human brain metastases identifies drivers of metastatic lung adenocarcinoma. PMID:32203465
Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes. PMID:32198887
A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping. PMID:32194587
Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells. PMID:32192535
De novo assembly of the cattle reference genome with single-molecule sequencing. PMID:32191811
Genomic and transcriptomic analysis of Candida intermedia reveals the genetic determinants for its xylose-converting capacity. PMID:32190113
Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns. PMID:32188845
Grape-RNA: A Database for the Collection, Evaluation, Treatment, and Data Sharing of Grape RNA-Seq Datasets. PMID:32188014
New genome assembly of the barn owl (Tyto alba alba). PMID:32184981
AtXRN4 Affects the Turnover of Chosen miRNA*s in Arabidopsis. PMID:32182993
What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen. PMID:32163141
Humans Are Selectively Exposed to Pneumocystis jirovecii. PMID:32156824
Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development. PMID:32152089
Large X-Linked Palindromes Undergo Arm-to-Arm Gene Conversion across Mus Lineages. PMID:32145018
The genome evolution and domestication of tropical fruit mango. PMID:32143734
Exploring the computational methods for protein-ligand binding site prediction. PMID:32140203
Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection. PMID:32134991
Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons. PMID:32126975
Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels. PMID:32125373
Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut. PMID:32099754
GSAlign: an efficient sequence alignment tool for intra-species genomes. PMID:32093618
Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates. PMID:32085667
MAC: Merging Assemblies by Using Adjacency Algebraic Model and Classification. PMID:32082361
MtSSPdb: The Medicago truncatula Small Secreted Peptide Database. PMID:32079733
Silent Infection of B and CD8+ T Lymphocytes by Influenza A Virus in Children with Tonsillar Hypertrophy. PMID:32075928
Assembly of Mitochondrial Complex I Requires the Low-Complexity Protein AMC1 in Chlamydomonas reinhardtii. PMID:32075865
Enterovirus 71 Infection Shapes Host T Cell Receptor Repertoire and Presumably Expands VP1-Specific TCRβ CDR3 Cluster. PMID:32075096
Current Trends in Diagnostics of Viral Infections of Unknown Etiology. PMID:32074965
The draft genome of mandrill (Mandrillus sphinx): An Old World monkey. PMID:32051450
Transcriptional Signatures of Tau and Amyloid Neuropathology. PMID:32049030
An inferred fitness consequence map of the rice genome. PMID:32042156
ZEBrA: Zebra finch Expression Brain Atlas-A resource for comparative molecular neuroanatomy and brain evolution studies. PMID:32037563
The complete mitochondrial genome of Talpa aquitania (Talpidae; Insectivora), a mole species endemic to northern Spain and southern France. PMID:32034626
Comprehensive molecular characterization of mitochondrial genomes in human cancers. PMID:32024997
Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling. PMID:32023871
Identification and characterization of ERV-W-like sequences in Platyrrhini species provides new insights into the evolutionary history of ERV-W in primates. PMID:32021657
REXTAL: Regional Extension of Assemblies Using Linked-Reads. PMID:32016171
Concentration-Dependent Recruitment of Mammalian Odorant Receptors. PMID:32015097
Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed. PMID:32012153
O6-Methylguanine-DNA Methyltransferase (MGMT): Challenges and New Opportunities in Glioma Chemotherapy. PMID:32010632
High-Quality Genome Assembly of Eriocheir japonica sinensis Reveals Its Unique Genome Evolution. PMID:32010195
Whole-genome and time-course dual RNA-Seq analyses reveal chronic pathogenicity-related gene dynamics in the ginseng rusty root rot pathogen Ilyonectria robusta. PMID:32005849
Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal. PMID:31996844
The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster. PMID:31992188
Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity. PMID:31988161
Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing. PMID:31986137
Expanded complement of Niemann-Pick type C2-like protein genes in Clonorchis sinensis suggests functions beyond sterol binding and transport. PMID:31973758
The landscape of chimeric RNAs in non-diseased tissues and cells. PMID:31965184
Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae. PMID:31949198
MRE11A Isoform Expression Associated with Outcome Following Radiotherapy in Muscle-Invasive Bladder Cancer does not Alter Cell Survival and DNA Double-Strand Break Repair Following Ionising Radiation. PMID:31942442
Cardiac mitochondrial function depends on BUD23 mediated ribosome programming. PMID:31939735
Enhanced genome assembly and a new official gene set for Tribolium castaneum. PMID:31937263
Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States. PMID:31936615
SWAV: a web-based visualization browser for sliding window analysis. PMID:31924845
Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy. PMID:31924795
Vanillin Production in Pseudomonas: Whole-Genome Sequencing of Pseudomonas sp. Strain 9.1 and Reannotation of Pseudomonas putida CalA as a Vanillin Reductase. PMID:31924622
Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding? PMID:31919520
ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity and breast cancer treatment response. PMID:31913353
Concordance of copy number abnormality detection using SNP arrays and Multiplex Ligation-dependent Probe Amplification (MLPA) in acute lymphoblastic leukaemia. PMID:31913349
An Automated Method To Predict Mouse Gene and Protein Sequences Using Variant Data. PMID:31911484
Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus). PMID:31904811
A shared genetic basis of mimicry across swallowtail butterflies points to ancestral co-option of doublesex. PMID:31900419
Targeted viral vector transduction of relaxin-3 neurons in the rat nucleus incertus using a novel cell-type specific promoter. PMID:31890981
Long walk to genomics: History and current approaches to genome sequencing and assembly. PMID:31890139
Atypical chromosome 22q11.2 deletions are complex rearrangements and have different mechanistic origins. PMID:31884517
Chromosome Translocation t(14;21)(q11;q22) Activates Both OLIG1 and OLIG2 in Pediatric T-cell Lymphoblastic Malignancies and May Signify Adverse Prognosis. PMID:31882550
Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis). PMID:31878322
Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1. PMID:31878043
Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups. PMID:31873088
Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus). PMID:31871636
Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing. PMID:31867041
Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. PMID:31853540
Genomes of early-diverging streptophyte algae shed light on plant terrestrialization. PMID:31844283
deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index. PMID:31842925
ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. PMID:31842745
SGID: a comprehensive and interactive database of the silkworm. PMID:31836898
Deciphering the microbiota data from termite mound soil in South Africa using shotgun metagenomics. PMID:31832528
From EST to structure models for functional inference of APP, BACE1, PSEN1, PSEN2 genes. PMID:31831959
Alignment-Free Sequence Analysis and Applications. PMID:31828235
Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken. PMID:31821332
A novel long noncoding RNA Linc-ASEN represses cellular senescence through multileveled reduction of p21 expression. PMID:31819156
Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). PMID:31816089
Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs. PMID:31803243
Deciphering the high-quality genome sequence of coriander that causes controversial feelings. PMID:31799788
Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei. PMID:31799430
QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut (Arachis hypogaea L.). PMID:31795931
Evaluation of Saccharomyces cerevisiae Wine Yeast Competitive Fitness in Enologically Relevant Environments by Barcode Sequencing. PMID:31792006
Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry. PMID:31788036
Identification and Characterization of Cis-Regulatory Elements for Photoreceptor-Type-Specific Transcription in ZebraFish. PMID:31786786
Programmed DNA elimination of germline development genes in songbirds. PMID:31784533
Minimal in vivo requirements for developmentally regulated cardiac long intergenic non-coding RNAs. PMID:31784461
Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010-2016. PMID:31783732
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. PMID:31782791
Retroelement Insertion in a CRISPR/Cas9 Editing Site in the Early Embryo Intensifies Genetic Mosaicism. PMID:31781562
Genome sequence of the model rice variety KitaakeX. PMID:31775618
Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera). PMID:31774498
A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary. PMID:31759823
Sequencing and Functional Annotation of the Whole Genome of Shiraia bambusicola. PMID:31712259
Identification of Single Nucleotide Polymorphism in Red Clover (Trifolium pratense L.) Using Targeted Genomic Amplicon Sequencing and RNA-seq. PMID:31708937
Exploration of intermediate-sized INDELs by next-generation multigene panel testing in Han Chinese patients with breast cancer. PMID:31700649
A New Chloroplast DNA Extraction Protocol Significantly Improves the Chloroplast Genome Sequence Quality of Foxtail Millet (Setaria italica (L.) P. Beauv.). PMID:31700055
From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. PMID:31694722
Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species. PMID:31694521
UCSC Genome Browser enters 20th year. PMID:31691824
Genetic Variations of Ultraconserved Elements in the Human Genome. PMID:31689173
Evidence for adaptive introgression of exons across a hybrid swarm in deer. PMID:31684869
Multi-Tissue Transcriptomes Yield Information on High-Altitude Adaptation and Sex-Determination in Scutiger cf. sikimmensis. PMID:31683620
In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum). PMID:31671113
An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. PMID:31667023
BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers. PMID:31665503
Preventive antibiotic treatment of calves: emergence of dysbiosis causing propagation of obese state-associated and mobile multidrug resistance-carrying bacteria. PMID:31663669
The transcription factor ETS1 promotes apoptosis resistance of senescent cholangiocytes by epigenetically up-regulating the apoptosis suppressor BCL2L1. PMID:31659122
Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae). PMID:31653891
Environmental transcriptomes of invasive dreissena, a model species in ecotoxicology and invasion biology. PMID:31653851
Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families. PMID:31651947
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier. PMID:31648300
A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. PMID:31647412
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Evolution of the new head by gradual acquisition of neural crest regulatory circuits. PMID:31645763
Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae. PMID:31641137
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. PMID:31639029
Exploring the basis of 2-propenyl and 3-butenyl glucosinolate synthesis by QTL mapping and RNA-sequencing in Brassica juncea. PMID:31626668
Satellite DNA content of B chromosomes in the characid fish Characidium gomesi supports their origin from sex chromosomes. PMID:31624915
A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona. PMID:31621849
Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing. PMID:31616471
The Structure, Evolution, and Gene Expression Within the Caprine Leukocyte Receptor Complex. PMID:31616444
Genome-wide association mapping of date palm fruit traits. PMID:31615981
A new species in the major malaria vector complex sheds light on reticulated species evolution. PMID:31611571
FusionScan: accurate prediction of fusion genes from RNA-Seq data. PMID:31610622
Alternative mRNA Splicing in Three Venom Families Underlying a Possible Production of Divergent Venom Proteins of the Habu Snake, Protobothrops flavoviridis. PMID:31600994
A chromosome-level genome assembly of Pyropia haitanensis (Bangiales, Rhodophyta). PMID:31600851
Genome Assembly of the A-Group Wolbachia in Nasonia oneida Using Linked-Reads Technology. PMID:31596462
RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. PMID:31593214
Realizing the potential of full-length transcriptome sequencing. PMID:31587638
A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae. PMID:31579586
The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies. PMID:31575853
Pedigree-based estimation of human mobile element retrotransposition rates. PMID:31575651
The sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies. PMID:31570724
RNA ligation precedes the retrotransposition of U6/LINE-1 chimeric RNA. PMID:31548405
BPSL1626: Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design against Burkholderia pseudomallei. PMID:31544878
The evolution study on Oryza rufipogon. dw by whole-genome sequencing. PMID:31544797
Rapid Detection of Genetic Engineering, Structural Variation, and Antimicrobial Resistance Markers in Bacterial Biothreat Pathogens by Nanopore Sequencing. PMID:31534162
A Puzzling Anomaly in the 4-Mer Composition of the Giant Pandoravirus Genomes Reveals a Stringent New Evolutionary Selection Process. PMID:31534042
Α de novo 3.8-Mb inversion affecting the EDA and XIST genes in a heterozygous female calf with generalized hypohidrotic ectodermal dysplasia. PMID:31533624
Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes. PMID:31528181
Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes. PMID:31525193
A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers. PMID:31521109
Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6. PMID:31519648
Comparative Transcriptomics Provides Insights into Reticulate and Adaptive Evolution of a Butterfly Radiation. PMID:31518398
The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer. PMID:31508512
Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae). PMID:31506321
Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations. PMID:31504750
Phytochrome Coordinates with a hnRNP to Regulate Alternative Splicing via an Exonic Splicing Silencer. PMID:31501299
Large miRNA survival analysis reveals a prognostic four-biomarker signature for triple negative breast cancer. PMID:31487369
Burkholderia pseudomallei, the causative agent of melioidosis, is rare but ecologically established and widely dispersed in the environment in Puerto Rico. PMID:31487287
The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. PMID:31471988
Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes. PMID:31455637
Profiling the Functional Diversity of Termite Mound Soil Bacteria as Revealed by Shotgun Sequencing. PMID:31450818
CNEr: A toolkit for exploring extreme noncoding conservation. PMID:31449516
Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway. PMID:31444106
Novel Locus Associated with Symmetrical Lupoid Onychodystrophy in the Bearded Collie. PMID:31443497
A SNP-Based High-Density Genetic Map of Leaf and Fruit Related Quantitative Trait Loci in Wolfberry (Lycium Linn.). PMID:31440266
Long-read sequencing and haplotype linkage analysis enabled preimplantation genetic testing for patients carrying pathogenic inversions. PMID:31439719
A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). PMID:31437279
Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome. PMID:31437148
Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris. PMID:31427456
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. PMID:31409808
Heterogeneous Nuclear Ribonucleoprotein H1 Coordinates with Phytochrome and the U1 snRNP Complex to Regulate Alternative Splicing in Physcomitrella patens. PMID:31409629
Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination. PMID:31399544
Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated. PMID:31395952
Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities. PMID:31388591
BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis. PMID:31387612
Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato. PMID:31377774
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. PMID:31375807
Exploring the molecular basis of neuronal excitability in a vocal learner. PMID:31375088
Uncovering missed indels by leveraging unmapped reads. PMID:31366961
Endogenous Retrovirus-Derived Long Noncoding RNA Enhances Innate Immune Responses via Derepressing RELA Expression. PMID:31363026
Challenges in funding and developing genomic software: roots and remedies. PMID:31358028
The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections. PMID:31355335
An expanded landscape of human long noncoding RNA. PMID:31350901
Dicyemid Mesozoans: A Unique Parasitic Lifestyle and a Reduced Genome. PMID:31347665
Impact of sequencing depth and technology on de novo RNA-Seq assembly. PMID:31337347
Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT. PMID:31324144
The genome assembly of asparagus bean, Vigna unguiculata ssp. sesquipedialis. PMID:31316072
Centromere Satellite Repeats Have Undergone Rapid Changes in Polyploid Wheat Subgenomes. PMID:31311836
Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change. PMID:31309157
Musa balbisiana genome reveals subgenome evolution and functional divergence. PMID:31308504
A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality. PMID:31308395
The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data. PMID:31308375
De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China. PMID:31307060
Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids. PMID:31293619
Genetic Diversity, Virulence, Race Profiling, and Comparative Genomic Analysis of the Fusarium oxysporum f. sp. conglutinans Strains Infecting Cabbages in China. PMID:31293534
Srrm234, but not canonical SR and hnRNP proteins, drive inclusion of Dscam exon 9 variable exons. PMID:31292260
Distribution of endogenous gammaretroviruses and variants of the Fv1 restriction gene in individual mouse strains and strain subgroups. PMID:31291374
Retroposed copies of RET gene: a somatically acquired event in medullary thyroid carcinoma. PMID:31288802
Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. PMID:31278252
Closing target trimming and CTTdocker programs for discovering hidden superfamily loci in genomes. PMID:31265455
Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa). PMID:31257419
HLA alleles and haplotypes observed in 263 US families. PMID:31256909
Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation. PMID:31248377
Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing. PMID:31243452
Long-read sequencing unveils IGH-DUX4 translocation into the silenced IGH allele in B-cell acute lymphoblastic leukemia. PMID:31243274
The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge). PMID:31241155
Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system. PMID:31238873
Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material. PMID:31236242
New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies. PMID:31231413
Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants. PMID:31223530
Deep sequencing of a recurrent oligodendroglioma and the derived xenografts reveals new insights into the evolution of human oligodendroglioma and candidate driver genes. PMID:31217899
Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Pleurotus Species. PMID:31212970
Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts. PMID:31193391
BarkBase: Epigenomic Annotation of Canine Genomes. PMID:31181663
Factors other than hTau overexpression that contribute to tauopathy-like phenotype in rTg4510 mice. PMID:31171783
Genome sequencing provides insights into the evolution and antioxidant activity of Chinese bayberry. PMID:31170907
High-Throughput Genotyping of CRISPR/Cas Edited Cells in 96-Well Plates. PMID:31164571
The Biodiversity and Geochemistry of Cryoconite Holes in Queen Maud Land, East Antarctica. PMID:31159414
Variable Baseline Papio cynocephalus Endogenous Retrovirus (PcEV) Expression Is Upregulated in Acutely SIV-Infected Macaques and Correlated to STAT1 Expression in the Spleen. PMID:31156613
Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.). PMID:31152165
Comment on "A comprehensive overview and evaluation of circular RNA detection tools". PMID:31150384
Altered microRNA expression profiles in large offspring syndrome and Beckwith-Wiedemann syndrome. PMID:31144574
HNCDB: An Integrated Gene and Drug Database for Head and Neck Cancer. PMID:31139565
Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for Berberis. PMID:31139202
Methanethiol and Dimethylsulfide Cycling in Stiffkey Saltmarsh. PMID:31134039
A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism. PMID:31133004
Microhomologies are prevalent at Cas9-induced larger deletions. PMID:31127293
Comprehensive Multiple eQTL Detection and Its Application to GWAS Interpretation. PMID:31123039
Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes. PMID:31121954
Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics. PMID:31114863
Pairwise alignment of nucleotide sequences using maximal exact matches. PMID:31113356
Transcript and metabolite changes during the early phase of abscisic acid-mediated induction of crassulacean acid metabolism in Talinum triangulare. PMID:31111894
How dynamic could be the 45S rDNA cistron? An intriguing variability in a grasshopper species revealed by integration of chromosomal and genomic data. PMID:31111199
Stenotrophomonas maltophilia Differential Gene Expression in Synthetic Cystic Fibrosis Sputum Reveals Shared and Cystic Fibrosis Strain-Specific Responses to the Sputum Environment. PMID:31109991
A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network. PMID:31107202
Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight. PMID:31104630
Draft genome of the big-headed turtle Platysternon megacephalum. PMID:31097710
CiliaCarta: An integrated and validated compendium of ciliary genes. PMID:31095607
Islands of retroelements are major components of Drosophila centromeres. PMID:31086362
Splice-Aware Multiple Sequence Alignment of Protein Isoforms. PMID:31080963
Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs. PMID:31080521
Genomic changes in the biological control agent Cryptolaemus montrouzieri associated with introduction. PMID:31080510
Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. PMID:31080084
Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. PMID:31080066
Insertion of a chimeric retrotransposon sequence in mouse Axin1 locus causes metastable kinky tail phenotype. PMID:31073336
A high-density genetic map developed by specific-locus amplified fragment (SLAF) sequencing and identification of a locus controlling anthocyanin pigmentation in stalk of Zicaitai (Brassica rapa L. ssp. chinensis var. purpurea). PMID:31064320
Exploiting selection at linked sites to infer the rate and strength of adaptation. PMID:31061475
Dietary Energy Level Promotes Rumen Microbial Protein Synthesis by Improving the Energy Productivity of the Ruminal Microbiome. PMID:31057531
Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. PMID:31050681
The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. PMID:31049561
Mitochondrial autoimmunity and MNRR1 in breast carcinogenesis. PMID:31046734
Functional adaptations in the cecal and colonic metagenomes associated with the consumption of transglycosylated starch in a pig model. PMID:31046662
SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data. PMID:31045209
Linkage-based genome assembly improvement of oil palm (Elaeis guineensis). PMID:31036825
Germline-restricted chromosome (GRC) is widespread among songbirds. PMID:31036668
Dauer signalling pathway model for Haemonchus contortus. PMID:31036054
Accurate high throughput alignment via line sweep-based seed processing. PMID:31028275
Instability of the Pseudoautosomal Boundary in House Mice. PMID:31028113
Agricultural Origins of a Highly Persistent Lineage of Vancomycin-Resistant Enterococcus faecalis in New Zealand. PMID:31028029
Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PMID:31026256
Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang. PMID:31022173
Chromosome-Level Assembly of the Chinese Seabass (Lateolabrax maculatus) Genome. PMID:31019525
TransLiG: a de novo transcriptome assembler that uses line graph iteration. PMID:31014374
Subtype classification and functional annotation of L1Md retrotransposon promoters. PMID:31007728
BHap: a novel approach for bacterial haplotype reconstruction. PMID:31004480
Shedding Light on a Secretive Tertiary urodelean Relict: Hynobiid salamanders (Paradactylodon persicus s.l.) from Iran, Illuminated by Phylogeographic, Developmental and Transcriptomic Data. PMID:31003559
Diversity, Virulence, and Antimicrobial Resistance in Isolates From the Newly Emerging Klebsiella pneumoniae ST101 Lineage. PMID:31001209
Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. PMID:30999938
Screening for mutations in selected miRNA genes in hypogonadotropic hypogonadism patients. PMID:30999277
Visualizing flow in an intact CSF network using optical coherence tomography: implications for human congenital hydrocephalus. PMID:30996265
Genome Sequence of an Arthroconidial Yeast, Saprochaete fungicola CBS 625.85. PMID:30975801
Whole genome sequencing reveals complexity in both HPV sequences present and HPV integrations in HPV-positive oropharyngeal squamous cell carcinomas. PMID:30975103
iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture. PMID:30967549
Low-cost assembly of a cacao crop genome is able to resolve complex heterozygous bubbles. PMID:30962937
Draft genome of the river water buffalo. PMID:30962899
Carbapenem-Susceptible OXA-23-Producing Proteus mirabilis in the French Community. PMID:30962345
Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication. PMID:30955886
A quick guide for student-driven community genome annotation. PMID:30943207
MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs. PMID:30942867
Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds. PMID:30936435
Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony. PMID:30926611
SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups. PMID:30925859
Deep-learning augmented RNA-seq analysis of transcript splicing. PMID:30923373
The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia tonsa Dana Improve the Understanding of Copepod Genome Size Evolution. PMID:30918947
Placenta Transcriptome Profiling in Intrauterine Growth Restriction (IUGR). PMID:30917529
Improving in-silico normalization using read weights. PMID:30914698
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. PMID:30902979
Cryo-EM structure of a light chain-derived amyloid fibril from a patient with systemic AL amyloidosis. PMID:30894526
Anaerotruncus massiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery. PMID:30891246
Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage. PMID:30888417
Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. PMID:30886425
Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects. PMID:30885123
Circular RNAs in human and vertebrate neural retinas. PMID:30874468
A reference-grade wild soybean genome. PMID:30872580
Memory and relatedness of transcriptional activity in mammalian cell lineages. PMID:30872573
Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin. PMID:30872351
Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome. PMID:30865260
Characterization of mammalian Lipocalin UTRs in silico: Predictions for their role in post-transcriptional regulation. PMID:30840684
Genome-wide analysis reveals the genomic features of the turkey vulture (Cathartes aura) as a scavenger. PMID:30834967
Genome Sequence of Flavor-Producing Yeast Saprochaete suaveolens NRRL Y-17571. PMID:30834381
A Modifying Autoantigen in Graves' Disease. PMID:30822352
Evolutionary Implications of the microRNA- and piRNA Complement of Lepidodermella squamata (Gastrotricha). PMID:30813358
Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis. PMID:30809240
Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus. PMID:30806641
Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis. PMID:30802244
Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler. PMID:30768175
Ribosomal DNA harbors an evolutionarily conserved clock of biological aging. PMID:30765617
Ipa1 Is an RNA Polymerase II Elongation Factor that Facilitates Termination by Maintaining Levels of the Poly(A) Site Endonuclease Ysh1. PMID:30759400
A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation. PMID:30741925
Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements. PMID:30735495
The sequence and de novo assembly of Oxygymnocypris stewartii genome. PMID:30720802
RNA sequencing discloses the genome‑wide profile of long noncoding RNAs in dilated cardiomyopathy. PMID:30720098
Ultrafast search of all deposited bacterial and viral genomic data. PMID:30718882
Evolution-guided evaluation of the inverted terminal repeats of the synthetic transposon Sleeping Beauty. PMID:30718656
Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina. PMID:30712875
Gene editing of the multi-copy H2A.B gene and its importance for fertility. PMID:30704500
Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis. PMID:30699955
Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina. PMID:30699175
The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. PMID:30698687
Environmental filtering of bacterial functional diversity along an aridity gradient. PMID:30696918
Genome structure and evolution of Antirrhinum majus L. PMID:30692677
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. PMID:30689848
Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy. PMID:30688658
Genomewide Association Study of Fracture Nonunion Using Electronic Health Records. PMID:30680360
Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome. PMID:30674356
Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data. PMID:30670076
Inflammation in Traumatic Brain Injury: Roles for Toxic A1 Astrocytes and Microglial-Astrocytic Crosstalk. PMID:30661228
Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophila simulans Wild-Type Strains. PMID:30658967
Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. PMID:30654561
pblat: a multithread blat algorithm speeding up aligning sequences to genomes. PMID:30646844
A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads. PMID:30646604
Comparative bioinformatic analysis suggests that specific dauer-like signalling pathway components regulate Toxocara canis development and migration in the mammalian host. PMID:30642380
Chromosome level comparative analysis of Brassica genomes. PMID:30632049
AtFusionDB: a database of fusion transcripts in Arabidopsis thaliana. PMID:30624648
SQuIRE reveals locus-specific regulation of interspersed repeat expression. PMID:30624635
Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps. PMID:30622124
