R31S69 last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:10.296503

The Sequence Read Archive (SRA)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

sra
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:10.296503

Other names: SRA, The Sequence Read Archive (SRA), sra

The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.

Webpage:

http://www.ncbi.nlm.nih.gov/sra

Licence:

Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
URL: http://opendatacommons.org/licenses/pddl/1.0/

Publications:

Publications
More detailed information about this field from each metasource.

The sequence read archive
PMID: 21062823
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:10.296503

Database resources of the National Center for Biotechnology Information
PMID: 18045790
metasource: Fairsharing.org
version: FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

The Sequence Read Archive: explosive growth of sequencing data
PMID: 22009675
metasource: Fairsharing.org
version: FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:10.296503

Investigation into the annotation of protocol sequencing steps in the sequence read archive
PMID: 25960871
metasource: Fairsharing.org
version: FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

The sequence read archive PubMed citations: 956.

956 articles citing: The sequence read archive

LncRNA-Based Classification of Triple Negative Breast Cancer Revealed Inherent Tumor Heterogeneity and Vulnerabilities. PMID:35893227
Proteotranscriptomics - A facilitator in omics research. PMID:35891789
FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling. PMID:35891785
Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage. PMID:35884206
OMiCC: An expanded and enhanced platform for meta-analysis of public gene expression data. PMID:35880119
Resistome Analysis of Global Livestock and Soil Microbiomes. PMID:35875563
A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. PMID:35847383
A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin. PMID:35821882
The Hidden Potential of High-Throughput RNA-Seq Re-Analysis, a Case Study for DHDPS, Key Enzyme of the Aspartate-Derived Lysine Biosynthesis Pathway and Its Role in Abiotic and Biotic Stress Responses in Soybean. PMID:35807714
Extending and Running the Mosquito Small RNA Genomics Resource Pipeline. PMID:35796973
Reciprocal recombination genomic signatures in the symbiotic arbuscular mycorrhizal fungi Rhizophagus irregularis. PMID:35776745
Genome-Wide Identification and Analysis of the Class III Peroxidase Gene Family in Tobacco (Nicotiana tabacum). PMID:35769995
A transcriptome atlas and interactive analysis platform for autoimmune disease. PMID:35758882
Detecting Medium and Large Insertions and Deletions with transIndel. PMID:35751809
Aspartyl Protease Inhibitors as Anti-Filarial Drugs. PMID:35745561
Not just a Snapshot: An Italian Longitudinal Evaluation of Stability of Gut Microbiota Findings in Parkinson's Disease. PMID:35741624
Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity. PMID:35739571
Sequences to Differences in Gene Expression: Analysis of RNA-Seq Data. PMID:35737247
In-depth comparative analysis of Tritrichomonas foetus transcriptomics reveals novel genes linked with adaptation to feline host. PMID:35710931
A Genomic Information Management System for Maintaining Healthy Genomic States and Application of Genomic Big Data in Clinical Research. PMID:35682641
Systematic analyses identify the anti-fibrotic role of lncRNA TP53TG1 in IPF. PMID:35661695
Intron losses and gains in the nematodes. PMID:35659725
The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets. PMID:35657102
What complete mitochondrial genomes tell us about the evolutionary history of the black soldier fly, Hermetia illucens. PMID:35650519
Systematic prediction of EMS-induced mutations in a sorghum mutant population. PMID:35647479
Hypoxia classifier for transcriptome datasets. PMID:35641902
mebipred: identifying metal binding potential in protein sequence. PMID:35639953
3D genome organization in the epithelial-mesenchymal transition spectrum. PMID:35637517
Variation at Spike position 142 in SARS-CoV-2 Delta genomes is a technical artifact caused by dropout of a sequencing amplicon. PMID:35634532
Assessment of the Safety and Efficacy of an Oral Probiotic-Based Vaccine Against Aspergillus Infection in Captive-Bred Humboldt Penguins (Spheniscus humboldti). PMID:35634323
Two Different Species of Mycoplasma Endosymbionts Can Influence Trichomonas vaginalis Pathophysiology. PMID:35608298
MutaXome: A Novel Database for Identified Somatic Variations of In silico Analyzed Cancer Exome Datasets. PMID:35586731
sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. PMID:35556129
Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach. PMID:35554915
Enhancing Data Integration, Interoperability, and Reuse to Address Complex and Emerging Environmental Health Problems. PMID:35549252
Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter. PMID:35545619
Genome-wide identification of associations between enhancer and alternative splicing in human and mouse. PMID:35534820
Distribution of Common and Rare Genetic Markers of Second-Line-Injectable-Drug Resistance in Mycobacterium tuberculosis Revealed by a Genome-Wide Association Study. PMID:35532237
Exploring synergies between plant metabolic modelling and machine learning. PMID:35521559
Biochemical and molecular characterization of three serologically different Vibrio harveyi strains isolated from farmed Dicentrarchus labrax from the Adriatic Sea. PMID:35508554
Large-scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression. PMID:35505892
Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences. PMID:35503575
The Arabidopsis gene co-expression network. PMID:35492683
Low Complexity Regions in Mammalian Proteins are Associated with Low Protein Abundance and High Transcript Abundance. PMID:35482425
Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking. PMID:35475639
ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data. PMID:35456896
Mitochondrial Genetics Reinforces Multiple Layers of Interaction in Alzheimer's Disease. PMID:35453630
An evolutionarily conserved stop codon enrichment at the 5' ends of mammalian piRNAs. PMID:35440552
The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia. PMID:35439302
Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures. PMID:35422847
Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species. PMID:35418239
RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor. PMID:35392801
Soil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome Assembly. PMID:35384699
The genomic basis of host and vector specificity in non-pathogenic trypanosomatids. PMID:35373253
Profiles of telomeric repeats in Insecta reveal diverse forms of telomeric motifs in Hymenopterans. PMID:35365574
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS. PMID:35361110
Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators. PMID:35357493
Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation. PMID:35353008
Integration of omics data to generate and analyse COVID-19 specific genome-scale metabolic models. PMID:35339845
An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using the Bentley-Saxe Transformation. PMID:35325039
New spinocerebellar ataxia subtype caused by SAMD9L mutation triggering mitochondrial dysregulation (SCA49). PMID:35310830
Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model. PMID:35310659
ECO: An Integrated Gene Expression Omnibus for Mouse Endothelial Cells In Vivo. PMID:35309132
Targeting SOX10-deficient cells to reduce the dormant-invasive phenotype state in melanoma. PMID:35296667
A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease. PMID:35286398
Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research. PMID:35285497
Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes. PMID:35277961
Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis. PMID:35251777
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters. PMID:35242361
Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome. PMID:35237850
Novel viruses discovered in the transcriptomes of agnathan fish. PMID:35235679
Advancing discovery in hearing research via biologist-friendly access to multi-omic data. PMID:35235019
FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis. PMID:35202087
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. PMID:35199087
Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach. PMID:35198001
HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly. PMID:35193521
SEAseq: a portable and cloud-based chromatin occupancy analysis suite. PMID:35193506
A-to-I mRNA editing controls spore death induced by a fungal meiotic drive gene in homologous and heterologous expression systems. PMID:35166849
Accurate and rapid prediction of tuberculosis drug resistance from genome sequence data using traditional machine learning algorithms and CNN. PMID:35165358
Overlooked and widespread pennate diatom-diazotroph symbioses in the sea. PMID:35145076
Widespread association of ERα with RMRP and tRNA genes in MCF-7 cells and breast cancers. PMID:35143945
Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes. PMID:35139905
Evolution and Stress Responses of CLO Genes and Potential Function of the GhCLO06 Gene in Salt Resistance of Cotton. PMID:35111180
Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies. PMID:35106579
Genomic patterns of transcription-replication interactions in mouse primary B cells. PMID:35100392
Petabase-scale sequence alignment catalyses viral discovery. PMID:35082445
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
In-Depth Analysis of Bacillus anthracis 16S rRNA Genes and Transcripts Reveals Intra- and Intergenomic Diversity and Facilitates Anthrax Detection. PMID:35076271
Betacoronavirus-specific alternate splicing. PMID:35074468
Influence of feeder cells on transcriptomic analysis of pluripotent stem cells. PMID:35060660
Characterization of Long Non-Coding RNAs in the Bollworm, Helicoverpa zea, and Their Possible Role in Cry1Ac-Resistance. PMID:35055855
Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. PMID:35048970
Darwinian genomics and diversity in the tree of life. PMID:35042807
Harnessing big data to characterize immune-related adverse events. PMID:35039679
CyVerse for Reproducible Research: RNA-Seq Analysis. PMID:35037200
Tissue specific expression of UMAMIT amino acid transporters in wheat. PMID:35013480
Meta-analysis of whole-genome gene expression datasets assessing the effects of IDH1 and IDH2 mutations in isogenic disease models. PMID:34997121
RNA sequencing and its applications in cancer and rare diseases. PMID:34988891
Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet. PMID:34988438
Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data. PMID:34980209
Transcriptome Dynamics of Human Neuronal Differentiation From iPSC. PMID:34970540
The first comprehensive database of germline pathogenic variants in East Asian cancer patients. PMID:34964846
Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019. PMID:34956117
Systematic Characterization of MicroRNA Processing Modes in Plants With Parallel Amplification of RNA Ends. PMID:34950175
Fast and accurate metagenotyping of the human gut microbiome with GT-Pro. PMID:34949778
Evolutionary Characterization of the Short Protein SPAAR. PMID:34946813
Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model. PMID:34944421
Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques. PMID:34938269
Foster thy young: enhanced prediction of orphan genes in assembled genomes. PMID:34928390
GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells. PMID:34928370
Genetic Variation and the Distribution of Variant Types in the Horse. PMID:34925451
The long non-coding RNA landscape of Candida yeast pathogens. PMID:34916523
A Comprehensive Annotation of the Channel Catfish (Ictalurus punctatus) T Cell Receptor Alpha/Delta, Beta, and Gamma Loci. PMID:34899754
Identification and Expression Analysis of G Protein-Coupled Receptors in the Miridae Insect Apolygus lucorum. PMID:34899608
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects. PMID:34890448
Transcriptomic Characterization of Cow, Donkey and Goat Milk Extracellular Vesicles Reveals Their Anti-Inflammatory and Immunomodulatory Potential. PMID:34884564
Kinase-dead mutation: A novel strategy for improving soybean resistance to soybean cyst nematode Heterodera glycines. PMID:34851539
Decoding the effects of synonymous variants. PMID:34850938
Addressing noise in co-expression network construction. PMID:34850822
TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data. PMID:34850130
PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process. PMID:34850118
Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures. PMID:34824813
High endogenous CCL2 expression promotes the aggressive phenotype of human inflammatory breast cancer. PMID:34824220
Maturation of 23S rRNA includes removal of helix H1 in many bacteria. PMID:34812116
Global Distribution and Richness of Armillaria and Related Species Inferred From Public Databases and Amplicon Sequencing Datasets. PMID:34803949
Identification of differentially expressed genomic repeats in primary hepatocellular carcinoma and their potential links to biological processes and survival. PMID:34803457
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. PMID:34791440
Evolution Analyses of CAMTA Transcription Factor in Plants and Its Enhancing Effect on Cold-tolerance. PMID:34790215
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison. PMID:34788838
Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. PMID:34780468
Evolutionary history of the vertebrate Piwi gene family. PMID:34760405
INDI-integrated nanobody database for immunoinformatics. PMID:34747487
Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing. PMID:34733267
Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing. PMID:34721349
Characterization of Basal Transcriptomes Identifies Potential Metabolic and Virulence-Associated Adaptations Among Diverse Nontyphoidal Salmonella enterica Serovars. PMID:34721328
MVIP: multi-omics portal of viral infection. PMID:34718748
isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data. PMID:34715772
Emerging and Established Trends to Support Secure Health Information Exchange. PMID:34713107
Transcriptional landscape associated with TNBC resistance to neoadjuvant chemotherapy revealed by single-cell RNA-seq. PMID:34703883
Comprehensive Analyses of NAC Transcription Factor Family in Almond (Prunus dulcis) and Their Differential Gene Expression during Fruit Development. PMID:34686009
Targeting Asparagine and Serine Metabolism in Germinal Centre-Derived B Cells Non-Hodgkin Lymphomas (B-NHL). PMID:34685569
Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics. PMID:34681121
Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019. PMID:34673924
Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa. PMID:34671335
Network-Based Approaches Reveal Potential Therapeutic Targets for Host-Directed Antileishmanial Therapy Driving Drug Repurposing. PMID:34668739
Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae. PMID:34664673
Quantifying full-length circular RNAs in cancer. PMID:34663689
Phylum-Spanning Neuropeptide GPCR Identification and Prioritization: Shaping Drug Target Discovery Pipelines for Nematode Parasite Control. PMID:34659113
Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. PMID:34657989
FusionAI: Predicting fusion breakpoint from DNA sequence with deep learning. PMID:34646994
Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions. PMID:34636851
SCovid: single-cell atlases for exposing molecular characteristics of COVID-19 across 10 human tissues. PMID:34634820
Conserved germ plasm characteristics across the Danio and Devario lineages. PMID:34617657
A standard knockout procedure alters expression of adjacent loci at the translational level. PMID:34606617
huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level. PMID:34606616
Systematic investigation of cytokine signaling activity at the tissue and single-cell levels. PMID:34594031
MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. PMID:34592929
Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa. PMID:34575741
Viral suppressor of RNA silencing in vascular plants also interferes with the development of the bryophyte Physcomitrella patens. PMID:34564869
Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions. PMID:34558825
Bias-invariant RNA-sequencing metadata annotation. PMID:34553213
Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data. PMID:34550971
The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid. PMID:34544144
Data Management and Modeling in Plant Biology. PMID:34539712
Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing. PMID:34527435
Synthetic Evaluation of MicroRNA-1-3p Expression in Head and Neck Squamous Cell Carcinoma Based on Microarray Chips and MicroRNA Sequencing. PMID:34485523
Whole-genome-based phylogenomic analysis of the Belgian 2016-2017 influenza A(H3N2) outbreak season allows improved surveillance. PMID:34477544
A Meta-Analysis of Bioelectric Data in Cancer, Embryogenesis, and Regeneration. PMID:34476377
DIANA-miTED: a microRNA tissue expression database. PMID:34469540
Linkage of community composition and function over short response time in anaerobic digestion systems with food fermentation wastewater. PMID:34466784
Statistical guidelines for quality control of next-generation sequencing techniques. PMID:34462322
Prevalence of IncFIB Plasmids Found among Salmonella enterica Serovar Schwarzengrund Isolates from Animal Sources in Taiwan Using Whole-Genome Sequencing. PMID:34451486
In silico analyses of neuropeptide-like protein (NLP) profiles in parasitic nematodes. PMID:34450132
RNA Sequencing Analyses for Deciphering Potato Molecular Responses. PMID:34448155
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Systematic Identification of circRNAs in Alzheimer's Disease. PMID:34440432
iRGvalid: A Robust in silico Method for Optimal Reference Gene Validation. PMID:34422018
Finding differentially expressed sRNA-Seq regions with srnadiff. PMID:34415926
Redondovirus Diversity and Evolution on Global, Individual, and Molecular Scales. PMID:34406857
Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases. PMID:34399612
Monomorphic Trypanozoon: towards reconciling phylogeny and pathologies. PMID:34397347
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. PMID:34379107
Quantifying the Impact of Human Leukocyte Antigen on the Human Gut Microbiota. PMID:34378979
INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosis. PMID:34376217
Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management. PMID:34362297
A Large-Scale and Serverless Computational Approach for Improving Quality of NGS Data Supporting Big Multi-Omics Data Analyses. PMID:34326863
Putatively cancer-specific exon-exon junctions are shared across patients and present in developmental and other non-cancer cells. PMID:34316681
Sequencing and Reconstructing Helminth Mitochondrial Genomes Directly from Genomic Next-Generation Sequencing Data. PMID:34313982
Genomic Evidence for Speciation with Gene Flow in Broadcast Spawning Marine Invertebrates. PMID:34311468
The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. PMID:34305969
Improving Mobilization of Foreign DNA into Zymomonas mobilis Strain ZM4 by Removal of Multiple Restriction Systems. PMID:34288704
Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources. PMID:34283824
Forming Consensus To Advance Urobiome Research. PMID:34282932
In silico model for miRNA-mediated regulatory network in cancer. PMID:34279571
Core of the saliva microbiome: an analysis of the MG-RAST data. PMID:34271900
Assessing conservation of alternative splicing with evolutionary splicing graphs. PMID:34266979
Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. PMID:34261503
Protocol for using TRIBE to study RNA-protein interactions and nuclear organization in mammalian cells. PMID:34258595
Practical selection of representative sets of RNA-seq samples using a hierarchical approach. PMID:34252927
Recommendations for the FAIRification of genomic track metadata. PMID:34249331
16S rRNA Gene Amplicon Sequencing Data from Flooded Rice Paddy Mesocosms Treated with Different Silicon-Rich Soil Amendments. PMID:34236218
Differential ATAC-seq and ChIP-seq peak detection using ROTS. PMID:34235431
Betacoronavirus-specific alternate splicing. PMID:34230929
Cell Death and Transcriptional Responses Induced in Larvae of the Nematode Haemonchus contortus by Toxins/Toxicants with Broad Phylogenetic Efficacy. PMID:34206464
Pincho: A Modular Approach to High Quality De Novo Transcriptomics. PMID:34206353
A Survey of Current Resources to Study lncRNA-Protein Interactions. PMID:34201302
Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry. PMID:34201152
Characterization of Human Genes Modulated by Porphyromonas gingivalis Highlights the Ribosome, Hypothalamus, and Cholinergic Neurons. PMID:34194426
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
Bioinformatic Analysis of Circular RNA Expression. PMID:34160817
ORFik: a comprehensive R toolkit for the analysis of translation. PMID:34147079
Herbaspirillum seropedicae strain HRC54 expression profile in response to sugarcane apoplastic fluid. PMID:34136329
Independent duplications of the Golgi phosphoprotein 3 oncogene in birds. PMID:34127736
PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses. PMID:34122478
Multiple Omics Integration Reveals Key Circular RNAs in Hepatocellular Carcinoma. PMID:34094907
Sporadic isolation of Tetratrichomonas species from the cattle urogenital tract. PMID:34078489
De novo genome assemblies of butterflies. PMID:34076242
Elucidating the Functions of Non-Coding RNAs from the Perspective of RNA Modifications. PMID:34065036
Genome-Wide Identification of Barley Long Noncoding RNAs and Analysis of Their Regulatory Interactions during Shoot and Grain Development. PMID:34064912
ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses. PMID:34055480
Optimal sample size for calibrating DNA methylation age estimators. PMID:34053192
Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa. PMID:34035952
The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron. PMID:34022814
Genome-Wide Analysis of c-MYC-Regulated mRNAs and miRNAs and c-MYC DNA-Binding by Next-Generation Sequencing. PMID:34019289
Endophytic Bacterial Isolates From Halophytes Demonstrate Phytopathogen Biocontrol and Plant Growth Promotion Under High Salinity. PMID:34017321
