NCBI Taxonomy Database

Names

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NCBI Taxonomy Database

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:33.962827

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ncbi_taxonomy_database

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:33.962827

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Other names: ncbi_taxonomy_database

Curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.

Webpage:

Publications:

Publications

More detailed information about this field from each metasource. ×

The NCBI Taxonomy database
PMID: 22139910

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:33.962827

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GenBank
PMID: 10592170

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:33.962827

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Database resources of the National Center for Biotechnology Information
PMID: 10592169

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:33.962827

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http://dx.doi.org/10.1093/nar/gki031

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:33.962827

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• The NCBI Taxonomy database PubMed citations: 468.

  468 articles citing: The NCBI Taxonomy database

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  Source files of the Carbohydrate Structure Database: the way to sophisticated analysis of natural glycans. PMID:35354826

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  Parallel sequence tagging for concept recognition. PMID:35331131

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  Structure and biosynthesis of carotenoids produced by a novel Planococcus sp. isolated from South Africa. PMID:35305628

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  TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets. PMID:35243369

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  Designing sensitive viral diagnostics with machine learning. PMID:35241837

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  Biochemical and Molecular Dynamics Study of a Novel GH 43 α-l-Arabinofuranosidase/β-Xylosidase From Caldicellulosiruptor saccharolyticus DSM8903. PMID:35223784

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  A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets. PMID:35205348

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  Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis. PMID:35191776

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  A positive correlation between GC content and growth temperature in prokaryotes. PMID:35139824

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  Isolation of a Dissimilatory Iodate-Reducing Aromatoleum sp. From a Freshwater Creek in the San Francisco Bay Area. PMID:35111143

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  AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite. PMID:35101114

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  Seasonal Diversity of Microeukaryotes in the Han River, Korea Through 18S rRNA Gene Metabarcoding. PMID:35095269

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  ExTaxsI: an exploration tool of biodiversity molecular data. PMID:35077538

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  Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus. PMID:35056480

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  Scripting Analyses of Genomes in Ensembl Plants. PMID:35037199

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  Bovine respiratory microbiota of feedlot cattle and its association with disease. PMID:35022062

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  SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss. PMID:35021210

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  GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids. PMID:34951622

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  The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects. PMID:34917063

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  Cryo-EM structures of human RNA polymerase I. PMID:34887565

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  An Overview of Biomedical Ontologies for Pandemics and Infectious Diseases Representation. PMID:34868401

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  The Sequence Read Archive: a decade more of explosive growth. PMID:34850094

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  The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health. PMID:34838100

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  A multitask transfer learning framework for the prediction of virus-human protein-protein interactions. PMID:34837942

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  Gcorn fungi: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi. PMID:34829248

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  Global Distribution and Richness of Armillaria and Related Species Inferred From Public Databases and Amplicon Sequencing Datasets. PMID:34803949

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  NP-MRD: the Natural Products Magnetic Resonance Database. PMID:34791429

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  Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. PMID:34787447

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  The Human Disease Ontology 2022 update. PMID:34755882

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  Oral Cyanobacteria and Hepatocellular Carcinoma. PMID:34697061

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  TAGOPSIN: collating taxa-specific gene and protein functional and structural information. PMID:34688246

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  Gene Network Analysis of Alzheimer's Disease Based on Network and Statistical Methods. PMID:34682089

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  Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics. PMID:34681121

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  Implications of divergence of methionine adenosyltransferase in archaea. PMID:34655277

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  Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy. PMID:34648558

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  virusMED: an atlas of hotspots of viral proteins. PMID:34614039

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  PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems. PMID:34593010

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  Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi. PMID:34575737

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  KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014

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  Structural characterization of NrnC identifies unifying features of dinucleotidases. PMID:34533457

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  Examination of the microbiota of normal cow milk using MinIONTM nanopore sequencing. PMID:34526421

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  Distribution of Denitrification among Haloarchaea: A Comprehensive Study. PMID:34442748