Simulation of heterogeneous tumour genomes with HeteroGenesis and in silico whole exome sequencing. PMID:30615054
Gorillas have been infected with the HERV-K (HML-2) endogenous retrovirus much more recently than humans and chimpanzees. PMID:30610173
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors. PMID:30606103
A benchmark study of sequence alignment methods for protein clustering. PMID:30598070
Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination. PMID:30592459
RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes. PMID:30583062
Multiple forms of selection shape reproductive isolation in a primate hybrid zone. PMID:30582763
QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing. PMID:30568674
A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs. PMID:30560136
Seasonality Drives Microbial Community Structure, Shaping both Eukaryotic and Prokaryotic Host⁻Viral Relationships in an Arctic Marine Ecosystem. PMID:30558156
Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis. PMID:30541446
The draft genomes of five agriculturally important African orphan crops. PMID:30535374
UM-HACC-2A: MYB-NFIB fusion-positive human adenoid cystic carcinoma cell line. PMID:30527239
Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle. PMID:30526490
The genomic landscape of molecular responses to natural drought stress in Panicum hallii. PMID:30523281
Off- and on-target effects of genome editing in mouse embryos. PMID:30518723
The Transcriptomic Landscape of Yaks Reveals Molecular Pathways for High Altitude Adaptation. PMID:30517636
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. PMID:30504855
Integrated Genomic, Epigenomic, and Expression Analyses of Ovarian Cancer Cell Lines. PMID:30485824
Profiling microRNA expression in Atlantic killifish (Fundulus heteroclitus) gill and responses to arsenic and hyperosmotic stress. PMID:30476744
Evaluation and application of RNA-Seq by MinION. PMID:30462165
De novo assembly and comparative transcriptome analysis: novel insights into terpenoid biosynthesis in Chamaemelum nobile L. PMID:30430213
Whole genome sequencing of Trypanosoma cruzi field isolates reveals extensive genomic variability and complex aneuploidy patterns within TcII DTU. PMID:30424726
Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome. PMID:30420487
SynerClust: a highly scalable, synteny-aware orthologue clustering tool. PMID:30418868
Defining TP53 pioneering capabilities with competitive nucleosome binding assays. PMID:30409772
A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. PMID:30409771
The UCSC Genome Browser database: 2019 update. PMID:30407534
imGLAD: accurate detection and quantification of target organisms in metagenomes. PMID:30405973
Assessing the impact of exact reads on reducing the error rate of read mapping. PMID:30400807
De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing. PMID:30398473
Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient. PMID:30397261
Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation. PMID:30397229
RNAcentral: a hub of information for non-coding RNA sequences. PMID:30395267
Wingless promotes EGFR signaling in follicle stem cells to maintain self-renewal. PMID:30389852
Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation. PMID:30381290
Genomic distribution of a novel Pyrenophora tritici-repentis ToxA insertion element. PMID:30379913
Whole-Genome Alignment and Comparative Annotation. PMID:30379572
Non-invasive genotyping with a massively parallel sequencing panel for the detection of SNPs in HPA-axis genes. PMID:30374157
Phenotypic characterization and whole genome analysis of extended-spectrum beta-lactamase-producing bacteria isolated from dogs in Germany. PMID:30365516
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. PMID:30365027
Characterization of the satellitome in lower vascular plants: the case of the endangered fern Vandenboschia speciosa. PMID:30357311
Structural and Comparative Analysis of the Complete Chloroplast Genome of Pyrus hopeiensis-"Wild Plants with a Tiny Population"-and Three Other Pyrus Species. PMID:30347837
Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health. PMID:30338244
A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues. PMID:30333510
High-resolution chromosome painting with repetitive and single-copy oligonucleotides in Arachis species identifies structural rearrangements and genome differentiation. PMID:30333010
Identification of Arbuscular Mycorrhiza Fungi Responsive microRNAs and Their Regulatory Network in Maize. PMID:30332850
REDfly: the transcriptional regulatory element database for Drosophila. PMID:30329093
The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. PMID:30325307
Firefly genomes illuminate parallel origins of bioluminescence in beetles. PMID:30324905
Phylogenetic analysis of the cytochrome P450 (CYP450) nucleotide sequences of the horse and predicted CYP450s of the white rhinoceros (Ceratotherium simum) and other mammalian species. PMID:30324017
Unicellular Origin of the Animal MicroRNA Machinery. PMID:30318349
Rapid preimplantation genetic screening using a handheld, nanopore-based DNA sequencer. PMID:30316437
The somatic piRNA pathway controls germline transposition over generations. PMID:30312469
"Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus. PMID:30304855
Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater. PMID:30297849
Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations. PMID:30297425
Genomic Characterization and Probiotic Potency of Bacillus sp. DU-106, a Highly Effective Producer of L-Lactic Acid Isolated From Fermented Yogurt. PMID:30294310
Repurposing of promoters and enhancers during mammalian evolution. PMID:30287902
CRISPRlnc: a manually curated database of validated sgRNAs for lncRNAs. PMID:30285246
MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks. PMID:30277499
Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms. PMID:30272673
Progress of analytical tools and techniques for human gut microbiome research. PMID:30267313
Structure and evolution of double minutes in diagnosis and relapse brain tumors. PMID:30267146
Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection. PMID:30262776
Chromosome Y-encoded antigens associate with acute graft-versus-host disease in sex-mismatched stem cell transplant. PMID:30262602
Opaque-2 Regulates a Complex Gene Network Associated with Cell Differentiation and Storage Functions of Maize Endosperm. PMID:30262552
Genetic mapping of anthocyanin accumulation-related genes in pepper fruits using a combination of SLAF-seq and BSA. PMID:30261055
De novo clustering of long reads by gene from transcriptomics data. PMID:30260405
Rare variants in the splicing regulatory elements of EXOC3L4 are associated with brain glucose metabolism in Alzheimer's disease. PMID:30255815
Fine mapping and candidate gene screening of the downy mildew resistance gene RPF1 in Spinach. PMID:30244393
The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication. PMID:30239729
Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae. PMID:30239695
Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation. PMID:30232334
Genomic analysis of MHC-based mate choice in the monogamous California mouse. PMID:30214134
QTL Mapping and Marker Identification for Sex-Determining: Indicating XY Sex Determination System in the Swimming Crab (Portunus trituberculatus). PMID:30210528
The genetic basis and cell of origin of mixed phenotype acute leukaemia. PMID:30209392
Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. PMID:30201725
Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration. PMID:30192940
Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units. PMID:30184074
Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians. PMID:30181897
Regulatory processes that control haploid expression of salmon sperm mRNAs. PMID:30176937
A novel panel of short mononucleotide repeats linked to informative polymorphisms enabling effective high volume low cost discrimination between mismatch repair deficient and proficient tumours. PMID:30157243
Comparative analysis of whole flower transcriptomes in the Zingiberales. PMID:30155368
Whole genome shotgun sequencing revealed highly polymorphic genome regions and genes in Escherichia coli O157:H7 isolates collected from a single feedlot. PMID:30153286
Repeated translocation of a gene cassette drives sex-chromosome turnover in strawberries. PMID:30148831
Complete sequence of kenaf (Hibiscus cannabinus) mitochondrial genome and comparative analysis with the mitochondrial genomes of other plants. PMID:30143661
Draft genome of Glyptosternon maculatum, an endemic fish from Tibet Plateau. PMID:30124856
Characterization of the β-defensin genes in giant panda. PMID:30120296
The landscape of the A-to-I RNA editome from 462 human genomes. PMID:30104667
Potent HIV-1-Specific CD8 T Cell Responses Induced in Mice after Priming with a Multiepitopic DNA-TMEP and Boosting with the HIV Vaccine MVA-B. PMID:30104537
The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana). PMID:30101322
Xenotropic Mouse Gammaretroviruses Isolated from Pre-Leukemic Tissues Include a Recombinant. PMID:30096897
Comparative genetic and genomic analysis of the novel fusellovirus Sulfolobus spindle-shaped virus 10. PMID:30094064
Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals. PMID:30093596
Evolutionary stability of topologically associating domains is associated with conserved gene regulation. PMID:30086749
Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave. PMID:30081833
No Evidence for Recent Selection at FOXP2 among Diverse Human Populations. PMID:30078708
Transcriptional profiling of HERV-K(HML-2) in amyotrophic lateral sclerosis and potential implications for expression of HML-2 proteins. PMID:30068350
Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging. PMID:30068345
Expanding the Mutation Spectrum in ABCA4: Sixty Novel Disease Causing Variants and Their Associated Phenotype in a Large French Stargardt Cohort. PMID:30060493
Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits. PMID:30059608
Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand. PMID:30057586
Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase. PMID:30052927
The habu genome reveals accelerated evolution of venom protein genes. PMID:30050104
Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks. PMID:30046115
Evolution of gene dosage on the Z-chromosome of schistosome parasites. PMID:30044216
Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction. PMID:30042472
Comparative Genomics of Escherichia coli Sequence Type 219 Clones From the Same Patient: Evolution of the IncI1 blaCMY-Carrying Plasmid in Vivo. PMID:30038606
Genome Plasticity in Cultured Leishmania donovani: Comparison of Early and Late Passages. PMID:30018594
Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American Voles. PMID:30002081
miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. PMID:29997117
Coinfections identified from metagenomic analysis of cervical lymph nodes from tularemia patients. PMID:29996780
The Genetics of a Behavioral Speciation Phenotype in an Island System. PMID:29996514
De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus. PMID:29983323
Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs. PMID:29967493
The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. PMID:29952048
Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus. PMID:29941016
Efficacy and safety of a clinically relevant foamy vector design in human hematopoietic repopulating cells. PMID:29935087
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant. PMID:29931210
Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract. PMID:29925834
SNP hot-spots in the clam parasite QPX. PMID:29925308
Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub. PMID:29917074
The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi. PMID:29914365
In silico read normalization using set multi-cover optimization. PMID:29912280
Detecting de Novo Homoeologous Recombination Events in Cultivated Brassica napus Using a Genome-Wide SNP Array. PMID:29907649
Association mapping from sequencing reads using k-mers. PMID:29897334
Transcriptional analyses provide new insight into the late-stage immune response of a diseased Caribbean coral. PMID:29892394
Hydrogen-Fueled Microbial Pathways in Biogas Upgrading Systems Revealed by Genome-Centric Metagenomics. PMID:29892275
A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. PMID:29892093
Blazing Signature Filter: a library for fast pairwise similarity comparisons. PMID:29890950
Investigating the Molecular Genetic Basis of Cytoplasmic Sex Determination Caused by Wolbachia Endosymbionts in Terrestrial Isopods. PMID:29890648
Genetic variation affecting exon skipping contributes to brain structural atrophy in Alzheimer's disease. PMID:29888056
Population resequencing reveals candidate genes associated with salinity adaptation of the Pacific oyster Crassostrea gigas. PMID:29875442
The Genomic Architecture of a Rapid Island Radiation: Recombination Rate Variation, Chromosome Structure, and Genome Assembly of the Hawaiian Cricket Laupala. PMID:29875253
phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R. PMID:29874797
A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women. PMID:29871690
Genomic Variations in Probiotic Lactobacillus plantarum P-8 in the Human and Rat Gut. PMID:29867805
Massive NGS data analysis reveals hundreds of potential novel gene fusions in human cell lines. PMID:29860514
Gene family innovation, conservation and loss on the animal stem lineage. PMID:29848444
Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes. PMID:29844299
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. PMID:29843602
The small RNA complement of adult Schistosoma haematobium. PMID:29813122
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data. PMID:29800452
Whole-genome sequencing reveals genomic signatures associated with the inflammatory microenvironments in Chinese NSCLC patients. PMID:29799009
Bidirectional regulation of adenosine-to-inosine (A-to-I) RNA editing by DEAH box helicase 9 (DHX9) in cancer. PMID:29796672
A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations. PMID:29794166
Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion. PMID:29793434
The Eukaryotic Proteome Is Shaped by E3 Ubiquitin Ligases Targeting C-Terminal Degrons. PMID:29779948
Association of Polygenic Risk Scores for Multiple Cancers in a Phenome-wide Study: Results from The Michigan Genomics Initiative. PMID:29779563
Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches. PMID:29776372
Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis). PMID:29774047
Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species. PMID:29771354
Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9. PMID:29770349
Mutant phenotypes for thousands of bacterial genes of unknown function. PMID:29769716
Population genomic data reveal genes related to important traits of quail. PMID:29762663
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells. PMID:29749794
Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs. PMID:29747566
Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing. PMID:29746484
Genome sequence of the progenitor of wheat A subgenome Triticum urartu. PMID:29743678
Improved de novo genomic assembly for the domestic donkey. PMID:29740610
Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. PMID:29732266
Applications and efficiencies of the first cat 63K DNA array. PMID:29728693
Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes. PMID:29728663
Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis. PMID:29722876
A new strategy to infer circularity applied to four new complete frog mitogenomes. PMID:29721275
Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups. PMID:29717207
Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. PMID:29716624
The genetic architecture of floral traits in the woody plant Prunus mume. PMID:29703940
CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data. PMID:29697367
Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys. PMID:29696004
Unsupervised, Statistically Based Systems Biology Approach for Unraveling the Genetics of Complex Traits: A Demonstration with Ethanol Metabolism. PMID:29689131
Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species. PMID:29689044
Chromosome-scale assembly of the Monopterus genome. PMID:29688346
Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity. PMID:29685100
Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memnon. PMID:29675466
Successful application of human-based methyl capture sequencing for methylome analysis in non-human primate models. PMID:29669513
The evolution of CpG density and lifespan in conserved primate and mammalian promoters. PMID:29661983
A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants. PMID:29661190
Insights into the Function of Long Noncoding RNAs in Sepsis Revealed by Gene Co-Expression Network Analysis. PMID:29657277
HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo. PMID:29650551
Replication-incompetent gammaretroviral and lentiviral vector-based insertional mutagenesis screens identify prostate cancer progression genes. PMID:29643985
L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. PMID:29643204
The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils. PMID:29634948
Genome-wide association identifies a novel locus for delirium risk. PMID:29631748
Detection and genotyping of human papillomavirus (HPV) in HIV-infected women and its relationship with HPV/HIV co-infection. PMID:29620669
G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences. PMID:29618053
Draft genome of the Peruvian scallop Argopecten purpuratus. PMID:29617765
De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. PMID:29615780
The constitutive differential transcriptome of a brain circuit for vocal learning. PMID:29614959
Homo sapiens-Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population. PMID:29608725
Unexpected conservation of the RNA splicing apparatus in the highly streamlined genome of Galdieria sulphuraria. PMID:29606099
Deep learning improves antimicrobial peptide recognition. PMID:29590297
HOXB7 overexpression in lung cancer is a hallmark of acquired stem-like phenotype. PMID:29576613
Long-lived rodents reveal signatures of positive selection in genes associated with lifespan. PMID:29570707
Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis. PMID:29560044
FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods. PMID:29559002
Candidate genes for first flower node identified in pepper using combined SLAF-seq and BSA. PMID:29558466
Long Non-Coding RNAs Responsive to Salt and Boron Stress in the Hyper-Arid Lluteño Maize from Atacama Desert. PMID:29558449
High-density genetic map construction and comparative genome analysis in asparagus bean. PMID:29555986
DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins. PMID:29551271
High-throughput analysis of satellite DNA in the grasshopper Pyrgomorpha conica reveals abundance of homologous and heterologous higher-order repeats. PMID:29549528
The diversity of ice algal communities on the Greenland Ice Sheet as revealed by oligotyping. PMID:29547098
Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform. PMID:29540443
Novel FR-900493 Analogues That Inhibit the Outgrowth of Clostridium difficile Spores. PMID:29503973
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. PMID:29500430
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads. PMID:29499650
Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni. PMID:29497070
Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. PMID:29489755
A Genetic Screen Identifies PRP18a, a Putative Second Step Splicing Factor Important for Alternative Splicing and a Normal Phenotype in Arabidopsis thaliana. PMID:29487188
Evolution of pyrrolizidine alkaloid biosynthesis in Apocynaceae: revisiting the defence de-escalation hypothesis. PMID:29479722
A translational silencing function of MCPIP1/Regnase-1 specified by the target site context. PMID:29471506
Genome-wide identification and analysis of A-to-I RNA editing events in bovine by transcriptome sequencing. PMID:29470549
Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum. PMID:29467168
Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki. PMID:29463761
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. PMID:29459707
Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline. PMID:29456082
Recently integrated Alu insertions in the squirrel monkey (Saimiri) lineage and application for population analyses. PMID:29449901
The Integrated Genomic Landscape of Thymic Epithelial Tumors. PMID:29438696
Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut. PMID:29435649
Identification of an (AC)n microsatellite in the Six1 gene promoter and its effect on production traits in Pietrain × Duroc × Landrace × Yorkshire pigs. PMID:29432614
5-Azacytidine prevents relapse and produces long-term complete remissions in leukemia xenografts treated with Moxetumomab pasudotox. PMID:29432154
Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria. PMID:29410661
Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade. PMID:29410443
Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches. PMID:29389989
Preferential use of unmutated immunoglobulin heavy variable region genes in Boxer dogs with chronic lymphocytic leukemia. PMID:29385200
MUMmer4: A fast and versatile genome alignment system. PMID:29373581
Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii). PMID:29367590
Genetical genomics of growth in a chicken model. PMID:29361907
HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini. PMID:29351742
Population size may shape the accumulation of functional mutations following domestication. PMID:29351740
HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees. PMID:29348708
Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D. PMID:29346625
Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes. PMID:29343494
SLAF-based high-density genetic map construction and QTL mapping for major economic traits in sea urchin Strongylocentrotus intermedius. PMID:29339742
Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells. PMID:29335803
seq-seq-pan: building a computational pan-genome data structure on whole genome alignment. PMID:29334898
The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes. PMID:29334897
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation. PMID:29329394
Analysis of DNA Methylation in Young People: Limited Evidence for an Association Between Victimization Stress and Epigenetic Variation in Blood. PMID:29325449
POU6f1 Mediates Neuropeptide-Dependent Plasticity in the Adult Brain. PMID:29305536
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins. PMID:29302007
Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. PMID:29301959
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. PMID:29297306
Scaling bioinformatics applications on HPC. PMID:29297287
A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome. PMID:29294012
Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003. PMID:29281966
Detection of de novo single nucleotide variants in offspring of atomic-bomb survivors close to the hypocenter by whole-genome sequencing. PMID:29279608
The Hidden Genomic and Transcriptomic Plasticity of Giant Marker Chromosomes in Cancer. PMID:29279323
An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench). PMID:29273003
Overexpressed HSF1 cancer signature genes cluster in human chromosome 8q. PMID:29268782
Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology. PMID:29267332
Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication. PMID:29263331
The coding and noncoding transcriptome of Neurospora crassa. PMID:29258423
Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree. PMID:29253216
Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA. PMID:29245011
Efficient transgenesis and annotated genome sequence of the regenerative flatworm model Macrostomum lignano. PMID:29242515
The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting. PMID:29233923
Whole-genome sequencing and SNV genotyping of 'Nebbiolo' (Vitis vinifera L.) clones. PMID:29229917
DNAAF1 links heart laterality with the AAA+ ATPase RUVBL1 and ciliary intraflagellar transport. PMID:29228333
CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations. PMID:29220491
RetrogeneDB-a database of plant and animal retrocopies. PMID:29220443
Transcription profiling and identification of infection-related genes in Phytophthora cactorum. PMID:29218408
Age-related gene expression changes, and transcriptome wide association study of physical and cognitive aging traits, in the Lothian Birth Cohort 1936. PMID:29207374
Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. PMID:29202864
Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera. PMID:29197336
Voluntary exposure to a toxin: the genetic influence on ethanol consumption. PMID:29196862
3C-PCR: a novel proximity ligation-based approach to phase chromosomal rearrangement breakpoints with distal allelic variants. PMID:29196799
A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. PMID:29195078
Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome. PMID:29186486
HLA genotyping by next-generation sequencing of complementary DNA. PMID:29179676
The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues. PMID:29176795
ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease. PMID:29162642
Fast batch searching for protein homology based on compression and clustering. PMID:29162030
Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. PMID:29149249
Age, estrogen, and immune response in breast adenocarcinoma and adjacent normal tissue. PMID:29147603
Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). PMID:29145861
The deep conservation of the Lepidoptera Z chromosome suggests a non-canonical origin of the W. PMID:29133797
The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA. PMID:29127278
Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.). PMID:29121864
The complete chloroplast genome of Primulina and two novel strategies for development of high polymorphic loci for population genetic and phylogenetic studies. PMID:29115917
The UCSC Genome Browser database: 2018 update. PMID:29106570
Stable Core Gut Microbiota across the Freshwater-to-Saltwater Transition for Farmed Atlantic Salmon. PMID:29101198
K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity. PMID:29100493
Stress amplifies sex differences in primate prefrontal profiles of gene expression. PMID:29096718
Genome-wide discovery of long intergenic noncoding RNAs and their epigenetic signatures in the rat. PMID:29093522
A distinct hematopoietic stem cell population for rapid multilineage engraftment in nonhuman primates. PMID:29093179
Variant Review with the Integrative Genomics Viewer. PMID:29092934
Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s. PMID:29085779
High rate of translocation-based gene birth on the Drosophila Y chromosome. PMID:29078298
Differences in the genetic control of early egg development and reproduction between C. elegans and its parthenogenetic relative D. coronatus. PMID:29075433
Keeping it complicated: Mitochondrial genome plasticity across diplonemids. PMID:29074957
Detecting large deletions at base pair level by combining split read and paired read data. PMID:29072143
Detection and quantification of mitochondrial DNA deletions from next-generation sequence data. PMID:29072135
sRNAnalyzer-a flexible and customizable small RNA sequencing data analysis pipeline. PMID:29069500
An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithm. PMID:29065853
Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents. PMID:29062974
Spontaneous circadian rhythms in a cold-adapted natural isolate of Aureobasidium pullulans. PMID:29062053
Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination. PMID:29052505
The genome draft of coconut (Cocos nucifera). PMID:29048487
Genome structure of Rosa multiflora, a wild ancestor of cultivated roses. PMID:29045613
Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. PMID:29038757
Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. PMID:29038424
MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. PMID:29028869
Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. PMID:29038424
MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. PMID:29028869
HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing. PMID:29026435
Dynamic landscape and regulation of RNA editing in mammals. PMID:29022589
The draft genome assembly of Rhododendron delavayi Franch. var. delavayi. PMID:29020749
Comprehensive benchmarking of SNV callers for highly admixed tumor data. PMID:29020110
DNA sequencing at 40: past, present and future. PMID:29019985
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data. PMID:29019934
The First Genetic Map in Sweet Osmanthus (Osmanthus fragrans Lour.) Using Specific Locus Amplified Fragment Sequencing. PMID:29018460
High-throughput analysis unveils a highly shared satellite DNA library among three species of fish genus Astyanax. PMID:29018237
Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. PMID:28988769
Genome-wide Mapping of Off-Target Events in Single-Stranded Oligodeoxynucleotide-Mediated Gene Repair Experiments. PMID:28988714
Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle. PMID:28985340
Optimal choice of word length when comparing two Markov sequences using a χ 2-statistic. PMID:28984181
Convergent evolution of Y chromosome gene content in flies. PMID:28978907
qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms. PMID:28977518
A Genetic Screen for Pre-mRNA Splicing Mutants of Arabidopsis thaliana Identifies Putative U1 snRNP Components RBM25 and PRP39a. PMID:28971960
A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3). PMID:28971018
Federation in genomics pipelines: techniques and challenges. PMID:28968781
EST-BASED ANALYSIS OF GENE EXPRESSION IN THE HUMAN COCHLEA. PMID:28967002
Evolution of Alu Subfamily Structure in the Saimiri Lineage of New World Monkeys. PMID:28957461
Accurate clinical genetic testing for autoinflammatory diseases using the next-generation sequencing platform MiSeq. PMID:28956000
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy. PMID:28931371
Comprehensive analysis of lncRNAs and mRNAs in skeletal muscle of rainbow trout (Oncorhynchus mykiss) exposed to estradiol. PMID:28924252
Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. PMID:28922755
Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. PMID:28922347
Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita. PMID:28916791
Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data. PMID:28900149
Approaches for in silico finishing of microbial genome sequences. PMID:28898352
Acidophilic green algal genome provides insights into adaptation to an acidic environment. PMID:28893987
Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis. PMID:28887541
Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine. PMID:28877764
A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri. PMID:28874118
Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley. PMID:28871634