Investigating the impact of reference assembly choice on genomic analyses in a cattle breed. PMID:34011274
Components of the Gut Microbiome That Influence Bone Tissue-Level Strength. PMID:33999456
TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis. PMID:33993215
Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome. PMID:33959106
Rengasvirus, a Circular Replication-Associated Protein-Encoding Single-Stranded DNA Virus-Related Genome That Is a Common Contaminant in Metagenomic Data. PMID:33958399
Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance. PMID:33945454
Integrative reconstruction of cancer genome karyotypes using InfoGenomeR. PMID:33927198
Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation. PMID:33917583
Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition. PMID:33914028
Population genomic evidence of Plasmodium vivax Southeast Asian origin. PMID:33910900
Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data. PMID:33888829
Identification of Inflammatory Genes, Pathways, and Immune Cells in Necrotizing Enterocolitis of Preterm Infant by Bioinformatics Approaches. PMID:33880370
Dual RNA Sequencing Meta-analysis in Plasmodium Infection Identifies Host-Parasite Interactions. PMID:33879496
H3ABioNet genomic medicine and microbiome data portals hackathon proceedings. PMID:33864455
A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes. PMID:33861991
Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. PMID:33852055
Artificial intelligence to deep learning: machine intelligence approach for drug discovery. PMID:33844136
Combining natural language processing and metabarcoding to reveal pathogen-environment associations. PMID:33826634
Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants. PMID:33822878
MolluscDB: a genome and transcriptome database for molluscs. PMID:33813885
Rice Transcriptome Analysis Reveals Nitrogen Starvation Modulates Differential Alternative Splicing and Transcript Usage in Various Metabolism-Related Genes. PMID:33801769
Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects. PMID:33794662
A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches. PMID:33789960
Large-scale labeling and assessment of sex bias in publicly available expression data. PMID:33784977
Assessing Ribosome Distribution Along Transcripts with Polarity Scores and Regression Slope Estimates. PMID:33765281
Shannon entropy as a metric for conditional gene expression in Neurospora crassa. PMID:33751112
Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP. PMID:33750297
Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. PMID:33726677
Draft Genome Sequence of the Type Strain Bacillus subtilis subsp. subtilis DSM10. PMID:33707332
Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes. PMID:33685485
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection. PMID:33674719
Assessing Trypanosoma cruzi Parasite Diversity through Comparative Genomics: Implications for Disease Epidemiology and Diagnostics. PMID:33669197
Chemogenomic approach to identifying nematode chemoreceptor drug targets in the entomopathogenic nematode Heterorhabditis bacteriophora. PMID:33667976
Molecular subtyping and functional validation of TTK, TPX2, UBE2C, and LRP8 in sensitivity of TNBC to paclitaxel. PMID:33665229
Single-cell mapper (scMappR): using scRNA-seq to infer the cell-type specificities of differentially expressed genes. PMID:33655208
Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape. PMID:33652953
Lower endoscopic delivery of freeze-dried intestinal microbiota results in more rapid and efficient engraftment than oral administration. PMID:33633264
Antidepressants fluoxetine and amitriptyline induce alterations in intestinal microbiota and gut microbiome function in rats exposed to chronic unpredictable mild stress. PMID:33602895
Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization. PMID:33600447
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. PMID:33575650
Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes. PMID:33575641
CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data. PMID:33575613
Reference-based QUantification Of gene Dispensability (QUOD). PMID:33563309
HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles. PMID:33557210
Clinical and Biological Subtypes of B-cell Lymphoma Revealed by Microenvironmental Signatures. PMID:33541860
Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly. PMID:33537807
Identification of RCC Subtype-Specific microRNAs-Meta-Analysis of High-Throughput RCC Tumor microRNA Expression Data. PMID:33535553
Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium. PMID:33522965
Identification of Key Pathways and Genes Related to the Development of Hair Follicle Cycle in Cashmere Goats. PMID:33513983
Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes. PMID:33510867
Bacterial meta-analysis of chicken cecal microbiota. PMID:33505795
Single-cell long noncoding RNA (lncRNA) transcriptome implicates MALAT1 in triple-negative breast cancer (TNBC) resistance to neoadjuvant chemotherapy. PMID:33495450
An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. PMID:33479725
Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae. PMID:33462193
Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice. PMID:33454277
Metals Alter Membership but Not Diversity of a Headwater Stream Microbiome. PMID:33452033
Improving tuberculosis surveillance by detecting international transmission using publicly available whole genome sequencing data. PMID:33446303
Deconstructing transcriptional variations and their effects on immunomodulatory function among human mesenchymal stromal cells. PMID:33422149
Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes. PMID:33411719
Current status of use of high throughput nucleotide sequencing in rheumatology. PMID:33408124
Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence. PMID:33402863
Trace gas oxidizers are widespread and active members of soil microbial communities. PMID:33398096
DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification. PMID:33396959
CorkOakDB-The Cork Oak Genome Database Portal. PMID:33382885
Antimicrobial Resistance and in silico Virulence Profiling of Aliarcobacter butzleri Strains From German Water Poultry. PMID:33381106
Structural Variability, Expression Profile, and Pharmacogenetic Properties of TMPRSS2 Gene as a Potential Target for COVID-19 Therapy. PMID:33375616
Molecular signatures of sexual communication in the phlebotomine sand flies. PMID:33370303
CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology. PMID:33364592
State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing. PMID:33362867
Essential interpretations of bioinformatics in COVID-19 pandemic. PMID:33349792
Using single-plant-omics in the field to link maize genes to functions and phenotypes. PMID:33346944
MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle. PMID:33338203
Modeling the human aging transcriptome across tissues, health status, and sex. PMID:33336875
Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses. PMID:33334055
Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses. PMID:33334055
RNA-Mediated Feedback Control of Transcriptional Condensates. PMID:33333019
Metagenomic Analysis Reveals the Distribution of Antibiotic Resistance Genes in a Large-Scale Population of Healthy Individuals and Patients With Varied Diseases. PMID:33330625
Data structures based on k-mers for querying large collections of sequencing data sets. PMID:33328168
Helixer: Cross-species gene annotation of large eukaryotic genomes using deep learning. PMID:33325516
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
Selective amplification of hypermethylated DNA from diverse tumor types via MSRE-PCR. PMID:33315971
ncDRMarker: a computational method for identifying non-coding RNA signatures of drug resistance based on heterogeneous network. PMID:33313140
Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom. PMID:33304470
Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution. PMID:33297939
A review of COVID-19 biomarkers and drug targets: resources and tools. PMID:33279954
Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations. PMID:33268804
Dissecting the DNA binding landscape and gene regulatory network of p63 and p53. PMID:33263276
HAHmiR.DB: a server platform for high-altitude human miRNA-gene coregulatory networks and associated regulatory circuits. PMID:33259604
ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy. PMID:33244314
The earliest diverging extant scleractinian corals recovered by mitochondrial genomes. PMID:33244171
Expression Partitioning of Duplicate Genes at Single Cell Resolution in Arabidopsis Roots. PMID:33240334
High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity. PMID:33236025
Anti-Tick Microbiota Vaccine Impacts Ixodes ricinus Performance during Feeding. PMID:33233316
RepeatFS: a file system providing reproducibility through provenance and automation. PMID:33230554
Variation under domestication in animal models: the case of the Mexican axolotl. PMID:33228551
A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies. PMID:33219668
Draft Genome Sequences of Lactococcus lactis Strains MS22314, MS22333, MS22336, and MS22337, Isolated from Fermented Camel Milk in Ethiopia. PMID:33214295
Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning. PMID:33212013
Methods for correcting inference based on outcomes predicted by machine learning. PMID:33208538
OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques. PMID:33206960
Using RNA Sequencing and Spike-in RNAs to Measure Intracellular Abundance of lncRNAs and mRNAs. PMID:33204768
A comprehensive analysis of cotton VQ gene superfamily reveals their potential and extensive roles in regulating cotton abiotic stress. PMID:33198654
Lower Airway Dysbiosis Affects Lung Cancer Progression. PMID:33177060
A comprehensive investigation of metagenome assembly by linked-read sequencing. PMID:33176883
Identifying candidate Aspergillus pathogenicity factors by annotation frequency. PMID:33176679
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. PMID:33175170
Genomic Characterization of Salmonella Minnesota Clonal Lineages Associated with Poultry Production in Brazil. PMID:33167341
Genomes OnLine Database (GOLD) v.8: overview and updates. PMID:33152092
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. PMID:33142722
Correcting for experiment-specific variability in expression compendia can remove underlying signals. PMID:33140829
Rapid determination of nematode cell and organ susceptibility to toxic treatments. PMID:33125935
The birth of a bacterial tRNA gene by large-scale, tandem duplication events. PMID:33124983
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. PMID:33119741
Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. PMID:33118035
Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists. PMID:33106560
Cathepsin F of Teladorsagia circumcincta is a recently evolved cysteine protease. PMID:33100828
The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition. PMID:33090199
Network-Based Coexpression Analysis Identifies Functional and Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma. PMID:33083449
MicroRNA dynamics during hibernation of the Australian central bearded dragon (Pogona vitticeps). PMID:33082398
Genome sequencing data for wild and cultivated bananas, plantains and abacá. PMID:33072825
In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides. PMID:33072042
tsRBase: a comprehensive database for expression and function of tsRNAs in multiple species. PMID:33068436
Legacy Effects Overshadow Tree Diversity Effects on Soil Fungal Communities in Oil Palm-Enrichment Plantations. PMID:33066264
An online coronavirus analysis platform from the National Genomics Data Center. PMID:33045776
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. PMID:33045728
TOP2A and CENPF are synergistic master regulators activated in cervical cancer. PMID:33023625
Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement. PMID:33023476
Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations. PMID:33016192
Database: web application for visualization of the cumulated RNAseq data against the salicylic acid (SA) and methyl jasmonate (MeJA) treatment of Arabidopsis thaliana. PMID:33008298
Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents. PMID:33007800
A systematic comparison of chloroplast genome assembly tools. PMID:32988404
Potential role of cellular miRNAs in coronavirus-host interplay. PMID:32983652
Spritz: A Proteogenomic Database Engine. PMID:32967423
T cell receptor sequence clustering and antigen specificity. PMID:32952933
Revealing antimicrobial resistance in stormwater with MinION. PMID:32947654
Unlocking the potential of plant phenotyping data through integration and data-driven approaches. PMID:32923745
TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets. PMID:32917036
Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads. PMID:32913631
Insights into glucocorticoid responses derived from omics studies. PMID:32910934
Multiple Known Mechanisms and a Possible Role of an Enhanced Immune System in Bt-Resistance in a Field Population of the Bollworm, Helicoverpa zea: Differences in Gene Expression with RNAseq. PMID:32906662
Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution. PMID:32900997
LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data. PMID:32883264
"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive". PMID:32883210
Computational and Transcriptome Analyses Revealed Preferential Induction of Chemotaxis and Lipid Synthesis by SARS-CoV-2. PMID:32882823
The Acidic Stress Response of the Intracellular Pathogen Brucella melitensis: New Insights from a Comparative, Genome-Wide Transcriptome Analysis. PMID:32872264
A comparison of statistical and machine learning methods for creating national daily maps of ambient PM2.5 concentration. PMID:32863727
Microbial Culture in Minimal Medium With Oil Favors Enrichment of Biosurfactant Producing Genes. PMID:32850771
Environmental prospecting of black yeast-like agents of human disease using culture-independent methodology. PMID:32848176
MicroRNAs Modulate the Pathogenesis of Alzheimer's Disease: An In Silico Analysis in the Human Brain. PMID:32846925
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community. PMID:32838759
HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis. PMID:32838738
The Interactive Effects of Crude Oil and Corexit 9500 on Their Biodegradation in Arctic Seawater. PMID:32826215
BrassicaEDB: A Gene Expression Database for Brassica Crops. PMID:32823802
Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets. PMID:32814578
Metagenomic Studies in Inflammatory Skin Diseases. PMID:32813091
Spider phylosymbiosis: divergence of widow spider species and their tissues' microbiomes. PMID:32811423
Strength of immune selection in tumors varies with sex and age. PMID:32807809
Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination. PMID:32796589
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection. PMID:32793903
ACValidator: A novel assembly-based approach for in silico verification of circular RNAs. PMID:32793805
Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities? PMID:32780777
Complete Genome Sequence of the Prototrophic Bacillus subtilis subsp. subtilis Strain SP1. PMID:32763948
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. PMID:32749457
Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays. PMID:32742811
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data. PMID:32735679
De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates. PMID:32722301
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts. PMID:32718933
MYB30 Orchestrates Systemic Reactive Oxygen Signaling and Plant Acclimation. PMID:32699028
Differential expression of receptors mediating receptor-mediated transcytosis (RMT) in brain microvessels, brain parenchyma and peripheral tissues of the mouse and the human. PMID:32698806
Identification and Analysis of p53-Regulated Enhancers in Hepatic Carcinoma. PMID:32695760
Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data. PMID:32693839
The oilseed rape developmental expression resource: a resource for the investigation of gene expression dynamics during the floral transition in oilseed rape. PMID:32693783
Comparative genomics and transcriptomics of 4 Paragonimus species provide insights into lung fluke parasitism and pathogenesis. PMID:32687148
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. PMID:32683045
Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality. PMID:32681306
Non-retroviral Endogenous Viral Element Limits Cognate Virus Replication in Aedes aegypti Ovaries. PMID:32679098
Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies. PMID:32669560
Obesity and load-induced posttraumatic osteoarthritis in the absence of fracture or surgical trauma. PMID:32658313
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets. PMID:32657392
VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development. PMID:32646368
Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response. PMID:32646047
A Comprehensive Coexpression Network Analysis in Vibrio cholerae. PMID:32636337
A First Insight into North American Plant Pathogenic Fungi Armillaria Sinapina Transcriptome. PMID:32635577
Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases. PMID:32621602
TeaCoN: a database of gene co-expression network for tea plant (Camellia sinensis). PMID:32620074
Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samples. PMID:32616845
URMAP, an ultra-fast read mapper. PMID:32612885
Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epithelial cells with metabolic and protein-protein interaction networks. PMID:32595353
Robust Virome Profiling and Whole Genome Reconstruction of Viruses and Viroids Enabled by Use of Available mRNA and sRNA-Seq Datasets in Grapevine (Vitis vinifera L.). PMID:32582126
Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution. PMID:32556167
Complete Genome Sequence and Annotation for Turicibacter sanguinis MOL361T (DSM 14220). PMID:32554789
Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing. PMID:32554554
Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin. PMID:32528502
High-Throughput Identification of Adapters in Single-Read Sequencing Data. PMID:32521604
MicroRNA Expression Profiling on Paired Primary and Lymph Node Metastatic Breast Cancer Revealed Distinct microRNA Profile Associated With LNM. PMID:32509578
Could the Heat Shock Proteins 70 Family Members Exacerbate the Immune Response in Multiple Sclerosis? An in Silico Study. PMID:32503176
LabxDB: versatile databases for genomic sequencing and lab management. PMID:32502232
Retrocopying expands the functional repertoire of APOBEC3 antiviral proteins in primates. PMID:32479260
Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB). PMID:32463383
MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons. PMID:32451429
GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins. PMID:32440658
The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts. PMID:32438695
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. PMID:32429287
Whole-Genome Sequences of Three Plant Growth-Promoting Rhizobacteria Isolated from Solanum tuberosum L. Rhizosphere in Tanzania. PMID:32409546
CoCoCoNet: conserved and comparative co-expression across a diverse set of species. PMID:32392296
Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. PMID:32383760
Revisiting the expression signature of pks15/1 unveils regulatory patterns controlling phenolphtiocerol and phenolglycolipid production in pathogenic mycobacteria. PMID:32379829
Transposable elements contribute to the genome plasticity of Ralstonia solanacearum species complex. PMID:32379020
miRSwitch: detecting microRNA arm shift and switch events. PMID:32356893
The two paralogous kiwellin proteins KWL1 and KWL1-b from maize are structurally related and have overlapping functions in plant defense. PMID:32350112
A complete domain-to-species taxonomy for Bacteria and Archaea. PMID:32341564
To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics. PMID:32338745
Resistance of Tick Gut Microbiome to Anti-Tick Vaccines, Pathogen Infection and Antimicrobial Peptides. PMID:32331444
Can Gut Microbiota Be a Good Predictor for Parkinson's Disease? A Machine Learning Approach. PMID:32325848
Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. PMID:32322240
Comparative Genome Analysis of Hungarian and Global Strains of Salmonella Infantis. PMID:32318036
More Accurate Transcript Assembly via Parameter Advising. PMID:32315544
Crosstalk Between Female Gonadal Hormones and Vaginal Microbiota Across Various Phases of Women's Gynecological Lifecycle. PMID:32296412
Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn's Disease Patients. PMID:32276386
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. PMID:32266012
A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila. PMID:32253450
Machine learning and clinical epigenetics: a review of challenges for diagnosis and classification. PMID:32245523
A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer's Disease. PMID:32231518
Exploring the Consistency of the Quality Scores with Machine Learning for Next-Generation Sequencing Experiments. PMID:32219145
Distinguishing cell phenotype using cell epigenotype. PMID:32206707
The genomic landscape of 8-oxodG reveals enrichment at specific inherently fragile promoters. PMID:32198884
RASflow: an RNA-Seq analysis workflow with Snakemake. PMID:32183729
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project. PMID:32153629
Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus. PMID:32152350
The single-cell eQTLGen consortium. PMID:32149610
Origin and evolution of the Rax homeobox gene by comprehensive evolutionary analysis. PMID:32144893
MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data. PMID:32143373
Enhancer occlusion transcripts regulate the activity of human enhancer domains via transcriptional interference: a computational perspective. PMID:32133533
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. PMID:32086366
Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites. PMID:32085510
Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls. PMID:32082269
Bacterial coexistence driven by motility and spatial competition. PMID:32076271
Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line. PMID:32058723
Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters. PMID:32054853
Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data. PMID:32038716
