Ensembl Fugu Genome Browser
Other names: ensembl_fugu_genome_browser
Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.
Description
More detailed information about this field from each metasource.
Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:43.046000
Webpage:
http://www.ensembl.org/Takifugu_rubripes/Info/IndexWebpage
More detailed information about this field from each metasource.
http://www.ensembl.org/Takifugu_rubripes/Info/Index
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:43.046000
Publications:
Publications
More detailed information about this field from each metasource.
The Ensembl genome database project
PMID: 11752248
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:43.046000
Publications
More detailed information about this field from each metasource.
The Ensembl genome database project
PMID: 11752248
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:43.046000
-
The Ensembl genome database project
PubMed citations: 653.
653 articles citing: The Ensembl genome database project
Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration. PMID:35882847
Ecosystem-specific microbiota and microbiome databases in the era of big data. PMID:35842686
PR-1-Like Protein as a Potential Target for the Identification of Fusarium oxysporum: An In Silico Approach. PMID:35822818
Molecular Analysis and Conformational Dynamics of Human MC4R Disease-Causing Mutations. PMID:35807283
SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19. PMID:35784208
Meta-Analysis Suggests That Intron Retention Can Affect Quantification of Transposable Elements from RNA-Seq Data. PMID:35741347
A Comparison of Methods for Gene-Based Testing That Account for Linkage Disequilibrium. PMID:35601489
Identifying common transcriptome signatures of cancer by interpreting deep learning models. PMID:35581644
Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment. PMID:35572582
In Silico Analysis Revealed Five Novel High-Risk Single-Nucleotide Polymorphisms (rs200384291, rs201163886, rs193141883, rs201139487, and rs201723157) in ELANE Gene Causing Autosomal Dominant Severe Congenital Neutropenia 1 and Cyclic Hematopoiesis. PMID:35571273
Dietary antigens suppress the proliferation of type 2 innate lymphoid cells by restraining homeostatic IL-25 production. PMID:35523930
Comparative analysis of web-based programs for single amino acid substitutions in proteins. PMID:35507592
Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle. PMID:35440545
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Splice Junction Identification using Long Short-Term Memory Neural Networks. PMID:35283668
A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts. PMID:35263568
Impact of deleterious missense PRKCI variants on structural and functional dynamics of protein. PMID:35260606
Small open reading frames in plant research: from prediction to functional characterization. PMID:35251879
Microautophagy Mediates Vacuolar Delivery of Storage Proteins in Maize Aleurone Cells. PMID:35251104
Insights into glucosinolate accumulation and metabolic pathways in Isatis indigotica Fort. PMID:35193497
WAFNRLTG: A Novel Model for Predicting LncRNA Target Genes Based on Weighted Average Fusion Network Representation Learning Method. PMID:35127729
Transcription factor motif activity as a biomarker of muscle aging. PMID:35083472
DANSR: A Tool for the Detection of Annotated and Novel Small RNAs. PMID:35076605
Genomic studies controvert the existence of the CUX1 p75 isoform. PMID:34997000
DNA methylation mediates the association between breastfeeding and early-life growth trajectories. PMID:34937578
Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. PMID:34900668
Investigation of Antidepressant Properties of Yohimbine by Employing Structure-Based Computational Assessments. PMID:34889886
Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies. PMID:34888349
Compound heterozygous c.598_612del and c.1746-20C > G CAPN3 genotype cause autosomal recessive limb-girdle muscular dystrophy-1: a case report. PMID:34863162
Unifying heterogeneous expression data to predict targets for CAR-T cell therapy. PMID:34858726
msRepDB: a comprehensive repetitive sequence database of over 80 000 species. PMID:34850956
Origins and Function of VL30 lncRNA Packaging in Small Extracellular Vesicles: Implications for Cellular Physiology and Pathology. PMID:34829970
Impact of Deleterious Mutations on Structure, Function and Stability of Serum/Glucocorticoid Regulated Kinase 1: A Gene to Diseases Correlation. PMID:34805284
The length scale of multivalent interactions is evolutionarily conserved in fungal and vertebrate phase-separating proteins. PMID:34791214
Evolution Analyses of CAMTA Transcription Factor in Plants and Its Enhancing Effect on Cold-tolerance. PMID:34790215
Contamination in Reference Sequence Databases: Time for Divide-and-Rule Tactics. PMID:34745061
Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0. PMID:34716342
Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders. PMID:34691999
Investigating single amino acid substitutions in PIM1 kinase: A structural genomics approach. PMID:34679086
ERp29 forms a feedback regulation loop with microRNA-135a-5p and promotes progression of colorectal cancer. PMID:34667160
caAtlas: An immunopeptidome atlas of human cancer. PMID:34622160
Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. PMID:34596551
Genetic predisposition to tinnitus in the UK Biobank population. PMID:34518561
Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction. PMID:34446935
Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. PMID:34418978
Spared Nerve Injury Causes Sexually Dimorphic Mechanical Allodynia and Differential Gene Expression in Spinal Cords and Dorsal Root Ganglia in Rats. PMID:34331199
Targeting cancer stem cells in medulloblastoma by inhibiting AMBRA1 dual function in autophagy and STAT3 signalling. PMID:34302498
Comparison of Transcriptional Response of C3 and C4 Plants to Drought Stress Using Meta-Analysis and Systems Biology Approach. PMID:34276729
A Methodology to Study Pseudogenized lincRNAs. PMID:34165708
A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression. PMID:34129840
PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial. PMID:34095775
Enhancement of myogenic differentiation and inhibition of rhabdomyosarcoma progression by miR-28-3p and miR-193a-5p regulated by SNAIL. PMID:34094709
The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans. PMID:34050022
Comparative proteomic analysis to annotate the structural and functional association of the hypothetical proteins of S. maltophilia k279a and predict potential T and B cell targets for vaccination. PMID:34043709
Differential gene expression profile by RNA sequencing study of elderly osteoporotic hip fracture patients with sarcopenia. PMID:34036042
Comprehensive transcriptome analysis of colorectal cancer risk of hyperglycemia in humans. PMID:34012653
Structural genomics approach to investigate deleterious impact of nsSNPs in conserved telomere maintenance component 1. PMID:33986331
Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure. PMID:33973996
Molecular evolutionary analysis of human primary microcephaly genes. PMID:33941077
The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins. PMID:33823809
Discovery of novel antagonists targeting the DNA binding domain of androgen receptor by integrated docking-based virtual screening and bioassays. PMID:33767381
Conserved dual-mode gene regulation programs in higher eukaryotes. PMID:33621342
Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia. PMID:33580198
MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. PMID:33482885
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms. PMID:33461501
Machine learning based CRISPR gRNA design for therapeutic exon skipping. PMID:33417623
Myogenic regulatory factors are key players in determining muscle mass and meat quality in Jeju native and Berkshire pigs. PMID:33372732
Multipath: An R Package to Generate Integrated Reproducible Pathway Models. PMID:33371258
Bioinformatic analysis and functional predictions of selected regeneration-associated transcripts expressed by zebrafish microglia. PMID:33287696
Early lung cancer diagnostic biomarker discovery by machine learning methods. PMID:33217646
Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction. PMID:33193626
Epigenetic Studies Revealed a Ghost Proteome in PC1/3 KD Macrophages under Antitumoral Resistance Induced by IL-10. PMID:33163760
Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption. PMID:33144645
Effects of early life stage exposure of largemouth bass to atrazine or a model estrogen (17α-ethinylestradiol). PMID:33072434
Bayesian Analysis of the Association between Casein Complex Haplotype Variants and Milk Yield, Composition, and Curve Shape Parameters in Murciano-Granadina Goats. PMID:33050522
Natural Selection on the Phase-Separation Properties of FUS during 160 My of Mammalian Evolution. PMID:33022038
lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA. PMID:33020484
Liquid lncRNA Biopsy for the Evaluation of Locally Advanced and Metastatic Squamous Cell Carcinomas of the Head and Neck. PMID:32947877
Identification of a Core Module for Bone Mineral Density through the Integration of a Co-expression Network and GWAS Data. PMID:32937138
The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia. PMID:32908143
Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network. PMID:32879328
MUTYH: Not just polyposis. PMID:32821650
The longevity-associated variant of BPIFB4 improves a CXCR4-mediated striatum-microglia crosstalk preventing disease progression in a mouse model of Huntington's disease. PMID:32683420
TH17 cells require ongoing classic IL-6 receptor signaling to retain transcriptional and functional identity. PMID:32680955
The transcriptional signature associated with human motile cilia. PMID:32616903
Genome-Wide Identification of RNA Silencing-Related Genes and Their Expressional Analysis in Response to Heat Stress in Barley (Hordeum vulgare L.). PMID:32570964
An improved clear cell renal cell carcinoma stage prediction model based on gene sets. PMID:32513106
Novel Comprehensive Bioinformatics Approaches to Determine the Molecular Genetic Susceptibility Profile of Moderate and Severe Asthma. PMID:32512817
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses. PMID:32449934
Effect of aging on the transcriptomic changes associated with the expression of the HERV-K (HML-2) provirus at 1q22. PMID:32435269
RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution. PMID:32427338
The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate-binding site. PMID:32355044
HMGA1-pseudogene7 transgenic mice develop B cell lymphomas. PMID:32341372
Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. PMID:32327568
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms. PMID:32272892
ADH7, miR-3065 and LINC01133 are associated with cervical cancer progression in different age groups. PMID:32194732
Integrating Casein Complex SNPs Additive, Dominance and Epistatic Effects on Genetic Parameters and Breeding Values Estimation for Murciano-Granadina Goat Milk Yield and Components. PMID:32183253
Role of non-coding RNA networks in leukemia progression, metastasis and drug resistance. PMID:32164715
Angiotensin-(1-9) prevents cardiomyocyte hypertrophy by controlling mitochondrial dynamics via miR-129-3p/PKIA pathway. PMID:32152556
Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development. PMID:32117919
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Mitochondrial transfer from MSCs to T cells induces Treg differentiation and restricts inflammatory response. PMID:31984629
ISOGO: Functional annotation of protein-coding splice variants. PMID:31974522
The landscape of chimeric RNAs in non-diseased tissues and cells. PMID:31965184
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. PMID:31956905
Long walk to genomics: History and current approaches to genome sequencing and assembly. PMID:31890139
Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. PMID:31885040
SpliceFinder: ab initio prediction of splice sites using convolutional neural network. PMID:31881982
Targeted sequencing of the LRRTM gene family in suicide attempters with bipolar disorder. PMID:31854516
Tasks, Techniques, and Tools for Genomic Data Visualization. PMID:31768085
Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently. PMID:31712655
Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling. PMID:31701028
Protease-associated import systems are widespread in Gram-negative bacteria. PMID:31613892
VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases. PMID:31317185
A novel CHD7 variant disrupting acceptor splice site in a patient with mild features of CHARGE syndrome: a case report. PMID:31315586
Toxins from scratch? Diverse, multimodal gene origins in the predatory robber fly Dasypogon diadema indicate a dynamic venom evolution in dipteran insects. PMID:31289835
Structural Analysis and Conformational Dynamics of STN1 Gene Mutations Involved in Coat Plus Syndrome. PMID:31245382
Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals. PMID:31221090
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
Rapid identification and interpretation of gene-environment associations using the new R.SamBada landscape genomics pipeline. PMID:31136078
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
Weighting sequence variants based on their annotation increases the power of genome-wide association studies in dairy cattle. PMID:31077144
An atypical pulmonary fibrosis is associated with co-inheritance of mutations in the calcium binding protein genes S100A3 and S100A13. PMID:31073086
De novo emergence and potential function of human-specific tandem repeats in brain-related loci. PMID:31069507
Identification of a long noncoding RNA signature to predict outcomes of glioblastoma. PMID:31059035
Structural and functional impact of non-synonymous SNPs in the CST complex subunit TEN1: structural genomics approach. PMID:31028137
Impact of Genetic Variation on CRISPR-Cas Targeting. PMID:31021199
Predicting synthetic lethal interactions using conserved patterns in protein interaction networks. PMID:30995217
Evolution of Deeper Rooting 1-like homoeologs in wheat entails the C-terminus mutations as well as gain and loss of auxin response elements. PMID:30947257
Prioritizing candidate genes for fertility in dairy cows using gene-based analysis, functional annotation and differential gene expression. PMID:30935378
PKD1 Duplicated regions limit clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of Autosomal Dominant Polycystic Kidney Disease. PMID:30858458
The sequence and de novo assembly of Oxygymnocypris stewartii genome. PMID:30720802
Risk gene-set and pathways in 22q11.2 deletion-related schizophrenia: a genealogical molecular approach. PMID:30710087
Identification of exon skipping events associated with Alzheimer's disease in the human hippocampus. PMID:30704480