Quantitative sequence characterization for repetitive DNA content in the supernumerary chromosome of the migratory locust. PMID:28868580
Efficient genome-wide association in biobanks using topic modeling identifies multiple novel disease loci. PMID:28861588
Transcriptome analysis reveals the host selection fitness mechanisms of the Rhizoctonia solani AG1IA pathogen. PMID:28860554
Persistent histone modifications at the BDNF and Cdk-5 promoters following extinction of nicotine-seeking in rats. PMID:28857504
A Glimpse into the Satellite DNA Library in Characidae Fish (Teleostei, Characiformes). PMID:28855916
Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids. PMID:28854624
De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance. PMID:28851357
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. PMID:28851275
Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains. PMID:28848533
Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion. PMID:28846694
Population genetic structure of Guiana dolphin (Sotalia guianensis) from the southwestern Atlantic coast of Brazil. PMID:28837691
An integrated expression atlas of miRNAs and their promoters in human and mouse. PMID:28829439
Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems. PMID:28821820
Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly. PMID:28821183
Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing. PMID:28812996
Transcriptome Association Identifies Regulators of Wheat Spike Architecture. PMID:28807930
Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ. PMID:28806931
A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing. PMID:28794490
Recombinant Origins of Pathogenic and Nonpathogenic Mouse Gammaretroviruses with Polytropic Host Range. PMID:28794032
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes. PMID:28778180
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. PMID:28778149
Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. PMID:28778145
High-Coverage Whole-Exome Sequencing Identifies Candidate Genes for Suicide in Victims with Major Depressive Disorder. PMID:28769055
Presence of a Shared 5'-Leader Sequence in Ancestral Human and Mammalian Retroviruses and Its Transduction into Feline Leukemia Virus. PMID:28768854
Elevated auxin biosynthesis and transport underlie high vein density in C4 leaves. PMID:28761000
Structural basis of head to head polyketide fusion by CorB. PMID:28757960
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. PMID:28756775
Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis. PMID:28750650
A systems approach to a spatio-temporal understanding of the drought stress response in maize. PMID:28747711
Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease. PMID:28739600
Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles. PMID:28738815
Differentiating Botulinum Neurotoxin-Producing Clostridia with a Simple, Multiplex PCR Assay. PMID:28733282
Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion. PMID:28732471
Dynamics of genomic innovation in the unicellular ancestry of animals. PMID:28726632
Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. PMID:28725468
Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. PMID:28722025
Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. PMID:28721231
Microbiome overview in swine lungs. PMID:28719637
Regulation of the activity of the promoter of RNA-induced silencing, C3PO. PMID:28714243
Splicing Activation by Rbfox Requires Self-Aggregation through Its Tyrosine-Rich Domain. PMID:28708999
LINE-1 Hypermethylation in Serum Cell-Free DNA of Relapsing Remitting Multiple Sclerosis Patients. PMID:28707075
Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation. PMID:28704649
The effects of sampling on the efficiency and accuracy of k-mer indexes: Theoretical and empirical comparisons using the human genome. PMID:28686614
Interpreting whole genome and exome sequencing data of individual gastric cancer samples. PMID:28683819
Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. PMID:28678784
Genome Sequences of Marine Shrimp Exopalaemon carinicauda Holthuis Provide Insights into Genome Size Evolution of Caridea. PMID:28678163
Expression of a SOX1 overlapping transcript in neural differentiation and cancer models. PMID:28674729
Automated tools for comparative sequence analysis of genic regions using the GenePalette application. PMID:28673819
A massively parallel strategy for STR marker development, capture, and genotyping. PMID:28666376
A Highly Dense Genetic Map for Ginkgo biloba Constructed Using Sequence-Based Markers. PMID:28663754
Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments. PMID:28652936
In Vivo Murine-Matured Human CD3+ Cells as a Preclinical Model for T Cell-Based Immunotherapies. PMID:28649577
Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta. PMID:28644839
McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data. PMID:28637810
Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution. PMID:28622346
Mapping and Preliminary Analysis of ABORTED MICROSPORES (AMS) as the Candidate Gene Underlying the Male Sterility (MS-5) Mutant in Melon (Cucumis melo L.). PMID:28611814
Gene silencing by RNA interference in Sarcoptes scabiei: a molecular tool to identify novel therapeutic targets. PMID:28601087
Whole genome sequencing of an ExPEC that caused fatal pneumonia at a pig farm in Changchun, China. PMID:28599670
Androgen receptor and miR-206 regulation in prostate cancer. PMID:28598253
CottonFGD: an integrated functional genomics database for cotton. PMID:28595571
Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus. PMID:28595343
A comprehensive overview and evaluation of circular RNA detection tools. PMID:28594838
A simple and economical method for improving whole genome alignment. PMID:28589863
Specific-Locus Amplified Fragment Sequencing Reveals Spontaneous Single-Nucleotide Mutations in Rice OsMsh6 Mutants. PMID:28589142
Identification of Proteases and Protease Inhibitors in Allergenic and Non-Allergenic Pollen. PMID:28587253
Analysis of LINE-1 Elements in DNA from Postmortem Brains of Individuals with Schizophrenia. PMID:28585566
Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes. PMID:28585529
Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content. PMID:28582424
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. PMID:28581499
The evolution and population diversity of human-specific segmental duplications. PMID:28580430
Analysis of Copy Number Variation in the Abp Gene Regions of Two House Mouse Subspecies Suggests Divergence during the Gene Family Expansions. PMID:28575204
The Agassiz's desert tortoise genome provides a resource for the conservation of a threatened species. PMID:28562605
Repeated divergent selection on pigmentation genes in a rapid finch radiation. PMID:28560331
A Review on Recent Computational Methods for Predicting Noncoding RNAs. PMID:28553651
An episomal vector-based CRISPR/Cas9 system for highly efficient gene knockout in human pluripotent stem cells. PMID:28539611
GCN2 phosphorylates HIV-1 integrase and decreases HIV-1 replication by limiting viral integration. PMID:28536474
Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). PMID:28523639
Reading LINEs within the cocaine addicted brain. PMID:28523221
MET Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma. PMID:28522754
Identification of Sex-determining Loci in Pacific White Shrimp Litopeneaus vannamei Using Linkage and Association Analysis. PMID:28508952
Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets. PMID:28507140
An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci. PMID:28505156
Expansion of the redox-sensitive proteome coincides with the plastid endosymbiosis. PMID:28504699
Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.). PMID:28503182
Short Read Mapping: An Algorithmic Tour. PMID:28502990
Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods. PMID:28501627
High-Density Genetic Map Construction and Gene Mapping of Basal Branching Habit and Flowers per Leaf Axil in Sesame. PMID:28496450
Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript sequences. PMID:28492983
GeSeq - versatile and accurate annotation of organelle genomes. PMID:28486635
Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. PMID:28484037
Heritable L1 retrotransposition in the mouse primordial germline and early embryo. PMID:28483779
High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing. PMID:28482802
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome. PMID:28482049
Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata. PMID:28475810
Comparative study of viromes from freshwater samples of the Ile-Balkhash region of Kazakhstan captured through metagenomic analysis. PMID:28466051
Geno- and phenotypic characteristics of a transfected Babesia bovis 6-Cys-E knockout clonal line. PMID:28464956
Evolutionary history of glucose-6-phosphatase encoding genes in vertebrate lineages: towards a better understanding of the functions of multiple duplicates. PMID:28464795
A-to-I RNA Editing in the Earliest-Diverging Eumetazoan Phyla. PMID:28453786
A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PMID:28448514
Draft genome of the lined seahorse, Hippocampus erectus. PMID:28444302
Mutational screening of SLC39A5, LEPREL1 and LRPAP1 in a cohort of 187 high myopia patients. PMID:28442722
Whole genome sequencing predicts novel human disease models in rhesus macaques. PMID:28438488
HirBin: high-resolution identification of differentially abundant functions in metagenomes. PMID:28431529
Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis. PMID:28431015
The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). PMID:28431014
Next generation mapping reveals novel large genomic rearrangements in prostate cancer. PMID:28423598
Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics. PMID:28420677
Contrasting evolutionary genome dynamics between domesticated and wild yeasts. PMID:28416820
gb4gv: a genome browser for geminivirus. PMID:28413726
TRE5-A retrotransposition profiling reveals putative RNA polymerase III transcription complex binding sites on the Dictyostelium extrachromosomal rDNA element. PMID:28406973
LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types. PMID:28398238
A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray. PMID:28390408
Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. PMID:28390096
HALC: High throughput algorithm for long read error correction. PMID:28381259
Kart: a divide-and-conquer algorithm for NGS read alignment. PMID:28379292
Comparative genomic identification and validation of β-defensin genes in the Ovis aries genome. PMID:28376793
Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq). PMID:28376721
A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana. PMID:28373290
Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants. PMID:28369350
Generation of mature T cells from human hematopoietic stem and progenitor cells in artificial thymic organoids. PMID:28369043
Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics. PMID:28368449
In silico analysis of the sequence features responsible for alternatively spliced introns in the model green alga Chlamydomonas reinhardtii. PMID:28364390
MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool. PMID:28350876
Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis. PMID:28348877
Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics. PMID:28348813
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. PMID:28347275
Different expression patterns of sperm motility-related genes in testis of diploid and tetraploid cyprinid fish†. PMID:28340181
Transcriptomic Complexity of Aspergillus terreus Velvet Gene Family under the Influence of Butyrolactone I. PMID:28335447
Efficient CNV breakpoint analysis reveals unexpected structural complexity and correlation of dosage-sensitive genes with clinical severity in genomic disorders. PMID:28334874
The mouse genome displays highly dynamic populations of KRAB-zinc finger protein genes and related genetic units. PMID:28334004
Time-course expression QTL-atlas of the global transcriptional response of wheat to Fusarium graminearum. PMID:28332274
Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species. PMID:28330894
MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach. PMID:28327976
GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data. PMID:28325279
Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis. PMID:28322295
Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi. PMID:28322291
Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing. PMID:28321219
An Analysis of Adenovirus Genomes Using Whole Genome Software Tools. PMID:28293072
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. PMID:28284188
A Frameshift Mutation in KIT is Associated with White Spotting in the Arabian Camel. PMID:28282952
The birth of a human-specific neural gene by incomplete duplication and gene fusion. PMID:28279197
Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia. PMID:28273067
Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome. PMID:28260531
SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions. PMID:28259144
Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus. PMID:28252665
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. PMID:28250805
RNA-Sequencing data supports the existence of novel VEGFA splicing events but not of VEGFAxxxb isoforms. PMID:28246395
An atlas of human long non-coding RNAs with accurate 5' ends. PMID:28241135
Mutational landscape reflects the biological continuum of plasma cell dyscrasias. PMID:28234344
Overexpression of hsa-miR-939 follows by NGFR down-regulation and apoptosis reduction. PMID:28229962
PEMapper and PECaller provide a simplified approach to whole-genome sequencing. PMID:28223510
A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array. PMID:28220206
Pneumococcal prophages are diverse, but not without structure or history. PMID:28218261
Convergent Evolution of the Osmoregulation System in Decapod Shrimps. PMID:28204969
An annotated draft genome for Radix auricularia (Gastropoda, Mollusca). PMID:28204581
Transcriptome analysis around the onset of strawberry fruit ripening uncovers an important role of oxidative phosphorylation in ripening. PMID:28195221
Functional preservation and variation in the cone opsin genes of nocturnal tarsiers. PMID:28193820
ETS Proto-oncogene 1 Transcriptionally Up-regulates the Cholangiocyte Senescence-associated Protein Cyclin-dependent Kinase Inhibitor 2A. PMID:28184004
Small genomic insertions form enhancers that misregulate oncogenes. PMID:28181482
Evolutionary mechanism and biological functions of 8-mers containing CG dinucleotide in yeast. PMID:28181048
Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits. PMID:28179367
Comparative genomics of canine hemoglobin genes reveals primacy of beta subunit delta in adult carnivores. PMID:28178945
PALADIN: protein alignment for functional profiling whole metagenome shotgun data. PMID:28158639
The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis. PMID:28158318
RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing. PMID:28149701
Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics. PMID:28148977
Improved annotation with de novo transcriptome assembly in four social amoeba species. PMID:28143409
Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome. PMID:28130382
Global and regional dissemination and evolution of Burkholderia pseudomallei. PMID:28112723
High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits. PMID:28111584
Photosynthesis in C3-C4 intermediate Moricandia species. PMID:28110276
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. PMID:28105025
Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression. PMID:28103240
Loss of AXIN1 drives acquired resistance to WNT pathway blockade in colorectal cancer cells carrying RSPO3 fusions. PMID:28100566
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. PMID:28100185
The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry. PMID:28094805
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. PMID:28092920
Identification of some main Streptococcus iniae associated proteins: relationship. PMID:28091882
Identification of misexpressed genetic elements in hybrids between Drosophila-related species. PMID:28091568
Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene in Giardia. PMID:28090405
A SNP-Enabled Assessment of Genetic Diversity, Evolutionary Relationships and the Identification of Candidate Genes in Chrysanthemum. PMID:28082602
Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes. PMID:28076377
Accurate Breakpoint Mapping in Apparently Balanced Translocation Families with Discordant Phenotypes Using Whole Genome Mate-Pair Sequencing. PMID:28072833
A molecular genetic toolbox for Yarrowia lipolytica. PMID:28066508
Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA. PMID:28066462
Transcriptome profiles reveal gene regulation of peanut (Arachis hypogaea L.) nodulation. PMID:28059169
MPD: multiplex primer design for next-generation targeted sequencing. PMID:28056760
Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies. PMID:28053115
Evolution of transcript modification by N6-methyladenosine in primates. PMID:28052920
ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data. PMID:28049418
A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis. PMID:28045132
A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies. PMID:28033318
Immunodominance of Antibody Recognition of the HIV Envelope V2 Region in Ig-Humanized Mice. PMID:28011932
SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly. PMID:28011768
Bioinformatic tools for analysis of CLIP ribonucleoprotein data. PMID:28008714
Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment. PMID:28007977
A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data. PMID:27998939
Complete plastid genome of Eriobotrya japonica (Thunb.) Lindl and comparative analysis in Rosaceae. PMID:27995013
Identification of a novel 15.5 kb SHOX deletion associated with marked intrafamilial phenotypic variability and analysis of its molecular origin. PMID:27994182
A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. PMID:27993777
Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis. PMID:27991530
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics. PMID:27980708
The intron-enriched HERV-K(HML-10) family suppresses apoptosis, an indicator of malignant transformation. PMID:27980690
Hotair Is Dispensible for Mouse Development. PMID:27977683
DNA Methylation Identifies Loci Distinguishing Hereditary Nonpolyposis Colorectal Cancer Without Germ-Line MLH1/MSH2 Mutation from Sporadic Colorectal Cancer. PMID:27977020
The seahorse genome and the evolution of its specialized morphology. PMID:27974754
RPAN: rice pan-genome browser for ∼3000 rice genomes. PMID:27940610
LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans. PMID:27934698
Acquired RAS or EGFR mutations and duration of response to EGFR blockade in colorectal cancer. PMID:27929064
A chromosome-level genome assembly of the Asian arowana, Scleropages formosus. PMID:27922628
A human microprotein that interacts with the mRNA decapping complex. PMID:27918561
Whole exome association of rare deletions in multiplex oral cleft families. PMID:27910131
The UCSC Genome Browser database: 2017 update. PMID:27899642
MEGARes: an antimicrobial resistance database for high throughput sequencing. PMID:27899569
RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk. PMID:27884183
Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods. PMID:27881416
Draft genome of the living fossil Ginkgo biloba. PMID:27871309
Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation. PMID:27862604
A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. PMID:27855707
AnnoLnc: a web server for systematically annotating novel human lncRNAs. PMID:27852242
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. PMID:27852011
Identification of new TRIP12 variants and detailed clinical evaluation of individuals with non-syndromic intellectual disability with or without autism. PMID:27848077
Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme. PMID:27843499
Genetic architecture of the maize kernel row number revealed by combining QTL mapping using a high-density genetic map and bulked segregant RNA sequencing. PMID:27842488
Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. PMID:27829365
LSCplus: a fast solution for improving long read accuracy by short read alignment. PMID:27829364
Circular RNAs and their associations with breast cancer subtypes. PMID:27829232
Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems? PMID:27822532
Postnatal regulation of MAMDC4 in the porcine intestinal epithelium is influenced by bacterial colonization. PMID:27821716
The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis. PMID:27812037
Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots. PMID:27804982
Computational workflow for the fine-grained analysis of metagenomic samples. PMID:27801291
Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors. PMID:27792127
TRPM8 genetic variations associated with COPD risk in the Chinese Han population. PMID:27789940
EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes. PMID:27785876
Transcriptomic resources and marker validation for diploid and polyploid Veronica (Plantaginaceae) from New Zealand and Europe. PMID:27785388
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries. PMID:27756200
Endogenous Multiple Exon Skipping and Back-Splicing at the DMD Mutation Hotspot. PMID:27754374
Morphological and Transcriptomic Analysis of a Beetle Chemosensory System Reveals a Gnathal Olfactory Center. PMID:27751175
Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance. PMID:27734962
Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan. PMID:27721649
Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. PMID:27717381
A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PMID:27711162
High expression of new genes in trochophore enlightening the ontogeny and evolution of trochozoans. PMID:27698463
Targeted next-generation sequencing for TP53, RAS, BRAF, ALK and NF1 mutations in anaplastic thyroid cancer. PMID:27696251
Feralisation targets different genomic loci to domestication in the chicken. PMID:27686863
Comprehensive analysis of microRNA signature of mouse pancreatic acini: overexpression of miR-21-3p in acute pancreatitis. PMID:27686613
A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens. PMID:27677796
Sex-Biased Transcriptome of Schistosoma mansoni: Host-Parasite Interaction, Genetic Determinants and Epigenetic Regulators Are Associated with Sexual Differentiation. PMID:27677173
Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient. PMID:27668083
C3 cotyledons are followed by C4 leaves: intra-individual transcriptome analysis of Salsola soda (Chenopodiaceae). PMID:27660482
Differing Alterations of Two Esca Associated Fungi, Phaeoacremonium aleophilum and Phaeomoniella chlamydospora on Transcriptomic Level, to Co-Cultured Vitis vinifera L. calli. PMID:27658052
Digital Gene Expression Profiling to Explore Differentially Expressed Genes Associated with Terpenoid Biosynthesis during Fruit Development in Litsea cubeba. PMID:27657027
The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers. PMID:27651357
Comparative genomic analysis between newly sequenced Brucella suis Vaccine Strain S2 and the Virulent Brucella suis Strain 1330. PMID:27645563
Exploring the transcriptome of Staphylococcus aureus in its natural niche. PMID:27641137
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. PMID:27633831
A novel TP53-KPNA3 translocation defines a de novo treatment-resistant clone in osteosarcoma. PMID:27626065
PGD: a pangolin genome hub for the research community. PMID:27616775
Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes. PMID:27613107
The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate. PMID:27609345
Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler. PMID:27595578
The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements. PMID:27588042
Prevalence and Abundance of Florfenicol and Linezolid Resistance Genes in Soils Adjacent to Swine Feedlots. PMID:27573068
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. PMID:27572438
Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement. PMID:27567261
Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution. PMID:27561724
Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T). PMID:27559429
High-quality genome assembly of channel catfish, Ictalurus punctatus. PMID:27549802
Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PMID:27547574
Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases. PMID:27540175
RES-Scanner: a software package for genome-wide identification of RNA-editing sites. PMID:27538485
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. PMID:27535938
Uncovering Earth's virome. PMID:27533034
Evaluation of Normalization Methods for RNA-Seq Gene Expression Estimation. PMID:27532058
Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). PMID:27531712
De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure. PMID:27527578
Satellite DNA content illuminates the ancestry of a supernumerary (B) chromosome. PMID:27522227
Proline Coordination with Fatty Acid Synthesis and Redox Metabolism of Chloroplast and Mitochondria. PMID:27512016
Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. PMID:27502555
Association of variations in HLA class II and other loci with susceptibility to EGFR-mutated lung adenocarcinoma. PMID:27501781
The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats. PMID:27501045
Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms. PMID:27499042
Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome. PMID:27489570
Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method. PMID:27487952
Meiotic pairing and gene expression disturbance in germ cells from an infertile boar with a balanced reciprocal autosome-autosome translocation. PMID:27484982
Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes. PMID:27474039
Identification of new branch points and unconventional introns in Saccharomyces cerevisiae. PMID:27473169
Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. PMID:27473065
Characterization of the T-cell receptor beta chain repertoire in tumor-infiltrating lymphocytes. PMID:27465739
TALEN-Mediated Mutagenesis and Genome Editing. PMID:27464798
SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence. PMID:27458203
On the origin and evolutionary consequences of gene body DNA methylation. PMID:27457936
Transcriptome Profiling of Huanglongbing (HLB) Tolerant and Susceptible Citrus Plants Reveals the Role of Basal Resistance in HLB Tolerance. PMID:27446161
The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features. PMID:27444405
Variant discovery and breakpoint region prediction for studying the human 22q11.2 deletion using BAC clone and whole genome sequencing analysis. PMID:27436579
Reciprocal genomic evolution in the ant-fungus agricultural symbiosis. PMID:27436133
Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole-Genome Sequences. PMID:27436010
RNA editing generates cellular subsets with diverse sequence within populations. PMID:27418407
Comorbid Analysis of Genes Associated with Autism Spectrum Disorders Reveals Differential Evolutionary Constraints. PMID:27414027
Microbiota Dysbiosis Controls the Neuroinflammatory Response after Stroke. PMID:27413153
Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain. PMID:27412987
Transcriptome analysis of woodland strawberry (Fragaria vesca) response to the infection by Strawberry vein banding virus (SVBV). PMID:27411713
CrispRVariants charts the mutation spectrum of genome engineering experiments. PMID:27404876
Identification and Validation of SNP Markers Linked to Dwarf Traits Using SLAF-Seq Technology in Lagerstroemia. PMID:27404662
The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity. PMID:27393338
Identification of Multiple Forms of RNA Transcripts Associated with Human-Specific Retrotransposed Gene Copies. PMID:27389689
Comparative Analysis of Human B Cell Epitopes Based on BCG Genomes. PMID:27382565
Structure and evolution of the gorilla and orangutan growth hormone loci. PMID:27376725
Natural Allelic Variations in Highly Polyploidy Saccharum Complex. PMID:27375658
Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges. PMID:27375355
A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome. PMID:27364915
Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut. PMID:27358740
The multicellularity genes of dictyostelid social amoebas. PMID:27357338
Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus). PMID:27352242
Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. PMID:27350259
Genome-Wide Survey of Gut Fungi (Harpellales) Reveals the First Horizontally Transferred Ubiquitin Gene from a Mosquito Host. PMID:27343289
CAP protein superfamily members in Toxocara canis. PMID:27342979
Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs. PMID:27339130
Overexpression of CHOP in Myelinating Cells Does Not Confer a Significant Phenotype under Normal or Metabolic Stress Conditions. PMID:27335410
PEP_scaffolder: using (homologous) proteins to scaffold genomes. PMID:27334475
Identification of polymorphic and off-target probe binding sites on the Illumina Infinium MethylationEPIC BeadChip. PMID:27330998
Microsatellite markers used for genome-wide association mapping of partial resistance to Sclerotinia sclerotiorum in a world collection of Brassica napus. PMID:27330402
TBR1 regulates autism risk genes in the developing neocortex. PMID:27325115
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. PMID:27322404
Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences. PMID:27318200
Identification of Coilin Mutants in a Screen for Enhanced Expression of an Alternatively Spliced GFP Reporter Gene in Arabidopsis thaliana. PMID:27317682
BLAT2DOLite: An Online System for Identifying Significant Relationships between Genetic Sequences and Diseases. PMID:27315278
Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PMID:27309962
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes. PMID:27307617
Evaluation of microRNA alignment techniques. PMID:27284164
Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): Inference from transcriptome-wide coalescence analyses. PMID:27282112
Aberrant PD-L1 expression through 3'-UTR disruption in multiple cancers. PMID:27281199
The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia. PMID:27279728
A Chromosome 7 Pericentric Inversion Defined at Single-Nucleotide Resolution Using Diagnostic Whole Genome Sequencing in a Patient with Hand-Foot-Genital Syndrome. PMID:27272187
Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems. PMID:27252693
Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing. PMID:27245094
Tricking Arthrinium malaysianum into Producing Industrially Important Enzymes Under 2-Deoxy D-Glucose Treatment. PMID:27242677
gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes. PMID:27242033
Draft Genome Sequence of Mycobacterium interjectum Strain ATCC 51457T. PMID:27231376
Draft Genome Sequence of Mycobacterium houstonense Strain ATCC 49403T. PMID:27231371
Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds. PMID:27230888
JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells. PMID:27225868
Expression Patterns and Functional Novelty of Ribonuclease 1 in Herbivorous Megalobrama amblycephala. PMID:27213364
Identification of human RNA editing sites: A historical perspective. PMID:27208508
Characterisation of Candida within the Mycobiome/Microbiome of the Lower Respiratory Tract of ICU Patients. PMID:27206014
Zinc Finger Domain of the PRDM9 Gene on Chromosome 1 Exhibits High Diversity in Ruminants but Its Paralog PRDM7 Contains Multiple Disruptive Mutations. PMID:27203728
Pleiotropic effect of thyroid hormones on gene expression in fish as exemplified from the blue bream Ballerus ballerus (Cyprinidae): Results of transcriptomic analysis. PMID:27193715
Viruses are a dominant driver of protein adaptation in mammals. PMID:27187613
An automated approach for global identification of sRNA-encoding regions in RNA-Seq data from Mycobacterium tuberculosis. PMID:27174874
A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. PMID:27172201
Development of new PCR multiplex system by the simultaneous detection of 10 miniSTRs, SE33, Penta E, Penta D, and four Y-STRs. PMID:27166705
Next-generation sequencing-based detection of germline L1-mediated transductions. PMID:27161561
A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. PMID:27158781
Genomic analysis of mouse VL30 retrotransposons. PMID:27158269
DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. PMID:27154274
Efficient privacy-preserving string search and an application in genomics. PMID:27153731
Informed kmer selection for de novo transcriptome assembly. PMID:27153653
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. PMID:27153593
Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome. PMID:27148310
Impact of Hypocaloric Hyperproteic Diet on Gut Microbiota in Overweight or Obese Patients with Nonalcoholic Fatty Liver Disease: A Pilot Study. PMID:27142672
Mitochondrial Genome and Nuclear Markers Provide New Insight into the Evolutionary History of Macaques. PMID:27135608
Redundans: an assembly pipeline for highly heterozygous genomes. PMID:27131372
Mechanical cell competition kills cells via induction of lethal p53 levels. PMID:27109213
Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools. PMID:27100792
Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products. PMID:27100228
LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots. PMID:27098918
Bitpacking techniques for indexing genomes: I. Hash tables. PMID:27095998
The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. PMID:27089831
Prediction of Toxin Genes from Chinese Yellow Catfish Based on Transcriptomic and Proteomic Sequencing. PMID:27089325
UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing. PMID:27083325
CDROM: Classification of Duplicate gene RetentiOn Mechanisms. PMID:27080514
Stress-induced gene expression and behavior are controlled by DNA methylation and methyl donor availability in the dentate gyrus. PMID:27078100
High-Density Genetic Mapping Identifies New Major Loci for Tolerance to Low-Phosphorus Stress in Soybean. PMID:27065041
Genomic Aberrations in Crizotinib Resistant Lung Adenocarcinoma Samples Identified by Transcriptome Sequencing. PMID:27045755
Toward Understanding the Genetic Basis of Yak Ovary Reproduction: A Characterization and Comparative Analyses of Estrus Ovary Transcriptiome in Yak and Cattle. PMID:27044040
Reactive Oxygen Species Play a Role in the Infection of the Necrotrophic Fungi, Rhizoctonia solani in Wheat. PMID:27031952
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. PMID:27029936
Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA. PMID:27029813
Placenta-Enriched LincRNAs MIR503HG and LINC00629 Decrease Migration and Invasion Potential of JEG-3 Cell Line. PMID:27023770
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites. PMID:27023428
Using a Candidate Gene-Based Genetic Linkage Map to Identify QTL for Winter Survival in Perennial Ryegrass. PMID:27010567
The real cost of sequencing: scaling computation to keep pace with data generation. PMID:27009100
Learning to cope with stress modulates anterior cingulate cortex stargazin expression in monkeys and mice. PMID:27003116
Mapping of a Novel Race Specific Resistance Gene to Phytophthora Root Rot of Pepper (Capsicum annuum) Using Bulked Segregant Analysis Combined with Specific Length Amplified Fragment Sequencing Strategy. PMID:26992080
RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. PMID:26984526
Unlocking the genetic diversity of Creole wheats. PMID:26976656
BBBomics-Human Blood Brain Barrier Transcriptomics Hub. PMID:26973449
Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5. PMID:26958346
Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains. PMID:26954687
Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris. PMID:26943850
Identification of mRNA isoform switching in breast cancer. PMID:26939613
Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia. PMID:26939550
A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. PMID:26934921
Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict. PMID:26934590
Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease. PMID:26932197
The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus. PMID:26921302
Host Mitochondrial Association Evolved in the Human Parasite Toxoplasma gondii via Neofunctionalization of a Gene Duplicate. PMID:26920761
Transcriptome Analysis in Domesticated Species: Challenges and Strategies. PMID:26917953
HsfA2 Controls the Activity of Developmentally and Stress-Regulated Heat Stress Protection Mechanisms in Tomato Male Reproductive Tissues. PMID:26917685
Discovery of a new repeat family in the Callithrix jacchus genome. PMID:26916108
γ-Crystallins of the chicken lens: remnants of an ancient vertebrate gene family in birds. PMID:26913478
Genetic features of Mycobacterium tuberculosis modern Beijing sublineage. PMID:26905026
Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. PMID:26904094
The genome of the miiuy croaker reveals well-developed innate immune and sensory systems. PMID:26902509
Resolving rates of mutation in the brain using single-neuron genomics. PMID:26901440
Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. PMID:26898953
Ensembl comparative genomics resources. PMID:26896847
BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data. PMID:26894997
Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek). PMID:26887961
Genetic mapping and molecular marker development for Pi65(t), a novel broad-spectrum resistance gene to rice blast using next-generation sequencing. PMID:26883042
TOPORS, a Dual E3 Ubiquitin and Sumo1 Ligase, Interacts with 26 S Protease Regulatory Subunit 4, Encoded by the PSMC1 Gene. PMID:26872363
Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon. PMID:26869021
Identification of Targets of CUG-BP, Elav-Like Family Member 1 (CELF1) Regulation in Embryonic Heart Muscle. PMID:26866591
Sequence Diversity, Intersubgroup Relationships, and Origins of the Mouse Leukemia Gammaretroviruses of Laboratory and Wild Mice. PMID:26865715
Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. PMID:26862001
Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary. PMID:26858690
New insights into the Plasmodium vivax transcriptome using RNA-Seq. PMID:26858037
Genome ARTIST: a robust, high-accuracy aligner tool for mapping transposon insertions and self-insertions. PMID:26855675
Genomes of Strongylocentrotus franciscanus and Lytechinus variegatus: are there any genomic explanations for the two order of magnitude difference in the lifespan of sea urchins? PMID:26851889
Homozygosity mapping identified a novel protein truncating mutation (p.Ser100Leufs*24) of the BBS9 gene in a consanguineous Pakistani family with Bardet Biedl syndrome. PMID:26846096
Reconstruction of the insulin-like signalling pathway of Haemonchus contortus. PMID:26842675
Mapping the Flavor Contributing Traits on "Fengwei Melon" (Cucumis melo L.) Chromosomes Using Parent Resequencing and Super Bulked-Segregant Analysis. PMID:26840947
Long Read Alignment with Parallel MapReduce Cloud Platform. PMID:26839887
A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PMID:26828929
Rapid Identification of Candidate Genes for Seed Weight Using the SLAF-Seq Method in Brassica napus. PMID:26824525
Genome Sequence and Analysis of Peptoclostridium difficile Strain ZJCDC-S82. PMID:26823648
Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos). PMID:26819540
Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. PMID:26818075
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. PMID:26814032
Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics. PMID:26810311
Sp1 and Sp3 Are the Transcription Activators of Human ek1 Promoter in TSA-Treated Human Colon Carcinoma Cells. PMID:26807725
The Mouse Solitary Odorant Receptor Gene Promoters as Models for the Study of Odorant Receptor Gene Choice. PMID:26794459
H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes. PMID:26789284
Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes. PMID:26781660
The Phenotypic and Genetic Underpinnings of Flower Size in Polemoniaceae. PMID:26779209
Expression of a Novel D4 Dopamine Receptor in the Lamprey Brain. Evolutionary Considerations about Dopamine Receptors. PMID:26778974
An evaluation of the accuracy and speed of metagenome analysis tools. PMID:26778510
PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events. PMID:26758031
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. PMID:26757703
Microvirga massiliensis sp. nov., the human commensal with the largest genome. PMID:26749561
Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies. PMID:26743510
Genetical Genomics of Behavior: A Novel Chicken Genomic Model for Anxiety Behavior. PMID:26733665
Effects of Gene Duplication, Positive Selection, and Shifts in Gene Expression on the Evolution of the Venom Gland Transcriptome in Widow Spiders. PMID:26733576
Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping. PMID:26729329
Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. PMID:26719891
Transposable element detection from whole genome sequence data. PMID:26719777
Application of a Novel "Pan-Genome"-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains. PMID:26717500
TauCstF-64 Mediates Correct mRNA Polyadenylation and Splicing of Activator and Repressor Isoforms of the Cyclic AMP-Responsive Element Modulator (CREM) in Mouse Testis. PMID:26700942
Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes. PMID:26699716
Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy. PMID:26695660
Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp. PMID:26695179
Engineering an allosteric transcription factor to respond to new ligands. PMID:26689263
Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis. PMID:26668163
Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the Earthworm Eisenia fetida. PMID:26659921
No association between HPV positive breast cancer and expression of human papilloma viral transcripts. PMID:26658849
Whole Genome Sequencing Defines the Genetic Heterogeneity of Familial Pancreatic Cancer. PMID:26658419
Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome. PMID:26658305
The MG-RAST metagenomics database and portal in 2015. PMID:26656948
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
De Novo Transcriptome Sequencing of the Orange-Fleshed Sweet Potato and Analysis of Differentially Expressed Genes Related to Carotenoid Biosynthesis. PMID:26649293
High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing. PMID:26647294
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation. PMID:26645680
De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite. PMID:26645667
A human 3'UTR clone collection to study post-transcriptional gene regulation. PMID:26645212
The Haemonchus contortus kinome--a resource for fundamental molecular investigations and drug discovery. PMID:26644012
ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly. PMID:26643039
Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca. PMID:26636322
Integrated 'Omics', Targeted Metabolite and Single-cell Analyses of Arctic Snow Algae Functionality and Adaptability. PMID:26635781
Defining the Schistosoma haematobium kinome enables the prediction of essential kinases as anti-schistosome drug targets. PMID:26635209
Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection. PMID:26627243
Fusion transcript loci share many genomic features with non-fusion loci. PMID:26626734
Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat. PMID:26625271
Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. PMID:26617401
The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling. PMID:26615215
Genome-wide association study of 8 carcass traits in Jinghai Yellow chickens using specific-locus amplified fragment sequencing technology. PMID:26614681
The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications. PMID:26609323
Advanced Applications of RNA Sequencing and Challenges. PMID:26609224
Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing. PMID:26599440
The UCSC Genome Browser database: 2016 update. PMID:26590259
Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. PMID:26587879
Stable recombination hotspots in birds. PMID:26586757
Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis. PMID:26586576
The role of biofilms as environmental reservoirs of antibiotic resistance. PMID:26583011
Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. PMID:26582927
HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. PMID:26578596
Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. PMID:26578579
Novel mutations in the genes TGM1 and ALOXE3 underlying autosomal recessive congenital ichthyosis. PMID:26578203
misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads. PMID:26573684
Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics. PMID:26569308
Dp412e: a novel human embryonic dystrophin isoform induced by BMP4 in early differentiated cells. PMID:26568816
The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression. PMID:26556591
Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. PMID:26546515
Draft Genome Sequence of Mycobacterium neworleansense Strain ATCC 49404T. PMID:26543131
Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development. PMID:26541409
Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin. PMID:26539826
Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare. PMID:26530316
Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data. PMID:26530187
Exocarp Properties and Transcriptomic Analysis of Cucumber (Cucumis sativus) Fruit Expressing Age-Related Resistance to Phytophthora capsici. PMID:26528543
Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae. PMID:26528397
Functionally conserved enhancers with divergent sequences in distant vertebrates. PMID:26519295
Lentiviral vector-mediated insertional mutagenesis screen identifies genes that influence androgen independent prostate cancer progression and predict clinical outcome. PMID:26512949
The essential gene set of a photosynthetic organism. PMID:26508635
A novel gammaretroviral shuttle vector insertional mutagenesis screen identifies SHARPIN as a breast cancer metastasis gene and prognostic biomarker. PMID:26506596
Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing. PMID:26505622
Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression. PMID:26503543
Discovery and characterization of Alu repeat sequences via precise local read assembly. PMID:26503250
mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. PMID:26500804
Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology. PMID:26500254
A catalogue of novel bovine long noncoding RNA across 18 tissues. PMID:26496443
Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis. PMID:26494905
Characterization and fine mapping of a novel barley Stage Green-Revertible Albino Gene (HvSGRA) by Bulked Segregant Analysis based on SSR assay and Specific Length Amplified Fragment Sequencing. PMID:26494145
Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes. PMID:26475107
An Exon-Capture System for the Entire Class Ophiuroidea. PMID:26474846
Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development. PMID:26474389
Novel RNA variants in colorectal cancers. PMID:26474385
Small RNA Sequencing Uncovers New miRNAs and moRNAs Differentially Expressed in Normal and Primary Myelofibrosis CD34+ Cells. PMID:26468945
Phylogenetic and genomic diversity in isolates from the globally distributed Acinetobacter baumannii ST25 lineage. PMID:26462752
Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution. PMID:26459856
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. PMID:26454280
MEPD: medaka expression pattern database, genes and more. PMID:26450962
NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision. PMID:26442529
Data in support of genome-wide identification of lineage-specific genes within Caenorhabditis elegans. PMID:26442285
Assembly and characterization of novel Alu inserts detected from next-generation sequencing data. PMID:26442170
Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis. PMID:26441894
Whole Blood Gene Expression Profiles of Patients with a Past Aneurysmal Subarachnoid Hemorrhage. PMID:26439625
Entropy-scaling search of massive biological data. PMID:26436140
Generation of a de novo transcriptome from equine lamellar tissue. PMID:26432030
Ovarian Transcriptome Analysis of Portunus trituberculatus Provides Insights into Genes Expressed during Phase III and IV Development. PMID:26431399
Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico. PMID:26421304
A novel locus of resistance to severe malaria in a region of ancient balancing selection. PMID:26416757
A catalog of the mouse gut metagenome. PMID:26414350
Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks. PMID:26392177
Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta). PMID:26391981
Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River. PMID:26388969
A comprehensive epigenome map of Plasmodium falciparum reveals unique mechanisms of transcriptional regulation and identifies H3K36me2 as a global mark of gene suppression. PMID:26388940
RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album. PMID:26388878
FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events. PMID:26384373
A novel retroviral mutagenesis screen identifies prognostic genes in RUNX1 mediated myeloid leukemogenesis. PMID:26384344
Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data. PMID:26382944
Identification of Ramie Genes in Response to Pratylenchus coffeae Infection Challenge by Digital Gene Expression Analysis. PMID:26378527
The genome of the vervet (Chlorocebus aethiops sabaeus). PMID:26377836
Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. PMID:26377088
Complex Population Structure and Virulence Differences among Serotype 2 Streptococcus suis Strains Belonging to Sequence Type 28. PMID:26375680
Genetic mapping uncovers cis-regulatory landscape of RNA editing. PMID:26373807
A draft genome sequence of an invasive mosquito: an Italian Aedes albopictus. PMID:26369436
Living without DAT: Loss and compensation of the dopamine transporter gene in sauropsids (birds and reptiles). PMID:26364979
Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication. PMID:26362289
A new amino acid substitution (Ala-205-Phe) in acetolactate synthase (ALS) confers broad spectrum resistance to ALS-inhibiting herbicides. PMID:26353912
Discovering New Biology through Sequencing of RNA. PMID:26353759
Tentacle: distributed quantification of genes in metagenomes. PMID:26351566
Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris. PMID:26346253
The Genome of the "Great Speciator" Provides Insights into Bird Diversification. PMID:26338191
Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates. PMID:26338187
Exploiting single-molecule transcript sequencing for eukaryotic gene prediction. PMID:26328666
High-resolution analysis of the human T-cell receptor repertoire. PMID:26324409
RASER: reads aligner for SNPs and editing sites of RNA. PMID:26323713
Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project. PMID:26319576
Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. PMID:26315624
Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini). PMID:26314297
SCR96, a small cysteine-rich secretory protein of Phytophthora cactorum, can trigger cell death in the Solanaceae and is important for pathogenicity and oxidative stress tolerance. PMID:26307454
Fecal Recovery of Ingested Cellular DNA: Implications for Noninvasive Detection of Upper Gastrointestinal Neoplasms. PMID:26297132
Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree. PMID:26290780
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. PMID:26283343
Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.). PMID:26283231
Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes. PMID:26283183
Comparative genome analysis of Mycoplasma pneumoniae. PMID:26275904
ApiAP2 Factors as Candidate Regulators of Stochastic Commitment to Merozoite Production in Theileria annulata. PMID:26273826
Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome. PMID:26272717
Identification, Phylogeny, and Function of fabp2 Paralogs in Two Non-Model Teleost Fish Species. PMID:26272429
High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L.). PMID:26262992
Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer. PMID:26253570
The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape. PMID:26253316
Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology. PMID:26252667
Draft Genome Sequence of Mycobacterium bohemicum Strain DSM 44277T. PMID:26251499
Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes. PMID:26250829
High speed BLASTN: an accelerated MegaBLAST search tool. PMID:26250111
The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat. PMID:26238519
A reanalysis of mouse ENCODE comparative gene expression data. PMID:26236466
Identification of heat-responsive genes in carnation (Dianthus caryophyllus L.) by RNA-seq. PMID:26236320
A high-density genetic map for P genome of Agropyron Gaertn. based on specific-locus amplified fragment sequencing (SLAF-seq). PMID:26232919
Analysis of paired end Pol II ChIP-seq and short capped RNA-seq in MCF-7 cells. PMID:26229744
Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. PMID:26228545
SuRankCo: supervised ranking of contigs in de novo assemblies. PMID:26224355
The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. PMID:26214836
Characterization of an APC Promoter 1B deletion in a Patient Diagnosed with Familial Adenomatous Polyposis via Whole Genome Shotgun Sequencing. PMID:26213617
Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex. PMID:26213557
Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley. PMID:26208213
GESPA: classifying nsSNPs to predict disease association. PMID:26206375
Draft Genome Sequence of Mycobacterium lentiflavum CSUR P1491. PMID:26205866
Genomic variations of the mevalonate pathway in porokeratosis. PMID:26202976
Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. PMID:26201400
Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing. PMID:26198742
Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans. PMID:26187050
Functional Analysis of Chicken IRF7 in Response to dsRNA Analog Poly(I:C) by Integrating Overexpression and Knockdown. PMID:26186542
The sequenced rat brain transcriptome--its use in identifying networks predisposing alcohol consumption. PMID:26183165
The molecular evolution of spiggin nesting glue in sticklebacks. PMID:26173374
BatAlign: an incremental method for accurate alignment of sequencing reads. PMID:26170239
Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data. PMID:26166306
BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data. PMID:26163275
Salix purpurea Stimulates the Expression of Specific Bacterial Xenobiotic Degradation Genes in a Soil Contaminated with Hydrocarbons. PMID:26161539
Genome Modeling System: A Knowledge Management Platform for Genomics. PMID:26158448
GenomePeek-an online tool for prokaryotic genome and metagenome analysis. PMID:26157610
An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches. PMID:26156552
Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress. PMID:26156140
Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants. PMID:26153459
Transcriptome Sequencing of Lima Bean (Phaseolus lunatus) to Identify Putative Positive Selection in Phaseolus and Legumes. PMID:26151849
VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing. PMID:26150117
An improved understanding of cancer genomics through massively parallel sequencing. PMID:26146607
High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. PMID:26132897
Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies. PMID:26131556
Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster. PMID:26129990
Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies. PMID:26125026
BlastXtract2: Improving early exploration of (meta) genomes. PMID:26124555
BGD: a database of bat genomes. PMID:26110276
Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon. PMID:26109355
Annotation of the Protein Coding Regions of the Equine Genome. PMID:26107351
Re-analysis of RNA-seq transcriptome data reveals new aspects of gene activity in Arabidopsis root hairs. PMID:26106402
Np9, a cellular protein of retroviral ancestry restricted to human, chimpanzee and gorilla, binds and regulates ubiquitin ligase MDM2. PMID:26103464
Analysis of Multiple Brachyspira hyodysenteriae Genomes Confirms That the Species Is Relatively Conserved but Has Potentially Important Strain Variation. PMID:26098837
A piRNA-like small RNA interacts with and modulates p-ERM proteins in human somatic cells. PMID:26095918
RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. PMID:26084484
piRNA-like small RNAs mark extended 3'UTRs present in germ and somatic cells. PMID:26076733
Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data. PMID:26072492
Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing. PMID:26069444
Draft Genome Sequence of Stenotrophomonas maltophilia Strain UV74 Reveals Extensive Variability within Its Genomic Group. PMID:26067959
Whole transcriptome analysis reveals changes in expression of immune-related genes during and after bleaching in a reef-building coral. PMID:26064625
Structural basis for retroviral integration into nucleosomes. PMID:26061770
Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). PMID:26059236
Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution. PMID:26058392
The radish genome and comprehensive gene expression profile of tuberous root formation and development. PMID:26056784
Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries. PMID:26056565
TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing. PMID:26056424
dbHiMo: a web-based epigenomics platform for histone-modifying enzymes. PMID:26055100
The distribution and evolution of Arabidopsis thaliana cis natural antisense transcripts. PMID:26054753
Recurrent somatic mutations in regulatory regions of human cancer genomes. PMID:26053494
Comprehensive Analysis of Disease-Related Genes in Chronic Lymphocytic Leukemia by Multiplex PCR-Based Next Generation Sequencing. PMID:26053404
Identification of Pathogen Signatures in Prostate Cancer Using RNA-seq. PMID:26053031
High-throughput monitoring of integration site clonality in preclinical and clinical gene therapy studies. PMID:26052530
Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. PMID:26044654
Mapping a Type 1 FHB resistance on chromosome 4AS of Triticum macha and deployment in combination with two Type 2 resistances. PMID:26040404
Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). PMID:26035838
Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. PMID:26028266
Genetic regulation of bone metabolism in the chicken: similarities and differences to Mammalian systems. PMID:26023928
Draft Genome Sequence of the Archiascomycetous Yeast Saitoella complicata. PMID:26021914
JAFFA: High sensitivity transcriptome-focused fusion gene detection. PMID:26019724
Towards computational improvement of DNA database indexing and short DNA query searching. PMID:26019584
Unravelling the genome of Holy basil: an "incomparable" "elixir of life" of traditional Indian medicine. PMID:26017011
The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing. PMID:26010095
Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU. PMID:26005439
Complete Genome Sequence of Streptococcus thermophilus SMQ-301, a Model Strain for Phage-Host Interactions. PMID:25999573
ImmuSort, a database on gene plasticity and electronic sorting for immune cells. PMID:25988315
Combining Next Generation Sequencing with Bulked Segregant Analysis to Fine Map a Stem Moisture Locus in Sorghum (Sorghum bicolor L. Moench). PMID:25984727
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. PMID:25983555
GraP: platform for functional genomics analysis of Gossypium raimondii. PMID:25982315
Lineage specific evolution of the VNTR composite retrotransposon central domain and its role in retrotransposition of gibbon LAVA elements. PMID:25981446
TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms. PMID:25979828
Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics. PMID:25978838
Flatworms have lost the right open reading frame kinase 3 gene during evolution. PMID:25976756
Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity. PMID:25976353
Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides. PMID:25971668
Bio301: A Web-Based EST Annotation Pipeline That Facilitates Functional Comparison Studies. PMID:25969743
Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. PMID:25968644
Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. PMID:25963125
Lactococcus garvieae: a small bacteria and a big data world. PMID:25960872
Design and bioinformatics analysis of genome-wide CLIP experiments. PMID:25958398
Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs. PMID:25956794
Differential Gene Expression Profiling of Dystrophic Dog Muscle after MuStem Cell Transplantation. PMID:25955839
Transcriptional profiling provides insights into metronomic cyclophosphamide-activated, innate immune-dependent regression of brain tumor xenografts. PMID:25952672
Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR. PMID:25945312
Gender-specific postnatal demethylation and establishment of epigenetic memory. PMID:25934504
Genome-wide amplification of proviral sequences reveals new polymorphic HERV-K(HML-2) proviruses in humans and chimpanzees that are absent from genome assemblies. PMID:25927962
Genome assembly using Nanopore-guided long and error-free DNA reads. PMID:25927464
Identification of a gene controlling variation in the salt tolerance of rapeseed (Brassica napus L.). PMID:25921693
Elucidating the composition and conservation of the autophagy pathway in photosynthetic eukaryotes. PMID:25915714
G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. PMID:25915121
The genomes of two key bumblebee species with primitive eusocial organization. PMID:25908251
Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. PMID:25893780
Evaluation and application of the strand-specific protocol for next-generation sequencing. PMID:25893191
BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. PMID:25889843
Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes. PMID:25888081
A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. PMID:25886949
RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets. PMID:25886935
The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. PMID:25883147
Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards. PMID:25880916
Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms. PMID:25880035
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. PMID:25879410
Numerous transitions of sex chromosomes in Diptera. PMID:25879221
Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation. PMID:25862382
Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants. PMID:25860123
Identification and functional analysis of genome mutations in a fluoride-resistant Streptococcus mutans strain. PMID:25856576
Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential. PMID:25856195
Transcriptome-wide identification of adenosine-to-inosine editing using the ICE-seq method. PMID:25855956
SANSparallel: interactive homology search against Uniprot. PMID:25855811
ALDB: a domestic-animal long noncoding RNA database. PMID:25853886
Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome. PMID:25853708
Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives. PMID:25849937
Acid sensitivity of the spinal dorsal root ganglia C-fiber nociceptors innervating the guinea pig esophagus. PMID:25846134
Transcriptional dynamics of Phytophthora infestans during sequential stages of hemibiotrophic infection of tomato. PMID:25845484
A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration. PMID:25841488
Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS. PMID:25830241
Influence of a non-hospital medical care facility on antimicrobial resistance in wastewater. PMID:25821977
A thesaurus of genetic variation for interrogation of repetitive genomic regions. PMID:25820428
An Rtf2 Domain-Containing Protein Influences Pre-mRNA Splicing and Is Essential for Embryonic Development in Arabidopsis thaliana. PMID:25819795
LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study. PMID:25819075
SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish. PMID:25813542
Population structure and antimicrobial resistance of invasive serotype IV group B Streptococcus, Toronto, Ontario, Canada. PMID:25811284
Analysis of the tomato leaf transcriptome during successive hemibiotrophic stages of a compatible interaction with the oomycete pathogen Phytophthora infestans. PMID:25808779
Genome-wide identification, characterization and evolutionary analysis of long intergenic noncoding RNAs in cucumber. PMID:25799544
De novo origin of VCY2 from autosome to Y-transposed amplicon. PMID:25799347
Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout. PMID:25793877
Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analyses. PMID:25786431
Identification of agonists for a group of human odorant receptors. PMID:25784876
Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives. PMID:25780758
Genome-wide characterization of developmental stage- and tissue-specific transcription factors in wheat. PMID:25766308
The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes. PMID:25765891
The exonuclease Nibbler regulates age-associated traits and modulates piRNA length in Drosophila. PMID:25754031
Development of a high-resolution NGS-based HLA-typing and analysis pipeline. PMID:25753671
A CRISPR/Cas9 vector system for tissue-specific gene disruption in zebrafish. PMID:25752963
Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PMID:25748510
Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. PMID:25740935
The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. PMID:25730766
Genome sequence-independent identification of RNA editing sites. PMID:25730491
Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite. PMID:25723966
Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. PMID:25723335
RNA-Seq: Improving Our Understanding of Retinal Biology and Disease. PMID:25722474
Multicolor CRISPR labeling of chromosomal loci in human cells. PMID:25713381
Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. PMID:25711833
IRcall and IRclassifier: two methods for flexible detection of intron retention events from RNA-Seq data. PMID:25707295
A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis). PMID:25707007
Whole transcriptome analysis using next-generation sequencing of sterile-cultured Eisenia andrei for immune system research. PMID:25706644
Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. PMID:25704602
Cigarette smoke mediates epigenetic repression of miR-217 during esophageal adenocarcinogenesis. PMID:25703328
A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD). PMID:25701871
Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum. PMID:25698879
A complex genome-microRNA interplay in human mitochondria. PMID:25695052
Molecular description of eye defects in the zebrafish Pax6b mutant, sunrise, reveals a Pax6b-dependent genetic network in the developing anterior chamber. PMID:25692557
Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. PMID:25689026
Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. PMID:25683379
A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. PMID:25679959
Whole-genome sequencing reveals absence of recent gene flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea. PMID:25677924
Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains. PMID:25673134
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. PMID:25666585
Nicotinic receptors in non-human primates: Analysis of genetic and functional conservation with humans. PMID:25661700
Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants. PMID:25652661
Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages. PMID:25652569
A single nucleotide polymorphism associated with isolated cleft lip and palate, thyroid cancer and hypothyroidism alters the activity of an oral epithelium and thyroid enhancer near FOXE1. PMID:25652407
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. PMID:25650807
The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio). PMID:25645996
Developmental genetic mechanisms of C4 syndrome based on transcriptome analysis of C3 cotyledons and C4 assimilating shoots in Haloxylon ammodendron. PMID:25643361
Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints. PMID:25640679
Identification of a recently active mammalian SINE derived from ribosomal RNA. PMID:25637222
Single-nucleotide polymorphism identification and genotyping in Camelina sativa. PMID:25620879
New cryptic karyotypic differences between cattle (Bos taurus) and goat (Capra hircus). PMID:25612562
Novel exons and splice variants in the human antibody heavy chain identified by single cell and single molecule sequencing. PMID:25611855
Evaluation of de novo transcriptome assemblies from RNA-Seq data. PMID:25608678
Vector design influences hepatic genotoxicity after adeno-associated virus gene therapy. PMID:25607839
Novel transcription factor variants through RNA-sequencing: the importance of being "alternative". PMID:25590302
The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau. PMID:25583503
Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing. PMID:25575840
Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm. PMID:25573960
Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure. PMID:25573196
A RESTful API for accessing microbial community data for MG-RAST. PMID:25569221
Three CCT domain-containing genes were identified to regulate heading date by candidate gene-based association mapping and transformation in rice. PMID:25563494
Extragenic suppressor mutations in ΔripA disrupt stability and function of LpxA. PMID:25551578
Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus. PMID:25543049
Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers. PMID:25526364
Tissue-specific transcriptomics, chromosomal localization, and phylogeny of chemosensory and odorant binding proteins from the red flour beetle Tribolium castaneum reveal subgroup specificities for olfaction or more general functions. PMID:25523483
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. PMID:25520706
Conserved syntenic clusters of protein coding genes are missing in birds. PMID:25518852
Smoking-Associated Site-Specific Differential Methylation in Buccal Mucosa in the COPDGene Study. PMID:25517428
Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. PMID:25517076
Recent advances in candidate-gene and whole-genome approaches to the discovery of anthelmintic resistance markers and the description of drug/receptor interactions. PMID:25516826
Genome-wide analysis of alternative splicing in Volvox carteri. PMID:25516378
Transcriptional consequence and impaired gametogenesis with high-grade aneuploidy in Arabidopsis thaliana. PMID:25514186
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data. PMID:25510498
Gene prediction and annotation in Penstemon (Plantaginaceae): A workflow for marker development from extremely low-coverage genome sequencing. PMID:25506519
Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PMID:25503521
Potassium stress growth characteristics and energetics in the haloarchaeon Haloarcula marismortui. PMID:25503059
Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. PMID:25496280
CLAST: CUDA implemented large-scale alignment search tool. PMID:25495907
Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max. PMID:25494922
Comparative genomics reveals molecular features unique to the songbird lineage. PMID:25494627
Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions. PMID:25487987
Integrative workflows for metagenomic analysis. PMID:25478562
Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. PMID:25477420
Triticeae resources in Ensembl Plants. PMID:25432969
Faster sequence homology searches by clustering subsequences. PMID:25432166
The UCSC Genome Browser database: 2015 update. PMID:25428374
BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers. PMID:25428359
MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes. PMID:25421434
Anti-centrosome antibodies in breast cancer are the expression of autoimmunity. PMID:25420961
Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces. PMID:25417012
Type I Interferon Regulates the Expression of Long Non-Coding RNAs. PMID:25414701
microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes. PMID:25414325
Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation. PMID:25411636
Diversification of bacterial genome content through distinct mechanisms over different timescales. PMID:25407023
RADIA: RNA and DNA integrated analysis for somatic mutation detection. PMID:25405470
Fast and sensitive protein alignment using DIAMOND. PMID:25402007
Species-specific exon loss in human transcriptomes. PMID:25398629
Definition of the cattle killer cell Ig-like receptor gene family: comparison with aurochs and human counterparts. PMID:25398326
Comparative genomic analysis shows that avian pathogenic Escherichia coli isolate IMT5155 (O2:K1:H5; ST complex 95, ST140) shares close relationship with ST95 APEC O1:K1 and human ExPEC O18:K1 strains. PMID:25397580
Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing. PMID:25396741
Evolution of an expanded mannose receptor gene family. PMID:25390371
Transcriptome of the invasive brown marmorated stink bug, Halyomorpha halys (Stål) (Heteroptera: Pentatomidae). PMID:25386688
Anchored multiplex PCR for targeted next-generation sequencing. PMID:25384085
Mutational spectrum of myeloid malignancies with inv(3)/t(3;3) reveals a predominant involvement of RAS/RTK signaling pathways. PMID:25381062
The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. PMID:25377941
Profiling the RNA editomes of wild-type C. elegans and ADAR mutants. PMID:25373143
MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing. PMID:25365329
The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing. PMID:25355294
Ensembl 2015. PMID:25352552
Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number. PMID:25348403
Host and viral determinants for MxB restriction of HIV-1 infection. PMID:25348155
Evaluation of a hybrid approach using UBLAST and BLASTX for metagenomic sequences annotation of specific functional genes. PMID:25347677
Intron evolution in Neurospora: the role of mutational bias and selection. PMID:25342722
Discovery of invariant T cells by next-generation sequencing of the human TCR α-chain repertoire. PMID:25339678
Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing. PMID:25339441
The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing. PMID:25338024
PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands. PMID:25336619
Disease variants in genomes of 44 centenarians. PMID:25333069
Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection. PMID:25325924
Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals. PMID:25312340
Divergence of gene body DNA methylation and evolution of plant duplicate genes. PMID:25310342
A PTCH1 homolog transcriptionally activated by p53 suppresses Hedgehog signaling. PMID:25296753
A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature. PMID:25273102
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. PMID:25271953
Population history and genomic signatures for high-altitude adaptation in Tibetan pigs. PMID:25270331
Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures. PMID:25267525
NSIT: novel sequence identification tool. PMID:25264906
Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes. PMID:25264628
Transcriptome sequencing and analysis of Plasmodium gallinaceum reveals polymorphisms and selection on the apical membrane antigen-1. PMID:25261185
Long distance linkage disequilibrium and limited hybridization suggest cryptic speciation in atlantic cod. PMID:25259573
Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification. PMID:25252941
Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq. PMID:25252653
Effective extraction and assembly methods for simultaneously obtaining plastid and mitochondrial genomes. PMID:25251391
circBase: a database for circular RNAs. PMID:25234927
Neutral nuclear variation in Baboons (genus Papio) provides insights into their evolutionary and demographic histories. PMID:25234435
LncRBase: an enriched resource for lncRNA information. PMID:25233092
Tangram: a comprehensive toolbox for mobile element insertion detection. PMID:25228379
Estimating overannotation across prokaryotic genomes using BLAST+, UBLAST, LAST and BLAT. PMID:25228073
Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics. PMID:25225629
Improved rat genome gene prediction by integration of ESTs with RNA-Seq information. PMID:25217576
Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge. PMID:25216354
De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms. PMID:25209985
Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon-primed, intron-spanning nuclear loci. PMID:25202534
Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers. PMID:25194325
Evidence for the persistence of an active endogenous retrovirus (ERVE) in humans. PMID:25192754
The expression profile of acid-sensing ion channel (ASIC) subunits ASIC1a, ASIC1b, ASIC2a, ASIC2b, and ASIC3 in the esophageal vagal afferent nerve subtypes. PMID:25190475
Genetic analysis of a consanguineous Pakistani family with Leber congenital amaurosis identifies a novel mutation in GUCY2D gene. PMID:25189253
Clone mapper: an online suite of tools for RNAi experiments in Caenorhabditis elegans. PMID:25187039
P2Y(12) receptor on the verge of a neuroinflammatory breakdown. PMID:25180027
Merging of multi-string BWTs with applications. PMID:25172922
Complete Genome Sequences of IncI1 Plasmids Carrying Extended-Spectrum β-Lactamase Genes. PMID:25169863
Comprehensive analysis of alternative splicing in Digitalis purpurea by strand-specific RNA-Seq. PMID:25167195
Lambda: the local aligner for massive biological data. PMID:25161219
A genome-wide map of hyper-edited RNA reveals numerous new sites. PMID:25158696
Genomic organization, transcriptomic analysis, and functional characterization of avian α- and β-keratins in diverse feather forms. PMID:25152353
Identification of oncogenic mutations and gene fusions in the follicular variant of papillary thyroid carcinoma. PMID:25148236
Potential for genomic instability associated with retrotranspositionally-incompetent L1 loci. PMID:25143528
Multiple groups of endogenous epsilon-like retroviruses conserved across primates. PMID:25142585
IRBIS: a systematic search for conserved complementarity. PMID:25142064
Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PMID:25140992
Parallel evolution of tetrodotoxin resistance in three voltage-gated sodium channel genes in the garter snake Thamnophis sirtalis. PMID:25135948
Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. PMID:25129133
The Babesia bovis gene and promoter model: an update from full-length EST analysis. PMID:25124460
Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. PMID:25129133
The Babesia bovis gene and promoter model: an update from full-length EST analysis. PMID:25124460
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations. PMID:25123903
A comprehensive survey of non-canonical splice sites in the human transcriptome. PMID:25123659
Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species. PMID:25122153
SNP identification by transcriptome sequencing and candidate gene-based association analysis for heat tolerance in the bay scallop Argopecten irradians. PMID:25121601
Gene-based SNP discovery and genetic mapping in pea. PMID:25119872
Plant vigour at establishment and following defoliation are both associated with responses to drought in perennial ryegrass (Lolium perenne L.). PMID:25104762
GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array. PMID:25099887
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. PMID:25091138
Identification and validation of genetic variants that influence transcription factor and cell signaling protein levels. PMID:25087611
A Bead-based Normalization for Uniform Sequencing depth (BeNUS) protocol for multi-samples sequencing exemplified by HLA-B. PMID:25087472
Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic cats. PMID:25085922
Haploinsufficiency of insulin gene enhancer protein 1 (ISL1) is associated with d-transposition of the great arteries. PMID:25077177
Gene Assembly from Chip-Synthesized Oligonucleotides. PMID:25077042
Corset: enabling differential gene expression analysis for de novo assembled transcriptomes. PMID:25063469
The nuclear hormone receptor family member NR5A2 controls aspects of multipotent progenitor cell formation and acinar differentiation during pancreatic organogenesis. PMID:25063451
Highly variable recombinational landscape modulates efficacy of natural selection in birds. PMID:25062920
Diversity in the preimmune immunoglobulin repertoire of SHR lines susceptible and resistant to end-organ injury. PMID:25056448
Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs. PMID:25056316
Repair of oxidative DNA base damage in the host genome influences the HIV integration site sequence preference. PMID:25051054
Genome-wide Association Study of Integrated Meat Quality-related Traits of the Duroc Pig Breed. PMID:25049955
Loss of oncogenic Notch1 with resistance to a PI3K inhibitor in T-cell leukaemia. PMID:25043004
The common marmoset genome provides insight into primate biology and evolution. PMID:25038751
Systematic identification and characterization of RNA editing in prostate tumors. PMID:25036877
NCI-60 whole exome sequencing and pharmacological CellMiner analyses. PMID:25032700
Epstein-Barr virus EBNA1 protein regulates viral latency through effects on let-7 microRNA and dicer. PMID:25031339
Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal. PMID:25028429
An integrated genomic and metabolomic framework for cell wall biology in rice. PMID:25023612
Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PMID:25013894
A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non-coding RNAs in cancers. PMID:25013169
First Complete Genome Sequence of Staphylococcus xylosus, a Meat Starter Culture and a Host to Propagate Staphylococcus aureus Phages. PMID:25013142
Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation. PMID:25010342
De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae). PMID:25000941
A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens. PMID:24999345
An integrated catalog of reference genes in the human gut microbiome. PMID:24997786
Complete genome assembly and characterization of an outbreak strain of the causative agent of swine erysipelas--Erysipelothrix rhusiopathiae SY1027. PMID:24993343
Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). PMID:24990609
Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species. PMID:24984952
Genotyping cancer-associated genes in chordoma identifies mutations in oncogenes and areas of chromosomal loss involving CDKN2A, PTEN, and SMARCB1. PMID:24983247
A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements. PMID:24981367
Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. PMID:24973796
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. PMID:24972667
Is the alcohol deprivation effect genetically mediated? Studies with HXB/BXH recombinant inbred rat strains. PMID:24961585
Genome assembly and annotation of a Drosophila simulans strain from Madagascar. PMID:24961367
BLAT-based comparative analysis for transposable elements: BLATCAT. PMID:24959585
Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone. PMID:24957517
The draft assembly of the radically organized Stylonychia lemnae macronuclear genome. PMID:24951568
The Chlamydomonas genome project: a decade on. PMID:24950814
Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (Lagopus lagopus scotica). PMID:24943398
A method for detecting long non-coding RNAs with tiled RNA expression microarrays. PMID:24937006
The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria. PMID:24935935
Efficient DNA fingerprinting based on the targeted sequencing of active retrotransposon insertion sites using a bench-top high-throughput sequencing platform. PMID:24935865
Multicilin drives centriole biogenesis via E2f proteins. PMID:24934224
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references. PMID:24932000
Genome and transcriptome of the porcine whipworm Trichuris suis. PMID:24929829
The American cranberry: first insights into the whole genome of a species adapted to bog habitat. PMID:24927653
Shared and unique proteins in human, mouse and rat saliva proteomes: Footprints of functional adaptation. PMID:24926433
MorusDB: a resource for mulberry genomics and genome biology. PMID:24923822
Evolutionary origin and methylation status of human intronic CpG islands that are not present in mouse. PMID:24923327
Unfixed endogenous retroviral insertions in the human population. PMID:24920817
Rewiring Host Lipid Metabolism by Large Viruses Determines the Fate of Emiliania huxleyi, a Bloom-Forming Alga in the Ocean. PMID:24920329
The genome of Eucalyptus grandis. PMID:24919147
Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape. PMID:24916661
A reference genome for common bean and genome-wide analysis of dual domestications. PMID:24908249
ABRA: improved coding indel detection via assembly-based realignment. PMID:24907369
Identification of potential therapeutic targets in a model of neuropathic pain. PMID:24904634
Novel principles of gamma-retroviral insertional transcription activation in murine leukemia virus-induced end-stage tumors. PMID:24886479
GAP-Seq: a method for identification of DNA palindromes. PMID:24885769
A novel approach to identify driver genes involved in androgen-independent prostate cancer. PMID:24885513
Predicting the fungal CUG codon translation with Bagheera. PMID:24885275
Identification of G protein-coupled receptors in Schistosoma haematobium and S. mansoni by comparative genomics. PMID:24884876
XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons. PMID:24884593
Heterochromatin controls γH2A localization in Neurospora crassa. PMID:24879124
Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data. PMID:24866698
GenomeVISTA--an integrated software package for whole-genome alignment and visualization. PMID:24860159
Characterization of natural antisense transcript, sclerotia development and secondary metabolism by strand-specific RNA sequencing of Aspergillus flavus. PMID:24849659
The ctenophore genome and the evolutionary origins of neural systems. PMID:24847885
APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition. PMID:24843014
Objective and comprehensive evaluation of bisulfite short read mapping tools. PMID:24839440
RBPmap: a web server for mapping binding sites of RNA-binding proteins. PMID:24829458
A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats. PMID:24824832
Alignment-Annotator web server: rendering and annotating sequence alignments. PMID:24813445
Detection of gene rearrangements in targeted clinical next-generation sequencing. PMID:24813172
DICER1 is essential for survival of postmitotic rod photoreceptor cells in mice. PMID:24812086
The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus. PMID:24811454
Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data. PMID:24810475
The tobacco genome sequence and its comparison with those of tomato and potato. PMID:24807620
Transcription-independent functions of an RNA polymerase II subunit, Rpb2, during genome rearrangement in the ciliate, Oxytricha trifallax. PMID:24793090
Development and characterization of a new 12-plex ChrX miniSTR system. PMID:24789265
A genome-wide analysis of genetic diversity in Trypanosoma cruzi intergenic regions. PMID:24784238
Toxoplasma effector MAF1 mediates recruitment of host mitochondria and impacts the host response. PMID:24781109
Mouse mammary tumor virus-based vector transduces non-dividing cells, enters the nucleus via a TNPO3-independent pathway and integrates in a less biased fashion than other retroviruses. PMID:24779422
Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens. PMID:24777346
Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. PMID:24773339
Origins and functional evolution of Y chromosomes across mammals. PMID:24759410
A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines. PMID:24758272
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. PMID:24755901
The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. PMID:24755649
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PMID:24749011
Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons. PMID:24748652
Describing sequencing results of structural chromosome rearrangements with a suggested next-generation cytogenetic nomenclature. PMID:24746958
Genome Sequence of Fusarium graminearum Isolate CS3005. PMID:24744326
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PMID:24743168
The impacts of read length and transcriptome complexity for de novo assembly: a simulation study. PMID:24736633
Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. PMID:24722551
A hybrid qPCR/SNP array approach allows cost efficient assessment of KIR gene copy numbers in large samples. PMID:24720548
Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines. PMID:24719854
Bioinformatics for next generation sequencing data. PMID:24710047
Measuring turnover of SIV DNA in resting CD4+ T cells using pyrosequencing: implications for the timing of HIV eradication therapies. PMID:24710023
Trapping DNA replication origins from the human genome. PMID:24705160
No evidence of clonal dominance after transplant of HOXB4-expanded cord blood cells in a nonhuman primate model. PMID:24704161
The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). PMID:24699266
A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. PMID:24682209
Comparative genomics of Taphrina fungi causing varying degrees of tumorous deformity in plants. PMID:24682155
CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma. PMID:24675677
Plant systems biology: insights, advances and challenges. PMID:24671625
RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin. PMID:24666749
Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. PMID:24653211
The Xenopus alcohol dehydrogenase gene family: characterization and comparative analysis incorporating amphibian and reptilian genomes. PMID:24649825
Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species. PMID:24642845
Patterns of divergence of a large family of nodule cysteine-rich peptides in accessions of Medicago truncatula. PMID:24635121
RepARK--de novo creation of repeat libraries from whole-genome NGS reads. PMID:24634442
AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae. PMID:24628857
Genome-wide signals of positive selection in human evolution. PMID:24619126
Orione, a web-based framework for NGS analysis in microbiology. PMID:24618473
Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1. PMID:24608750
Detection of chromosomal breakpoints in patients with developmental delay and speech disorders. PMID:24603971
BambooGDB: a bamboo genome database with functional annotation and an analysis platform. PMID:24602877
doublesex is a mimicry supergene. PMID:24598547
Systematic design and functional analysis of artificial microRNAs. PMID:24598260
Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. PMID:24594072
MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. PMID:24589583
Genomic networks of hybrid sterility. PMID:24586194
Estimating differential expression from multiple indicators. PMID:24586062
Benchmarking of methods for genomic taxonomy. PMID:24574292
On the optimal trimming of high-throughput mRNA sequence data. PMID:24567737
OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly. PMID:24564959
A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units. PMID:24564714
Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum. PMID:24564352
A base composition analysis of natural patterns for the preprocessing of metagenome sequences. PMID:24564274
De novo sequencing, assembly, and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding. PMID:24563685
Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi. PMID:24559402
Evolution of primate α and θ defensins revealed by analysis of genomes. PMID:24557891
Molecular evolution and functional divergence of the metallothionein gene family in vertebrates. PMID:24557429
Mirror movement-like defects in startle behavior of zebrafish dcc mutants are caused by aberrant midline guidance of identified descending hindbrain neurons. PMID:24553931
Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia. PMID:24551246
Suppression of cell wall-related genes associated with stunting of Oryza glaberrima infected with Rice tungro spherical virus. PMID:24550897
Analysis of the floral transcriptome of Tarenaya hassleriana (Cleomaceae), a member of the sister group to the Brassicaceae: towards understanding the base of morphological diversity in Brassicales. PMID:24548348
Haploinsufficiency of Sf3b1 leads to compromised stem cell function but not to myelodysplasia. PMID:24535406
Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes. PMID:24520158
The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants. PMID:24516393
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. PMID:24512684