Integrating Computational Methods to Investigate the Macroecology of Microbiomes. PMID:32010196
Domain-specific introduction to machine learning terminology, pitfalls and opportunities in CRISPR-based gene editing. PMID:32008042
Identification of RELN variant p.(Ser2486Gly) in an Iranian family with ankylosing spondylitis; the first association of RELN and AS. PMID:32001840
Applying a New REFINE Approach in Zymomonas mobilis Identifies Novel sRNAs That Confer Improved Stress Tolerance Phenotypes. PMID:31998271
Immune correlates of tuberculosis disease and risk translate across species. PMID:31996462
A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening. PMID:31992236
QuantTB - a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data. PMID:31992201
Ontology-driven integrative analysis of omics data through Onassis. PMID:31959844
Accumulation of genetic variants associated with immunity in the selective breeding of broilers. PMID:31952471
ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them. PMID:31942977
Machine learning applied to whole-blood RNA-sequencing data uncovers distinct subsets of patients with systemic lupus erythematosus. PMID:31921420
Quantitative Trait Loci Mapping and Candidate Gene Analysis of Low Temperature Tolerance in Cucumber Seedlings. PMID:31921263
Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo. PMID:31921150
Tryptophan Metabolism by Gut Microbiome and Gut-Brain-Axis: An in silico Analysis. PMID:31920519
ASCOT identifies key regulators of neuronal subtype-specific splicing. PMID:31919425
A functional twintron, 'zombie' twintrons and a hypermobile group II intron invading itself in plant mitochondria. PMID:31915815
Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize. PMID:31900107
Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota. PMID:31878183
Human sperm displays rapid responses to diet. PMID:31877125
JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants. PMID:31874631
Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads. PMID:31849338
FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures. PMID:31847917
An Online Database for Exploring Over 2,000 Arabidopsis Small RNA Libraries. PMID:31843802
Engaging a community to enable disease-centric data sharing with the NF Data Portal. PMID:31836719
A Hierarchical Machine Learning Model to Discover Gleason Grade-Specific Biomarkers in Prostate Cancer. PMID:31835700
Parental origin of the allotetraploid tobacco Nicotiana benthamiana. PMID:31833111
Drug screening approach combines epigenetic sensitization with immunochemotherapy in cancer. PMID:31829282
Expression Profile Analysis of Differentially Expressed Circular RNAs in Steroid-Induced Osteonecrosis of the Femoral Head. PMID:31827647
TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model. PMID:31824778
A comprehensive resource for retrieving, visualizing, and integrating functional genomics data. PMID:31818883
Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya. PMID:31818257
Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes. PMID:31809632
Transcriptome-wide miRNA identification of Bacopa monnieri: a cross-kingdom approach. PMID:31797719
Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients. PMID:31796020
Integrating the Ribonucleic Acid Sequencing Data From Various Studies for Exploring the Multiple Sclerosis-Related Long Noncoding Ribonucleic Acids and Their Functions. PMID:31781177
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
Characterization of antibiotic resistance genes in the species of the rumen microbiota. PMID:31748524
PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks. PMID:31725858
Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP Webtool. PMID:31708960
VARUS: sampling complementary RNA reads from the sequence read archive. PMID:31703556
Mash Screen: high-throughput sequence containment estimation for genome discovery. PMID:31690338
Analysis of the structural variability of topologically associated domains as revealed by Hi-C. PMID:31687663
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. PMID:31679514
Epstein-Barr virus circRNAome as host miRNA sponge regulates virus infection, cell cycle, and oncogenesis. PMID:31668120
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. PMID:31640809
Upregulation of miR‑132‑3p in cholangiocarcinoma tissues: A study based on RT‑qPCR, The Cancer Genome Atlas miRNA sequencing, Gene Expression Omnibus microarray data and bioinformatics analyses. PMID:31638221
Comprehensive RNA-Seq Data Analysis Identifies Key mRNAs and lncRNAs in Atrial Fibrillation. PMID:31632440
Genome-wide association study of the seed transmission rate of soybean mosaic virus and associated traits using two diverse population panels. PMID:31630210
PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing. PMID:31617559
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
SEAweb: the small RNA Expression Atlas web application. PMID:31598718
Molecular evolution of the meiotic recombination pathway in mammals. PMID:31579931
Oregano essential oil vapour prevents Plasmopara viticola infection in grapevine (Vitis Vinifera) and primes plant immunity mechanisms. PMID:31560730
Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model. PMID:31529043
NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements. PMID:31527408
Molecular Profiling of the Drosophila Antenna Reveals Conserved Genes Underlying Olfaction in Insects. PMID:31527046
Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes. PMID:31525193
Is reliance on an inaccurate genome sequence sabotaging your experiments? PMID:31513692
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. PMID:31510699
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. PMID:31510660
QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data. PMID:31503285
High-Quality Draft Genome Sequence of the Causal Agent of the Current Panama Disease Epidemic. PMID:31488538
RNA-Seq de Novo Assembly and Differential Transcriptome Analysis of Chaga (Inonotus obliquus) Cultured with Different Betulin Sources and the Regulation of Genes Involved in Terpenoid Biosynthesis. PMID:31487924
Prospects of genomic resources available at the global databases for the flora of United Arab Emirates. PMID:31475085
The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases. PMID:31475030
Dose-Dependent Alterations to In Vitro Human Microbiota Composition and Butyrate Inhibition by a Supercritical Carbon Dioxide Hops Extract. PMID:31438572
CFEA: a cell-free epigenome atlas in human diseases. PMID:31428785
TDNAscan: A Software to Identify Complete and Truncated T-DNA Insertions. PMID:31428129
Microbial Exposure Enhances Immunity to Pathogens Recognized by TLR2 but Increases Susceptibility to Cytokine Storm through TLR4 Sensitization. PMID:31412243
Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human. PMID:31400206
Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins. PMID:31390792
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. PMID:31375807
Malaria.tools-comparative genomic and transcriptomic database for Plasmodium species. PMID:31372645
Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. PMID:31358912
An expanded landscape of human long noncoding RNA. PMID:31350901
Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns. PMID:31344123
Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0. PMID:31343654
A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses. PMID:31324840
Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data. PMID:31323892
Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development. PMID:31302154
Microbial Succession of Anaerobic Chitin Degradation in Freshwater Sediments. PMID:31285190
Cross-species functional modules link proteostasis to human normal aging. PMID:31269015
Long non-coding RNA (lncRNA) transcriptional landscape in breast cancer identifies LINC01614 as non-favorable prognostic biomarker regulated by TGFβ and focal adhesion kinase (FAK) signaling. PMID:31263577
Multimapping confounds ribosome profiling analysis: A case-study of the Hsp90 molecular chaperone. PMID:31254414
Dynamics of Vaginal and Rectal Microbiota Over Several Menstrual Cycles in Female Cynomolgus Macaques. PMID:31249812
Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences. PMID:31239292
New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies. PMID:31231413
Two Separation-of-Function Isoforms of Human TPP1 Dictate Telomerase Regulation in Somatic and Germ Cells. PMID:31216472
Deciphering the non-coding RNA-level response to arsenic stress in rice (Oryza sativa). PMID:31187662
BarkBase: Epigenomic Annotation of Canine Genomes. PMID:31181663
Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia. PMID:31174959
Comparison of the microbiomes of two drinking water distribution systems-with and without residual chloramine disinfection. PMID:31174608
Evaluation of introgressive hybridization among Cervidae in Japan's Kinki District via two novel genetic markers developed from public NGS data. PMID:31160985
Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew. PMID:31160924
Bridging the gap between reference and real transcriptomes. PMID:31159855
Events of alternative splicing in head and neck cancer via RNA sequencing - an update. PMID:31159745
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
Expression dynamics of repetitive DNA in early human embryonic development. PMID:31151386
RNAmod: an integrated system for the annotation of mRNA modifications. PMID:31147718
Integrating Molecular Biology and Bioinformatics Education. PMID:31145692
sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression. PMID:31114926
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. PMID:31114675
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data. PMID:31110304
Multiple genetic loci affect place learning and memory performance in Drosophila melanogaster. PMID:31095869
Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness. PMID:31071295
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia. PMID:31066139
Human contamination in bacterial genomes has created thousands of spurious proteins. PMID:31064768
BacTag - a pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing. PMID:31060512
Microbiome Learning Repo (ML Repo): A public repository of microbiome regression and classification tasks. PMID:31042284
Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease. PMID:31015293
Broad domains of histone 3 lysine 4 trimethylation are associated with transcriptional activation in CA1 neurons of the hippocampus during memory formation. PMID:31002880
RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs. PMID:30962443
The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1. PMID:30959844
exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. PMID:30951672
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. PMID:30951143
Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach. PMID:30947707
Pixel: a content management platform for quantitative omics data. PMID:30944779
Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World. PMID:30942856
OMICfpp: a fuzzy approach for paired RNA-Seq counts. PMID:30940089
Identification of rfk-1, a Meiotic Driver Undergoing RNA Editing in Neurospora. PMID:30918007
Predicting enhancers in mammalian genomes using supervised hidden Markov models. PMID:30917778
Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs. PMID:30915105
Sterol regulatory element binding protein 1 couples mechanical cues and lipid metabolism. PMID:30902980
Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: Neisseria meningitidis as a Proof-of-Concept. PMID:30894839
Lightweight data management with dtool. PMID:30867992
New insights from uncultivated genomes of the global human gut microbiome. PMID:30867587
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. PMID:30864657
Extracting allelic read counts from 250,000 human sequencing runs in Sequence Read Archive. PMID:30864322
Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework. PMID:30863673
Ploidy Determination in the Pathogenic Fungus Sporothrix spp. PMID:30858833
Integrative Analysis Reveals Key Circular RNA in Atrial Fibrillation. PMID:30838031
Federated discovery and sharing of genomic data using Beacons. PMID:30833764
Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease. PMID:30827497
An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria. PMID:30816249
Integration of Transcriptomic Data Identifies Global and Cell-Specific Asthma-Related Gene Expression Signatures. PMID:30815178
FAIRness and Usability for Open-access Omics Data Systems. PMID:30815061
The Active Sulfate-Reducing Microbial Community in Littoral Sediment of Oligotrophic Lake Constance. PMID:30814991
A Near Chromosome Assembly of the Dromedary Camel Genome. PMID:30804979
FairBase: a comprehensive database of fungal A-to-I RNA editing. PMID:30788499
New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation. PMID:30782641
Leukemia multiclass assessment and classification from Microarray and RNA-seq technologies integration at gene expression level. PMID:30753220
Transcriptomic Analysis of Planarians under Simulated Microgravity or 8 g Demonstrates That Alteration of Gravity Induces Genomic and Cellular Alterations That Could Facilitate Tumoral Transformation. PMID:30743987
A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks. PMID:30733664
The Fe(II)-oxidizing Zetaproteobacteria: historical, ecological and genomic perspectives. PMID:30715272
De Novo Transcriptome Assembly of Agave H11648 by Illumina Sequencing and Identification of Cellulose Synthase Genes in Agave Species. PMID:30704153
Urotensin-related gene transcripts mark developmental emergence of the male forebrain vocal control system in songbirds. PMID:30692609
First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_. PMID:30691411
Waldron et al. Reply to "Commentary on the HMP16SData Bioconductor Package". PMID:30689687
CMEP: a database for circulating microRNA expression profiling. PMID:30668638
Cross-species hybridization and the origin of North African date palms. PMID:30642962
Decrease of gene expression diversity during domestication of animals and plants. PMID:30634914
Immune genes are hotspots of shared positive selection across birds and mammals. PMID:30620335
Re-annotation of eight Drosophila genomes. PMID:30599046
Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. PMID:30594132
High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report. PMID:30592451
Plant stress RNA-seq Nexus: a stress-specific transcriptome database in plant cells. PMID:30587128
MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data. PMID:30577750
The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer. PMID:30577431
Draft Genome Sequence of Lactococcus lactis subsp. lactis W8, a Potential Nisin-Producing Starter Culture for Indian Traditional Fermented Milk (Dahi). PMID:30574584
An integrative approach for building personalized gene regulatory networks for precision medicine. PMID:30567569
Rapid Next-Generation Sequencing Method for Prediction of Prostate Cancer Risks. PMID:30553750
Impact of Rearing Conditions on the Ambrosia Beetle's Microbiome. PMID:30551580
Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. PMID:30544207
"Omics" data integration and functional analyses link Enoyl-CoA hydratase, short chain 1 to drug refractory dilated cardiomyopathy. PMID:30541556
DeepIsoFun: a deep domain adaptation approach to predict isoform functions. PMID:30535380
PDX Finder: A portal for patient-derived tumor xenograft model discovery. PMID:30535239
Reproductive and Behavior Dysfunction Induced by Maternal Androgen Exposure and Obesity Is Likely Not Gut Microbiome-Mediated. PMID:30534630
Whole-Genome Sequences of Two Arthrobacter sp. Strains, 4041 and 4042, Potentially Usable in Agriculture and Environmental Depollution. PMID:30533628
Whole-Genome Sequence of Pseudomonas sp. Strain 1239, Isolated from Soil in Western France. PMID:30533625
Whole-Genome Sequence of Pseudomonas aeruginosa Strain 4014, Isolated from Soil in France. PMID:30533620
Whole-Genome Sequence of Pseudomonas putida Strain 1312, a Potential Biostimulant Developed for Agriculture. PMID:30533614
Advances in genomic hepatocellular carcinoma research. PMID:30521023
Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis. PMID:30487815
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. PMID:30481257
Computational enhancement of single-cell sequences for inferring tumor evolution. PMID:30423071
A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. PMID:30420870
Leishmania Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification. PMID:30401775
Species-Wide Variation in Shoot Nitrate Concentration, and Genetic Loci Controlling Nitrate, Phosphorus and Potassium Accumulation in Brassica napus L. PMID:30386356
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. PMID:30365027
Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi). PMID:30356240
Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites. PMID:30355348
Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression. PMID:30324181
Next-Generation Sequencing Strategies. PMID:30323017
Complete Genome Sequence of the Model Halovirus PhiH1 (ΦH1). PMID:30322017
Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox). PMID:30315079
Exploring biogeographic patterns of bacterioplankton communities across global estuaries. PMID:30303297
Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. PMID:30291328
Genes significantly associated with lineage II food isolates of Listeria monocytogenes. PMID:30253738
Elucidation and analyses of the regulatory networks of upland and lowland ecotypes of switchgrass in response to drought and salt stresses. PMID:30248119
Mitochondrial transcription factor A (TFAM) shapes metabolic and invasion gene signatures in melanoma. PMID:30242167
Effects of hydroxyurea on CNV induction in the mouse germline. PMID:30218578
Deep learning in biomedicine. PMID:30188539
Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. PMID:30175688
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories. PMID:30166985
Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica. PMID:30158193
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. PMID:30148503
bioSyntax: syntax highlighting for computational biology. PMID:30134911
An Integrated, High-Throughput Strategy for Multiomic Systems Level Analysis. PMID:30114907
Cecal microbiome profile altered by Salmonella enterica, serovar Enteritidis inoculation in chicken. PMID:30087697
A population genomic characterization of copy number variation in the opportunistic fungal pathogen Aspergillus fumigatus. PMID:30071059
exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes. PMID:30053265
The mRNA cap methyltransferase gene TbCMT1 is not essential in vitro but is a virulence factor in vivo for bloodstream form Trypanosoma brucei. PMID:30040830
Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms. PMID:30037148
Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them. PMID:30018876
Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling. PMID:30010675
Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. PMID:29986751
Trends in the development of miRNA bioinformatics tools. PMID:29982332
Extensive screening of microRNA populations identifies hsa-miR-375 and hsa-miR-133a-3p as selective markers for human rectal and colon cancer. PMID:29930763
Gene Discovery of Characteristic Metabolic Pathways in the Tea Plant (Camellia sinensis) Using 'Omics'-Based Network Approaches: A Future Perspective. PMID:29915604
The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish. PMID:29909776
Genome sequence data from 17 accessions of Ensete ventricosum, a staple food crop for millions in Ethiopia. PMID:29896517
Comparative transcriptomics reveals shared gene expression changes during independent evolutionary origins of stem and hypocotyl/root tubers in Brassica (Brassicaceae). PMID:29856865
Landscape of Microsatellite Instability Across 39 Cancer Types. PMID:29850653
Genome-Wide Screening and Characterization of the Dof Gene Family in Physic Nut (Jatropha curcas L.). PMID:29844264
Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs. PMID:29789629
Revised Phylogeny of the Cellulose Synthase Gene Superfamily: Insights into Cell Wall Evolution. PMID:29780036
Core non-coding RNAs of Piscirickettsia salmonis. PMID:29768466
Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis. PMID:29764361
A Multi-Omics Database for Parasitic Nematodes and Trematodes. PMID:29761465
CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses. PMID:29718322
The Presence of Genotoxic and/or Pro-inflammatory Bacterial Genes in Gut Metagenomic Databases and Their Possible Link With Inflammatory Bowel Diseases. PMID:29692798
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. PMID:29688354
Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases. PMID:29666611
Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data. PMID:29643990
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees. PMID:29641248
A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms. PMID:29632618
taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time. PMID:29588360
BEARscc determines robustness of single-cell clusters using simulated technical replicates. PMID:29567991
Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis. PMID:29545614
Discovery and validation of a glioblastoma co-expressed gene module. PMID:29541392
Improving the value of public RNA-seq expression data by phenotype prediction. PMID:29514223
ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. PMID:29485622
Recently Evolved Tumor Suppressor Transcript TP73-AS1 Functions as Sponge of Human-Specific miR-941. PMID:29474580
msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data. PMID:29391490
Method for the Identification of Taxon-Specific k-mers from Chloroplast Genome: A Case Study on Tomato Plant (Solanum lycopersicum). PMID:29387080
Variations in diet cause alterations in microbiota and metabolites that follow changes in disease severity in a multiple sclerosis model. PMID:29380645
Cloud computing for genomic data analysis and collaboration. PMID:29379135
Biclustering of transcriptome sequencing data reveals human tissue-specific circular RNAs. PMID:29363420
The Expressed MicroRNA-mRNA Interactions of Toxoplasma gondii. PMID:29354114
Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications. PMID:29320804
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PMID:29300748
The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations. PMID:29220445