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  KEGG mapping tools for uncovering hidden features in biological data. PMID:34423492

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  Mining Natural Products with Anticancer Biological Activity through a Systems Biology Approach. PMID:34422220

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  Amadis: A Comprehensive Database for Association Between Microbiota and Disease. PMID:34335304

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  Proteomics, Lipidomics, Metabolomics, and 16S DNA Sequencing of Dental Plaque From Patients With Diabetes and Periodontal Disease. PMID:34332123

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  Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. PMID:34325658

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  Forming Consensus To Advance Urobiome Research. PMID:34282932

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  The Infectious Disease Ontology in the age of COVID-19. PMID:34275487

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  Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum. PMID:34254817

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  Evolutionary Origins of Drought Tolerance in Spermatophytes. PMID:34239520

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  Identification and Characterization of Mycobacterial Species Using Whole-Genome Sequences. PMID:34235665

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  Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures. PMID:34203511

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  TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes. PMID:34197621

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  Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. PMID:34187366

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  Divide-and-conquer: machine-learning integrates mammalian and viral traits with network features to predict virus-mammal associations. PMID:34172731

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  Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP. PMID:34168213

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  A standardized archaeal taxonomy for the Genome Taxonomy Database. PMID:34155373

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  Screening potential insect vectors in a museum biorepository reveals undiscovered diversity of plant pathogens in natural areas. PMID:34141234

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  Deciphering the diet of a wandering spider (Phoneutria boliviensis; Araneae: Ctenidae) by DNA metabarcoding of gut contents. PMID:34141195

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  Simulation study and comparative evaluation of viral contiguous sequence identification tools. PMID:34130621

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  Functional prediction of environmental variables using metabolic networks. PMID:34108539

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  An Unsupervised Algorithm for Host Identification in Flaviviruses. PMID:34069049

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  ML-AdVInfect: A Machine-Learning Based Adenoviral Infection Predictor. PMID:34026828

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  Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. PMID:34021239

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  Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank. PMID:34020714

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  Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19. PMID:34009288

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  Kokumi taste perception is functional in a model carnivore, the domestic cat (Felis catus). PMID:34006911

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  Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators. PMID:34006865

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  DOE JGI Metagenome Workflow. PMID:34006627

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  An overview of graph databases and their applications in the biomedical domain. PMID:34003247

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  Learning adaptive representations for entity recognition in the biomedical domain. PMID:34001263

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  ProteoVision: web server for advanced visualization of ribosomal proteins. PMID:33999189

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  ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies. PMID:33996287

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  Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries. PMID:33993214

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  IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298

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  OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life. PMID:33970279

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  Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient. PMID:33906949

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  Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi. PMID:33906412

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  ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis. PMID:33895137

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  Gut microbiota in Immunoglobulin A Nephropathy: a Malaysian Perspective. PMID:33882859

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  Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning. PMID:33878118

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  Near-Complete Genome Sequences of Eight Human Astroviruses Recovered from Diarrheal Stool Samples of Hospitalized Children in Coastal Kenya in 2019. PMID:33858926

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  Phylogenomic Analyses of Nucleotide-Sugar Biosynthetic and Interconverting Enzymes Illuminate Cell Wall Composition in Fungi. PMID:33849982

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  Prokaryotic taxonomy and nomenclature in the age of big sequence data. PMID:33824426

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  Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria. PMID:33815349

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  Maximum levels of global phylogenetic diversity efficiently capture plant services for humankind. PMID:33782579

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  animalcules: interactive microbiome analytics and visualization in R. PMID:33775256

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  An immunologically friendly classification of non-peptidic ligands. PMID:33772585

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  Analysis of human total antibody repertoires in TIF1γ autoantibody positive dermatomyositis. PMID:33772100

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  Ancient DNA preserved in small bone fragments from the P.W. Lund collection. PMID:33717442

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  DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions. PMID:33673098

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  Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences. PMID:33654096

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  Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. PMID:33649554

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  Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage. PMID:33642591