Genotyping of BCL11A and HBS1L-MYB SNPs associated with fetal haemoglobin levels: a SNaPshot minisequencing approach. PMID:24502199
Large inverted duplications in the human genome form via a fold-back mechanism. PMID:24497845
The Cryptococcus neoformans transcriptome at the site of human meningitis. PMID:24496797
Differential locus expansion distinguishes Toxoplasmatinae species and closely related strains of Toxoplasma gondii. PMID:24496792
Improved search heuristics find 20,000 new alignments between human and mouse genomes. PMID:24493737
Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data. PMID:24489615
The imprinted NPAP1 gene in the Prader-Willi syndrome region belongs to a POM121-related family of retrogenes. PMID:24482533
Finding the missing honey bee genes: lessons learned from a genome upgrade. PMID:24479613
Current challenges in the bioinformatics of single cell genomics. PMID:24478987
Absence of Genomic Ikaros/IKZF1 Deletions in Pediatric B-Precursor Acute Lymphoblastic Leukemia. PMID:24478816
C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human. PMID:24475127
Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications. PMID:24465857
New microRNAs in Drosophila--birth, death and cycles of adaptive evolution. PMID:24465220
Functional divergence and evolutionary turnover in mammalian phosphoproteomes. PMID:24465218
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. PMID:24463464
Genetic dysregulation in recurrent respiratory papillomatosis. PMID:24449512
Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data. PMID:24443445
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut. PMID:24438450
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PMID:24427317
Somatic RHOA mutation in angioimmunoblastic T cell lymphoma. PMID:24413737
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. PMID:24413732
A bioinformatician's guide to the forefront of suffix array construction algorithms. PMID:24413184
Genome-wide eQTLs and heritability for gene expression traits in unrelated individuals. PMID:24405759
SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching. PMID:24404406
Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. PMID:24398233
Computational approaches in detecting non- coding RNA. PMID:24396270
Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads. PMID:24391826
NCYM, a Cis-antisense gene of MYCN, encodes a de novo evolved protein that inhibits GSK3β resulting in the stabilization of MYCN in human neuroblastomas. PMID:24391509
Assessing the state of substitution models describing noncoding RNA evolution. PMID:24391153
Identification of Hematopoietic Stem Cell Engraftment Genes in Gene Therapy Studies. PMID:24383045
Evolutionary genetics and implications of small size and twinning in callitrichine primates. PMID:24379383
Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. PMID:24375144
Epigenetic regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islets. PMID:24374217
The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda. PMID:24373391
An integrative bioinformatics pipeline for the genomewide identification of novel porcine microRNA genes. PMID:24371181
A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae. PMID:24367647
Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia. PMID:24367274
A guide to bioinformatics for immunologists. PMID:24363654
Obligate mutualism within a host drives the extreme specialization of a fig wasp genome. PMID:24359812
Comparative transcriptome analysis of two rice varieties in response to rice stripe virus and small brown planthoppers during early interaction. PMID:24358146
Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis. PMID:24352427
Rapid diversification of FoxP2 in teleosts through gene duplication in the teleost-specific whole genome duplication event. PMID:24349554
Evaluation of assembly strategies using RNA-seq data associated with grain development of wheat (Triticum aestivum L.). PMID:24349528
Genetic screen of African Americans with Fuchs endothelial corneal dystrophy. PMID:24348007
Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours. PMID:24336498
A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes. PMID:24320546
The high polyphenol content of grapevine cultivar tannat berries is conferred primarily by genes that are not shared with the reference genome. PMID:24319081
Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. PMID:24316981
Transparency tools in gene patenting for informing policy and practice. PMID:24316644
ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection. PMID:24308000
TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. PMID:24307552
Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. PMID:24307551
Biochemical and molecular characterization of Treponema phagedenis-like spirochetes isolated from a bovine digital dermatitis lesion. PMID:24304812
Detection limit of intragenic deletions with targeted array comparative genomic hybridization. PMID:24304607
The GATA transcription factor/MTA-1 homolog egr-1 promotes longevity and stress resistance in Caenorhabditis elegans. PMID:24304470
Metagenomic Analysis of the Dynamic Changes in the Gut Microbiome of the Participants of the MARS-500 Experiment, Simulating Long Term Space Flight. PMID:24303207
Genome-block expression-assisted association studies discover malaria resistance genes in Anopheles gambiae. PMID:24297936
megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. PMID:24285304
Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. PMID:24282021
Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. PMID:24279325
Minke whale genome and aquatic adaptation in cetaceans. PMID:24270359
Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats. PMID:24262036
Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data. PMID:24261984
UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing. PMID:24259430
MEGANTE: a web-based system for integrated plant genome annotation. PMID:24253915
Data compression for sequencing data. PMID:24252160
A new family of predicted Krüppel-like factor genes and pseudogenes in placental mammals. PMID:24244731
Cross-platform prediction of gene expression signatures. PMID:24244455
Systems approaches to modeling chronic mucosal inflammation. PMID:24228254
Spatial-temporal targeting of lung-specific mesenchyme by a Tbx4 enhancer. PMID:24225400
Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues. PMID:24225116
Global transcriptome analysis of Lactococcus garvieae strains in response to temperature. PMID:24223997
Optimal scaling of digital transcriptomes. PMID:24223126
Assembly errors cause false tandem duplicate regions in the chicken (Gallus gallus) genome sequence. PMID:24213641
Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data. PMID:24211736
Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-Seq. PMID:24204709
Variant splicing and influence of ionizing radiation on human endogenous retrovirus K (HERV-K) transcripts in cancer cell lines. PMID:24204631
Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. PMID:24201445
Rhizosphere microbiome assemblage is affected by plant development. PMID:24196324
A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells. PMID:24194746
Genomic divergence between nine- and three-spined sticklebacks. PMID:24188282
Systematic evaluation of spliced alignment programs for RNA-seq data. PMID:24185836
GWIPS-viz: development of a ribo-seq genome browser. PMID:24185699
Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. PMID:24183450
Transcriptome interrogation of human myometrium identifies differentially expressed sense-antisense pairs of protein-coding and long non-coding RNA genes in spontaneous labor at term. PMID:24168098
Large-scale detection of in vivo transcription errors. PMID:24167253
Ensembl Genomes 2013: scaling up access to genome-wide data. PMID:24163254
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. PMID:24162736
An evolutionary screen highlights canonical and noncanonical candidate antiviral genes within the primate TRIM gene family. PMID:24158625
An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. PMID:24142994
Draft genome of the kiwifruit Actinidia chinensis. PMID:24136039
Identification of novel microRNAs in primates by using the synteny information and small RNA deep sequencing data. PMID:24135875
Sense-antisense gene pairs: sequence, transcription, and structure are not conserved between human and mouse. PMID:24133500
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency. PMID:24131564
The spliced leader trans-splicing mechanism in different organisms: molecular details and possible biological roles. PMID:24130571
Fungal alternative splicing is associated with multicellular complexity and virulence: a genome-wide multi-species study. PMID:24122896
Comprehensive analysis of human endogenous retrovirus group HERV-W locus transcription in multiple sclerosis brain lesions by high-throughput amplicon sequencing. PMID:24109235
Revealing of Mycobacterium marinum transcriptome by RNA-seq. PMID:24098731
ToPS: a framework to manipulate probabilistic models of sequence data. PMID:24098098
Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa). PMID:24096890
Transcriptome analyses of a Chinese hazelnut species Corylus mandshurica. PMID:24093758
An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. PMID:24083400
Hominoid fission of chromosome 14/15 and the role of segmental duplications. PMID:24077392
Reliable identification of genomic variants from RNA-seq data. PMID:24075185
A SNP profiling panel for sample tracking in whole-exome sequencing studies. PMID:24070238
BlastGraph: a comparative genomics tool based on BLAST and graph algorithms. PMID:24068035
Advancing our understanding of the human microbiome using QIIME. PMID:24060131
Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing. PMID:24060091
The landscape of somatic mutations in Down syndrome-related myeloid disorders. PMID:24056718
The tiger genome and comparative analysis with lion and snow leopard genomes. PMID:24045858
Transcript assembly and quantification by RNA-Seq reveals differentially expressed genes between soft-endocarp and hard-endocarp hawthorns. PMID:24039819
Acquired genetic mechanisms of a multiresistant bacterium isolated from a treatment plant receiving wastewater from antibiotic production. PMID:24038701
Admixture mapping of prostate cancer in African Americans participating in the North Carolina-Louisiana Prostate Cancer Project (PCaP). PMID:24037755
CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. PMID:24037212
Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (apocynaceae). PMID:24029811
Substantial loss of conserved and gain of novel MicroRNA families in flatworms. PMID:24025793
Complete genome analysis of a Haemophilus parasuis serovar 12 strain from China. PMID:24023711
RNA-Seq reveals infection-related gene expression changes in Phytophthora capsici. PMID:24019970
Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area. PMID:24015321
Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation. PMID:24015111
Lizards and LINEs: selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis). PMID:24013105
L_RNA_scaffolder: scaffolding genomes with transcripts. PMID:24010822
Divergent evolutionary and expression patterns between lineage specific new duplicate genes and their parental paralogs in Arabidopsis thaliana. PMID:24009676
Genome sequences of six wheat-infecting fusarium species isolates. PMID:24009115
Web Apollo: a web-based genomic annotation editing platform. PMID:24000942
Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis. PMID:23991058
The shared genomic architecture of human nucleolar organizer regions. PMID:23990606
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. PMID:23985341
Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families. PMID:23981484
Genome sequencing and analysis of BCG vaccine strains. PMID:23977002
The perfect neuroimaging-genetics-computation storm: collision of petabytes of data, millions of hardware devices and thousands of software tools. PMID:23975276
MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads. PMID:23967014
Assembler for de novo assembly of large genomes. PMID:23966565
GnpIS: an information system to integrate genetic and genomic data from plants and fungi. PMID:23959375
Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies. PMID:23957733
De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. PMID:23957668
Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. PMID:23955599
HIV latency and integration site placement in five cell-based models. PMID:23953889
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies. PMID:23941359
Comprehensive genomic characterization of campylobacter genus reveals some underlying mechanisms for its genomic diversification. PMID:23940551
Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. PMID:23937694
Mena/VASP and αII-Spectrin complexes regulate cytoplasmic actin networks in cardiomyocytes and protect from conduction abnormalities and dilated cardiomyopathy. PMID:23937664
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. PMID:23934149
Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20. PMID:23925440
Analysis of unannotated equine transcripts identified by mRNA sequencing. PMID:23922931
Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly. PMID:23922726
Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens. PMID:23922691
Improving transcriptome assembly through error correction of high-throughput sequence reads. PMID:23904992
Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. PMID:23904502
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. PMID:23899370
Insertional mutagenesis using Tnt1 retrotransposon in potato. PMID:23898040
PECONPI: a novel software for uncovering pathogenic copy number variations in non-syndromic sensorineural hearing loss and other genetically heterogeneous disorders. PMID:23897863
A computational workflow to identify allele-specific expression and epigenetic modification in maize. PMID:23891706
The transcriptional response of Arabidopsis leaves to Fe deficiency. PMID:23888164
Integrative genomic analysis of the human immune response to influenza vaccination. PMID:23878721
Genome survey sequencing and genetic background characterization of Gracilariopsis lemaneiformis (Rhodophyta) based on next-generation sequencing. PMID:23875008
A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa. PMID:23874666
High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications. PMID:23874421
Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. PMID:23873082
Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. PMID:23865674
MisPred: a resource for identification of erroneous protein sequences in public databases. PMID:23864220
Populus euphratica: the transcriptomic response to drought stress. PMID:23857471
Detection of Human Endogenous Retrovirus K (HERV-K) Transcripts in Human Prostate Cancer Cell Lines. PMID:23847768
Genomics analysis of potassium channel genes in songbirds reveals molecular specializations of brain circuits for the maintenance and production of learned vocalizations. PMID:23845108
nhmmer: DNA homology search with profile HMMs. PMID:23842809
Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances. PMID:23842651
EGN: a wizard for construction of gene and genome similarity networks. PMID:23841456
Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia. PMID:23832011
Endogenous gammaretrovirus acquisition in Mus musculus subspecies carrying functional variants of the XPR1 virus receptor. PMID:23824809
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. PMID:23817568
IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels. PMID:23813001
Mapping gene activity of Arabidopsis root hairs. PMID:23800126
Separating homeologs by phasing in the tetraploid wheat transcriptome. PMID:23800085
Integrated molecular analysis of clear-cell renal cell carcinoma. PMID:23797736
MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. PMID:23793516
Reversal of an ancient sex chromosome to an autosome in Drosophila. PMID:23792562
Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray. PMID:23776682
Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. PMID:23773524
Combined methylation mapping of 5mC and 5hmC during early embryonic stages in bovine. PMID:23773395
Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients. PMID:23773324
Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions. PMID:23771142
The development of 7E chromosome-specific molecular markers for Thinopyrum elongatum based on SLAF-seq technology. PMID:23762296
Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation. PMID:23742985
Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq. PMID:23740984
Spliced DNA sequences in the Paramecium germline: their properties and evolutionary potential. PMID:23737328
Genome-wide characterization of adaptation and speciation in tiger swallowtail butterflies using de novo transcriptome assemblies. PMID:23737327
Mutually exclusive alterations in secondary metabolism are critical for the uptake of insoluble iron compounds by Arabidopsis and Medicago truncatula. PMID:23735511
Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots. PMID:23735510
Bellerophon: a hybrid method for detecting interchromosomal rearrangements at base pair resolution using next-generation sequencing data. PMID:23734783
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. PMID:23731509
Dual host-virus arms races shape an essential housekeeping protein. PMID:23723737
Integrated analysis of recurrent properties of cancer genes to identify novel drivers. PMID:23718799
VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PMID:23717618
Compensation of the metabolic costs of antibiotic resistance by physiological adaptation in Escherichia coli. PMID:23716056
Phase-defined complete sequencing of the HLA genes by next-generation sequencing. PMID:23714642
Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. PMID:23708188
WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes. PMID:23700307
Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles. PMID:23696454
Neuropilin-2 promotes extravasation and metastasis by interacting with endothelial α5 integrin. PMID:23689123
Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos. PMID:23684812
Human GGT2 does not autocleave into a functional enzyme: A cautionary tale for interpretation of microarray data on redox signaling. PMID:23682772
ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats. PMID:23677944
WebScipio: Reconstructing alternative splice variants of eukaryotic proteins. PMID:23677611
Draft genome sequence of the Tibetan antelope. PMID:23673643
Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. PMID:23672450
Inactivation of the RB family prevents thymus involution and promotes thymic function by direct control of Foxn1 expression. PMID:23669396
Transcriptome of the Lymantria dispar (gypsy moth) larval midgut in response to infection by Bacillus thuringiensis. PMID:23658687
Genomic diversity and fitness of E. coli strains recovered from the intestinal and urinary tracts of women with recurrent urinary tract infection. PMID:23658245
Reprever: resolving low-copy duplicated sequences using template driven assembly. PMID:23658221
DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. PMID:23657089
High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. PMID:23651622
Population genomics of post-vaccine changes in pneumococcal epidemiology. PMID:23644493
Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly. PMID:23638091
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PMID:23637635
Somatic alterations contributing to metastasis of a castration-resistant prostate cancer. PMID:23636849
Metagenomic evidence for sulfur lithotrophy by Epsilonproteobacteria as the major energy source for primary productivity in a sub-aerial arctic glacial deposit, Borup Fiord Pass. PMID:23626586
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. PMID:23624526
Phylogenomics of strongylocentrotid sea urchins. PMID:23617542
Widespread divergence of the CEACAM/PSG genes in vertebrates and humans suggests sensitivity to selection. PMID:23613906
Mechanisms of intron loss and gain in the fission yeast Schizosaccharomyces. PMID:23613904
Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants. PMID:23598527
Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the Drosophila retina. PMID:23597484
Computational solutions for omics data. PMID:23594911
Development of peptide nucleic acid probes for detection of the HER2 oncogene. PMID:23593123
Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery. PMID:23589517
CD34(+) expansion with Delta-1 and HOXB4 promotes rapid engraftment and transfusion independence in a Macaca nemestrina cord blood transplant model. PMID:23587923
Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. PMID:23583100
Overexpression of full-length centrobin rescues limb malformation but not male fertility of the hypodactylous (hd) rats. PMID:23577170
Monocular inhibition reveals temporal and spatial changes in gene expression in the primary visual cortex of marmoset. PMID:23576954
The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice. PMID:23576519
Construction of customized sub-databases from NCBI-nr database for rapid annotation of huge metagenomic datasets using a combined BLAST and MEGAN approach. PMID:23573212
Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches. PMID:23572138
OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. PMID:23571760
Defining the functional potential and active community members of a sediment microbial community in a high-arctic hypersaline subzero spring. PMID:23563939
Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus. PMID:23562481
Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing. PMID:23561577
Transcriptome analysis of the differentially expressed genes in the male and female shrub willows (Salix suchowensis). PMID:23560075
Probabilistic error correction for RNA sequencing. PMID:23558750
Genome-wide characterization and linkage mapping of simple sequence repeats in mei (Prunus mume Sieb. et Zucc.). PMID:23555708
Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. PMID:23555216
Transduction-specific ATLAS reveals a cohort of highly active L1 retrotransposons in human populations. PMID:23553801
PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. PMID:23550143
TRACER: a resource to study the regulatory architecture of the mouse genome. PMID:23547943
Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PMID:23547111
Development and characterization of cDNA resources for the common marmoset: one of the experimental primate models. PMID:23543116
The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. PMID:23542700
Contrasting patterns of transposable element and satellite distribution on sex chromosomes (XY1Y2) in the dioecious plant Rumex acetosa. PMID:23542206
The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. PMID:23542700
Contrasting patterns of transposable element and satellite distribution on sex chromosomes (XY1Y2) in the dioecious plant Rumex acetosa. PMID:23542206
Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium System in a comparison of multiple genomics core facilities. PMID:23542132
Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude. PMID:23537097
Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.). PMID:23537070
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. PMID:23537068
Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences. PMID:23537002
The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). PMID:23536760
Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms. PMID:23527231
SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PMID:23527008
Genetic-genomic replication to identify candidate mouse atherosclerosis modifier genes. PMID:23525445
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. PMID:23525075
Genomics of Loa loa, a Wolbachia-free filarial parasite of humans. PMID:23525074
The Reference Genome of the Halophytic Plant Eutrema salsugineum. PMID:23518688
Microhomology-mediated mechanisms underlie non-recurrent disease-causing microdeletions of the FOXL2 gene or its regulatory domain. PMID:23516377
Association of intron loss with high mutation rate in Arabidopsis: implications for genome size evolution. PMID:23516254
Mobilomics in Saccharomyces cerevisiae strains. PMID:23514613
Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research. PMID:23512102
PSimScan: algorithm and utility for fast protein similarity search. PMID:23505522
Analysis of metagenomic data containing high biodiversity levels. PMID:23505458
Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. PMID:23497673
Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong? PMID:23486611
Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA. PMID:23482460
Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont. PMID:23475938
Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR). PMID:23474544
An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. PMID:23471004
Transforming growth factor beta receptor 2 (TGFBR2) changes sialylation in the microsatellite unstable (MSI) Colorectal cancer cell line HCT116. PMID:23468914
Modeling host genetic regulation of influenza pathogenesis in the collaborative cross. PMID:23468633
Evolutionary Genomics of Salmonella enterica Subspecies. PMID:23462113
RCPedia: a database of retrocopied genes. PMID:23457042
Estimating the population mutation rate from a de novo assembled Bactrian camel genome and cross-species comparison with dromedary ESTs. PMID:23454912
Comparative analysis of microRNA promoters in Arabidopsis and rice. PMID:23453017
Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. PMID:23452981
Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues. PMID:23450259
Nucleotide resolution analysis of TMPRSS2 and ERG rearrangements in prostate cancer. PMID:23447416
Circular RNAs are a large class of animal RNAs with regulatory potency. PMID:23446348
RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics. PMID:23442262
Genome sequencing identifies two nearly unchanged strains of persistent Listeria monocytogenes isolated at two different fish processing plants sampled 6 years apart. PMID:23435887
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. PMID:23433480
Transcriptome analysis of Inbred Long Sleep and Inbred Short Sleep mice. PMID:23433184
Genome sequence-based species delimitation with confidence intervals and improved distance functions. PMID:23432962
Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora. PMID:23432754
Alternative polyadenylation in glioblastoma multiforme and changes in predicted RNA binding protein profiles. PMID:23421905
Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta. PMID:23419129
TNPO3 protects HIV-1 replication from CPSF6-mediated capsid stabilization in the host cell cytoplasm. PMID:23414560
Genetic diversity, linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers. PMID:23409110
TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data. PMID:23408855
The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PMID:23382650
Draft genome sequence of the rubber tree Hevea brasiliensis. PMID:23375136
Genomic diversity and evolution of the head crest in the rock pigeon. PMID:23371554
HDAM: a resource of human disease associated mutations from next generation sequencing studies. PMID:23369322
Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish. PMID:23368736
A multispecies polyadenylation site model. PMID:23368518
Gene copy-number polymorphism caused by retrotransposition in humans. PMID:23359205
Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PMID:23357949
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. PMID:23354103
Cloning, annotation and developmental expression of the chicken intestinal MUC2 gene. PMID:23349743
Trivalent live attenuated influenza-simian immunodeficiency virus vaccines: efficacy and evolution of cytotoxic T lymphocyte escape in macaques. PMID:23345519
Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes. PMID:23343042
A survey of tools for variant analysis of next-generation genome sequencing data. PMID:23341494
Identification of biologically relevant enhancers in human erythroid cells. PMID:23341446
Deep sequencing of RNA from ancient maize kernels. PMID:23326310
A structural-based strategy for recognition of transcription factor binding sites. PMID:23320072
Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. PMID:23319649
Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. PMID:23316438
Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. PMID:23314698
A heterozygous moth genome provides insights into herbivory and detoxification. PMID:23313953
A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly. PMID:23303782
Lack of evidence for existence of noncanonical RNA editing. PMID:23302925
Henipavirus pathogenesis in human respiratory epithelial cells. PMID:23302882
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. PMID:23299411
The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s. PMID:23297357
Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidates. PMID:23282184
A specific family of interspersed repeats (SINEs) facilitates meiotic synapsis in mammals. PMID:23276256
rDNA-directed integration by an HIV-1 integrase--I-PpoI fusion protein. PMID:23275537
Spreading of heterochromatin is limited to specific families of maize retrotransposons. PMID:23271981
The genome of Prunus mume. PMID:23271652
A genomic scale map of genetic diversity in Trypanosoma cruzi. PMID:23270511
Identification of stanniocalcin 2 as a novel aryl hydrocarbon receptor target gene. PMID:23269473
A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. PMID:23263692
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). PMID:23263233
Genomic pathology of SLE-associated copy-number variation at the FCGR2C/FCGR3B/FCGR2B locus. PMID:23261299
Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes. PMID:23260012
Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing. PMID:23259534
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. PMID:23257886
TrueSight: a new algorithm for splice junction detection using RNA-seq. PMID:23254332
An integrated approach of comparative genomics and heritability analysis of pig and human on obesity trait: evidence for candidate genes on human chromosome 2. PMID:23253381
Genome-wide analysis of DNA methylation differences in muscle and fat from monozygotic twins discordant for type 2 diabetes. PMID:23251491
Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes. PMID:23249957
Latent regulatory potential of human-specific repetitive elements. PMID:23246434
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PMID:23236275
ENU mutagenesis reveals that Notchless homolog 1 (Drosophila) affects Cdkn1a and several members of the Wnt pathway during murine pre-implantation development. PMID:23231322
The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci. PMID:23224333
Flexible and efficient genome tiling design with penalized uniqueness score. PMID:23216884
Using chimaeric expression sequence tag as the reference to identify three-dimensional chromosome contacts. PMID:23213109