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site. PMID:29196557
Functional sequencing read annotation for high precision microbiome analysis. PMID:29194524
Decontaminating eukaryotic genome assemblies with machine learning. PMID:29191179
Identification of Candidate Genes for Calcium and Magnesium Accumulation in Brassica napus L. by Association Genetics. PMID:29187860
In Silico Analysis of Putrefaction Pathways in Bacteria and Its Implication in Colorectal Cancer. PMID:29163445
Ethylene Receptors Signal via a Noncanonical Pathway to Regulate Abscisic Acid Responses. PMID:29158332
Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling. PMID:29157215
Independent degradation in genes of the plastid ndh gene family in species of the orchid genus Cymbidium (Orchidaceae; Epidendroideae). PMID:29140976
Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice. PMID:29123534
Missing data and technical variability in single-cell RNA-sequencing experiments. PMID:29121214
Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer. PMID:29115931
Evolutionary Conserved Cysteines Function as cis-Acting Regulators of Arabidopsis PIN-FORMED 2 Distribution. PMID:29109378
Cancer cell line specific co-factors modulate the FOXM1 cistrome. PMID:29100329
Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomas. PMID:29099869
A molecular roadmap of the AGM region reveals BMPER as a novel regulator of HSC maturation. PMID:29093060
ARSDA: A New Approach for Storing, Transmitting and Analyzing Transcriptomic Data. PMID:29079682
Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents. PMID:29062974
Parallel sequencing lives, or what makes large sequencing projects successful. PMID:29048533
LiverWiki: a wiki-based database for human liver. PMID:29029599
De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data. PMID:29018311
Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes. PMID:29017442
Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. PMID:28992302
DART: a fast and accurate RNA-seq mapper with a partitioning strategy. PMID:28968831
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples. PMID:28968689
Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis. PMID:28955037
Strains, functions and dynamics in the expanded Human Microbiome Project. PMID:28953883
Insights into DDT Resistance from the Drosophila melanogaster Genetic Reference Panel. PMID:28935691
Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates. PMID:28923023
SEXCMD: Development and validation of sex marker sequences for whole-exome/genome and RNA sequencing. PMID:28886064
Mycobacterium bovis Bacillus Calmette-Guérin Alters Melanoma Microenvironment Favoring Antitumor T Cell Responses and Improving M2 Macrophage Function. PMID:28848560
Integrated Genomic Medicine: A Paradigm for Rare Diseases and Beyond. PMID:28838357
Analysis of repetitive amino acid motifs reveals the essential features of spider dragline silk proteins. PMID:28832627
Using omics approaches to understand pulmonary diseases. PMID:28774304
Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data. PMID:28768814
Pancreatic PYY but not PPY expression is responsive to short-term nutritional state and the pancreas constitutes the major site of PYY mRNA expression in chickens. PMID:28694054
Comparative analysis of lincRNA in insect species. PMID:28673235
Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica. PMID:28672765
An RNA Recognition Motif-Containing Protein Functions in Meiotic Silencing by Unpaired DNA. PMID:28667016
Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data. PMID:28625989
A Primer on Infectious Disease Bacterial Genomics. PMID:28590251
Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. PMID:28590247
Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene. PMID:28583129
Deeper Insight in Beehives: Metagenomes of Royal Jelly, Pollen, and Honey from Lavender, Chestnut, and Fir Honeydew and Epiphytic and Endophytic Microbiota of Lavender and Rose Flowers. PMID:28572315
The common transcriptional subnetworks of the grape berry skin in the late stages of ripening. PMID:28558655
Metagenomes and Metatranscriptomes of Activated Sludge from a Sewage Plant, with or without Aerobic Granule Enrichment. PMID:28546481
An environment-dependent transcriptional network specifies human microglia identity. PMID:28546318
RNA-Seq Comparison of Larval and Adult Malpighian Tubules of the Yellow Fever Mosquito Aedes aegypti Reveals Life Stage-Specific Changes in Renal Function. PMID:28536536
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. PMID:28535296
OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations. PMID:28521726
Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes. PMID:28474674
A Metagenomics Investigation of Carbohydrate-Active Enzymes along the Gastrointestinal Tract of Saudi Sheep. PMID:28473812
LncRNAs2Pathways: Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method. PMID:28425476
Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity. PMID:28408746
miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. PMID:28407097
Omicseq: a web-based search engine for exploring omics datasets. PMID:28402462
A framework for space-efficient read clustering in metagenomic samples. PMID:28361710
Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi. PMID:28361700
Small chromosomal regions position themselves autonomously according to their chromatin class. PMID:28341771
Listeriomics: an Interactive Web Platform for Systems Biology of Listeria. PMID:28317029
TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. PMID:28250416
A fuzzy method for RNA-Seq differential expression analysis in presence of multireads. PMID:28185579
Natural antisense transcripts are significantly involved in regulation of drought stress in maize. PMID:28175341
LncSubpathway: a novel approach for identifying dysfunctional subpathways associated with risk lncRNAs by integrating lncRNA and mRNA expression profiles and pathway topologies. PMID:28152521
Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization. PMID:28133571
miRmine: a database of human miRNA expression profiles. PMID:28108447
Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size. PMID:28087770
Discovery of flavivirus-derived endogenous viral elements in Anopheles mosquito genomes supports the existence of Anopheles-associated insect-specific flaviviruses. PMID:28078104
Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges. PMID:28076869
Identifying stably expressed genes from multiple RNA-Seq data sets. PMID:28028467
Performance evaluation for rapid detection of pan-cancer microsatellite instability with MANTIS. PMID:27980218
Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments. PMID:27966672
The ability of human nuclear DNA to cause false positive low-abundance heteroplasmy calls varies across the mitochondrial genome. PMID:27955616
PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs). PMID:27936097
MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing. PMID:27924023
TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species. PMID:27899608
Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data. PMID:27875984
A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. PMID:27855707
A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions. PMID:27824113
The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation. PMID:27821409
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. PMID:27803195
The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5' Leader Featuring the sRNA UpsM. PMID:27802301
Cooperative binding of AP-1 and TEAD4 modulates the balance between vascular smooth muscle and hemogenic cell fate. PMID:27802171
Multiple Evolutionary Origins of Ubiquitous Cu2+ and Zn2+ Binding in the S100 Protein Family. PMID:27764152
Comparative Transcriptomic Analysis of Two Brassica napus Near-Isogenic Lines Reveals a Network of Genes That Influences Seed Oil Accumulation. PMID:27746810
Global and cell-type specific properties of lincRNAs with ribosome occupancy. PMID:27738133
Genome-wide compendium and functional assessment of in vivo heart enhancers. PMID:27703156
IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. PMID:27659943
Complementary feature selection from alternative splicing events and gene expression for phenotype prediction. PMID:27587658
Subtractive transcriptome analysis of leaf and rhizome reveals differentially expressed transcripts in Panax sokpayensis. PMID:27586658
Avian Leukosis Virus Activation of an Antisense RNA Upstream of TERT in B-Cell Lymphomas. PMID:27512065
Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus. PMID:27507588
Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005-2009. PMID:27366170
Genome wide analysis of protein production load in Trichoderma reesei. PMID:27354857
Integration of Telomere Length Dynamics into Systems Biology Framework: A Review. PMID:27346946
WRKY transcription factor genes in wild rice Oryza nivara. PMID:27345721
Extent of pre-translational regulation for the control of nucleocytoplasmic protein localization. PMID:27342569
A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema. PMID:27324572
A Meiotic Drive Element in the Maize Pathogen Fusarium verticillioides Is Located Within a 102 kb Region of Chromosome V. PMID:27317777
Boiler: lossy compression of RNA-seq alignments using coverage vectors. PMID:27298258
The A, C, G, and T of Genome Assembly. PMID:27247941
Empirical estimation of sequencing error rates using smoothing splines. PMID:27102907
High-throughput sequencing of immune repertoires in multiple sclerosis. PMID:27081660
Data set for transcriptional response to depletion of the Shoc2 scaffolding protein. PMID:27077079
Using Small RNA Deep Sequencing Data to Detect Human Viruses. PMID:27066498
The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales. PMID:27026101
The real cost of sequencing: scaling computation to keep pace with data generation. PMID:27009100
CCAR1 5' UTR as a natural miRancer of miR-1254 overrides tamoxifen resistance. PMID:27002217
Genome Update. Let the consumer beware: Streptomyces genome sequence quality. PMID:26986204
Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils. PMID:26969694
Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis. PMID:26966169
Missed, Not Missing: Phylogenomic Evidence for the Existence of Avian FoxP3. PMID:26938477
MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression. PMID:26895947
Single-cell Transcriptome Study as Big Data. PMID:26876720
Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions. PMID:26869583
Draft Genome Sequence of Pseudomonas syringae pv. syringae ALF3 Isolated from Alfalfa. PMID:26868403
Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants. PMID:26868395
Fast search of thousands of short-read sequencing experiments. PMID:26854477
Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants. PMID:26847218
RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data. PMID:26817607
"Life in Data"--Outcome of a Multi-Disciplinary, Interactive Biobanking Conference Session on Sample Data. PMID:26808538
Multi-species sequence comparison reveals conservation of ghrelin gene-derived splice variants encoding a truncated ghrelin peptide. PMID:26792793
4Pipe4--A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information. PMID:26787189
REPURPOSING GERMLINE EXOMES OF THE CANCER GENOME ATLAS DEMANDS A CAUTIOUS APPROACH AND SAMPLE-SPECIFIC VARIANT FILTERING. PMID:26776187
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. PMID:26757703
Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera). PMID:26755583
Characterizing root-associated fungal communities and soils of Douglas-fir (Pseudotsuga menziesii) stands that naturally produce Oregon white truffles (Tuber oregonense and Tuber gibbosum). PMID:26743427
WheatExp: an RNA-seq expression database for polyploid wheat. PMID:26705106
Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. PMID:26698853
Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner. PMID:26684652
Analysis of Biobanked Serum from a Mycobacterium avium subsp paratuberculosis Bovine Infection Model Confirms the Remarkable Stability of Circulating miRNA Profiles and Defines a Bovine Serum miRNA Repertoire. PMID:26675426
The International Nucleotide Sequence Database Collaboration. PMID:26657633
An Evolutionarily Young Polar Bear (Ursus maritimus) Endogenous Retrovirus Identified from Next Generation Sequence Data. PMID:26610552
Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars. PMID:26573226
Information Commons for Rice (IC4R). PMID:26519466
Altered Gene Expression Associated with microRNA Binding Site Polymorphisms. PMID:26496489
A mutation in the nucleoporin-107 gene causes XX gonadal dysgenesis. PMID:26485283
Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler. PMID:26484285
Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. PMID:26466991
Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities. PMID:26458130
CircNet: a database of circular RNAs derived from transcriptome sequencing data. PMID:26450965
A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq. PMID:26427366
Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays. PMID:26357913
Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing. PMID:26341416
Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact. PMID:26308346
Draft Genome Sequences of 19 Salmonella enterica Serovar Typhimurium [4,5:i:-] Strains Resistant to Nalidixic Acid from a Long-Term Outbreak in Italy. PMID:26294627
Effects of subsampling on characteristics of RNA-seq data from triple-negative breast cancer patients. PMID:26253000
Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project. PMID:26216192
C2H2 zinc finger proteins of the SP/KLF, Wilms tumor, EGR, Huckebein, and Klumpfuss families in metazoans and beyond. PMID:26187067
Rapid mapping of insertional mutations to probe cell wall regulation in Cryptococcus neoformans. PMID:26112692
TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing. PMID:26056424
Light-weight reference-based compression of FASTQ data. PMID:26051252
SeedsGraph: an efficient assembler for next-generation sequencing data. PMID:26044652
Integrative analyses of cancer data: a review from a statistical perspective. PMID:26041968
BioMiner: Paving the Way for Personalized Medicine. PMID:26005322
Investigation into the annotation of protocol sequencing steps in the sequence read archive. PMID:25960871
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse. PMID:25953081
Computel: computation of mean telomere length from whole-genome next-generation sequencing data. PMID:25923330
The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine. PMID:25915124
Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa. PMID:25897488
CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts. PMID:25887563
Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform. PMID:25860802
NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome. PMID:25849067
Small RNA sequencing for profiling microRNAs in long-term preserved formalin-fixed and paraffin-embedded non-small cell lung cancer tumor specimens. PMID:25812157
Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles. PMID:25774498
Similarities and differences of X and Y chromosome homologous genes, SRY and SOX3, in regulating the renin-angiotensin system promoters. PMID:25759379
CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002. PMID:25632108
Transcriptional control of an essential ribozyme in Drosophila reveals an ancient evolutionary divide in animals. PMID:25569672
Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis. PMID:25566309
Compression of next-generation sequencing quality scores using memetic algorithm. PMID:25474747
The evolutionary fate of the horizontally transferred agrobacterial mikimopine synthase gene in the genera Nicotiana and Linaria. PMID:25420106
Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation. PMID:25411636
Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases? PMID:25399113
GeneFriends: a human RNA-seq-based gene and transcript co-expression database. PMID:25361971
Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins. PMID:25348801
Measuring the effect of inter-study variability on estimating prediction error. PMID:25330348
MetaProx: the database of metagenomic proximons. PMID:25288655
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. PMID:25270877
Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. PMID:25270025
We are all individuals... bioinformatics in the personalized medicine era. PMID:25204962
Parallel selection on gene copy number variations through evolution of three-spined stickleback genomes. PMID:25168270
Efficient detection of unpaired DNA requires a member of the rad54-like family of homologous recombination proteins. PMID:25146971
Defining the estimated core genome of bacterial populations using a Bayesian decision model. PMID:25144616
Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'. PMID:25083931
Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS. PMID:25026199
Identification and characterization of CYP79D16 and CYP71AN24 catalyzing the first and second steps in L-phenylalanine-derived cyanogenic glycoside biosynthesis in the Japanese apricot, Prunus mume Sieb. et Zucc. PMID:25015725
A virulent strain of deformed wing virus (DWV) of honeybees (Apis mellifera) prevails after Varroa destructor-mediated, or in vitro, transmission. PMID:24968198
A critical component of meiotic drive in Neurospora is located near a chromosome rearrangement. PMID:24931406
Last-gen nostalgia: a lighthearted rant and reflection on genome sequencing culture. PMID:24904646
The use of metagenomic approaches to analyze changes in microbial communities. PMID:24826073
The use of metagenomic approaches to analyze changes in microbial communities. PMID:24826073
NFI transcription factors interact with FOXA1 to regulate prostate-specific gene expression. PMID:24801505
Natural variation of histone modification and its impact on gene expression in the rat genome. PMID:24793478
Identification of candidate genes for drought tolerance by whole-genome resequencing in maize. PMID:24684805
Navigating and mining modENCODE data. PMID:24636835
Integrative analysis of many RNA-seq datasets to study alternative splicing. PMID:24583115
An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads. PMID:24564333
Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline. PMID:24478219
DevMouse, the mouse developmental methylome database and analysis tools. PMID:24408217
An extensive evaluation of read trimming effects on Illumina NGS data analysis. PMID:24376861
Time for the zebrafish ENCODE. PMID:24371190
High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method. PMID:24369432
A metagenomic framework for the study of airborne microbial communities. PMID:24349140
A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PMID:24324667
Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application). PMID:24256031
Deep sequencing identification of novel glucocorticoid-responsive miRNAs in apoptotic primary lymphocytes. PMID:24250753
Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PMID:24244129
Phylogenomic analysis identifies gene gains that define Salmonella enterica subspecies I. PMID:24204679
The BET family of proteins targets moloney murine leukemia virus integration near transcription start sites. PMID:24183673
Genomics meets proteomics: identifying the culprits in disease. PMID:24135908
Genome-wide study of NAGNAG alternative splicing in Arabidopsis. PMID:24097263
Integrative 'omic' approach towards understanding the nature of human diseases. PMID:24052743
A directed approach for the identification of transcripts harbouring the spliced leader sequence and the effect of trans-splicing knockdown in Schistosoma mansoni. PMID:24037192
Metagenomic guilt by association: an operonic perspective. PMID:23940763
WEP: a high-performance analysis pipeline for whole-exome data. PMID:23815231
Quantifying single nucleotide variant detection sensitivity in exome sequencing. PMID:23773188
QualComp: a new lossy compressor for quality scores based on rate distortion theory. PMID:23758828
DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. PMID:23657089
Genome sequencing unveils a novel sea enterotoxin-carrying PVL phage in Staphylococcus aureus ST772 from India. PMID:23544121
TIARA genome database: update 2013. PMID:23515433
Comprehensive structural annotation of Pichia pastoris transcriptome and the response to various carbon sources using deep paired-end RNA sequencing. PMID:23276294
Multiscale integration of -omic, imaging, and clinical data in biomedical informatics. PMID:23231990
A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences. PMID:23231464
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue. PMID:22957051
Compression of next-generation sequencing reads aided by highly efficient de novo assembly. PMID:22904078
Metagenomic annotation networks: construction and applications. PMID:22879885
Estimation of sequencing error rates in short reads. PMID:22846331
Determinants of exon-level evolutionary rates in Arabidopsis species. PMID:22844194
Standardized collection of MNase-seq experiments enables unbiased dataset comparisons. PMID:22559821
Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research. PMID:22312447
The Lymantria dispar IPLB-Ld652Y cell line transcriptome comprises diverse virus-associated transcripts. PMID:22163348
RecountDB: a database of mapped and count corrected transcribed sequences. PMID:22139942
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. PMID:22087737
Major submissions tool developments at the European Nucleotide Archive. PMID:22080548
The Sequence Read Archive: explosive growth of sequencing data. PMID:22009675
High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. PMID:21940835
BioMart: a data federation framework for large collaborative projects. PMID:21930506
Differential expression in RNA-seq: a matter of depth. PMID:21903743
Systematic clustering of transcription start site landscapes. PMID:21887249
Cistrome: an integrative platform for transcriptional regulation studies. PMID:21859476
Databases and resources for human small non-coding RNAs. PMID:21504869
The properties and applications of single-molecule DNA sequencing. PMID:21349208
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:21177655
The International Nucleotide Sequence Database Collaboration. PMID:21106499
Database resources of the National Center for Biotechnology Information. PMID:21097890
GenBank. PMID:21071399
Database resources of the National Center for Biotechnology Information PubMed citations: 421.