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  Identification of Stress-Related Genes and a Comparative Analysis of the Amino Acid Compositions of Translated Coding Sequences Based on Draft Genome Sequences of Antarctic Yeasts. PMID:33633709

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  Resistome analysis of bloodstream infection bacterial genomes reveals a specific set of proteins involved in antibiotic resistance and drug efflux. PMID:33575606

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  Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing. PMID:33575567

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  Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states. PMID:33558764

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  biotoolsSchema: a formalized schema for bioinformatics software description. PMID:33506265

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  Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef. PMID:33499977

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  Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution. PMID:33499799

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  A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses. PMID:33482803

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  Oral exposure to environmental cyanobacteria toxins: Implications for cancer risk. PMID:33465665

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  Review on natural products databases: where to find data in 2020. PMID:33431011

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  A review on viral data sources and search systems for perspective mitigation of COVID-19. PMID:33348368

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  Possible Transmission Flow of SARS-CoV-2 Based on ACE2 Features. PMID:33322198

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  COVID-19 Knowledge Extractor (COKE): A Tool and a Web Portal to Extract Drug - Target Protein Associations from the CORD-19 Corpus of Scientific Publications on COVID-19. PMID:33269341

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  New Names for Fungi of Medical Importance: Can We Have Our Cake and Eat It Too? PMID:33268539

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  Data-Driven Modeling for Species-Level Taxonomic Assignment From 16S rRNA: Application to Human Microbiomes. PMID:33262743

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  DNA methylation signatures to predict the cervicovaginal microbiome status. PMID:33228781

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  BRENDA, the ELIXIR core data resource in 2021: new developments and updates. PMID:33211880

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  Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR. PMID:33211099

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  Widespread endogenization of giant viruses shapes genomes of green algae. PMID:33208937

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  The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. PMID:33205138

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  Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads. PMID:33198651

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  OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836

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  COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database. PMID:33175089

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  High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method. PMID:33158461

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  Searching for target-specific and multi-targeting organics for Covid-19 in the Drugbank database with a double scoring approach. PMID:33154404

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  Genomes OnLine Database (GOLD) v.8: overview and updates. PMID:33152092

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  Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata. PMID:33150057

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  KEGG: integrating viruses and cellular organisms. PMID:33125081

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  MASI: microbiota-active substance interactions database. PMID:33125077

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  An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature. PMID:33123100

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  Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy. PMID:33112882

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  Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation. PMID:33105659

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  Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia. PMID:33082403

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  Peryton: a manual collection of experimentally supported microbe-disease associations. PMID:33080028

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  Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country. PMID:33066371

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  A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease. PMID:33053371

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  The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820

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  Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics. PMID:33013807

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  A systematic comparison of chloroplast genome assembly tools. PMID:32988404

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  When mycologists describe new species, not all relevant information is provided (clearly enough). PMID:32982558

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  Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction. PMID:32932905

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  METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies-Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses. PMID:32897080

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  Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. PMID:32883995

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  The Best-Practice Organism for Single-Species Studies of Antimicrobial Efficacy against Biofilms Is Pseudomonas aeruginosa. PMID:32872560

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  Assembling Reads Improves Taxonomic Classification of Species. PMID:32824429

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  Metagenomic Studies in Inflammatory Skin Diseases. PMID:32813091

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  ReDU: a framework to find and reanalyze public mass spectrometry data. PMID:32807955

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  The diversity of maternal-age effects upon pre-adult survival across animal species. PMID:32781953

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  NCBI Taxonomy: a comprehensive update on curation, resources and tools. PMID:32761142

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  The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community. PMID:32756341

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  Guidelines for human gene nomenclature. PMID:32747822

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  In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles. PMID:32719673

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  Novel aspects of Cell Division Cycle and Apoptosis Regulator 1 (CCAR1) protein in Morus notabilis: an in silico approach. PMID:32693681

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  Bacterial chemolithoautotrophy via manganese oxidation. PMID:32669693

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  Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. PMID:32661357