Regulation of RNA editing by RNA-binding proteins in human cells. PMID:30652130
Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance. PMID:30643692
Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation. PMID:30638445
Genome-wide mapping of nucleotide excision repair with XR-seq. PMID:30552409
Functional genomics of the digestive tract in broilers. PMID:30545300
Aging-associated patterns in the expression of human endogenous retroviruses. PMID:30513106
RNA-sequencing analysis of umbilical cord plasma microRNAs from healthy newborns. PMID:30507953
Variant information systems for precision oncology. PMID:30463544
Optimised isolation method for RNA extraction suitable for RNA sequencing from feline teeth collected in a clinical setting and at post mortem. PMID:30402716
Arena-Idb: a platform to build human non-coding RNA interaction networks. PMID:30367585
Sc-ncDNAPred: A Sequence-Based Predictor for Identifying Non-coding DNA in Saccharomyces cerevisiae. PMID:30258427
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Targeted Genomic Screen Reveals Focal Long Non-Coding RNA Copy Number Alterations in Cancer Cell Lines. PMID:30217017
HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation. PMID:30196115
Prioritizing candidate genes post-GWAS using multiple sources of data for mastitis resistance in dairy cattle. PMID:30189836
Detecting long non-coding RNA biomarkers in prostate cancer liquid biopsies: Hype or hope? PMID:30159441
ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. PMID:30143675
Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli. PMID:30089658
Integrative omics analyses broaden treatment targets in human cancer. PMID:30053901
Making genome browsers portable and personal. PMID:30016986
RabGTD: a comprehensive database of rabbit genome and transcriptome. PMID:30010730
Loose ends: almost one in five human genes still have unresolved coding status. PMID:29982784
Transcriptome Analysis Provides Insight into the Molecular Mechanisms Underlying gametophyte factor 2-Mediated Cross-Incompatibility in Maize. PMID:29899298
Genetic variation affecting exon skipping contributes to brain structural atrophy in Alzheimer's disease. PMID:29888056
Kinact: a computational approach for predicting activating missense mutations in protein kinases. PMID:29788456
Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. PMID:29716624
Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation. PMID:29703132
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Curated compendium of human transcriptional biomarker data. PMID:29664470
Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. PMID:29593678
SpliceDetector: a software for detection of alternative splicing events in human and model organisms directly from transcript IDs. PMID:29567976
Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks. PMID:29504915
Δ9-Tetrahydrocannabinol changes the brain lipidome and transcriptome differentially in the adolescent and the adult. PMID:29408467
Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis. PMID:29387452
Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly. PMID:29342277
Integrated sequencing of exome and mRNA of large-sized single cells. PMID:29321653
Cancer transcriptome profiling at the juncture of clinical translation. PMID:29279605
Non-coding RNAs profiling in head and neck cancers. PMID:29263803
In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research. PMID:29220465
Construction of PRDM9 allele-specific recombination maps in cattle using large-scale pedigree analysis and genome-wide single sperm genomics. PMID:29186399
Genome-wide DNase hypersensitivity, and occupancy of RUNX2 and CTCF reveal a highly dynamic gene regulome during MC3T3 pre-osteoblast differentiation. PMID:29176792
Ensembl 2018. PMID:29155950
Dynamic Visualization and Comparative Analysis of Multiple Collinear Genomic Data. PMID:29119144
Tracing the spatio-temporal dynamics of endangered fin whales (Balaenoptera physalus) within baleen whale (Mysticeti) lineages: a mitogenomic perspective. PMID:29103106
Structure-mediated modulation of mRNA abundance by A-to-I editing. PMID:29093448
Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system. PMID:29087374
Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease. PMID:29069510
DNA sequencing at 40: past, present and future. PMID:29019985
HUMA: A platform for the analysis of genetic variation in humans. PMID:28967693
De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance. PMID:28851357
The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates. PMID:28795237
Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs. PMID:28776031
Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes. PMID:28760689
Prognostic cancer gene signatures share common regulatory motifs. PMID:28684851
Bridging Plant and Human Radiation Response and DNA Repair through an In Silico Approach. PMID:28587301
Properties of genes essential for mouse development. PMID:28562614
UPR transducer BBF2H7 allows export of type II collagen in a cargo- and developmental stage-specific manner. PMID:28500182
Microbial Biogeography and Core Microbiota of the Rat Digestive Tract. PMID:28374781
Identification of long non-coding transcripts with feature selection: a comparative study. PMID:28335739
Pan-cancer analysis distinguishes transcriptional changes of aneuploidy from proliferation. PMID:28320919
Identification and Expression of Equine MER-Derived miRNAs. PMID:28320202
Facial cutaneo-mucosal venous malformations can develop independently of mutation of TEK gene but may be associated with excessive expression of Src and p-Src. PMID:28316284
NEUROD2 Regulates Stim1 Expression and Store-Operated Calcium Entry in Cortical Neurons. PMID:28303257
Development of Bioinformatics Infrastructure for Genomics Research. PMID:28302555
Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level. PMID:28302551
Genomic characterisation of Eμ-Myc mouse lymphomas identifies Bcor as a Myc co-operative tumour-suppressor gene. PMID:28262675
Integrative multi-omics analysis revealed SNP-lncRNA-mRNA (SLM) networks in human peripheral blood mononuclear cells. PMID:28243742
Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues. PMID:28178989
Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing. PMID:27989103
DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles. PMID:27923386
Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction. PMID:27807179
Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data. PMID:27803687
Transcriptome Sequencing Identified Genes and Gene Ontologies Associated with Early Freezing Tolerance in Maize. PMID:27774095
Differential morphology and transcriptome profile between the incompletely fused carpels ovary and its wild-type in maize. PMID:27587343
Structure and regulation of human troponin genes. PMID:27520667
How to talk about protein-level false discovery rates in shotgun proteomics. PMID:27503675
Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method. PMID:27478829
Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation. PMID:27436282
CAT7 and cat7l Long Non-coding RNAs Tune Polycomb Repressive Complex 1 Function during Human and Zebrafish Development. PMID:27405765
The Ensembl gene annotation system. PMID:27337980
ELAVL2-regulated transcriptional and splicing networks in human neurons link neurodevelopment and autism. PMID:27260404
Cloning the Horse RNA Polymerase I Promoter and Its Application to Studying Influenza Virus Polymerase Activity. PMID:27258298