421 articles citing: Database resources of the National Center for Biotechnology Information

Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes. PMID:35821377
Prior exposure to microcystin alters host gut resistome and is associated with dysregulated immune homeostasis in translatable mouse models. PMID:35799048
RegEl corpus: identifying DNA regulatory elements in the scientific literature. PMID:35758881
Robust fingerprinting of genomic databases. PMID:35758787
Design of a Multi-Epitopes Based Chimeric Vaccine against Enterobacter cloacae Using Pan-Genome and Reverse Vaccinology Approaches. PMID:35746494
Splice-site identification for exon prediction using bidirectional LSTM-RNN approach. PMID:35663929
Sequence-based pangenomic core detection. PMID:35663029
First two mitochondrial genomes for the order Filobasidiales reveal novel gene rearrangements and intron dynamics of Tremellomycetes. PMID:35501936
Characterization of differential gene expression of broiler chicken to thermal stress in discrete developmental stages. PMID:35479510
Cathelicidin-3 Associated With Serum Extracellular Vesicles Enables Early Diagnosis of a Transmissible Cancer. PMID:35422813
Transcriptomic Analysis of Liver Indicates Novel Vaccine to Porcine Reproductive and Respiratory Virus Promotes Homeostasis in T-Cell and Inflammatory Immune Responses Compared to a Commercial Vaccine in Pigs. PMID:35400088
Exploring the Lethality of Human-Adapted Coronavirus Through Alignment-Free Machine Learning Approaches Using Genomic Sequences. PMID:35386190
Establishment of an Artificial Neural Network Model Using Immune-Infiltration Related Factors for Endometrial Receptivity Assessment. PMID:35214598
GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring. PMID:35087491
Bacterial gasdermins reveal an ancient mechanism of cell death. PMID:35025633
Identification of Cross-Talk and Pyroptosis-Related Genes Linking Periodontitis and Rheumatoid Arthritis Revealed by Transcriptomic Analysis. PMID:35003389
Characterization of the mitochondrial genomes of three powdery mildew pathogens reveals remarkable variation in size and nucleotide composition. PMID:34890311
Integrative COVID-19 biological network inference with probabilistic core decomposition. PMID:34791019
TopoFun: a machine learning method to improve the functional similarity of gene co-expression modules. PMID:34761220
The complete mitochondrial genome of Dictyostelium intermedium. PMID:34746396
Multi-Similarities Bilinear Matrix Factorization-Based Method for Predicting Human Microbe-Disease Associations. PMID:34721543
Identifying disease-gene associations using a convolutional neural network-based model by embedding a biological knowledge graph with entity descriptions. PMID:34653225
RFCM-PALM: In-Silico Prediction of S-Palmitoylation Sites in the Synaptic Proteins for Male/Female Mouse Data. PMID:34576064
Genome assembly of a Mesoamerican derived variety of lima bean: a foundational cultivar in the Mid-Atlantic USA. PMID:34542584
Characterization of a novel multidomain CE15-GH8 enzyme encoded by a polysaccharide utilization locus in the human gut bacterium Bacteroides eggerthii. PMID:34480044
Architecture Insight of Bifidobacterial α-L-Fucosidases. PMID:34445166
Editorial: Integration of Multi-Omics Techniques in Cancer. PMID:34434225
Databases for Protein-Protein Interactions. PMID:34236665
The mitochondrial genome of the grape powdery mildew pathogen Erysiphe necator is intron rich and exhibits a distinct gene organization. PMID:34230575
Prevalence and spectrum of DNA mismatch repair gene variation in the general Chinese population. PMID:34172528
Development of a Dissemination Platform for Spatiotemporal and Phylogenetic Analysis of Avian Infectious Bronchitis Virus. PMID:34017870
The Role of Network Science in Glioblastoma. PMID:33801334
Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest. PMID:33680580
In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE2. PMID:33560990
The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2. PMID:33555346
TagSeq for gene expression in non-model plants: A pilot study at the Santa Rita Experimental Range NEON core site. PMID:33304661
Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy. PMID:33302373
Functional Diversification of the Dihydroflavonol 4-Reductase from Camellia nitidissima Chi. in the Control of Polyphenol Biosynthesis. PMID:33198369
Contaminating DNA in human saliva alters the detection of variants from whole genome sequencing. PMID:33159102
Exploration of surface glycoprotein to design multi-epitope vaccine for the prevention of Covid-19. PMID:33043110
Molecular evolutionary and structural analysis of human UCHL1 gene demonstrates the relevant role of intragenic epistasis in Parkinson's disease and other neurological disorders. PMID:33028204
Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans. PMID:32993015
Tissue-specific usage of transposable element-derived promoters in mouse development. PMID:32988383
Bulk and Active Sediment Prokaryotic Communities in the Mariana and Mussau Trenches. PMID:32765444
The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2. PMID:32714120
Role of SARS-CoV-2 in altering the RNA binding protein and miRNA directed post-transcriptional regulatory networks in humans. PMID:32676599
Co-Expression Networks for Causal Gene Identification Based on RNA-Seq Data of Corynebacterium pseudotuberculosis. PMID:32674507
Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria. PMID:32518115
Genome Sequences of Newcastle Disease Virus Strains from Two Outbreaks in Indonesia. PMID:32499364
Insight into Evolution and Conservation Patterns of B1-Subfamily Members of GPCR. PMID:32421105
Fungicides Reduce the Abundance of Yeast-like Symbionts and Survival of White-Backed Planthopper Sogatella furcifera (Homoptera: Delphacidae). PMID:32230918
An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms. PMID:32055857
Transcriptome Sequencing of Listeria monocytogenes Reveals Major Gene Expression Changes in Response to Lactic Acid Stress Exposure but a Less Pronounced Response to Oxidative Stress. PMID:32038553
A novel lncRNA as a positive regulator of carotenoid biosynthesis in Fusarium. PMID:31959816
Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata. PMID:31860080
Predicting and designing therapeutics against the Nipah virus. PMID:31830030
FlySilico: Flux balance modeling of Drosophila larval growth and resource allocation. PMID:31748517
Lipid Related Genes Altered in NASH Connect Inflammation in Liver Pathogenesis Progression to HCC: A Canonical Pathway. PMID:31717414
Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP). PMID:31644802
Molecular Characterization of Leishmania RNA virus 2 in Leishmania major from Uzbekistan. PMID:31640177
Single-cell RNA-seq variant analysis for exploration of genetic heterogeneity in cancer. PMID:31267007
Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments. PMID:31035578
Draft genome of the river water buffalo. PMID:30962899
RNA-sequencing in ophthalmology research: considerations for experimental design and analysis. PMID:30911735
Carbon Fixation by Marine Ultrasmall Prokaryotes. PMID:30903144
Measuring the importance of vertices in the weighted human disease network. PMID:30901770
Molecular evolutionary and structural analysis of familial exudative vitreoretinopathy associated FZD4 gene. PMID:30849938
The Membrane Proximal Domain of TRPV1 and TRPV2 Channels Mediates Protein⁻Protein Interactions and Lipid Binding In Vitro. PMID:30764505
Compression of Large Sets of Sequence Data Reveals Fine Diversification of Functional Profiles in Multigene Families of Proteins: A Study for Peptidyl-Prolyl cis/trans Isomerases (PPIase). PMID:30754725
Drug-Target Interaction Prediction via Dual Laplacian Graph Regularized Matrix Completion. PMID:30627536
Capsule network for protein post-translational modification site prediction. PMID:30520972
Aequatus: an open-source homology browser. PMID:30395211
Molecular docking studies of human MCT8 protein with soy isoflavones in Allan-Herndon-Dudley syndrome (AHDS). PMID:30345146
Multiple paralogues of α-SNAP in Giardia lamblia exhibit independent subcellular localization and redistribution during encystation and stress. PMID:30286802
DNArCdb: A database of cancer biomarkers in DNA repair genes that includes variants related to multiple cancer phenotypes. PMID:30098577
Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations. PMID:30046134
RabGTD: a comprehensive database of rabbit genome and transcriptome. PMID:30010730
Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation. PMID:29970463
Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities. PMID:29732264
The role of the Human Metabolome Database in inborn errors of metabolism. PMID:29663269
The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida. PMID:29587633
Synopsis of the SOFL Plant-Specific Gene Family. PMID:29467189
Time-consistent reconciliation maps and forbidden time travel. PMID:29441122
Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle. PMID:29439661
The regulatory network analysis of long noncoding RNAs in human colorectal cancer. PMID:29374362
Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues. PMID:29337142
Detailed secondary structure models of invertebrate 7SK RNAs. PMID:29219696
An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression. PMID:29109288
HCMDB: the human cancer metastasis database. PMID:29088455
Peptidylprolyl Isomerases as In Vivo Carriers for Drugs That Target Various Intracellular Entities. PMID:28961224
Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations. PMID:28912564
Biologically feasible gene trees, reconciliation maps and informative triples. PMID:28861118
Exoproteome Analysis of the Seaweed Pathogen Nautella italica R11 Reveals Temperature-Dependent Regulation of RTX-Like Proteins. PMID:28706511
Daily Changes in Composition and Diversity of the Intestinal Microbiota in Patients with Anorexia Nervosa: A Series of Three Cases. PMID:28586130
Meta Analysis of Human AlzGene Database: Benefits and Limitations of Using C. elegans for the Study of Alzheimer's Disease and Co-morbid Conditions. PMID:28553317
Identifying pathogenicity of human variants via paralog-based yeast complementation. PMID:28542158
Models of global gene expression define major domains of cell type and tissue identity. PMID:28426095
Leucine to proline substitution by SNP at position 197 in Caspase-9 gene expression leads to neuroblastoma: a bioinformatics analysis. PMID:28324374
Selection and Prioritization of Candidate Drug Targets for Amyotrophic Lateral Sclerosis Through a Meta-Analysis Approach. PMID:28236105
UFGT: The Key Enzyme Associated with the Petals Variegation in Japanese Apricot. PMID:28223989
A novel RNA sequencing data analysis method for cell line authentication. PMID:28192450
Mixing omics: combining genetics and metabolomics to study rheumatic diseases. PMID:28148918
Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads. PMID:28122610
Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. PMID:28049628
γ-Protocadherin structural diversity and functional implications. PMID:27782885
Evaluation of Normalization Methods for RNA-Seq Gene Expression Estimation. PMID:27532058
Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA. PMID:27526722
Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq. PMID:27385103
A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs. PMID:27195295
Drug Repurposing Is a New Opportunity for Developing Drugs against Neuropsychiatric Disorders. PMID:27073698
Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients. PMID:27068610
EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data. PMID:27004791
From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories. PMID:26967999
Unique PFK regulatory property from some mosquito vectors of disease, and from Drosophila melanogaster. PMID:26911930
Extensive Transcriptome Changes Underlying the Flower Color Intensity Variation in Paeonia ostii. PMID:26779235
Extensive regulation of nicotinate phosphoribosyltransferase (NAPRT) expression in human tissues and tumors. PMID:26675378
Gene Expression Reaction Norms Unravel the Molecular and Cellular Processes Underpinning the Plastic Phenotypes of Alternanthera Philoxeroides in Contrasting Hydrological Conditions. PMID:26617628
Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. PMID:26602695
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. PMID:26493560
Marine amoebae with cytoplasmic and perinuclear symbionts deeply branching in the Gammaproteobacteria. PMID:26303516
Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma. PMID:26177267
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. PMID:26154165
The WUSCHEL-RELATED HOMEOBOX 3 gene PaWOX3 regulates lateral organ formation in Norway spruce. PMID:26115363
A new alkaline lipase obtained from the metagenome of marine sponge Ircinia sp. PMID:25921581
Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. PMID:25853883
Impact of the CFTR-potentiator ivacaftor on airway microbiota in cystic fibrosis patients carrying a G551D mutation. PMID:25853698
SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish. PMID:25813542
Improved detection of artifactual viral minority variants in high-throughput sequencing data. PMID:25657642
Medical and biomedical research productivity from the Kingdom of Saudi Arabia (2008-2012). PMID:25657608
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach. PMID:25632945
OntoMate: a text-mining tool aiding curation at the Rat Genome Database. PMID:25619558
First co-expression of a lipase and its specific foldase obtained by metagenomics. PMID:25510188
Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. PMID:25501035
Assessment of airway microbiota and inflammation in cystic fibrosis using multiple sampling methods. PMID:25474078
Computational prediction of microRNAs from Toxoplasma gondii potentially regulating the hosts' gene expression. PMID:25462155
Non-coding RNA gene families in the genomes of anopheline mosquitoes. PMID:25432596
Dissecting the human protein-protein interaction network via phylogenetic decomposition. PMID:25412639
Fast and sensitive protein alignment using DIAMOND. PMID:25402007
Fingerprints of a message: integrating positional information on the transcriptome. PMID:25364746
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. PMID:25361952
A transcriptomic analysis of Chrysanthemum nankingense provides insights into the basis of low temperature tolerance. PMID:25277256
DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. PMID:25267467
Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life. PMID:25238539
Orthology detection combining clustering and synteny for very large datasets. PMID:25137074
Curation and analysis of multitargeting agents for polypharmacological modeling. PMID:25133604
miRSeq: a user-friendly standalone toolkit for sequencing quality evaluation and miRNA profiling. PMID:25114903
Quality control on the frontier. PMID:24904650
Proteomic analysis of Mecistocirrus digitatus and Haemonchus contortus intestinal protein extracts and subsequent efficacy testing in a vaccine trial. PMID:24901227
Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome. PMID:24844236
EpimiR: a database of curated mutual regulation between miRNAs and epigenetic modifications. PMID:24682734
A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach. PMID:24595269
Life in an unusual intracellular niche: a bacterial symbiont infecting the nucleus of amoebae. PMID:24500618
The vertebrate RCAN gene family: novel insights into evolution, structure and regulation. PMID:24465593
An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines. PMID:24441647
A novel GABRG2 mutation, p.R136*, in a family with GEFS+ and extended phenotypes. PMID:24407264
A human torque teno virus encodes a microRNA that inhibits interferon signaling. PMID:24367263
MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. PMID:24306534
Structure of Patt1 human proapoptotic histone acetyltransferase. PMID:24248912
Fine mapping and identification of a candidate gene for a major locus controlling maturity date in peach. PMID:24148786
New hyperekplexia mutations provide insight into glycine receptor assembly, trafficking, and activation mechanisms. PMID:24108130
Use of MSAP markers to analyse the effects of salt stress on DNA methylation in rapeseed (Brassica napus var. oleifera). PMID:24086583
Next-generation sequence analysis of cancer xenograft models. PMID:24086345
Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae. PMID:23949660
Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors. PMID:23880963
A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change. PMID:23826735
Fine-tuning of microRNA-mediated repression of mRNA by splicing-regulated and highly repressive microRNA recognition element. PMID:23819653
Construction of a full-length enriched cDNA library and preliminary analysis of expressed sequence tags from Bengal Tiger Panthera tigris tigris. PMID:23708105
ExtremeDB: a unified web repository of extremophilic archaea and bacteria. PMID:23696792
Discovering chromatin motifs using FAIRE sequencing and the human diploid genome. PMID:23656909
Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PMID:23646159
Guard cell purification and RNA isolation suitable for high-throughput transcriptional analysis of cell-type responses to biotic stresses. PMID:23634837
Functional classification of immune regulatory proteins. PMID:23583034
Growth temperature and genome size in bacteria are negatively correlated, suggesting genomic streamlining during thermal adaptation. PMID:23563968
Evaluating purifying selection in the mitochondrial DNA of various mammalian species. PMID:23533597
Alternating hemiplegia of childhood-related neural and behavioural phenotypes in Na+,K+-ATPase α3 missense mutant mice. PMID:23527305
Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation. PMID:23418180
Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish. PMID:23368736
MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis. PMID:23341152
Insulin and IGF1 receptors are essential for XX and XY gonadal differentiation and adrenal development in mice. PMID:23300479
Polypharmacology: drug discovery for the future. PMID:23272792
ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species. PMID:23180770
Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers. PMID:23056629
Crystal structure of HutZ, a heme storage protein from Vibrio cholerae: A structural mismatch observed in the region of high sequence conservation. PMID:23013214
In silico directed mutagenesis identifies the CD81/claudin-1 hepatitis C virus receptor interface. PMID:22897233
Ontologies as integrative tools for plant science. PMID:22847540
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. PMID:22684630
Development of a pharmaceutical hepatotoxicity biomarker panel using a discovery to targeted proteomics approach. PMID:22527513
Orthology relations, symbolic ultrametrics, and cographs. PMID:22456957
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. PMID:22434826
Recent advances of metabolomics in plant biotechnology. PMID:22308170
Convergent evolution in structural elements of proteins investigated using cross profile analysis. PMID:22244085
Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. PMID:22159132
Human genetics and genomics a decade after the release of the draft sequence of the human genome. PMID:22155605