Comprehensive human transcription factor binding site map for combinatory binding motifs discovery. PMID:23209563
A forward genetic screen reveals that calcium-dependent protein kinase 3 regulates egress in Toxoplasma. PMID:23209419
Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma. PMID:23202128
Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. PMID:23197571
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. PMID:23193278
The evolution of the class A scavenger receptors. PMID:23181696
The chemical interactome space between the human host and the genetically defined gut metabotypes. PMID:23178670
Steric antisense inhibition of AMPA receptor Q/R editing reveals tight coupling to intronic editing sites and splicing. PMID:23172291
Activity-regulated RNA editing in select neuronal subfields in hippocampus. PMID:23172290
Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome. PMID:23171245
Comparative analysis of genome sequences covering the seven cronobacter species. PMID:23166675
Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PMID:23166598
Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis). PMID:23166587
A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. PMID:23152986
Strong signatures of selection in the domestic pig genome. PMID:23151514
The genome of the pear (Pyrus bretschneideri Rehd.). PMID:23149293
A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing. PMID:23144753
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. PMID:23143107
Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. PMID:23136377
Comparative genomics of neuroglobin reveals its early origins. PMID:23133533
Variants affecting exon skipping contribute to complex traits. PMID:23133393
Current analysis platforms and methods for detecting copy number variation. PMID:23132758
Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. PMID:23124323
Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms. PMID:23119097
A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish. PMID:23118857
Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: a comparative transcriptomic analysis of two ranid frogs, Rana chensinensis and R. kukunoris. PMID:23116153
Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. PMID:23114024
The τCstF-64 polyadenylation protein controls genome expression in testis. PMID:23110235
Comparative evaluation of intron prediction methods and detection of plant genome annotation using intron length distributions. PMID:23105930
STAR: ultrafast universal RNA-seq aligner. PMID:23104886
Genome update of Botrytis cinerea strains B05.10 and T4. PMID:23104368
Sex-biased transcriptome evolution in Drosophila. PMID:23097318
CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex. PMID:23085716
A hybrid distance measure for clustering expressed sequence tags originating from the same gene family. PMID:23071763
Gene and genome parameters of mammalian liver circadian genes (LCGs). PMID:23071677
The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences. PMID:23071448
SPLOOCE: a new portal for the analysis of human splicing variants. PMID:23064119
Computational tools for viral metagenomics and their application in clinical research. PMID:23062738
Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data. PMID:23056904
Selective constraint on copy number variation in human piwi-interacting RNA Loci. PMID:23056369
RNA-Seq Assembly - Are We There Yet? PMID:23056003
A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads. PMID:23049702
A multi-omic map of the lipid-producing yeast Rhodosporidium toruloides. PMID:23047670
Conserved epigenetic sensitivity to early life experience in the rat and human hippocampus. PMID:23045659
Next-generation sequencing and de novo assembly, genome organization, and comparative genomic analyses of the genomes of two Helicobacter pylori isolates from duodenal ulcer patients in India. PMID:23045484
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. PMID:23044549
Hundreds of conserved non-coding genomic regions are independently lost in mammals. PMID:23042682
Discovery and characterization of human exonic transcriptional regulatory elements. PMID:23029400
Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A. PMID:23028950
Tethering of the conserved piggyBac transposase fusion protein CSB-PGBD3 to chromosomal AP-1 proteins regulates expression of nearby genes in humans. PMID:23028371
A novel rhabdovirus associated with acute hemorrhagic fever in central Africa. PMID:23028323
Noncoder: a web interface for exon array-based detection of long non-coding RNAs. PMID:23012263
Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300. PMID:23009684
ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins. PMID:23009561
The minimal active human SVA retrotransposon requires only the 5'-hexamer and Alu-like domains. PMID:23007156
High-resolution genotyping and mapping of recombination and gene conversion in the protozoan Theileria parva using whole genome sequencing. PMID:22998600
Rat Mcs1b is concordant to the genome-wide association-identified breast cancer risk locus at human 5q11.2 and MIER3 is a candidate cancer susceptibility gene. PMID:22993404
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. PMID:22988817
Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329. PMID:22978491
Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. PMID:22978381
Highly improved homopolymer aware nucleotide-protein alignments with 454 data. PMID:22971057
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model. PMID:22962492
MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample. PMID:22962452
Activity-dependent human brain coding/noncoding gene regulatory networks. PMID:22960213
RON is not a prognostic marker for resectable pancreatic cancer. PMID:22958871
Long noncoding RNAs are rarely translated in two human cell lines. PMID:22955977
Ruler arrays reveal haploid genomic structural variation. PMID:22952647
The GENCODE pseudogene resource. PMID:22951037
Genotypic and phenotypic evaluation of the evolution of high-level daptomycin nonsusceptibility in vancomycin-resistant Enterococcus faecium. PMID:22948885
SKIP is a component of the spliceosome linking alternative splicing and the circadian clock in Arabidopsis. PMID:22942380
Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. PMID:22941634
Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. PMID:22937793
An alu-based phylogeny of lemurs (infraorder: Lemuriformes). PMID:22937148
Mechanisms of dietary response in mice and primates: a role for EGR1 in regulating the reaction to human-specific nutritional content. PMID:22937124
A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. PMID:22936249
Tissue-restricted transcription from a conserved intragenic CpG island in the Klf1 gene in mice. PMID:22933519
Integrase-deficient lentiviral vectors mediate efficient gene transfer to human vascular smooth muscle cells with minimal genotoxic risk. PMID:22931362
Identification and analysis of pig chimeric mRNAs using RNA sequencing data. PMID:22925561
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides. PMID:22925230
Characterization of the standard and recommended CODIS markers. PMID:22925064
Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing. PMID:22923523
The diversity of class II transposable elements in mammalian genomes has arisen from ancestral phylogenetic splits during ancient waves of proliferation through the genome. PMID:22923465
The human transcriptome: an unfinished story. PMID:22916334
Eco-geographical diversification of bitter taste receptor genes (TAS2Rs) among subspecies of chimpanzees (Pan troglodytes). PMID:22916235
Identification and functional analysis of three isoforms of bovine BST-2. PMID:22911799
Personal receptor repertoires: olfaction as a model. PMID:22908908
The UCSC genome browser and associated tools. PMID:22908213
CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes. PMID:22901030
Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. PMID:22900609
Mating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27 nt small RNAs derived from the parental macronucleus. PMID:22900016
Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. PMID:22891638
FoxO-dependent regulation of diacylglycerol kinase α gene expression. PMID:22890845
Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system. PMID:22884033
SAP--a sequence mapping and analyzing program for long sequence reads alignment and accurate variants discovery. PMID:22880129
Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. PMID:22871084
Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing. PMID:22866951
A genomic approach to investigate expression profiles in Slovenian patients with gastric cancer. PMID:22866164
Identification of 34 novel proinflammatory proteins in a genome-wide macrophage functional screen. PMID:22860121
The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion. PMID:22859968
Spatio-temporal regulation of ADAR editing during development in porcine neural tissues. PMID:22858680
Evolutionary patterns of RNA-based gene duplicates in Caenorhabditis nematodes coincide with their genomic features. PMID:22853807
Complementary proteome and transcriptome profiling in phosphate-deficient Arabidopsis roots reveals multiple levels of gene regulation. PMID:22843991
Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles. PMID:22839428
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. PMID:22839106
Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles. PMID:22839428
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. PMID:22839106
Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti. PMID:22833609
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. PMID:22833495
YAHA: fast and flexible long-read alignment with optimal breakpoint detection. PMID:22829624
FAST-SeqS: a simple and efficient method for the detection of aneuploidy by massively parallel sequencing. PMID:22815955
Novel RNAi-mediated approach to G protein-coupled receptor deorphanization: proof of principle and characterization of a planarian 5-HT receptor. PMID:22815820
Comparative genomic and transcriptional analyses of CRISPR systems across the genus Pyrobaculum. PMID:22811677
Restricted gene flow among hospital subpopulations of Enterococcus faecium. PMID:22807567
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. PMID:22801500
Large-scale transcriptome analysis of retroelements in the migratory locust, Locusta migratoria. PMID:22792363
Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species. PMID:22783241
Compressive genomics. PMID:22781691
Ultrafast clustering algorithms for metagenomic sequence analysis. PMID:22772836
Functional assignment of metagenomic data: challenges and applications. PMID:22772835
Oomycete Transcriptomics Database: a resource for oomycete transcriptomes. PMID:22768977
A pronounced evolutionary shift of the pseudoautosomal region boundary in house mice. PMID:22763584
Hybrid error correction and de novo assembly of single-molecule sequencing reads. PMID:22750884
Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species. PMID:22747887
Bovine polledness--an autosomal dominant trait with allelic heterogeneity. PMID:22737241
Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.). PMID:22736259
Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae). PMID:22731878
Expressed pseudogenes in the transcriptional landscape of human cancers. PMID:22726445
Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida. PMID:22726260
Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. PMID:22724064
Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping. PMID:22724063
A tumour suppressor network relying on the polyamine-hypusine axis. PMID:22722845
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. PMID:22720753
Skipping of exons by premature termination of transcription and alternative splicing within intron-5 of the sheep SCF gene: a novel splice variant. PMID:22719917
A SEL1L mutation links a canine progressive early-onset cerebellar ataxia to the endoplasmic reticulum-associated protein degradation (ERAD) machinery. PMID:22719266
Field monitoring of avian influenza viruses: whole-genome sequencing and tracking of neuraminidase evolution using 454 pyrosequencing. PMID:22718944
The molecular mechanism of action of the CR6261-Azichromycin combination found through computational analysis. PMID:22693576
UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes. PMID:22693428
Novel domain combinations in proteins encoded by chimeric transcripts. PMID:22689780
SEQuel: improving the accuracy of genome assemblies. PMID:22689760
Dissect: detection and characterization of novel structural alterations in transcribed sequences. PMID:22689759
Xenome--a tool for classifying reads from xenograft samples. PMID:22689758
MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity. PMID:22689644
Multi-locus phylogeographic and population genetic analysis of Anolis carolinensis: historical demography of a genomic model species. PMID:22685573
An Alu-based phylogeny of gibbons (hylobatidae). PMID:22683814
High accuracy mutation detection in leukemia on a selected panel of cancer genes. PMID:22675565
Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PMID:22675423
Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. PMID:22674328
Genomic variation in natural populations of Drosophila melanogaster. PMID:22673804
A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs. PMID:22672252
Regulated Expression of Chromobox Homolog 5 Revealed in Tumors of Apc(Min) (/+) ROSA11 Gene Trap Mice. PMID:22670227
The iPlant Collaborative: Cyberinfrastructure for Plant Biology. PMID:22645531
Mutation at the human D1S80 minisatellite locus. PMID:22645469
Transcriptome analysis of a North American songbird, Melospiza melodia. PMID:22645122
Epigenetics in the human brain. PMID:22643929
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts. PMID:22641850
VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era. PMID:22618869
Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PMID:22615578
Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform. PMID:22607986
Rapid transcriptional pulsing dynamics of high expressing retroviral transgenes in embryonic stem cells. PMID:22606340
jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. PMID:22600739
Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene. PMID:22591852
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. PMID:22588898
Metagenomics - a guide from sampling to data analysis. PMID:22587947
On the analysis of the illumina 450k array data: probes ambiguously mapped to the human genome. PMID:22586432
SIS: a program to generate draft genome sequence scaffolds for prokaryotes. PMID:22583530
Reference genome sequence of the model plant Setaria. PMID:22580951
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. PMID:22580950
GHOSTM: a GPU-accelerated homology search tool for metagenomics. PMID:22574135
Meta-analysis of genetic association studies on bipolar disorder. PMID:22573399
Extended survival of glioblastoma patients after chemoprotective HSC gene therapy. PMID:22572881
Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells. PMID:22570599
Transcript profiling identifies dynamic gene expression patterns and an important role for Nrf2/Keap1 pathway in the developing mouse esophagus. PMID:22567161
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. PMID:22563071
Bioinformatic clonality analysis of next-generation sequencing-derived viral vector integration sites. PMID:22559057
Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam]. PMID:22558397
Experimental verification of a predicted intronic microRNA in human NGFR gene with a potential pro-apoptotic function. PMID:22558167
Elephant transcriptome provides insights into the evolution of eutherian placentation. PMID:22546564
Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers. PMID:22541534
A context-based approach to identify the most likely mapping for RNA-seq experiments. PMID:22537048
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. PMID:22537044
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. PMID:22537006
Tachyon search speeds up retrieval of similar sequences by several orders of magnitude. PMID:22531216
Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. PMID:22529356
A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. PMID:22524439
lobSTR: A short tandem repeat profiler for personal genomes. PMID:22522390
A beginner's guide to eukaryotic genome annotation. PMID:22510764
Mapping of gene expression reveals CYP27A1 as a susceptibility gene for sporadic ALS. PMID:22509407
A genome resource to address mechanisms of developmental programming: determination of the fetal sheep heart transcriptome. PMID:22508961
The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens. PMID:22506068
Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin. PMID:22496776
Search for an aetiological virus candidate in chronic lymphocytic leukaemia by extensive transcriptome analysis. PMID:22489537
Characterisation of bovine leukocyte Ig-like receptors. PMID:22485161
Exploring the switchgrass transcriptome using second-generation sequencing technology. PMID:22479570
Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. PMID:22475018
Whole genome expression differences in human left and right atria ascertained by RNA sequencing. PMID:22474228
Identification of allele-specific alternative mRNA processing via transcriptome sequencing. PMID:22467206
A quantitative atlas of polyadenylation in five mammals. PMID:22454233
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. PMID:22443449
Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. PMID:22417298
Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines. PMID:22414013
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. PMID:22403033
High Levels of Sequence Diversity in the 5' UTRs of Human-Specific L1 Elements. PMID:22400009
Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. PMID:22396667
Using BLAT to find sequence similarity in closely related genomes. PMID:22389010
Molecular cloning of large alternative transcripts based on comparative phylogenetic analysis and exploration of an EST database. PMID:22387390
Expression quantitative trait Loci for extreme host response to influenza a in pre-collaborative cross mice. PMID:22384400
Organizational heterogeneity of vertebrate genomes. PMID:22384143
FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads. PMID:22379138
Rapid identification of non-human sequences in high-throughput sequencing datasets. PMID:22377895
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. PMID:22373417
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. PMID:22373054
Interrogation of alternative splicing events in duplicated genes during evolution. PMID:22369477
Profiling ascidian promoters as the primordial type of vertebrate promoter. PMID:22369359
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. PMID:22368243
Hospital and community ampicillin-resistant Enterococcus faecium are evolutionarily closely linked but have diversified through niche adaptation. PMID:22363425
Joint analysis of multiple metagenomic samples. PMID:22359490
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. PMID:22355574
Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PMID:22347999
Virus identification in unknown tropical febrile illness cases using deep sequencing. PMID:22347512
Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PMID:22347367
A differential sequencing-based analysis of the C. elegans noncoding transcriptome. PMID:22345127
Effect of periodontal pathogens on the metatranscriptome of a healthy multispecies biofilm model. PMID:22328675
CAPRG: sequence assembling pipeline for next generation sequencing of non-model organisms. PMID:22319566
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. PMID:22293517
The chimpanzee GH locus: composition, organization, and evolution. PMID:22290452
A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation. PMID:22289569
R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. PMID:22287631
Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs. PMID:22282338
Detection of base substitution-type somatic mosaicism of the NLRP3 gene with >99.9% statistical confidence by massively parallel sequencing. PMID:22279087
Adrenal androgen production in catarrhine primates and the evolution of adrenarche. PMID:22271526
A recurrent translocation is mediated by homologous recombination between HERV-H elements. PMID:22260357
Evidence for transcript networks composed of chimeric RNAs in human cells. PMID:22238572
Entry of human T-cell leukemia virus type 1 is augmented by heparin sulfate proteoglycans bearing short heparin-like structures. PMID:22238310
Investigation of the origin and spread of a Mammalian transposable element based on current sequence diversity. PMID:22222953
A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon. PMID:22219511
Common promoter elements in odorant and vomeronasal receptor genes. PMID:22216168
Functional RNA interference (RNAi) screen identifies system A neutral amino acid transporter 2 (SNAT2) as a mediator of arsenic-induced endoplasmic reticulum stress. PMID:22215663
Genome-wide expression profiling of schizophrenia using a large combined cohort. PMID:22212594
SCOREM: statistical consolidation of redundant expression measures. PMID:22210887
Probe mapping across multiple microarray platforms. PMID:22199380
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program. PMID:22199257
Phenotype-specific effect of chromosome 1q21.1 rearrangements and GJA5 duplications in 2436 congenital heart disease patients and 6760 controls. PMID:22199024
Molecular mechanisms of EGF signaling-dependent regulation of pipe, a gene crucial for dorsoventral axis formation in Drosophila. PMID:22198544
Analysis of expression sequence tags from a full-length-enriched cDNA library of developing sesame seeds (Sesamum indicum). PMID:22195973
Genome-wide signatures of 'rearrangement hotspots' within segmental duplications in humans. PMID:22194928
Transcriptome analyses to investigate the pathogenesis of RNA splicing factor retinitis pigmentosa. PMID:22183372
A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi. PMID:22180794
Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. PMID:22180530
The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs. PMID:22171608
Neuroglobin-deficiency exacerbates Hif1A and c-FOS response, but does not affect neuronal survival during severe hypoxia in vivo. PMID:22164238
MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates. PMID:22162950
Polymorphic NumtS trace human population relationships. PMID:22160368
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. PMID:22158310
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. PMID:22156394
Hematopoietic stem cell expansion facilitates multilineage engraftment in a nonhuman primate cord blood transplantation model. PMID:22155723
STELLAR: fast and exact local alignments. PMID:22151882
The repertoire of G protein-coupled receptors in the human parasite Schistosoma mansoni and the model organism Schmidtea mediterranea. PMID:22145649
Identification of a genomic reservoir for new TRIM genes in primate genomes. PMID:22144910
Estimated comparative integration hotspots identify different behaviors of retroviral gene transfer vectors. PMID:22144885
RecountDB: a database of mapped and count corrected transcribed sequences. PMID:22139942
Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster. PMID:22135405
Dr.VIS: a database of human disease-related viral integration sites. PMID:22135288
Revealing the missing expressed genes beyond the human reference genome by RNA-Seq. PMID:22133125
Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. PMID:22096216
Characterizing complex structural variation in germline and somatic genomes. PMID:22094265
High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. PMID:22090119
Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. PMID:22086488
Effects of genome-wide copy number variation on expression in mammalian cells. PMID:22085887
CADRE: the Central Aspergillus Data REpository 2012. PMID:22080563
Evolutionary history and functional characterization of the amphibian xenosensor CAR. PMID:22074953
Drosophila duplication hotspots are associated with late-replicating regions of the genome. PMID:22072977
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. PMID:22067447
Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. PMID:22067224
Approaches to Fungal Genome Annotation. PMID:22059117
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. PMID:22057054
A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle. PMID:22056929
RNA-Seq improves annotation of protein-coding genes in the cucumber genome. PMID:22047402
A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. PMID:22045999
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. PMID:22039206
Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. PMID:22038251
Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. PMID:22034492
Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines. PMID:22032724
Ascaris suum draft genome. PMID:22031327
Silencing, positive selection and parallel evolution: busy history of primate cytochromes C. PMID:22028846
Graph accordance of next-generation sequence assemblies. PMID:22025481
The draft genome of the carcinogenic human liver fluke Clonorchis sinensis. PMID:22023798
Regional selection acting on the OFD1 gene family. PMID:22022562
Very few RNA and DNA sequence differences in the human transcriptome. PMID:22022455
MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PMID:22022286
Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PMID:22022265
The draft genome and transcriptome of Cannabis sativa. PMID:22014239
Conditional CD8+ T cell escape during acute simian immunodeficiency virus infection. PMID:22013056
De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes. PMID:21995639
The UCSC Genome Browser. PMID:21975940
Methylation of L1Hs promoters is lower on the inactive X, has a tendency of being higher on autosomes in smaller genomes and shows inter-individual variability at some loci. PMID:21972244
Kaviar: an accessible system for testing SNV novelty. PMID:21965822
Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. PMID:21964414
Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. PMID:21960545
Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. PMID:21948523
Alu pair exclusions in the human genome. PMID:21943335
Genome of a novel isolate of Paracoccus denitrificans capable of degrading N,N-dimethylformamide. PMID:21914898
Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. PMID:21914852
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. PMID:21909094
A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes. PMID:21906286
Next-generation transcriptome assembly. PMID:21897427
The human gut virome: inter-individual variation and dynamic response to diet. PMID:21880779
In silico reconstruction of viral genomes from small RNAs improves virus-derived small interfering RNA profiling. PMID:21880776
Protein-binding microarray analysis of tumor suppressor AP2α target gene specificity. PMID:21876733
A comprehensive map of mobile element insertion polymorphisms in humans. PMID:21876680
Whole-genome sequencing of multiple Arabidopsis thaliana populations. PMID:21874002
Activation of the glucocorticoid receptor is associated with poor prognosis in estrogen receptor-negative breast cancer. PMID:21868756
Parallelized short read assembly of large genomes using de Bruijn graphs. PMID:21867511
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. PMID:21864382
Discovery of lost diversity of paternal horse lineages using ancient DNA. PMID:21863017
Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. PMID:21863010
Transcriptional profiling of human liver identifies sex-biased genes associated with polygenic dyslipidemia and coronary artery disease. PMID:21858147
Molecular genetic analyses of polytene chromosome region 72A-D in Drosophila melanogaster reveal a gene desert in 72D. PMID:21853143
Three periods of regulatory innovation during vertebrate evolution. PMID:21852499
Comparative deep transcriptional profiling of four developing oilseeds. PMID:21851431
Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited. PMID:21850235
The head-regeneration transcriptome of the planarian Schmidtea mediterranea. PMID:21846378
Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. PMID:21840973
A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome inactivation. PMID:21840866
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. PMID:21835007
The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PMID:21829493
An unbiased genome-wide analysis of zinc-finger nuclease specificity. PMID:21822255
The fat body transcriptomes of the yellow fever mosquito Aedes aegypti, pre- and post- blood meal. PMID:21818341
Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio. PMID:21798037
Identification of genomic indels and structural variations using split reads. PMID:21787423
Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. PMID:21785424
The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones. PMID:21777481
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). PMID:21775302
Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PMID:21750662
Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma. PMID:21750257
Mutational analysis of 12 patients with the phenotype of Ehlers-Danlos syndrome type VIB shows no linkage to the zinc transporter gene SLC39A13. PMID:21739577
Microbial diversity in the midguts of field and lab-reared populations of the European corn borer Ostrinia nubilalis. PMID:21738787
Gene expression in Trypanosoma brucei: lessons from high-throughput RNA sequencing. PMID:21737348
Phosphorylation network rewiring by gene duplication. PMID:21734643
Deep sequencing of the human TCRγ and TCRβ repertoires suggests that TCRβ rearranges after αβ and γδ T cell commitment. PMID:21734177
Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies. PMID:21731731
Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines. PMID:21731642
Evolution of the V, D, and J gene segments used in the primate gammadelta T-cell receptor reveals a dichotomy of conservation and diversity. PMID:21730193
Exome-wide DNA capture and next generation sequencing in domestic and wild species. PMID:21729323
Reproductive tissue-specific expression profiling and genetic variation across a 19 gene bovine β-defensin cluster. PMID:21713586
Evolution of C4 photosynthesis in the genus Flaveria: how many and which genes does it take to make C4? PMID:21705644
Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus. PMID:21699734
Nuclear outsourcing of RNA interference components to human mitochondria. PMID:21695135
Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India. PMID:21685291
Meta-IDBA: a de Novo assembler for metagenomic data. PMID:21685107
Transcriptome analysis of sarracenia, an insectivorous plant. PMID:21676972
Comparative analysis of the ATRX promoter and 5' regulatory region reveals conserved regulatory elements which are linked to roles in neurodevelopment, alpha-globin regulation and testicular function. PMID:21676266