Research Resources for Nuclear Receptor Signaling Pathways. PMID:27216565
Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare. PMID:27130220
Evolutionary constraints over microsatellite abundance in larger mammals as a potential mechanism against carcinogenic burden. PMID:27125812
Molecular evolution of WDR62, a gene that regulates neocorticogenesis. PMID:27114917
Molecular Basis of the Ligand Binding Specificity of αvβ8 Integrin. PMID:27033701
The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects. PMID:27006757
Analysis of computational footprinting methods for DNase sequencing experiments. PMID:26901649
Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. PMID:26897376
An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs. PMID:26847462
Insulin-like growth factor axis in pregnancies affected by fetal growth disorders. PMID:26823688
Cascade: an RNA-seq visualization tool for cancer genomics. PMID:26810393
Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. PMID:26787667
The drug target genes show higher evolutionary conservation than non-target genes. PMID:26716901
Light-RCV: a lightweight read coverage viewer for next generation sequencing data. PMID:26680734
Prioritizing and selecting likely novel miRNAs from NGS data. PMID:26635395
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. PMID:26602693
The UCSC Genome Browser database: 2016 update. PMID:26590259
Expression of microRNAs and isomiRs in the porcine endometrium: implications for gene regulation at the maternal-conceptus interface. PMID:26546342
DNA Editing of LTR Retrotransposons Reveals the Impact of APOBECs on Vertebrate Genomes. PMID:26541172
Coexpression Network Analysis of miRNA-142 Overexpression in Neuronal Cells. PMID:26539539
Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels. PMID:26515589
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
Whole exome sequencing of microdissected splenic marginal zone lymphoma: a study to discover novel tumor-specific mutations. PMID:26498442
Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays. PMID:26431201
New genes drive the evolution of gene interaction networks in the human and mouse genomes. PMID:26424194
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. PMID:26379229
The Structural Characterization of Tumor Fusion Genes and Proteins. PMID:26347798
Data integration in biological research: an overview. PMID:26336651
Selection of recombinant anti-SH3 domain antibodies by high-throughput phage display. PMID:26332758
The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity. PMID:26332131
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer. PMID:26253570
Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation. PMID:26177635
Differential and coherent processing patterns from small RNAs. PMID:26166713
QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation. PMID:26126663
The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human. PMID:26115450
Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data. PMID:26100580
Possible Human Papillomavirus 38 Contamination of Endometrial Cancer RNA Sequencing Samples in The Cancer Genome Atlas Database. PMID:26085148
Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization. PMID:26076386
A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data. PMID:25990738
GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development. PMID:25982314
Variation in DNAH1 may contribute to primary ciliary dyskinesia. PMID:25927852
Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene. PMID:25918715
NOTCH1 regulates matrix gla protein and calcification gene networks in human valve endothelium. PMID:25871831
MAFCO: a compression tool for MAF files. PMID:25816229
RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation. PMID:25783031
GASS: genome structural annotation for Eukaryotes based on species similarity. PMID:25764973
The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio). PMID:25645996
Prioritizing causal disease genes using unbiased genomic features. PMID:25633252
Cetaceans evolution: insights from the genome sequences of common minke whales. PMID:25609461
plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. PMID:25566282
microRNA profiling in three main stages during porcine spermatogenesis. PMID:25563581
RNA-binding proteins in pluripotency, differentiation, and reprogramming. PMID:25554730
Comparative genomics reveals molecular features unique to the songbird lineage. PMID:25494627
The UCSC Genome Browser database: 2015 update. PMID:25428374
Role of recurrent hypoxia-ischemia in preterm white matter injury severity. PMID:25390897
Identification of candidate long noncoding RNAs associated with left ventricular hypertrophy. PMID:25382655
APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals. PMID:25378337
An update on LNCipedia: a database for annotated human lncRNA sequences. PMID:25378313
A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. PMID:25348400
Comparative analyses of C₄ and C₃ photosynthesis in developing leaves of maize and rice. PMID:25306245
Balancing selection on CDH2 may be related to the behavioral features of the Belgian Malinois. PMID:25303325
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
Genome-wide analysis of noncoding regulatory mutations in cancer. PMID:25261935
Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease. PMID:25252782
Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog. PMID:25210846
We are all individuals... bioinformatics in the personalized medicine era. PMID:25204962
MiR-7 promotes epithelial cell transformation by targeting the tumor suppressor KLF4. PMID:25181544
Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB. PMID:25178365
Parallel selection on gene copy number variations through evolution of three-spined stickleback genomes. PMID:25168270
Computational Methods for MicroRNA Target Prediction. PMID:25153283
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. PMID:25149441
Annotated features of domestic cat - Felis catus genome. PMID:25143822
Differential Evolution between Monotocous and Polytocous Species. PMID:25049975
Notch signaling functions in retinal pericyte survival. PMID:25015359
RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing. PMID:24960161
BLAT-based comparative analysis for transposable elements: BLATCAT. PMID:24959585
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. PMID:24939910
Identification of potential therapeutic targets in a model of neuropathic pain. PMID:24904634
Infinium monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis). PMID:24815017
Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. PMID:24727769
Molecular evolution of the vertebrate FK506 binding protein 25. PMID:24724077
Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3. PMID:24667746
Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PMID:24651478
Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution. PMID:24602261
Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. PMID:24594072
A novel two-layer SVM model in miRNA Drosha processing site detection. PMID:24565218
Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data. PMID:24564528
Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline. PMID:24478219
The gene family of dehydration responsive element-binding transcription factors in grape (Vitis vinifera): genome-wide identification and analysis, expression profiles, and involvement in abiotic stress resistance. PMID:24402876