The UCSC Archaeal Genome Browser: 2012 update. PMID:22080555
Characterization of the human ornithine transcarbamylase 3' untranslated regulatory region. PMID:22054066
Accelerated recruitment of new brain development genes into the human genome. PMID:22028629
Meta-analysis and genome-wide interpretation of genetic susceptibility to drug addiction. PMID:21999673
The energy landscape analysis of cancer mutations in protein kinases. PMID:21998754
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. PMID:21911355
Integrating GPCR-specific information with full text articles. PMID:21910883
In silico approach to inhibition of signaling pathways of Toll-like receptors 2 and 4 by ST2L. PMID:21897866
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. PMID:21878105
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. PMID:21851591
Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae). PMID:21833037
Identification and characterization of a new true lipase isolated through metagenomic approach. PMID:21762508
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. PMID:21750106
Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies. PMID:21731731
An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins. PMID:21731483
Independent subtilases expansions in fungi associated with animals. PMID:21727238
Improving pan-genome annotation using whole genome multiple alignment. PMID:21718539
Analysis of insertion sequences in thermophilic cyanobacteria: exploring the mechanisms of establishing, maintaining, and withstanding high insertion sequence abundance. PMID:21666019
Sharing and archiving nucleic acid structure mapping data. PMID:21610212
Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing. PMID:21605378
hERGAPDbase: a database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds. PMID:21586548
The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors. PMID:21575214
A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes. PMID:21551137
The Booly aliasing resource: a database of grouped biological identifiers. PMID:21544171
A suspected parasite spill-back of two novel Myxidium spp. (Myxosporea) causing disease in Australian endemic frogs found in the invasive Cane toad. PMID:21541340
Proteinortho: detection of (co-)orthologs in large-scale analysis. PMID:21526987
Voxelwise gene-wide association study (vGeneWAS): multivariate gene-based association testing in 731 elderly subjects. PMID:21497199
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. PMID:21450710
Apolipoprotein M gene (APOM) polymorphism modifies metabolic and disease traits in type 2 diabetes. PMID:21390319
The properties and applications of single-molecule DNA sequencing. PMID:21349208
Comorbidity of bipolar disorder with substance abuse: selection of prioritized genes for translational research. PMID:21347170
Screening for antimicrobial resistance genes and virulence factors via genome sequencing. PMID:21335393
Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing. PMID:21310711
Functional relevance of CpG island length for regulation of gene expression. PMID:21288871
Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis. PMID:21232103
Structure-function relationship of cytoplasmic and nuclear IκB proteins: an in silico analysis. PMID:21203422
BiologicalNetworks 2.0--an integrative view of genome biology data. PMID:21190573
De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). PMID:21182800
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
The Notch target Hes1 directly modulates Gli1 expression and Hedgehog signaling: a potential mechanism of therapeutic resistance. PMID:21169257
Predicting DNA-binding specificities of eukaryotic transcription factors. PMID:21152420
Mugsy: fast multiple alignment of closely related whole genomes. PMID:21148543
LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria. PMID:21092245
VnD: a structure-centric database of disease-related SNPs and drugs. PMID:21051351
GlycomeDB--a unified database for carbohydrate structures. PMID:21045056
The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms. PMID:21036862
Nucleotide parasitism by Simkania negevensis (Chlamydiae). PMID:20971898
EuroDia: a beta-cell gene expression resource. PMID:20940178
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. PMID:20927658
Public data archives for genomic structural variation. PMID:20877315
Accurately assessing the risk of schizophrenia conferred by rare copy-number variation affecting genes with brain function. PMID:20838587
Two naturally occurring mutations in the type 1 melanin-concentrating hormone receptor abolish agonist-induced signaling. PMID:20833795
A score of the ability of a three-dimensional protein model to retrieve its own sequence as a quantitative measure of its quality and appropriateness. PMID:20830209
Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. PMID:20799350
The X as model for RNA's niche in epigenomic regulation. PMID:20739414
ReCGiP, a database of reproduction candidate genes in pigs based on bibliomics. PMID:20707928
Expression of the transcription factor, TFII-I, during post-implantation mouse embryonic development. PMID:20642858
Integration and visualization of systems biology data in context of the genome. PMID:20642854
Human variation databases. PMID:20639550
CGDSNPdb: a database resource for error-checked and imputed mouse SNPs. PMID:20624716
OpenFluDB, a database for human and animal influenza virus. PMID:20624713
Affinity of aporphines for the human 5-HT2A receptor: insights from homology modeling and molecular docking studies. PMID:20621490
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. PMID:20537162
A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing. PMID:20531933
Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase. PMID:20455263
Genome-wide assessment of differential roles for p300 and CBP in transcription regulation. PMID:20435671
The glycinergic system in human startle disease: a genetic screening approach. PMID:20407582
A human-specific de novo protein-coding gene associated with human brain functions. PMID:20376170
Bioinformatics and molecular modeling in glycobiology. PMID:20364395
MLTrends: Graphing MEDLINE term usage over time. PMID:20333611
Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales. PMID:20333207
MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. PMID:20215419
Word add-in for ontology recognition: semantic enrichment of scientific literature. PMID:20181245
Identification of 28 novel mutations in the Bardet-Biedl syndrome genes: the burden of private mutations in an extensively heterogeneous disease. PMID:20177705
A large and accurate collection of peptidase cleavages in the MEROPS database. PMID:20157488
ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies. PMID:20157487
Management of High-Throughput DNA Sequencing Projects: Alpheus. PMID:20151039
A pattern analysis of gene conversion literature. PMID:20148076
Complete-proteome mapping of human influenza A adaptive mutations: implications for human transmissibility of zoonotic strains. PMID:20140252
DIGA--a database of improved gene annotation for phytopathogens. PMID:20089203
TollML: a database of toll-like receptor structural motifs. PMID:20084417
A protocol for generating a high-quality genome-scale metabolic reconstruction. PMID:20057383
Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser. PMID:20031585
Two-stage joint selection method to identify candidate markers from genome-wide association studies. PMID:20018019
Advances in translational bioinformatics: computational approaches for the hunting of disease genes. PMID:20007728
Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria. PMID:20007606
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species. PMID:20003425
Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis. PMID:20003344
Archiving next generation sequencing data. PMID:19965774
ANEXdb: an integrated animal ANnotation and microarray EXpression database. PMID:19936830
Detection of treatment-induced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data. PMID:19903850
Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. PMID:19892720
Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches. PMID:19847304
ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses. PMID:19846609
Proteomics analysis of A33 immunoaffinity-purified exosomes released from the human colon tumor cell line LIM1215 reveals a tissue-specific protein signature. PMID:19837982
Sequence and structure signatures of cancer mutation hotspots in protein kinases. PMID:19834613
The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice. PMID:19825586
Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD). PMID:19814812
Comparison of human chromosome 19q13 and syntenic region on mouse chromosome 7 reveals absence, in man, of 11.6 Mb containing four mouse calcium-sensing receptor-related sequences: relevance to familial benign hypocalciuric hypercalcaemia type 3. PMID:19809483
Optimization and comparison of different methods for RNA isolation for cDNA library construction from the reindeer lichen Cladonia rangiferina. PMID:19804636
Current Screens Based on the AlphaScreen Technology for Deciphering Cell Signalling Pathways. PMID:19794881
Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics. PMID:19781082
Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb. PMID:19758468
Pepsin homologues in bacteria. PMID:19758436
Prediction and identification of tumor-specific noncoding RNAs from human UniGene. PMID:19757216
Context-driven discovery of gene cassettes in mobile integrons using a computational grammar. PMID:19735578
Candidate genes involved in neural plasticity and the risk for attention-deficit hyperactivity disorder: a meta-analysis of 8 common variants. PMID:19721846
Comparative analyses of plant transcription factor databases. PMID:19721806
BatchGenAna: a batch platform for large-scale genomic analysis of mammalian small RNAs. PMID:19707298
The human protein coevolution network. PMID:19696150
Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. PMID:19684108
Linking genes to diseases: it's all in the data. PMID:19678910
Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. PMID:19654296
A novel putative miRNA target enhancer signal. PMID:19649282
CLEAN: CLustering Enrichment ANalysis. PMID:19640299
OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. PMID:19615117
Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis. PMID:19615109
Integrative sequence and tissue expression profiling of chicken and mammalian aquaporins. PMID:19607658
HAPPI: an online database of comprehensive human annotated and predicted protein interactions. PMID:19594875
Differences in duplication age distributions between human GPCRs and their downstream genes from a network prospective. PMID:19594873
aGEM: an integrative system for analyzing spatial-temporal gene-expression information. PMID:19592395
DDEC: Dragon database of genes implicated in esophageal cancer. PMID:19580656
Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs. PMID:19558667
Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PMID:19557189
The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes. PMID:19545381
Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin. PMID:19535502
Homology modeling of human Toll-like receptors TLR7, 8, and 9 ligand-binding domains. PMID:19521997
Reflect: augmented browsing for the life scientist. PMID:19513049
LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs. PMID:19500380
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. PMID:19498102
Computational biology methods and their application to the comparative genomics of endocellular symbiotic bacteria of insects. PMID:19495914
ProGMap: an integrated annotation resource for protein orthology. PMID:19494185
Sexy gene conversions: locating gene conversions on the X-chromosome. PMID:19487239
Origin of saxitoxin biosynthetic genes in cyanobacteria. PMID:19484122
Family classification without domain chaining. PMID:19478015
Small RNAs derived from snoRNAs. PMID:19474147
Sim4cc: a cross-species spliced alignment program. PMID:19429899
The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches. PMID:19427324
PCOPGene-Net: holistic characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships. PMID:19426548
A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro. PMID:19351829
A signature-based method for indexing cell cycle phase distribution from microarray profiles. PMID:19331659
Location, location, (ChIP-)location! Mapping chromatin landscapes one immunoprecipitation at a time. PMID:19308935
Functional classification of genome-scale metabolic networks. PMID:19300528
RBF-TSS: identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies. PMID:19287502
Bioinformatic characterizations and prediction of K+ and Na+ ion channels effector toxins. PMID:19284552
Recent developments in StemBase: a tool to study gene expression in human and murine stem cells. PMID:19284540
Identification of Atg5-dependent transcriptional changes and increases in mitochondrial mass in Atg5-deficient T lymphocytes. PMID:19276668
CNV-seq, a new method to detect copy number variation using high-throughput sequencing. PMID:19267900
FragIdent--automatic identification and characterisation of cDNA-fragments. PMID:19254371
Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. PMID:19232096
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. PMID:19219566
Tuberculosis drug resistance mutation database. PMID:19209951
Meta-analysis of age-related gene expression profiles identifies common signatures of aging. PMID:19189975
Detailed transcriptome atlas of the pancreatic beta cell. PMID:19146692
Immunome knowledge base (IKB): an integrated service for immunome research. PMID:19134210
RepPop: a database for repetitive elements in Populus trichocarpa. PMID:19134208
Global similarity with local differences in linkage disequilibrium between the Dutch and HapMap-CEU populations. PMID:19127282
Genomic and genetic database resources for the grasses. PMID:19126704
GenomeGraphs: integrated genomic data visualization with R. PMID:19123956
Reconstruction of biochemical networks in microorganisms. PMID:19116616
Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway. PMID:19109899
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases. PMID:19091018
Evolutionary origin and phylogenetic analysis of the novel oocyte-specific eukaryotic translation initiation factor 4E in Tetrapoda. PMID:19089447
PSI-BLAST pseudocounts and the minimum description length principle. PMID:19088134
GeneDistiller--distilling candidate genes from linkage intervals. PMID:19057649
A bioinformatician's guide to metagenomics. PMID:19052320
Ensembl 2009. PMID:19033362
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. PMID:19029536
Cataloguing the HIV type 1 human protein interaction network. PMID:19025396
M148R and M149R are two virulence factors for myxoma virus pathogenesis in the European rabbit. PMID:19019281
Medium- and short-chain dehydrogenase/reductase gene and protein families : the MDR superfamily. PMID:19011751
The protein structure initiative structural genomics knowledgebase. PMID:19010965
Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. PMID:19001483
The UCSC Genome Browser Database: update 2009. PMID:18996895
INTERFEROME: the database of interferon regulated genes. PMID:18996892
Chemical databases for environmental health and clinical research. PMID:18996453
Molecular genetics of addiction and related heritable phenotypes: genome-wide association approaches identify "connectivity constellation" and drug target genes with pleiotropic effects. PMID:18991966
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. PMID:18989261
Human Protein Reference Database--2009 update. PMID:18988627
PIPs: human protein-protein interaction prediction database. PMID:18988626
Mouse phenome database. PMID:18987003
MoKCa database--mutations of kinases in cancer. PMID:18986996
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. PMID:18984625
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. PMID:18984624
CDD: specific functional annotation with the Conserved Domain Database. PMID:18984618
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. PMID:18984617
Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. PMID:18978788
An integrated software system for analyzing ChIP-chip and ChIP-seq data. PMID:18978777
Petabyte-scale innovations at the European Nucleotide Archive. PMID:18978013
SysZNF: the C2H2 zinc finger gene database. PMID:18974185
The role of CLCA proteins in inflammatory airway disease. PMID:18954282
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. PMID:18953038
GOBASE: an organelle genome database. PMID:18953030
MODBASE, a database of annotated comparative protein structure models and associated resources. PMID:18948282
IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels. PMID:18948278
UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. PMID:18945703
PEDANT covers all complete RefSeq genomes. PMID:18940859
NCBI GEO: archive for high-throughput functional genomic data. PMID:18940857
MMsINC: a large-scale chemoinformatics database. PMID:18931373
Human immunodeficiency virus type 1, human protein interaction database at NCBI. PMID:18927109
Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform 'Open Genome Resource' (OGeR). PMID:18854354
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. PMID:18845571
MetaSim: a sequencing simulator for genomics and metagenomics. PMID:18841204
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. PMID:18838390
Linking genes to literature: text mining, information extraction, and retrieval applications for biology. PMID:18834499
Modeling gene-by-environment interaction in comorbid depression with alcohol use disorders via an integrated bioinformatics approach. PMID:18822146
Presenting and exploring biological pathways with PathVisio. PMID:18817533
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules. PMID:18790807
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. PMID:18782832
The Degradome database: mammalian proteases and diseases of proteolysis. PMID:18776217
Big data: The future of biocuration. PMID:18769432
Methods and tools for comparative genomics of foodborne pathogens. PMID:18713064
Guidelines for the nomenclature of the human heat shock proteins. PMID:18663603
Fine mapping of the GLC1K juvenile primary open-angle glaucoma locus and exclusion of candidate genes. PMID:18648523
A gene wiki for community annotation of gene function. PMID:18613750
Lawsonia intracellularis contains a gene encoding a functional rickettsia-like ATP/ADP translocase for host exploitation. PMID:18606736
TriMEDB: a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae. PMID:18590523
The ontology of biological taxa. PMID:18586729
BIOSMILE web search: a web application for annotating biomedical entities and relations. PMID:18515840
BioLit: integrating biological literature with databases. PMID:18515836
ENDEAVOUR update: a web resource for gene prioritization in multiple species. PMID:18508807
MADNet: microarray database network web server. PMID:18480121
OREST: the online resource for EST analysis. PMID:18463135
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks. PMID:18440972
Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. PMID:18416670
The CGView Server: a comparative genomics tool for circular genomes. PMID:18411202
GenBank. PMID:18073190
The Sequence Read Archive: explosive growth of sequencing data PubMed citations: 405.