CREST maps somatic structural variation in cancer genomes with base-pair resolution. PMID:21666668
Human teneurin-1 is a direct target of the homeobox transcription factor EMX2 at a novel alternate promoter. PMID:21651764
Towards the human colorectal cancer microbiome. PMID:21647227
A novel mitofusin 2 mutation causes canine fetal-onset neuroaxonal dystrophy. PMID:21643798
Computational analysis of drought stress-associated miRNAs and miRNA co-regulation network in Physcomitrella patens. PMID:21641561
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. PMID:21633356
Genome-wide identification of conserved regulatory function in diverged sequences. PMID:21628450
Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection. PMID:21627829
Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PMID:21625384
De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). PMID:21623354
Computational methods for transcriptome annotation and quantification using RNA-seq. PMID:21623353
Finding cancer-associated miRNAs: methods and tools. PMID:21607762
piRNA profiling during specific stages of mouse spermatogenesis. PMID:21602304
Inhibition of RNA interference and modulation of transposable element expression by cell death in Drosophila. PMID:21596898
Bioinformatics challenges for personalized medicine. PMID:21596790
Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing. PMID:21592371
The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships. PMID:21589882
Sequence-specific error profile of Illumina sequencers. PMID:21576222
RAPSearch: a fast protein similarity search tool for short reads. PMID:21575167
Full-length transcriptome assembly from RNA-Seq data without a reference genome. PMID:21572440
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. PMID:21565797
Functional divergences of GAPDH isoforms during early development in two perciform fish species. PMID:21559871
Enhancing genome assemblies by integrating non-sequence based data. PMID:21554765
Sequence alignment as hypothesis testing. PMID:21554016
Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing. PMID:21551146
TparvaDB: a database to support Theileria parva vaccine development. PMID:21546359
CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome. PMID:21544197
Methods and strategies for gene structure curation in WormBase. PMID:21543339
Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. PMID:21542930
De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. PMID:21536722
Identification of piRNAs in the central nervous system. PMID:21515829
Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient. PMID:21515762
Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori. PMID:21508430
Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore. PMID:21507265
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. PMID:21505035
The sequence, structure and evolutionary features of HOTAIR in mammals. PMID:21496275
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. PMID:21493686
Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma. PMID:21490616
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. PMID:21478890
A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. PMID:21457569
A vertebrate case study of the quality of assemblies derived from next-generation sequences. PMID:21453517
Rice-Map: a new-generation rice genome browser. PMID:21450055
Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite. PMID:21439036
Fast local fragment chaining using sum-of-pair gap costs. PMID:21418573
Targeted deep resequencing of the human cancer genome using next-generation technologies. PMID:21415896
A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences. PMID:21415121
Rhythms and synchronization patterns in gene expression in the Aedes aegypti mosquito. PMID:21414217
Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos). PMID:21410945
Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PMID:21408183
Metatranscriptomic approach to analyze the functional human gut microbiota. PMID:21408168
Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PMID:21408061
Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta. PMID:21402862
Disease and phenotype data at Ensembl. PMID:21400687
A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PMID:21383968
Genome sequence of Neisseria meningitidis serogroup B strain H44/76. PMID:21378179
Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. PMID:21367939
Abundant human DNA contamination identified in non-primate genome databases. PMID:21358816
Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning. PMID:21352520
FoSTeS, MMBIR and NAHR at the human proximal Xp region and the mechanisms of human Xq isochromosome formation. PMID:21349920
PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences. PMID:21347141
Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs. PMID:21346809
Annotating genes and genomes with DNA sequences extracted from biomedical articles. PMID:21325301
Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays. PMID:21324185
Neuronal genes for subcutaneous fat thickness in human and pig are identified by local genomic sequencing and combined SNP association study. PMID:21311593
Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination. PMID:21307298
Quantitative trait loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L.) through targeted genome scan. PMID:21304996
Considering transposable element diversification in de novo annotation approaches. PMID:21304975
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. PMID:21304686
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. PMID:21304684
Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. PMID:21297981
The effects of EBV transformation on gene expression levels and methylation profiles. PMID:21289059
Genomic sequencing and analysis of a Chinese hamster ovary cell line using Illumina sequencing technology. PMID:21269493
Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. PMID:21266659
S-adenosylmethionine decreases lipopolysaccharide-induced phosphodiesterase 4B2 and attenuates tumor necrosis factor expression via cAMP/protein kinase A pathway. PMID:21266552
Narrowing a region on rat chromosome 13 that protects against hypertension in Dahl SS-13BN congenic strains. PMID:21257920
Activation-induced cytidine deaminase induces reproducible DNA breaks at many non-Ig Loci in activated B cells. PMID:21255732
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. PMID:21251332
Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. PMID:21247460
Identifying viral integration sites using SeqMap 2.0. PMID:21245052
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. PMID:21245033
Comparison of Current BLAST Software on Nucleotide Sequences. PMID:21243090
Bioinformatic identification of novel protein phosphatases in the dog genome. PMID:21240543
Expression, splicing, and evolution of the myosin gene family in plants. PMID:21233331
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. PMID:21233167
A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation. PMID:21226900
Adaptive seeds tame genomic sequence comparison. PMID:21209072
Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea. PMID:21194483
Aromatase is a direct target of FOXL2: C134W in granulosa cell tumors via a single highly conserved binding site in the ovarian specific promoter. PMID:21188138
The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach. PMID:21187908
The solute carrier families have a remarkably long evolutionary history with the majority of the human families present before divergence of Bilaterian species. PMID:21186191
Extraordinary sequence divergence at Tsga8, an X-linked gene involved in mouse spermiogenesis. PMID:21186189
Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. PMID:21177970
Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. PMID:21177965
The Drosophila melanogaster transcriptome by paired-end RNA sequencing. PMID:21177959
Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera. PMID:21171999
Disease-associated XMRV sequences are consistent with laboratory contamination. PMID:21171979
Gene duplication and divergence of long wavelength-sensitive opsin genes in the guppy, Poecilia reticulata. PMID:21170644
Genome-wide interrogation of Mammalian stem cell fate determinants by nested chromosome deletions. PMID:21170304
A case-by-case evolutionary analysis of four imprinted retrogenes. PMID:21166792
Initial steps towards a production platform for DNA sequence analysis on the grid. PMID:21156038
Genomic mRNA profiling reveals compensatory mechanisms for the requirement of the essential splicing factor U2AF. PMID:21149581
Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. PMID:21149391
Identifying novel genes in C. elegans using SAGE tags. PMID:21143975
Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. PMID:21131573
Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. PMID:21128942
Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. PMID:21126361
The parental non-equivalence of imprinting control regions during mammalian development and evolution. PMID:21124941
Analyses of copy number variation of GK rat reveal new putative type 2 diabetes susceptibility loci. PMID:21124896
Structure-function analyses point to a polynucleotide-accommodating groove essential for APOBEC3A restriction activities. PMID:21123384
Pseudogene: lessons from PCR bias, identification and resurrection. PMID:21116863
Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis. PMID:21115709
Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene. PMID:21109525
Recurrent interstitial 1p36 deletions: Evidence for germline mosaicism and complex rearrangement breakpoints. PMID:21108392
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. PMID:21106091
Genetic diversity in India and the inference of Eurasian population expansion. PMID:21106085
The rapid generation of chimerical genes expanding protein diversity in zebrafish. PMID:21106061
Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster. PMID:21104067
Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PMID:21103372
dbDNV: a resource of duplicated gene nucleotide variants in human genome. PMID:21097891
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. PMID:21092284
Nme gene family evolutionary history reveals pre-metazoan origins and high conservation between humans and the sea anemone, Nematostella vectensis. PMID:21085602
HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PMID:21079731
Expression of type II chorionic gonadotropin genes supports a role in the male reproductive system. PMID:21078876
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. PMID:21076406
Identification of alternatively spliced transcripts using a proteomic informatics approach. PMID:21063957
Genomic tools development for Aquilegia: construction of a BAC-based physical map. PMID:21059242
Dating primate divergences through an integrated analysis of palaeontological and molecular data. PMID:21051775
Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data. PMID:21044359
Enrichment of mRNA-like noncoding RNAs in the divergence of Drosophila males. PMID:21041796
Epigenetic control of retrotransposon expression in human embryonic stem cells. PMID:21041477
Scaffolding a Caenorhabditis nematode genome with RNA-seq. PMID:20980554
Computational Epigenetics: the new scientific paradigm. PMID:20978607
An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research. PMID:20976139
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. PMID:20973991
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. PMID:20964841
The UCSC Genome Browser database: update 2011. PMID:20959295
Identification and characterisation of the BPI/LBP/PLUNC-like gene repertoire in chickens reveals the absence of a LBP gene. PMID:20959152
Genome of Helicobacter pylori strain 908. PMID:20952566
Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. PMID:20952408
Comparing de novo assemblers for 454 transcriptome data. PMID:20950480
Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay. PMID:20946641
Quail Genomics: a knowledgebase for Northern bobwhite. PMID:20946596
Discovery and characterization of mammalian endogenous parvoviruses. PMID:20943964
GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing. PMID:20939910
Geoseq: a tool for dissecting deep-sequencing datasets. PMID:20939882
T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. PMID:20937630
De novo assembly and analysis of RNA-seq data. PMID:20935650
Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin. PMID:20935062
The evolution and expression of the snaR family of small non-coding RNAs. PMID:20935053
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. PMID:20932287
Cloning and characterization of a novel alternatively spliced transcript of the human CHD7 putative helicase. PMID:20925924
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. PMID:20924354
Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera. PMID:20920358
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. PMID:20924354
Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera. PMID:20920358
Identification of disease-causing mutations in autosomal dominant retinitis pigmentosa (adRP) using next-generation DNA sequencing. PMID:20861475
Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome. PMID:20860831
The FLIGHT Drosophila RNAi database: 2010 update. PMID:20855970
Long- and short-term selective forces on malaria parasite genomes. PMID:20838588
Exploring zebrafish genomic, functional and phenotypic data using ZFIN. PMID:20836073
Genome rearrangements detected by SNP microarrays in individuals with intellectual disability referred with possible Williams syndrome. PMID:20824207
FragGeneScan: predicting genes in short and error-prone reads. PMID:20805240
SAW: a method to identify splicing events from RNA-Seq data based on splicing fingerprints. PMID:20706591
A network of conserved co-occurring motifs for the regulation of alternative splicing. PMID:20702423
Exon-level transcriptome profiling in murine breast cancer reveals splicing changes specific to tumors with different metastatic abilities. PMID:20700505
Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing. PMID:20671722
Isolation of SPINK6 in human skin: selective inhibitor of kallikrein-related peptidases. PMID:20667819
Polyploidy did not predate the evolution of nodulation in all legumes. PMID:20661290
Gene duplication and environmental adaptation within yeast populations. PMID:20660110
Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates. PMID:20659325
Heritability in the efficiency of nonsense-mediated mRNA decay in humans. PMID:20657766
Inherited neuroaxonal dystrophy in dogs causing lethal, fetal-onset motor system dysfunction and cerebellar hypoplasia. PMID:20653033
A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping. PMID:20650293
Tissue-specific regulatory regions of the PTH gene localized by novel chromosome 11 rearrangement breakpoints in a parathyroid adenoma. PMID:20641034
Quantitative gene expression profiles in real time from expressed sequence tag databases. PMID:20635574
Integration preferences of wildtype AAV-2 for consensus rep-binding sites at numerous loci in the human genome. PMID:20628575
The role of nucleosome positioning in the evolution of gene regulation. PMID:20625544
Semi-automated library preparation for high-throughput DNA sequencing platforms. PMID:20625503
Evolution of a bitter taste receptor gene cluster in a New World sparrow. PMID:20624740
Serious limitations of the QTL/microarray approach for QTL gene discovery. PMID:20624276
Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. PMID:20622855
Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes. PMID:20622018
Characterization of C1q in teleosts: insight into the molecular and functional evolution of C1q family and classical pathway. PMID:20615881
LINE-1 retrotransposition activity in human genomes. PMID:20602998
RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. PMID:20587772
Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer. PMID:20587502
Local alignment of generalized k-base encoded DNA sequence. PMID:20576157
Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. PMID:20565788
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. PMID:20565764
Design and evaluation of genome-wide libraries for RNA interference screens. PMID:20550664
Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. PMID:20547834
An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. PMID:20543093
Genomic SELEX: a discovery tool for genomic aptamers. PMID:20541015
Prevalence of alternative splicing choices in Arabidopsis thaliana. PMID:20525311
Challenges of sequencing human genomes. PMID:20519329
Most "dark matter" transcripts are associated with known genes. PMID:20502517
SFmap: a web server for motif analysis and prediction of splicing factor binding sites. PMID:20501600
Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication. PMID:20500887
Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. PMID:20487544
A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6. PMID:20487517
Towards a comprehensive structural variation map of an individual human genome. PMID:20482838
Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly. PMID:20479877
Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. PMID:20472684
Classification of DNA sequences using Bloom filters. PMID:20472541
BAGEL2: mining for bacteriocins in genomic data. PMID:20462861
A survey of sequence alignment algorithms for next-generation sequencing. PMID:20460430
eHive: an artificial intelligence workflow system for genomic analysis. PMID:20459813
Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. PMID:20455209
Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen. PMID:20453089
Natural selection on cis and trans regulation in yeasts. PMID:20445163
E-RNAi: a web application for the multi-species design of RNAi reagents--2010 update. PMID:20444868
Organization of the variable region of the immunoglobulin heavy-chain gene locus of the rat. PMID:20442993
Molecular genetic analysis of Chd3 and polytene chromosome region 76B-D in Drosophila melanogaster. PMID:20439780
The molecular evolution of PL10 homologs. PMID:20438638
An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags. PMID:20433739
Cgaln: fast and space-efficient whole-genome alignment. PMID:20433723
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. PMID:20430781
A novel role for minimal introns: routing mRNAs to the cytosol. PMID:20419085
Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. PMID:20418490
BS Seeker: precise mapping for bisulfite sequencing. PMID:20416082
MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. PMID:20407027
Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana. PMID:20406451
EuGène-maize: a web site for maize gene prediction. PMID:20400755
Replacement of Rbpj with Rbpjl in the PTF1 complex controls the final maturation of pancreatic acinar cells. PMID:20398665
Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome. PMID:20385588
Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites. PMID:20385579
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. PMID:20360389
Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. PMID:20360267
Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri. PMID:20353595
Histone H3 trimethylated at lysine 4 is enriched at probable transcription start sites in Trypanosoma brucei. PMID:20347883
Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila melanogaster. PMID:20333226
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. PMID:20331785
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. PMID:20308636
Analysis of the genome content of Lactococcus garvieae by genomic interspecies microarray hybridization. PMID:20233401
Agrobacterium-meditated gene disruption using split-marker in Grosmannia clavigera, a mountain pine beetle associated pathogen. PMID:20229292
Heads or tails: L1 insertion-associated 5' homopolymeric sequences. PMID:20226075
Gallin; an antimicrobial peptide member of a new avian defensin family, the ovodefensins, has been subject to recent gene duplication. PMID:20226050
Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin. PMID:20224866
Testing the coding potential of conserved short genomic sequences. PMID:20224812
KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PMID:20221260
Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. PMID:20219969
PanCGHweb: a web tool for genotype calling in pangenome CGH data. PMID:20219865
Validation and application of normalization factors for gene expression studies in rubella virus-infected cell lines with quantitative real-time PCR. PMID:20217898
High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates. PMID:20212022
Alterations in the steroid hormone receptor co-chaperone FKBPL are associated with male infertility: a case-control study. PMID:20210997
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. PMID:20210993
Genome-wide synteny through highly sensitive sequence alignment: Satsuma. PMID:20208069
Efficient discovery of ASCL1 regulatory sequences through transgene pooling. PMID:20206680
A human gut microbial gene catalogue established by metagenomic sequencing. PMID:20203603
Gene family size conservation is a good indicator of evolutionary rates. PMID:20194423
Chaperonin genes on the rise: new divergent classes and intense duplication in human and other vertebrate genomes. PMID:20193073
Chromosomal position effects on AAV-mediated gene targeting. PMID:20185563
Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0. PMID:20178631
Evolution of spliceosomal introns following endosymbiotic gene transfer. PMID:20178587
Endothelial cell processing and alternatively spliced transcripts of factor VIII: potential implications for coagulation cascades and pulmonary hypertension. PMID:20174619
Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems. PMID:20169186
Comparative analysis of nuclear tRNA genes of Nasonia vitripennis and other arthropods, and relationships to codon usage bias. PMID:20167017
Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. PMID:20163725
Acceleration of Ungapped Extension in Mercury BLAST. PMID:20160873
Gramene QTL database: development, content and applications. PMID:20157478
Proviruses selected for high and stable expression of transduced genes accumulate in broadly transcribed genome areas. PMID:20147411
Fast and SNP-tolerant detection of complex variants and splicing in short reads. PMID:20147302
Parameters for accurate genome alignment. PMID:20144198
Human and non-human primate genomes share hotspots of positive selection. PMID:20140238
Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. PMID:20137068
Defining transcribed regions using RNA-seq. PMID:20134426
MicroRNA regulation of IFN-beta protein expression: rapid and sensitive modulation of the innate immune response. PMID:20130213
Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. PMID:20128909
hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes. PMID:20127503
Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma. PMID:20116306
Periostin shows increased evolutionary plasticity in its alternatively spliced region. PMID:20109226
Fast and accurate long-read alignment with Burrows-Wheeler transform. PMID:20080505
Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction. PMID:20078885
A manual collection of Syt, Esyt, Rph3a, Rph3al, Doc2, and Dblc2 genes from 46 metazoan genomes--an open access resource for neuroscience and evolutionary biology. PMID:20078875
A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements. PMID:20067640
A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. PMID:20059953
Characterization of the zebrafish T cell receptor beta locus. PMID:20054533
Phylogenetic comparative assembly. PMID:20047659
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. PMID:20047656
Evidence for bacterial origin of heat shock RNA-1. PMID:20040589
Microarray probes and probe sets. PMID:20036881
Genes targeted by the estrogen and progesterone receptors in the human endometrial cell lines HEC1A and RL95-2. PMID:20034404
Large intron 14 rearrangement in APC results in splice defect and attenuated FAP. PMID:20033212
Targets of the Tal1 transcription factor in erythrocytes: E2 ubiquitin conjugase regulation by Tal1. PMID:20028976
Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. PMID:20026622
A SNP discovery method to assess variant allele probability from next-generation resequencing data. PMID:20019143
ECRG4 is a candidate tumor suppressor gene frequently hypermethylated in colorectal carcinoma and glioma. PMID:20017917
r2cat: synteny plots and comparative assembly. PMID:20015948
Fine-scale variation and genetic determinants of alternative splicing across individuals. PMID:20011102
Sex-specific and lineage-specific alternative splicing in primates. PMID:20009012
BLAST+: architecture and applications. PMID:20003500
A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome. PMID:20000637
Building the sequence map of the human pan-genome. PMID:19997067
PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. PMID:19995808
Comprehensive genomic access to vector integration in clinical gene therapy. PMID:19966782
RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation. PMID:19958502
COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System. PMID:19958500
PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs. PMID:19958497
An empirical study of choosing efficient discriminative seeds for oligonucleotide design. PMID:19958494
BOAT: Basic Oligonucleotide Alignment Tool. PMID:19958483
MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads. PMID:19958476
The UCSC Genome Browser. PMID:19957273
Tandem repeats modify the structure of human genes hosted in segmental duplications. PMID:19954527
Runx2 regulates survivin expression in prostate cancer cells. PMID:19949374
Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. PMID:19948818
Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas. PMID:19941159
Discovery of Plasmodium modulators by genome-wide analysis of circulating hemocytes in Anopheles gambiae. PMID:19940242
Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs. PMID:19936069
Fine-scale phylogenetic discordance across the house mouse genome. PMID:19936022
MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains. PMID:19933259
Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species. PMID:19930683
Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis. PMID:19925684
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. PMID:19923232
Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis. PMID:19922648
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. PMID:19922616
The Pfam protein families database. PMID:19920124
Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500 K SNP array genomic hybridization. PMID:19917086
Development of a DNA microarray to detect antimicrobial resistance genes identified in the National Center for Biotechnology Information database. PMID:19916789
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update. PMID:19910367
Correlation of microsynteny conservation and disease gene distribution in mammalian genomes. PMID:19909546
The effect of sequencing errors on metagenomic gene prediction. PMID:19909532
BFAST: an alignment tool for large scale genome resequencing. PMID:19907642
The UCSC Genome Browser database: update 2010. PMID:19906737
ChimerDB 2.0--a knowledgebase for fusion genes updated. PMID:19906715
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays. PMID:19906711
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. PMID:19906710
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. PMID:19906700
An expression database for roots of the model legume Medicago truncatula under salt stress. PMID:19906315
High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians. PMID:19900272
Computational prediction of splicing regulatory elements shared by Tetrapoda organisms. PMID:19889216
Detection, validation, and downstream analysis of allelic variation in gene expression. PMID:19884314
An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. PMID:19881495
inGAP: an integrated next-generation genome analysis pipeline. PMID:19880367
iTriplet, a rule-based nucleic acid sequence motif finder. PMID:19874606
Genetical genomic determinants of alcohol consumption in rats and humans. PMID:19874574
Hematopoietic immortalizing function of the NKL-subclass homeobox gene TLX1. PMID:19862821
A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. PMID:19860896
Nme protein family evolutionary history, a vertebrate perspective. PMID:19852809
G-compass: a web-based comparative genome browser between human and other vertebrate genomes. PMID:19846439
A syndrome of short stature, microcephaly and speech delay is associated with duplications reciprocal to the common Sotos syndrome deletion. PMID:19844260
Positive selection for the male functionality of a co-retroposed gene in the hominoids. PMID:19832993
Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell. PMID:19832986
The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice. PMID:19825586
Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. PMID:19821981
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. PMID:19821977
BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. PMID:19820115
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. PMID:19820112
A modified sleeping beauty transposon system that can be used to model a wide variety of human cancers in mice. PMID:19808965
A Caenorhabditis elegans RNA-directed RNA polymerase in sperm development and endogenous RNA interference. PMID:19805814
Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. PMID:19800577
A scalable method for analysis and display of DNA sequences. PMID:19798412
Extensive structural renovation of retrogenes in the evolution of the Populus genome. PMID:19789289
Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus. PMID:19785770
An N- and C-terminal truncated isoform of zinc finger X-linked duplicated C protein represses MHC class II transcription. PMID:19777325
Direct RNA sequencing. PMID:19776739
Many LINE1 elements contribute to the transcriptome of human somatic cells. PMID:19772661
The completion of the Mammalian Gene Collection (MGC). PMID:19767417
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. PMID:19758566
Distribution and neuronal expression of phosphatidylinositol phosphate kinase IIgamma in the mouse brain. PMID:19757494
Characterization of a novel human HMBOX1 splicing variant lacking the homeodomain and with attenuated transcription repressor activity. PMID:19757162
Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth. PMID:19747392
Blimp-1/Prdm1 alternative promoter usage during mouse development and plasma cell differentiation. PMID:19737919
GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline. PMID:19730684
Recent de novo origin of human protein-coding genes. PMID:19726446
Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis. PMID:19723631
Systematic identification and characterization of chicken (Gallus gallus) ncRNAs. PMID:19720738
Somatic cell nuclear transfer in zebrafish. PMID:19718031