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  ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. PMID:32657362

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  The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990

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  Data-Driven Inference Reveals Distinct and Conserved Dynamic Pathways of Tool Use Emergence across Animal Taxa. PMID:32629611

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  MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding. PMID:32620910

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  LEMMI: a continuous benchmarking platform for metagenomics classifiers. PMID:32616517

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  Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer. PMID:32611311

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  COVID-KOP: Integrating Emerging COVID-19 Data with the ROBOKOP Database. PMID:32601612

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  The Presence of Plant-Associated Bacteria Alters Responses to N-acyl Homoserine Lactone Quorum Sensing Signals that Modulate Nodulation in Medicago Truncatula. PMID:32580337

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  GTDB: an integrated resource for glycosyltransferase sequences and annotations. PMID:32542364

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  Comprehensive database and evolutionary dynamics of U12-type introns. PMID:32484558

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  Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads. PMID:32471343

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  Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians. PMID:32450885

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  Impact of C-terminal amino acid composition on protein expression in bacteria. PMID:32449593

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  An Unusual Amino Acid Substitution Within Hummingbird Cytochrome c Oxidase Alters a Key Proton-Conducting Channel. PMID:32444359

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  Faecal calprotectin and gut microbiota do not predict enteropathy in very preterm infants. PMID:32418251

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  SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction. PMID:32411695

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  Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank. PMID:32398145

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  EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. PMID:32392342

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  SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. PMID:32379317

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  Species Classification for Neuroscience Literature Based on Span of Interest Using Sequence-to-Sequence Learning Model. PMID:32372933

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  Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities - a proof of concept under laboratory conditions. PMID:32355612

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  CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data. PMID:32345331

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  Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939

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  Repositories for Taxonomic Data: Where We Are and What is Missing. PMID:32298457

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  R-loop-forming Sequences Analysis in Thousands of Viral Genomes Identify A New Common Element in Herpesviruses. PMID:32286400

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  Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts. PMID:32209692

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  Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA. PMID:32184999

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  Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV. PMID:32142938

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  Characteristics of the endometrium in menstruating species: lessons learned from the animal kingdom†. PMID:32129461

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  The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here? PMID:32115818

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  Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential. PMID:32106565

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  Dead Rhizophagus irregularis biomass mysteriously stimulates plant growth. PMID:32062707

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  Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping. PMID:31941798

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  Automatic construction of metabolic models with enzyme constraints. PMID:31937255

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  CAMITAX: Taxon labels for microbial genomes. PMID:31909794

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  Emergence and Evolution of ERM Proteins and Merlin in Metazoans. PMID:31851361

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  GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804

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  Transcriptome and microbiome of coconut rhinoceros beetle (Oryctes rhinoceros) larvae. PMID:31818246

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  Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PMID:31800571

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  Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. PMID:31792218

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  New C-Terminal Conserved Regions of Tafazzin, a Catalyst of Cardiolipin Remodeling. PMID:31781330

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  Improved metagenomic analysis with Kraken 2. PMID:31779668

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  Myofibril diameter is set by a finely tuned mechanism of protein oligomerization in Drosophila. PMID:31746737

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  Geography and habitat predominate over climate influences on arbuscular mycorrhizal fungal communities of mid-European meadows. PMID:31724087

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  In Silico Study of Rett Syndrome Treatment-Related Genes, MECP2, CDKL5, and FOXG1, by Evolutionary Classification and Disordered Region Assessment. PMID:31717404

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  Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia. PMID:31709051

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  PlantRegMap: charting functional regulatory maps in plants. PMID:31701126

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  How the past impacts the future: modelling the performance of evolutionarily distinct mammals through time. PMID:31679492

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  The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. PMID:31667520

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  Brevibacillus antibioticus sp. nov., with a broad range of antibacterial activity, isolated from soil in the Nakdong River. PMID:31659685

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  MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PMID:31648227

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  Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. PMID:31640809

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  CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. PMID:31624845

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  Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618