405 articles citing: The Sequence Read Archive: explosive growth of sequencing data

Comparative Plastid Genomics of Green-Colored Dinoflagellates Unveils Parallel Genome Compaction and RNA Editing. PMID:35898209
The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. PMID:35889831
Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data. PMID:35871895
Primary Sjögren's syndrome combined with Chlamydia psittaci infection. PMID:35832704
Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system. PMID:35819579
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. PMID:35789323
Organoid-derived intestinal epithelial cells are a suitable model for preclinical toxicology and pharmacokinetic studies. PMID:35754737
A database of animal metagenomes. PMID:35710683
GeMI: interactive interface for transformer-based Genomic Metadata Integration. PMID:35657113
Systematic prediction of EMS-induced mutations in a sorghum mutant population. PMID:35647479
3D genome organization in the epithelial-mesenchymal transition spectrum. PMID:35637517
The state of Medusozoa genomics: current evidence and future challenges. PMID:35579552
Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking. PMID:35475639
Decay of TRPV3 as the genomic trace of epidermal structure changes in the land-to-sea transition of mammals. PMID:35342611
Integration of omics data to generate and analyse COVID-19 specific genome-scale metabolic models. PMID:35339845
An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using the Bentley-Saxe Transformation. PMID:35325039
Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection. PMID:35306876
ADDAGMA: A database for domestic animal gut microbiome atlas. PMID:35222847
Hsa-miR-183-5p Modulates Cell Adhesion by Repression of ITGB1 Expression in Prostate Cancer. PMID:35202085
SeqWho: Reliable, Rapid Determination of Sequence File Identity using k-mer Frequencies in Random Forest Classifiers. PMID:35134110
VirStrain: a strain identification tool for RNA viruses. PMID:35101081
Using metagenomic data to boost protein structure prediction and discovery. PMID:35070166
A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics. PMID:35053129
Single-Cell Analysis Identify Transcription Factor BACH1 as a Master Regulator Gene in Vascular Cells During Aging. PMID:35004685
Comparative Analysis of Neuropeptides in Homologous Interneurons and Prohormone Annotation in Nudipleuran Sea Slugs. PMID:35002782
Fast and memory-efficient mapping of short bisulfite sequencing reads using a two-letter alphabet. PMID:34988438
Gene regulation network analyses of pistil development in papaya. PMID:34983382
Comparison of Oxidative and Hypoxic Stress Responsive Genes from Meta-Analysis of Public Transcriptomes. PMID:34944646
The Sequence Read Archive: a decade more of explosive growth. PMID:34850094
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure. PMID:34791105
Genetic Diversity in Chimpanzee Transcriptomics Does Not Represent Wild Populations. PMID:34788801
Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius. PMID:34777307
Rice RS2-9, which is bound by transcription factor OSH1, blocks enhancer-promoter interactions in plants. PMID:34773305
Complete Mitochondrial Genome Sequences of Nine Aspergillus flavus Strains. PMID:34761953
DNA Data Bank of Japan (DDBJ) update report 2021. PMID:34751405
Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing. PMID:34733267
MVIP: multi-omics portal of viral infection. PMID:34718748
mBodyMap: a curated database for microbes across human body and their associations with health and diseases. PMID:34718713
Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa. PMID:34671335
RE-SELEX: restriction enzyme-based evolution of structure-switching aptamer biosensors. PMID:34659704
Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants. PMID:34649506
CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria. PMID:34614159
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. PMID:34591957
Bile acid metabolism dysregulation associates with cancer cachexia: roles of liver and gut microbiome. PMID:34585527
Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa. PMID:34575741
scMethBank: a database for single-cell whole genome DNA methylation maps. PMID:34570235
CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response. PMID:34570230
Animal-eRNAdb: a comprehensive animal enhancer RNA database. PMID:34551433
STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions. PMID:34544477
ISA API: An open platform for interoperable life science experimental metadata. PMID:34528664
Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing. PMID:34527435
DIANA-miTED: a microRNA tissue expression database. PMID:34469540
Genome-wide characterization and expression profiling of the Phospholipase C (PLC) gene family in three orchids of economic importance. PMID:34420115
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. PMID:34403477
Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning. PMID:34379786
MiREDiBase, a manually curated database of validated and putative editing events in microRNAs. PMID:34349127
Using bioinformatics approaches to investigate driver genes and identify BCL7A as a prognostic gene in colorectal cancer. PMID:34306573
piRNAclusterDB 2.0: update and expansion of the piRNA cluster database. PMID:34302483
Genome-Wide Comparative Analysis of Heat Shock Transcription Factors Provides Novel Insights for Evolutionary History and Expression Characterization in Cotton Diploid and Tetraploid Genomes. PMID:34168673
pyrpipe: a Python package for RNA-Seq workflows. PMID:34085037
A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. PMID:34083435
Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes. PMID:34065451
AniProtDB: A Collection of Consistently Generated Metazoan Proteomes for Comparative Genomics Studies. PMID:34048573
Genome-Wide Analysis of c-MYC-Regulated mRNAs and miRNAs and c-MYC DNA-Binding by Next-Generation Sequencing. PMID:34019289
Systematic in silico Evaluation of Leishmania spp. Proteomes for Drug Discovery. PMID:33987166
Potential role of chimeric genes in pathway-related gene co-expression modules. PMID:33980272
A method for achieving complete microbial genomes and improving bins from metagenomics data. PMID:33961626
M6ADD: a comprehensive database of m6A modifications in diseases. PMID:33906563
A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. PMID:33850120
Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data. PMID:33846313
Sequencing error profiles of Illumina sequencing instruments. PMID:33817639
Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2. PMID:33757279
Phylotranscriptomic analysis of Dillenia indica L. (Dilleniales, Dilleniaceae) and its systematics implication. PMID:33732040
riboCIRC: a comprehensive database of translatable circRNAs. PMID:33685493
DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions. PMID:33673098
Meta-Analysis of Oxidative Transcriptomes in Insects. PMID:33669076
Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly. PMID:33537807
Effect of Paternal Genome Excess on the Developmental and Gene Expression Profiles of Polyspermic Zygotes in Rice. PMID:33525652
Improvement, identification, and target prediction for miRNAs in the porcine genome by using massive, public high-throughput sequencing data. PMID:33493272
Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level. PMID:33468706
Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. PMID:33453123
PM4NGS, a project management framework for next-generation sequencing data analysis. PMID:33410471
Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer. PMID:33397462
Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods. PMID:33363701
The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis. PMID:33339309
NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index. PMID:33322070
Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features. PMID:33292532
GTRD: an integrated view of transcription regulation. PMID:33231677
Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting. PMID:33226702
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. PMID:33221926
Lower Airway Dysbiosis Affects Lung Cancer Progression. PMID:33177060
A Novel Anphevirus in Aedes albopictus Mosquitoes Is Distributed Worldwide and Interacts with the Host RNA Interference Pathway. PMID:33172032
Genome Variation Map: a worldwide collection of genome variations across multiple species. PMID:33170268
DDBJ update: streamlining submission and access of human data. PMID:33156332
ATACdb: a comprehensive human chromatin accessibility database. PMID:33125076
Innovations to culturing the uncultured microbial majority. PMID:33093661
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data. PMID:33023248
Ten simple rules for annotating sequencing experiments. PMID:33017400
Animal-APAdb: a comprehensive animal alternative polyadenylation database. PMID:32986825
A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model. PMID:32913254
The Expression and Potential Role of Tubulin Alpha 1b in Wilms' Tumor. PMID:32908931
Plant science decadal vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future. PMID:32904806
"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive". PMID:32883210
Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State. PMID:32879348
Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett). PMID:32867696
The archives are half-empty: an assessment of the availability of microbial community sequencing data. PMID:32859925
Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference. PMID:32859263
The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides. PMID:32817170
Method development for cross-study microbiome data mining: Challenges and opportunities. PMID:32802279
In Silico Evaluation of Putative S100B Interacting Proteins in Healthy and IBD Gut Microbiota. PMID:32679810
The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. PMID:32556166
Integrated analysis of a compendium of RNA-Seq datasets for splicing factors. PMID:32546682
Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments. PMID:32469363
Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps. PMID:32422044
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. PMID:32383760
Genome-wide analysis of glycerol-3-phosphate O-acyltransferase gene family and functional characterization of two cutin group GPATs in Brassica napus. PMID:32246349
Master Regulator Analysis of the SARS-CoV-2/Human Interactome. PMID:32244779
Bioinformatics services for analyzing massive genomic datasets. PMID:32224841
Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-D-phosphohexomutase superfamily. PMID:32221390
Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. PMID:32200634
Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis. PMID:32178397
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments. PMID:32170312
vtRNA2-1/nc886 Produces a Small RNA That Contributes to Its Tumor Suppression Action through the microRNA Pathway in Prostate Cancer. PMID:32093270
All of gene expression (AOE): An integrated index for public gene expression databases. PMID:31978081
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. PMID:31956905
Meta-Analysis of Hypoxic Transcriptomes from Public Databases. PMID:31936636
Comparative analysis on the expression of L1 loci using various RNA-Seq preparations. PMID:31921361
Exploring the taxonomic composition of two fungal communities on the Swedish west coast through metabarcoding. PMID:31871405
Improved metagenomic analysis with Kraken 2. PMID:31779668
Food authentication from shotgun sequencing reads with an application on high protein powders. PMID:31754632
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. PMID:31728526
DDBJ Database updates and computational infrastructure enhancement. PMID:31724722
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species. PMID:31694521
Evolutionary Analysis of Bile Acid-Conjugating Enzymes Reveals a Complex Duplication and Reciprocal Loss History. PMID:31670760
Epstein-Barr virus circRNAome as host miRNA sponge regulates virus infection, cell cycle, and oncogenesis. PMID:31668120
BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers. PMID:31665503
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
PmiREN: a comprehensive encyclopedia of plant miRNAs. PMID:31602478
APAatlas: decoding alternative polyadenylation across human tissues. PMID:31586392
Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation. PMID:31584087
Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. PMID:31579821
NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements. PMID:31527408
Building Containerized Workflows Using the BioDepot-Workflow-Builder. PMID:31521606
GMrepo: a database of curated and consistently annotated human gut metagenomes. PMID:31504765
FQStat: a parallel architecture for very high-speed assessment of sequencing quality metrics. PMID:31416440
Genetic basis of functional variability in adhesion G protein-coupled receptors. PMID:31363148
A principled strategy for mapping enhancers to genes. PMID:31363138
Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella. PMID:31354679
A spliceosomal twin intron (stwintron) participates in both exon skipping and evolutionary exon loss. PMID:31289343
Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend. PMID:31275764
SRAssembler: Selective Recursive local Assembly of homologous genomic regions. PMID:31266441
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. PMID:31258543
MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae. PMID:31240103
Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection. PMID:31222199
Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers. PMID:31221760
HMMRATAC: a Hidden Markov ModeleR for ATAC-seq. PMID:31199868
Differential analysis of combinatorial protein complexes with CompleXChange. PMID:31159772
Genomics and data science: an application within an umbrella. PMID:31142351
Big Data to the Bench: Transcriptome Analysis for Undergraduates. PMID:31074696
DNAscan: personal computer compatible NGS analysis, annotation and visualisation. PMID:31029080
A computational system for identifying operons based on RNA-seq data. PMID:30953757
Digital expression explorer 2: a repository of uniformly processed RNA sequencing data. PMID:30942868
YESdb: integrative analysis of environmental stress in yeast. PMID:30821814
An estimate of the total number of true human miRNAs. PMID:30820533
An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria. PMID:30816249
Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PMID:30718421
Conserved regulation of RNA processing in somatic cell reprogramming. PMID:30704403
Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data. PMID:30697483
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. PMID:30668832
The use of next generation sequencing for improving food safety: Translation into practice. PMID:30621881
Rhizosphere Microenvironments of Eight Common Deciduous Fruit Trees Were Shaped by Microbes in Northern China. PMID:30619213
Mining data and metadata from the gene expression omnibus. PMID:30594974
Genome-wide mapping of nucleotide excision repair with XR-seq. PMID:30552409
Draft Genome Sequences of the Type Strains of Three Clavibacter Subspecies and Atypical Peach-Colored Strains Isolated from Tomato. PMID:30533783
A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae). PMID:30498089
From sequencing data to gene functions: co-functional network approaches. PMID:30460054
Parallel identification of novel antimicrobial peptide sequences from multiple anuran species by targeted DNA sequencing. PMID:30458708
GTRD: a database on gene transcription regulation-2019 update. PMID:30445619
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. PMID:30371820
SEdb: a comprehensive human super-enhancer database. PMID:30371817
DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data. PMID:30357349
RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling. PMID:30335166
Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. PMID:30245936
microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions. PMID:30190538
Cecal microbiome profile altered by Salmonella enterica, serovar Enteritidis inoculation in chicken. PMID:30087697
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. PMID:30086717
Diversity of Fungal Communities in Heshang Cave of Central China Revealed by Mycobiome-Sequencing. PMID:30061866
Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them. PMID:30018876
Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling. PMID:30010675
Clustering huge protein sequence sets in linear time. PMID:29959318
Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals. PMID:29953435
Biological classification with RNA-seq data: Can alternatively spliced transcript expression enhance machine learning classifiers? PMID:29941426
Bioinformatic Workflows for Generating Complete Plastid Genome Sequences-An Example from Cabomba (Cabombaceae) in the Context of the Phylogenomic Analysis of the Water-Lily Clade. PMID:29933597
MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data. PMID:29901703
Disbiome database: linking the microbiome to disease. PMID:29866037
Divergent and convergent evolution of housekeeping genes in human-pig lineage. PMID:29844985
The aquatic animals' transcriptome resource for comparative functional analysis. PMID:29764375
Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. PMID:29745848
Genome-wide identification of hexokinase gene family in Brassica napus: structure, phylogenetic analysis, expression, and functional characterization. PMID:29644447
Prevalent Homozygous Deletions of Type I Interferon and Defensin Genes in Human Cancers Associate with Immunotherapy Resistance. PMID:29618619
riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions. PMID:29608703
A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. PMID:29572503
A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection. PMID:29564396
Improving Reproducibility and Candidate Selection in Transcriptomics Using Meta-analysis. PMID:29511359
Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches. PMID:29363422
TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. PMID:29272447
SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis. PMID:29270443
Potential Diagnostic Power of Blood Circular RNA Expression in Active Pulmonary Tuberculosis. PMID:29248507
Living Organisms Author Their Read-Write Genomes in Evolution. PMID:29211049
A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa. PMID:29178822
Expression Atlas: gene and protein expression across multiple studies and organisms. PMID:29165655
MethBank 3.0: a database of DNA methylomes across a variety of species. PMID:29161430
Genome-wide identification of long non-coding RNA genes and their association with insecticide resistance and metamorphosis in diamondback moth, Plutella xylostella. PMID:29158595
DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. PMID:29156006
Transition to an Aquatic Habitat Permitted the Repeated Loss of the Pleiotropic KLK8 Gene in Mammals. PMID:29145610
GenBank. PMID:29140468
Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer. PMID:29115931
Generalist species drive microbial dispersion and evolution. PMID:29079803
ARSDA: A New Approach for Storing, Transmitting and Analyzing Transcriptomic Data. PMID:29079682
Don't just dump your data and run: Authors should submit as much experimental information as possible when uploading sequence data. PMID:29079656
Genome Variation Map: a data repository of genome variations in BIG Data Center. PMID:29069473
Pervasive Transcription of Mitochondrial, Plastid, and Nucleomorph Genomes across Diverse Plastid-Bearing Species. PMID:29048528
PCSD: a plant chromatin state database. PMID:29040761
DNA Data Bank of Japan: 30th anniversary. PMID:29040613
miRCarta: a central repository for collecting miRNA candidates. PMID:29036653
'Multi-omic' data analysis using O-miner. PMID:28981577
Viewing RNA-seq data on the entire human genome. PMID:28979763
GWIPS-viz: 2018 update. PMID:28977460
PATRIC as a unique resource for studying antimicrobial resistance. PMID:28968762
Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists. PMID:28935754
Long noncoding RNAs in the model species Brachypodium distachyon. PMID:28900227
Novel endogenous retrovirus-derived transcript expressed in the bovine placenta is regulated by WNT signaling. PMID:28899944
Forensic Human Identification Using Skin Microbiomes. PMID:28887423
Development of hop transcriptome to support research into host-viroid interactions. PMID:28886174
Novel nuclear barcode regions for the identification of flatfish species. PMID:28867876
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes. PMID:28850115
Automated identification of reference genes based on RNA-seq data. PMID:28830520
Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs. PMID:28786034
Transcriptome Analysis of the Sm-Mediated Hypersensitive Response to Stemphylium lycopersici in Tomato. PMID:28769960
Evolution of the cAMP-dependent protein kinase (PKA) catalytic subunit isoforms. PMID:28742821
Assessment of genome annotation using gene function similarity within the gene neighborhood. PMID:28724412
ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data. PMID:28693417
Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data. PMID:28625989
CottonFGD: an integrated functional genomics database for cotton. PMID:28595571
A Primer on Infectious Disease Bacterial Genomics. PMID:28590251
Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best. PMID:28586479
Transcriptomics technologies. PMID:28545146
Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive. PMID:28449062
An auditory display tool for DNA sequence analysis. PMID:28438115
Omicseq: a web-based search engine for exploring omics datasets. PMID:28402462
Reproducible RNA-seq analysis using recount2. PMID:28398307
PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive. PMID:28369246
Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. PMID:28334818
Salmon provides fast and bias-aware quantification of transcript expression. PMID:28263959
A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data. PMID:28155657
TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. PMID:28111364
Controlling new knowledge: Genomic science, governance and the politics of bioinformatics. PMID:28056721
Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data. PMID:28043950
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. PMID:27924024
DNA Data Bank of Japan. PMID:27924010
Virus Variation Resource - improved response to emergent viral outbreaks. PMID:27899678
DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. PMID:27899673
The BIG Data Center: from deposition to integration to translation. PMID:27899658
The dbGaP data browser: a new tool for browsing dbGaP controlled-access genomic data. PMID:27899644
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. PMID:27899627
GenBank. PMID:27899564
DFAST and DAGA: web-based integrated genome annotation tools and resources. PMID:27867804
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. PMID:27794040
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). PMID:27679477
Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq bioinformatics pipeline. PMID:27677960
The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. PMID:27670113
ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells. PMID:27582018
Toward Accurate and Quantitative Comparative Metagenomics. PMID:27565341
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. PMID:27560171
OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid. PMID:27499617
SoyNet: a database of co-functional networks for soybean Glycine max. PMID:27492285
ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress. PMID:27402360
Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond. PMID:27383682
Sensing Enzymatic Activity by Exposure and Selection of DNA-Encoded Probes. PMID:27355201
Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science. PMID:27339634
Antimicrobial Resistance Prediction in PATRIC and RAST. PMID:27297683
GenVisR: Genomic Visualizations in R. PMID:27288499
Quality Assessment of Domesticated Animal Genome Assemblies. PMID:27279738
Bioinformatics resources for pollen. PMID:27271281
A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants. PMID:27261064
High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti. PMID:27161480
Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes. PMID:27092515
PGP repository: a plant phenomics and genomics data publication infrastructure. PMID:27087305
Can data repositories help find effective treatments for complex diseases? PMID:27018167
NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data. PMID:26848255
NEAT: a framework for building fully automated NGS pipelines and analyses. PMID:26830846
Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. PMID:26818008
Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes. PMID:26793234
Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PMID:26789269
Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. PMID:26731733
Proteogenomics from a bioinformatics angle: A growing field. PMID:26670565
Systematic comparison of variant calling pipelines using gold standard personal exome variants. PMID:26639839
Database resources of the National Center for Biotechnology Information. PMID:26615191
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Reads2Type: a web application for rapid microbial taxonomy identification. PMID:26608174
GenBank. PMID:26590407
SEA: a super-enhancer archive. PMID:26578594
DNA data bank of Japan (DDBJ) progress report. PMID:26578571
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564
LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes. PMID:26578557
The Widening Gulf between Genomics Data Generation and Consumption: A Practical Guide to Big Data Transfer Technology. PMID:26568680
DASHR: database of small human noncoding RNAs. PMID:26553799
OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes. PMID:26543854
The evolutionary landscape of intergenic trans-splicing events in insects. PMID:26521696
Information Commons for Rice (IC4R). PMID:26519466
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes. PMID:26459560
Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities. PMID:26458130
Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens. PMID:26437919
BacWGSTdb, a database for genotyping and source tracking bacterial pathogens. PMID:26433226
Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing. PMID:26407912
RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets. PMID:26323714
Quantification of DNA cleavage specificity in Hi-C experiments. PMID:26264668
FusionCancer: a database of cancer fusion genes derived from RNA-seq data. PMID:26215638
A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads. PMID:26052341
RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application. PMID:26046471
Databases for Microbiologists. PMID:26013493
Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome. PMID:25853708
Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution. PMID:25848874
Biological databases for human research. PMID:25712261
Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities. PMID:25709713
IIIDB: a database for isoform-isoform interactions and isoform network modules. PMID:25707505
De novo assembly of bacterial transcriptomes from RNA-seq data. PMID:25583448
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing. PMID:25553907
The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. PMID:25477381
De novo transcriptome assembly, gene annotation, marker development, and miRNA potential target genes validation under abiotic stresses in Oenanthe javanica. PMID:25416420
GenBank. PMID:25414350
Database resources of the National Center for Biotechnology Information. PMID:25398906
Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome. PMID:25398096
COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems. PMID:25392420
The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. PMID:25378343
GeneFriends: a human RNA-seq-based gene and transcript co-expression database. PMID:25361971
The parasite Trichomonas vaginalis expresses thousands of pseudogenes and long non-coding RNAs independently from functional neighbouring genes. PMID:25326207
High-resolution digital profiling of the epigenome. PMID:25297728
MetaProx: the database of metagenomic proximons. PMID:25288655
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. PMID:25271953
Managing large-scale genomic datasets and translation into clinical practice. PMID:25123745
Towards a HPC-oriented parallel implementation of a learning algorithm for bioinformatics applications. PMID:25077818
e!DAL--a framework to store, share and publish research data. PMID:24958009
Changes in the bacterial community of soybean rhizospheres during growth in the field. PMID:24955843
Chromatin landscapes of retroviral and transposon integration profiles. PMID:24721906
Genome-wide sequencing reveals two major sub-lineages in the genetically monomorphic pathogen xanthomonas campestris pathovar musacearum. PMID:24704974
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). PMID:24667251
INsPeCT: INtegrative Platform for Cancer Transcriptomics. PMID:24653643
Benchmarking of methods for genomic taxonomy. PMID:24574292
Life in an unusual intracellular niche: a bacterial symbiont infecting the nucleus of amoebae. PMID:24500618
Finding the missing honey bee genes: lessons learned from a genome upgrade. PMID:24479613
MetaMetaDB: a database and analytic system for investigating microbial habitability. PMID:24475242
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. PMID:24467687
DevMouse, the mouse developmental methylome database and analysis tools. PMID:24408217
ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants. PMID:24334350
TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. PMID:24330842
INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PMID:24324765
RefSeq microbial genomes database: new representation and annotation strategy. PMID:24316578
miRBase: annotating high confidence microRNAs using deep sequencing data. PMID:24275495
Database resources of the National Center for Biotechnology Information. PMID:24259429
Data compression for sequencing data. PMID:24252160
GenBank. PMID:24217914
DOOR 2.0: presenting operons and their functions through dynamic and integrated views. PMID:24214966
DDBJ progress report: a new submission system for leading to a correct annotation. PMID:24194602
Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive. PMID:24167589
Gene expression rate comparison for multiple high-throughput datasets. PMID:24067413
Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. PMID:24038472
The detection of microRNA associated with Alzheimer's disease in biological fluids using next-generation sequencing technologies. PMID:23964286
Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae. PMID:23949660
Metagenomic guilt by association: an operonic perspective. PMID:23940763
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. PMID:23879659
Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data. PMID:23800020
A meta-analysis of the genomic and transcriptomic composition of complex life. PMID:23759593
Routine performance and errors of 454 HLA exon sequencing in diagnostics. PMID:23731822
Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA. PMID:23671186
Transcription factors that convert adult cell identity are differentially polycomb repressed. PMID:23650565
The Fluid Mechanics of Genome Mapping. PMID:23641116
Sequence squeeze: an open contest for sequence compression. PMID:23596984
Existing and emerging technologies for tumor genomic profiling. PMID:23589546
The future of DNA sequence archiving. PMID:23587147
OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. PMID:23571760
TIARA genome database: update 2013. PMID:23515433
Uncovering hidden duplicated content in public transcriptomics data. PMID:23487185
New insights from existing sequence data: generating breakthroughs without a pipette. PMID:23438857
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. PMID:23368412
Interactions of nitrifying bacteria and heterotrophs: identification of a Micavibrio-like putative predator of Nitrospira spp. PMID:23335755
OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. PMID:23203890
Finding microRNA targets in plants: current status and perspectives. PMID:23200136
NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse. PMID:23196988
GenBank. PMID:23193287
Database resources of the National Center for Biotechnology Information. PMID:23193264
The International Nucleotide Sequence Database Collaboration. PMID:23180798
DDBJ new system and service refactoring. PMID:23180790
NGC: lossless and lossy compression of aligned high-throughput sequencing data. PMID:23066097
SCALCE: boosting sequence compression algorithms using locally consistent encoding. PMID:23047557
Metagenomic annotation networks: construction and applications. PMID:22879885
Molecular signatures from omics data: from chaos to consensus. PMID:22528809
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. PMID:22110025
The International Nucleotide Sequence Database Collaboration. PMID:22080546
Investigation into the annotation of protocol sequencing steps in the sequence read archive PubMed citations: 10.