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PMID:24391926
Lack of TEK Gene Mutation in Patients with Cutaneomucosal Venous Malformations from the North-Western Region of Algeria. PMID:24386570
Genomics of alternative splicing: evolution, development and pathophysiology. PMID:24378600
Time for the zebrafish ENCODE. PMID:24371190
The roles of FMRP-regulated genes in autism spectrum disorder: single- and multiple-hit genetic etiologies. PMID:24207117
Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. PMID:24175627
Exploring evolution of brain genes involved in microcephaly through phylogeny and synteny analysis. PMID:24148351
NSD1 mitigates caspase-1 activation by listeriolysin O in macrophages. PMID:24058709
PharmGKB summary: very important pharmacogene information for the epidermal growth factor receptor. PMID:23962910
GnpIS: an information system to integrate genetic and genomic data from plants and fungi. PMID:23959375
Identification of differentially evolved genes: an alternative approach to detection of accelerated molecular evolution from genome-wide comparative data. PMID:23926417
Unraveling genomic variation from next generation sequencing data. PMID:23885890
GEMINI: integrative exploration of genetic variation and genome annotations. PMID:23874191
Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. PMID:23827707
bioNerDS: exploring bioinformatics' database and software use through literature mining. PMID:23768135
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location. PMID:23761436
Alternative splicing tends to avoid partial removals of protein-protein interaction sites. PMID:23758645
Computational framework to support integration of biomolecular and clinical data within a translational approach. PMID:23742129
Identification of novel arthropod vector G protein-coupled receptors. PMID:23705687
Equivalent indels--ambiguous functional classes and redundancy in databases. PMID:23658777
Hypertension and genetic variation in endothelial-specific genes. PMID:23637959
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. PMID:23629695
Peeling back the evolutionary layers of molecular mechanisms responsive to exercise-stress in the skeletal muscle of the racing horse. PMID:23580538
The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. PMID:23558341
HCFC1 is a common component of active human CpG-island promoters and coincides with ZNF143, THAP11, YY1, and GABP transcription factor occupancy. PMID:23539139
Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer. PMID:23527012
Prediction of structure of human WNT-CRD (FZD) complex for computational drug repurposing. PMID:23372744
Finding protein-coding genes through human polymorphisms. PMID:23349826
Large-scale reverse docking profiles and their applications. PMID:23282219
Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage. PMID:23264566
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. PMID:23237380
iPiG: integrating peptide spectrum matches into genome browser visualizations. PMID:23226516
Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques. PMID:23226328
Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PMID:23209562
Variants affecting exon skipping contribute to complex traits. PMID:23133393
NOD2 Polymorphisms and Their Impact on Haematopoietic Stem Cell Transplant Outcome. PMID:23119165
29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PMID:22952639
Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. PMID:22923516
Human developmental enhancers conserved between deuterostomes and protostomes. PMID:22876195
Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles. PMID:22839428
Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms. PMID:22826460
Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions. PMID:22788692
Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus. PMID:22726727
IMGT-ONTOLOGY 2012. PMID:22654892
Comparative analysis and visualization of multiple collinear genomes. PMID:22536897
High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. PMID:22524474
Fast homozygosity mapping and identification of a zebrafish ENU-induced mutation by whole-genome sequencing. PMID:22496837
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. PMID:22446687
Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio). PMID:22424280
Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. PMID:22344696
When one and one gives more than two: challenges and opportunities of integrative omics. PMID:22303399
Fishing the molecular bases of Treacher Collins syndrome. PMID:22295061
R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. PMID:22287631
ABrowse--a customizable next-generation genome browser framework. PMID:22222089
Organization, complexity and allelic diversity of the porcine (Sus scrofa domestica) immunoglobulin lambda locus. PMID:22186825
Overview of biological database mapping services for interoperation between different 'omics' datasets. PMID:22155608
Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. PMID:22115825
Evolution of the porcine (Sus scrofa domestica) immunoglobulin kappa locus through germline gene conversion. PMID:22109540
The UCSC Genome Browser database: extensions and updates 2011. PMID:22086951
Segtor: rapid annotation of genomic coordinates and single nucleotide variations using segment trees. PMID:22069465
Deep proteome and transcriptome mapping of a human cancer cell line. PMID:22068331
gViz, a novel tool for the visualization of co-expression networks. PMID:22032859
No excess gene movement is detected off the avian or lepidopteran Z chromosome. PMID:22024813
Novel germline PALB2 truncating mutations in African American breast cancer patients. PMID:21932393
Retinal disease course in Usher syndrome 1B due to MYO7A mutations. PMID:21873662
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. PMID:21873452
Three periods of regulatory innovation during vertebrate evolution. PMID:21852499
Positive Darwinian selection drives the evolution of the morphology-related gene, EPCAM, in particularly species-rich lineages of African cichlid fishes. PMID:21811860
Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome. PMID:21765411
S3QL: a distributed domain specific language for controlled semantic integration of life sciences data. PMID:21756325
Extensive relationship between antisense transcription and alternative splicing in the human genome. PMID:21719572
Protein 4.1R regulates cell adhesion, spreading, migration and motility of mouse keratinocytes by modulating surface expression of beta1 integrin. PMID:21693581
Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif. PMID:21649932
ParkDB: a Parkinson's disease gene expression database. PMID:21593080
PSAR: measuring multiple sequence alignment reliability by probabilistic sampling. PMID:21576232
Integrating human genome database into electronic health record with sequence alignment and compression mechanism. PMID:21559844
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. PMID:21504591
MAISTAS: a tool for automatic structural evaluation of alternative splicing products. PMID:21498402
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. PMID:21460061
Rice-Map: a new-generation rice genome browser. PMID:21450055
Fast local fragment chaining using sum-of-pair gap costs. PMID:21418573
Knowledge management for systems biology a general and visually driven framework applied to translational medicine. PMID:21375767
FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. PMID:21287609