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  SEAweb: the small RNA Expression Atlas web application. PMID:31598718

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  gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. PMID:31584099

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  Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. PMID:31584075

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  Ensemble QSAR Modeling to Predict Multispecies Fish Toxicity Lethal Concentrations and Points of Departure. PMID:31560848

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  Genetic robustness of let-7 miRNA sequence-structure pairs. PMID:31548338

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  Gephebase, a database of genotype-phenotype relationships for natural and domesticated variation in Eukaryotes. PMID:31544935

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  Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis. PMID:31523127

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  GMrepo: a database of curated and consistently annotated human gut metagenomes. PMID:31504765

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  Challenges in the construction of knowledge bases for human microbiome-disease associations. PMID:31488215

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  A Structure-Informed Atlas of Human-Virus Interactions. PMID:31474372

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  Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life. PMID:31462411

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  A corpus of plant-disease relations in the biomedical domain. PMID:31461491

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  ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database. PMID:31412866

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  Clinical gamasoidosis and antibody response in two patients infested with Ornithonyssus bursa (Acari: Gamasida: Macronyssidae). PMID:31367978

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  Herb-Induced Liver Injury: Phylogenetic Relationship, Structure-Toxicity Relationship, and Herb-Ingredient Network Analysis. PMID:31349548

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  JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface. PMID:31331268

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  geneHummus: an R package to define gene families and their expression in legumes and beyond. PMID:31319791

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  Multiple origins of reverse transcriptases linked to CRISPR-Cas systems. PMID:31276437

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  An ontology for representing hematologic malignancies: the cancer cell ontology. PMID:31272372

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  metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes. PMID:31235611

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  Metabolic route computation in organism communities. PMID:31174602

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  PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. PMID:31160594

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  Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218

  ---

  Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves. PMID:31151997

  ---

  Solr-Plant: efficient extraction of plant names from text. PMID:31117932

  ---

  AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. PMID:31081040

  ---

  The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria. PMID:31052562

  ---

  A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal Jelly. PMID:31051140

  ---

  Conserved Secondary Structures in Viral mRNAs. PMID:31035717

  ---

  The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups. PMID:31032842

  ---

  Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants. PMID:31029164

  ---

  A degeneration-reducing criterion for optimal digital mapping of genetic codes. PMID:30984363

  ---

  Recentrifuge: Robust comparative analysis and contamination removal for metagenomics. PMID:30958827

  ---

  GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies. PMID:30943284

  ---

  Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer. PMID:30868063

  ---

  Promiscuous terpene synthases from Prunella vulgaris highlight the importance of substrate and compartment switching in terpene synthase evolution. PMID:30843212

  ---

  Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory. PMID:30834996

  ---

  How Sustainable are Biomedical Ontologies? PMID:30815087

  ---

  Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. PMID:30791939

  ---

  Introduction of 'Generalized Genomic Signatures' for the quantification of neighbour preferences leads to taxonomy- and functionality-based distinction among sequences. PMID:30737442

  ---

  Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves. PMID:30705313

  ---

  Exact variance component tests for longitudinal microbiome studies. PMID:30623484

  ---

  STADIUM: Species-Specific tRNA Adaptive Index Compendium. PMID:30602089

  ---

  Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle. PMID:30600356

  ---

  Predicting wildlife reservoirs and global vulnerability to zoonotic Flaviviruses. PMID:30575757

  ---

  Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics. PMID:30532202

  ---

  A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae). PMID:30498089

  ---

  SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541

  ---

  Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research. PMID:30412219

  ---

  Human Disease Ontology 2018 update: classification, content and workflow expansion. PMID:30407550

  ---

  The Gene Ontology Resource: 20 years and still GOing strong. PMID:30395331

  ---

  OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. PMID:30395283

  ---

  BRENDA in 2019: a European ELIXIR core data resource. PMID:30395242

  ---

  OrthoInspector 3.0: open portal for comparative genomics. PMID:30380106

  ---

  The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. PMID:30371820

  ---

  Multiple model species selection for transcriptomics analysis of non-model organisms. PMID:30367568