10 articles citing: Investigation into the annotation of protocol sequencing steps in the sequence read archive

Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing. PMID:34527435
In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia. PMID:34502522
Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive. PMID:34379632
Investigating Molecular Determinants of Cancer Cell Resistance to Ionizing Radiation Through an Integrative Bioinformatics Approach. PMID:33898418
Ten simple rules for annotating sequencing experiments. PMID:33017400
Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca). PMID:31635158
Comprehensive analysis of circRNA expression profiles in humans by RAISE. PMID:29039477
A Novel Method to Detect Bias in Short Read NGS Data. PMID:28941355
Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive. PMID:28449062
Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology. PMID:28234981

Tags:

Tags
More detailed information about this field from each metasource.

allele
metasource: Fairsharing.org
version: FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

gene
metasource: Fairsharing.org
version: FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

nucleic acid sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

nucleotide
metasource: Fairsharing.org
version: FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

region
metasource: Fairsharing.org
version: FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

international nucleotide sequence database collaboration
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

chemicals
metasource: re3data.org
version: re3data.org: Sequence Read Archive; editing status 2022-08-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31S69 last accessed: 2022-11-04

dna
metasource: re3data.org
version: re3data.org: Sequence Read Archive; editing status 2022-08-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31S69 last accessed: 2022-11-04

genes
metasource: re3data.org
version: re3data.org: Sequence Read Archive; editing status 2022-08-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31S69 last accessed: 2022-11-04

proteins
metasource: re3data.org
version: re3data.org: Sequence Read Archive; editing status 2022-08-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31S69 last accessed: 2022-11-04

rna
metasource: re3data.org
version: re3data.org: Sequence Read Archive; editing status 2022-08-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31S69 last accessed: 2022-11-04

sequencing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:10.296503

database management
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:10.296503

sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:10.296503

allele dna sequences gene nucleic acid sequence alignment nucleotide sequence alignment region nucleic acid sequence international nucleotide sequence database collaboration chemicals dna gene proteins rna sequencing data management sequence analysis

More to explore:

1/20

Previous Next

Need help integrating and/or managing biomedical data?

Webpage:

Licence:

More to explore:

1/20

DDBJ Sequence Read Archive

Short Read Archive eXtensible Markup Language

NCBI Trace Archive

NCBI Trace Archives

DNA Data Bank of Japan

GenBank

European Nucleotide Archive

BioSystems

Genome Sequence Archive

Gene Expression Omnibus

NCBI BioSample

Expressed Sequence Tags database

DDBJ Trace Archive

HumanMetagenomeDB

NCBI Gene

National Omics Data Encyclopedia

Conserved Domain Database

NCBI Taxonomy

Molecular Modeling Database

NCBI BioProject