The gene regulatory cascade linking proneural specification with differentiation in Drosophila sensory neurons. PMID:21283833
RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti. PMID:21276245
The Genomic HyperBrowser: inferential genomics at the sequence level. PMID:21182759
The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PMID:21179244
Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human. PMID:21124763
LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana. PMID:21071420
dbCRID: a database of chromosomal rearrangements in human diseases. PMID:21051346
Evaluation of SPARC as a candidate gene of juvenile-onset primary open-angle glaucoma by mutation and copy number analyses. PMID:21042566
The GMOD Drupal bioinformatic server framework. PMID:20971988
PathEx: a novel multi factors based datasets selector web tool. PMID:20969778
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. PMID:20964841
Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. PMID:20952408
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. PMID:20946618
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. PMID:20929876
Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes. PMID:20885980
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PMID:20617162
Using semantic web rules to reason on an ontology of pseudogenes. PMID:20529940
SOBA: sequence ontology bioinformatics analysis. PMID:20494974
Flanking region sequence information to refine microRNA target predictions. PMID:20413915
Detection of novel 3' untranslated region extensions with 3' expression microarrays. PMID:20346121
Testing the coding potential of conserved short genomic sequences. PMID:20224812
Mutations in Grxcr1 are the basis for inner ear dysfunction in the pirouette mouse. PMID:20137774
An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome. PMID:20126623
A unified method for purification of basic proteins. PMID:20109435
Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. PMID:20108112
SoyDB: a knowledge database of soybean transcription factors. PMID:20082720
Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis. PMID:19925684
Next-generation gap. PMID:19844227
KAIKObase: an integrated silkworm genome database and data mining tool. PMID:19843344
The completion of the Mammalian Gene Collection (MGC). PMID:19767417
Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics. PMID:19737408
Forging links between human mental retardation-associated CNVs and mouse gene knockout models. PMID:19557186
Validation of a primer optimisation matrix to improve the performance of reverse transcription - quantitative real-time PCR assays. PMID:19549292
OmicBrowse: a Flash-based high-performance graphics interface for genomic resources. PMID:19528066
Development of an integrative database with 499 novel microsatellite markers for Macaca fascicularis. PMID:19497132
Evidence of maternal QTL affecting growth and obesity in adult mice. PMID:19399551
Gene expression during the oocyte-to-embryo transition in mammals. PMID:19363788
Molecular evolution of the junctophilin gene family. PMID:19318539
Angiotensin-converting enzyme is a modifier of hypertensive end organ damage. PMID:19307186
Next generation tools for the annotation of human SNPs. PMID:19181721
Studying alternative splicing regulatory networks through partial correlation analysis. PMID:19133160
Inferring selection on amino acid preference in protein domains. PMID:19095755
Genotype-phenotype databases: challenges and solutions for the post-genomic era. PMID:19065136
The HuRef Browser: a web resource for individual human genomics. PMID:19036787
Ensembl 2009. PMID:19033362
Fast gene ontology based clustering for microarray experiments. PMID:19025591
Accurate whole human genome sequencing using reversible terminator chemistry. PMID:18987734
HGVbaseG2P: a central genetic association database. PMID:18948288
Quality of regulatory elements in Drosophila retrogenes. PMID:18848618
Prioritization of candidate cancer genes--an aid to oncogenomic studies. PMID:18710882
The Synergizer service for translating gene, protein and other biological identifiers. PMID:18697767
Reduced purifying selection prevails over positive selection in human copy number variant evolution. PMID:18687881
Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium. PMID:18682805
Identify alternative splicing events based on position-specific evolutionary conservation. PMID:18665247
Towards Interoperability in Genome Databases: The MAtDB (MIPS Arabidopsis Thaliana Database) Experience. PMID:18629123
The Gene Ontology Annotation (GOA) Project--Application of GO in SWISS-PROT, TrEMBL and InterPro. PMID:18629103
The Xenopus FcR family demonstrates continually high diversification of paired receptors in vertebrate evolution. PMID:18485190
Conserved co-expression for candidate disease gene prioritization. PMID:18433471
Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PMID:18384235
Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution. PMID:18252209
In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PMID:18052534
Genome-wide changes in expression profile of murine endogenous retroviruses (MuERVs) in distant organs after burn injury. PMID:18045489
Immunoglobulin light chain (IgL) genes in zebrafish: Genomic configurations and inversional rearrangements between (V(L)-J(L)-C(L)) gene clusters. PMID:18022691
The vertebrate genome annotation (Vega) database. PMID:18003653
Lactation transcriptomics in the Australian marsupial, Macropus eugenii: transcript sequencing and quantification. PMID:17997866
Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites. PMID:17978194
Characterization of oligopeptide patterns in large protein sets. PMID:17908308
Linking microarray reporters with protein functions. PMID:17897448
Deep analysis of cellular transcriptomes - LongSAGE versus classic MPSS. PMID:17892551
An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer. PMID:17683518
oPOSSUM: integrated tools for analysis of regulatory motif over-representation. PMID:17576675
Genome-wide association study identifies novel breast cancer susceptibility loci. PMID:17529967
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. PMID:17526514
Discovery of tissue-specific exons using comprehensive human exon microarrays. PMID:17456239
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. PMID:17395691
Species-specific evolution of the FcR family in endothermic vertebrates. PMID:17356879
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. PMID:17316440
TICdb: a collection of gene-mapped translocation breakpoints in cancer. PMID:17257420
DiscoverySpace: an interactive data analysis application. PMID:17210078
CYCLONET--an integrated database on cell cycle regulation and carcinogenesis. PMID:17202170
A consensus prognostic gene expression classifier for ER positive breast cancer. PMID:17076897
Local mutagenic impact of insertions of LTR retrotransposons on the mouse genome. PMID:17075698
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs. PMID:17064411
MMASS: an optimized array-based method for assessing CpG island methylation. PMID:17041235
Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins. PMID:17029626
yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. PMID:16859520
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. PMID:16855290
Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies. PMID:16855283
Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. PMID:16817963