  ---

  GenBank. PMID:30365038

  ---

  Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales). PMID:30356815

  ---

  LION LBD: a literature-based discovery system for cancer biology. PMID:30304355

  ---

  The jPOST environment: an integrated proteomics data repository and database. PMID:30295851

  ---

  The Comparative Toxicogenomics Database: update 2019. PMID:30247620

  ---

  EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PMID:30222734

  ---

  One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review. PMID:30214898

  ---

  Flexibility and constraint: Evolutionary remodeling of the sporulation initiation pathway in Firmicutes. PMID:30212463

  ---

  DES-Mutation: System for Exploring Links of Mutations and Diseases. PMID:30190574

  ---

  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

  ---

  Traitpedia: a collaborative effort to gather species traits. PMID:30165582

  ---

  A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. PMID:30148503

  ---

  Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs. PMID:30140690

  ---

  Glycomics@ExPASy: Bridging the Gap. PMID:30097532

  ---

  Predicting MicroRNA Mediated Gene Regulation between Human and Viruses. PMID:30096814

  ---

  An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights. PMID:30065857

  ---

  Liberating links between datasets using lightweight data publishing: an example using plant names and the taxonomic literature. PMID:30065607

  ---

  Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments. PMID:30018864

  ---

  CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108

  ---

  Visual tuning in the flashlight fish Anomalops katoptron to detect blue, bioluminescent light. PMID:29995896

  ---

  Non-Coding RNA Analysis Using the Rfam Database. PMID:29927072

  ---

  Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker. PMID:29912385

  ---

  In silico Phylogenetic Analysis of hAT Transposable Elements in Plants. PMID:29882803

  ---

  phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R. PMID:29874797

  ---

  Disbiome database: linking the microbiome to disease. PMID:29866037

  ---

  Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. PMID:29792589

  ---

  ComplexContact: a web server for inter-protein contact prediction using deep learning. PMID:29790960

  ---

  Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments. PMID:29762668

  ---

  Structural biology data archiving - where we are and what lies ahead. PMID:29749603

  ---

  Uniform resolution of compact identifiers for biomedical data. PMID:29737976

  ---

  Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities. PMID:29732264

  ---

  Modeling one thousand intron length distributions with fitild. PMID:29722882

  ---

  MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. PMID:29686086

  ---

  Impact of spatial organization on a novel auxotrophic interaction among soil microbes. PMID:29572468

  ---

  A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection. PMID:29564396

  ---

  Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle. PMID:29515524

  ---

  Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. PMID:29410430

  ---

  Mapping HLA-A2, -A3 and -B7 supertype-restricted T-cell epitopes in the ebolavirus proteome. PMID:29363421

  ---

  ReprDB and panDB: minimalist databases with maximal microbial representation. PMID:29347966

  ---

  DataMed - an open source discovery index for finding biomedical datasets. PMID:29346583

  ---

  Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems. PMID:29263101

  ---

  Historical Biogeography of endemic seed plant genera in the Caribbean: Did GAARlandia play a role? PMID:29238545

  ---

  Gas diffusion electrodes improve hydrogen gas mass transfer for a hydrogen oxidizing bioanode. PMID:29200586

  ---

  The international nucleotide sequence database collaboration. PMID:29190397

  ---

  The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578

  ---

  SATORI: a system for ontology-guided visual exploration of biomedical data repositories. PMID:29186292

  ---

  GenBank. PMID:29140468

  ---

  Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits. PMID:29138307

  ---

  Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability. PMID:29126205

  ---

  PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160

  ---

  A method for named entity normalization in biomedical articles: application to diseases and plants. PMID:29029598

  ---

  A review of methods and databases for metagenomic classification and assembly. PMID:29028872

  ---

  Unbiased Taxonomic Annotation of Metagenomic Samples. PMID:29028181

  ---

  Gearing up to handle the mosaic nature of life in the quest for orthologs. PMID:28968857

  ---

  Phenetic Comparison of Prokaryotic Genomes Using k-mers. PMID:28957508

  ---

  Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists. PMID:28935754

  ---

  Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding. PMID:28877740

  ---

  Lingual microbiota profiles of patients with geographic tongue. PMID:28839519

  ---

  MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling. PMID:28807044

  ---

  Automated assembly of a reference taxonomy for phylogenetic data synthesis. PMID:28765728

  ---

  The Colorful World of Extracellular Electron Shuttles. PMID:28731847

  ---

  DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. PMID:28729549

  ---

  Cyanobacterial Diversity in Microbial Mats from the Hypersaline Lagoon System of Araruama, Brazil: An In-depth Polyphasic Study. PMID:28713360

  ---

  biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831

  ---

  Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes. PMID:28659871

  ---

  Resurrecting the Dead (Molecules). PMID:28652896

  ---

  Expansion of the redox-sensitive proteome coincides with the plastid endosymbiosis. PMID:28504699

  ---

  Class III Histidine Kinases: a Recently Accessorized Kinase Domain in Putative Modulators of Type IV Pilus-Based Motility. PMID:28484044

  ---

  The EBI search engine: EBI search as a service-making biological data accessible for all. PMID:28472374

  ---

  Cryptic diversity of the subfamily Calaphidinae (Hemiptera: Aphididae) revealed by comprehensive DNA barcoding. PMID:28448639

  ---

  Variable habitat conditions drive species covariation in the human microbiota. PMID:28448493

  ---

  Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics. PMID:28420677

  ---

  DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. PMID:28387604

  ---

  SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare? PMID:28361695

  ---

  NOVOPlasty: de novo assembly of organelle genomes from whole genome data. PMID:28204566

  ---

  Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. PMID:28199101

  ---

  Novel Approach to Classify Plants Based on Metabolite-Content Similarity. PMID:28164123

  ---

  treeman: an R package for efficient and intuitive manipulation of phylogenetic trees. PMID:28061884

  ---

  Functional constraints on adaptive evolution of protein ubiquitination sites. PMID:28054638

  ---

  BRENDA in 2017: new perspectives and new tools in BRENDA. PMID:27924025

  ---

  DNA Data Bank of Japan. PMID:27924010

  ---

  Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov. PMID:27902180

  ---

  KEGG: new perspectives on genomes, pathways, diseases and drugs. PMID:27899662

  ---

  jPOSTrepo: an international standard data repository for proteomes. PMID:27899654

  ---

  IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex. PMID:27899604

  ---

  OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. PMID:27899580

  ---

  GenBank. PMID:27899564

  ---

  Aquerium: A web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree. PMID:27802571

  ---

  Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. PMID:27794040

  ---

  PMDBase: a database for studying microsatellite DNA and marker development in plants. PMID:27733507

  ---

  A corpus for plant-chemical relationships in the biomedical domain. PMID:27650402

  ---

  Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa. PMID:27616324

  ---

  Species-function relationships shape ecological properties of the human gut microbiome. PMID:27573110

  ---

  Using a Novel Ontology to Inform the Discovery of Therapeutic Peptides from Animal Venoms. PMID:27570672

  ---

  LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes. PMID:27515739

  ---

  Wnt signal transduction pathways: modules, development and evolution. PMID:27490822

  ---

  The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response. PMID:27489856

  ---

  Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches. PMID:27481788

  ---

  The ontology of medically related social entities: recent developments. PMID:27406187

  ---

  COMODI: an ontology to characterise differences in versions of computational models in biology. PMID:27401413

  ---

  Informational laws of genome structures. PMID:27354155

  ---

  Challenges with using names to link digital biodiversity information. PMID:27346955

  ---

  A novel skew analysis reveals substitution asymmetries linked to genetic code GC-biases and PolIII a-subunit isoforms. PMID:27345720