BioMediator data integration: beyond genomics to neuroscience data. PMID:16779146
The abundance of short proteins in the mammalian proteome. PMID:16683031
Pseudo-messenger RNA: phantoms of the transcriptome. PMID:16683022
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes. PMID:16630345
Predicting disease genes using protein-protein interactions. PMID:16611749
Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold. PMID:16522806
Tracking the evolution of alternatively spliced exons within the Dscam family. PMID:16483367
Bias of selection on human copy-number variants. PMID:16482228
Role of positive selection in the retention of duplicate genes in mammalian genomes. PMID:16461903
MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. PMID:16433928
Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. PMID:16420668
Micro-array analyses decipher exceptional complex familial chromosomal rearrangement. PMID:16395598
Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination. PMID:16380909
Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion. PMID:16344558
Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. PMID:16344557
Mapping and characterization of the amplicon near APOA2 in 1q23 in human sarcomas by FISH and array CGH. PMID:16274472
Emergence of young human genes after a burst of retroposition in primates. PMID:16201836
Diversification of stem cell molecular repertoire by alternative splicing. PMID:16183747
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PMID:16118666
A sequence sub-sampling algorithm increases the power to detect distant homologues. PMID:16006623
Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones. PMID:15998469
FACT--a framework for the functional interpretation of high-throughput experiments. PMID:15985174
RPBS: a web resource for structural bioinformatics. PMID:15980507
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families. PMID:15980440
Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. PMID:15959677
Protein length in eukaryotic and prokaryotic proteomes. PMID:15951512
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies. PMID:15949044
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals. PMID:15882449
Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser. PMID:15826305
NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. PMID:15760844
FISH analysis of hematological neoplasias with 1p36 rearrangements allows the definition of a cluster of 2.5 Mb included in the minimal region deleted in 1p36 deletion syndrome. PMID:15744521
Gene expression profiling in murine autoimmune arthritis during the initiation and progression of joint inflammation. PMID:15743466
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. PMID:15716312
Characterization of a centromeric marker on mouse chromosome 11 and its introgression in a domesticus/musculus hybrid zone. PMID:15672596
Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases. PMID:15642112
Significant expansion of exon-bordering protein domains during animal proteome evolution. PMID:15640447
Gene and alternative splicing annotation with AIR. PMID:15632090
The Rat Genome Database (RGD): developments towards a phenome database. PMID:15608243
The Universal Protein Resource (UniProt). PMID:15608167
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. PMID:15608166
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. PMID:15601538
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence. PMID:15588320
Consensus clustering and functional interpretation of gene-expression data. PMID:15535870
Systematic recovery and analysis of full-ORF human cDNA clones. PMID:15489330
Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. PMID:15466287
A comprehensive transcript index of the human genome generated using microarrays and computational approaches. PMID:15461792
Fast and effective prediction of microRNA/target duplexes. PMID:15383676
What can we learn from noncoding regions of similarity between genomes? PMID:15369604
Genetic analysis of X-linked hybrid sterility in the house mouse. PMID:15366371
Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse. PMID:15364904
A catalog of human cDNA expression clones and its application to structural genomics. PMID:15345055
Effects of G-protein mutations on skin color. PMID:15322542
The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. PMID:15292448
C-type lectin-like domains in Fugu rubripes. PMID:15285787
Global survey of chromatin accessibility using DNA microarrays. PMID:15231753
Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. PMID:15219233
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. PMID:15215412
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. PMID:15215395
POBO, transcription factor binding site verification with bootstrapping. PMID:15215385
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences. PMID:15215376
SNPbox: web-based high-throughput primer design from gene to genome. PMID:15215373
Public web-based services from the European Bioinformatics Institute. PMID:15215339
Structure-function evolution of the transforming acidic coiled coil genes revealed by analysis of phylogenetically diverse organisms. PMID:15207008
Genome-wide identification of genes likely to be involved in human genetic disease. PMID:15181176
eShadow: a tool for comparing closely related sequences. PMID:15173121
Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. PMID:15173108
Comprehensive analysis of the base composition around the transcription start site in Metazoa. PMID:15171795
Complete MHC haplotype sequencing for common disease gene mapping. PMID:15140828
eL-DASionator: an LDAS upload file generator. PMID:15132760
Sockeye: a 3D environment for comparative genomics. PMID:15123592
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PMID:15103394
Pegasys: software for executing and integrating analyses of biological sequences. PMID:15096276
Visualization of multiple genome annotations and alignments with the K-BROWSER. PMID:15060015
Automated whole-genome multiple alignment of rat, mouse, and human. PMID:15060011
Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing. PMID:15060008
Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents. PMID:15060000
Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. PMID:15059996
The DNA sequence and analysis of human chromosome 13. PMID:15057823
Identifying transcriptional regulatory sites in the human genome using an integrated system. PMID:15051813
FRAGS: estimation of coding sequence substitution rates from fragmentary data. PMID:15005802
Diverse and specific gene expression responses to stresses in cultured human cells. PMID:15004229
A functional domain of Dof that is required for fibroblast growth factor signaling. PMID:14993266
Identification of biochemical adaptations in hyper- or hypocontractile hearts from phospholamban mutant mice by expression proteomics. PMID:14982994
Numerous novel annotations of the human genome sequence supported by a 5'-end-enriched cDNA collection. PMID:14962985
Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping. PMID:14960710
The bioinformatics challenges in comparative analysis of cereal genomes-an overview. PMID:14770300
Gene structure conservation aids similarity based gene prediction. PMID:14764925
Large-scale identification of disease genes involved in acute myeloid leukemia. PMID:14747562
MicroRNA targets in Drosophila. PMID:14709173
EnsMart: a generic system for fast and flexible access to biological data. PMID:14707178
The mouse salivary androgen-binding protein (ABP) gene cluster on chromosomes 7: characterization and evolutionary relationships. PMID:14694904
Transcriptome analysis of mouse stem cells and early embryos. PMID:14691545
The mouse Gene Expression Database (GXD): updates and enhancements. PMID:14681482
The Centre for Modeling Human Disease Gene Trap resource. PMID:14681480
SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes. PMID:14681474
HGVbase: a curated resource describing human DNA variation and phenotype relationships. PMID:14681471
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. PMID:14681438
UniProt: the Universal Protein knowledgebase. PMID:14681372
A genome-wide survey of human pseudogenes. PMID:14656963
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. PMID:14656962
The German cDNA network: cDNAs, functional genomics and proteomics. PMID:14649292
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PMID:14624247
Bioinformatics Resources for In Silico Proteome Analysis. PMID:14615630
Fugu ESTs: new resources for transcription analysis and genome annotation. PMID:14613980
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. PMID:14611660
GeneViTo: visualizing gene-product functional and structural features in genomic datasets. PMID:14594459
Exegesis: a procedure to improve gene predictions and its use to find immunoglobulin superfamily proteins in the human and mouse genomes. PMID:14576296
Functionality of system components: conservation of protein function in protein feature space. PMID:14559779
Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population. PMID:14525928
Transposon mutagenesis of the mouse germline. PMID:14504232
cDNA2Genome: a tool for mapping and annotating cDNAs. PMID:12964951
Fugu rubripes possesses genes for the entire set of the ITAM-bearing transmembrane signal subunits. PMID:12955357
GANESH: software for customized annotation of genome regions. PMID:12952886
Different evolutionary patterns between young duplicate genes in the human genome. PMID:12952535
Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis. PMID:12888525
Biopipe: a flexible framework for protocol-based bioinformatics analysis. PMID:12869579
The 2R hypothesis and the human genome sequence. PMID:12836689
OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms. PMID:12824422
FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes. PMID:12824363
GenePublisher: Automated analysis of DNA microarray data. PMID:12824347
Connecting sequence and biology in the laboratory mouse. PMID:12819150
GeneLynx mouse: integrated portal to the mouse genome. PMID:12819149
Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome. PMID:12819141
Mouse proteome analysis. PMID:12819131
Cytokine-related genes identified from the RIKEN full-length mouse cDNA data set. PMID:12819128
Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs. PMID:12783626
Human-mouse gene identification by comparative evidence integration and evolutionary analysis. PMID:12743024
Conservation of human alternative splice events in mouse. PMID:12736303
Duplication and selection in the evolution of primate beta-defensin genes. PMID:12734011
DAVID: Database for Annotation, Visualization, and Integrated Discovery. PMID:12734009
Otubains: a new family of cysteine proteases in the ubiquitin pathway. PMID:12704427
ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data. PMID:12702210
Comparative genomic tools and databases: providing insights into the human genome. PMID:12697725
GALA, a database for genomic sequence alignments and annotations. PMID:12671007
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. PMID:12654719
Toucan: deciphering the cis-regulatory logic of coregulated genes. PMID:12626717
The transcriptional activity of human Chromosome 22. PMID:12600945
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. PMID:12552088
Apollo: a sequence annotation editor. PMID:12537571
Strategies and tools for whole-genome alignments. PMID:12529308
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. PMID:12529305
Cross-species sequence comparisons: a review of methods and available resources. PMID:12529301
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. PMID:12520037
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. PMID:12519986
MOsDB: an integrated information resource for rice genomics. PMID:12519979
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. PMID:12519968
The SNP Consortium website: past, present and future. PMID:12519964
MTID: a database of Sleeping Beauty transposon insertions in mice. PMID:12519952
ParaDB: a tool for paralogy mapping in vertebrate genomes. PMID:12519948
CORG: a database for COmparative Regulatory Genomics. PMID:12519946
The UCSC Genome Browser Database. PMID:12519945
The European Bioinformatics Institute's data resources. PMID:12519944
Ensembl 2002: accommodating comparative genomics. PMID:12519943
The EMBL Nucleotide Sequence Database: major new developments. PMID:12519939
SeqVISTA: a graphical tool for sequence feature visualization and comparison. PMID:12513700
Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence. PMID:12498619
ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files. PMID:12493080
Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes. PMID:12490704
Genomic expansion and clustering of ZAD-containing C2H2 zinc-finger genes in Drosophila. PMID:12446571
Signatures of domain shuffling in the human genome. PMID:12421750
A major susceptibility locus for systemic lupus erythemathosus maps to chromosome 1q31. PMID:12373647
The Bioperl toolkit: Perl modules for the life sciences. PMID:12368254
The generic genome browser: a building block for a model organism system database. PMID:12368253
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. PMID:12368239
Current methods of gene prediction, their strengths and weaknesses. PMID:12364589
Genomic rearrangements resulting in PLP1 deletion occur by nonhomologous end joining and cause different dysmyelinating phenotypes in males and females. PMID:12297985
Prediction of MHC class I binding peptides, using SVMHC. PMID:12225620
Sushi gets serious: the draft genome sequence of the pufferfish Fugu rubripes. PMID:12225591
Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. PMID:12213774
Exploring alternative models for sex-linked quantitative trait loci in outbred populations: application to an iberian x landrace pig intercross. PMID:12196405
Large-scale protein annotation through gene ontology. PMID:11997345
Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data? PMID:11991940
The EMBL Nucleotide Sequence Database. PMID:11752244
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human biology
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whole genome sequencing
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version: extracted_at: 2022-11-04T11:34:43.046000
gene transcripts
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More detailed information about this field from each metasource.
human biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:43.046000
genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:43.046000
database management
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:43.046000
whole genome sequencing
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:43.046000
gene transcripts
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:43.046000
human genomics data management whole genome sequencing gene transcripts
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