  ---

  A comprehensive view of the web-resources related to sericulture. PMID:27307138

  ---

  The Orthology Ontology: development and applications. PMID:27259657

  ---

  The Evolution of COP9 Signalosome in Unicellular and Multicellular Organisms. PMID:27044515

  ---

  HerDing: herb recommendation system to treat diseases using genes and chemicals. PMID:26980517

  ---

  Towards Plant Species Identification in Complex Samples: A Bioinformatics Pipeline for the Identification of Novel Nuclear Barcode Candidates. PMID:26807711

  ---

  Precise genotyping and recombination detection of Enterovirus. PMID:26678286

  ---

  Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems. PMID:26673755

  ---

  Database resources of the National Center for Biotechnology Information. PMID:26615191

  ---

  GenBank. PMID:26590407

  ---

  ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases. PMID:26581408

  ---

  DNA data bank of Japan (DDBJ) progress report. PMID:26578571

  ---

  Predicting RAD-seq Marker Numbers across the Eukaryotic Tree of Life. PMID:26537225

  ---

  FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses. PMID:26504853

  ---

  KEGG as a reference resource for gene and protein annotation. PMID:26476454

  ---

  Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PMID:26436773

  ---

  Evolutionary history exposes radical diversification among classes of interaction partners of the MLLE domain of plant poly(A)-binding proteins. PMID:26377114

  ---

  Structural Bridges through Fold Space. PMID:26372166

  ---

  Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy. PMID:26370248

  ---

  Bacterial Landscape of Bloodstream Infections in Neutropenic Patients via High Throughput Sequencing. PMID:26270467

  ---

  Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes. PMID:26252577

  ---

  Trends in genome dynamics among major orders of insects revealed through variations in protein families. PMID:26251035

  ---

  De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. PMID:26228684

  ---

  Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes. PMID:26227972

  ---

  Basidioascus undulatus: genome, origins, and sexuality. PMID:26203425

  ---

  Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570

  ---

  The contribution of co-reference resolution to supervised relation detection between bacteria and biotopes entities. PMID:26201352

  ---

  Genome Diversity of Spore-Forming Firmicutes. PMID:26184964

  ---

  A large-scale crop protection bioassay data set. PMID:26175909

  ---

  Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream. PMID:26133389

  ---

  BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. PMID:26130132

  ---

  kpath: integration of metabolic pathway linked data. PMID:26055101

  ---

  R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server. PMID:26048960

  ---

  ProCARs: Progressive Reconstruction of Ancestral Gene Orders. PMID:26040958

  ---

  Databases for Microbiologists. PMID:26013493

  ---

  Visualisation of BioPAX Networks using BioLayout Express (3D). PMID:25949802

  ---

  Making species checklists understandable to machines - a shift from relational databases to ontologies. PMID:25937880

  ---

  novPTMenzy: a database for enzymes involved in novel post-translational modifications. PMID:25931459

  ---

  Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses. PMID:25905099

  ---

  Protein complexes in bacteria. PMID:25723151

  ---

  Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. PMID:25648696

  ---

  Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes. PMID:25607983

  ---

  Parallel detection of ancient pathogens via array-based DNA capture. PMID:25487327

  ---

  OntoGene web services for biomedical text mining. PMID:25472638

  ---

  Expanded microbial genome coverage and improved protein family annotation in the COG database. PMID:25428365

  ---

  NCBI viral genomes resource. PMID:25428358

  ---

  GenBank. PMID:25414350

  ---

  Database resources of the National Center for Biotechnology Information. PMID:25398906

  ---

  DDMGD: the database of text-mined associations between genes methylated in diseases from different species. PMID:25398897

  ---

  Current advances in systems and integrative biology. PMID:25379142

  ---

  BRENDA in 2015: exciting developments in its 25th year of existence. PMID:25378310

  ---

  The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161

  ---

  Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. PMID:25240328

  ---

  Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records. PMID:25197497

  ---

  Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation. PMID:25165633

  ---

  Insights into the evolution and domain structure of Ataxin-2 proteins across eukaryotes. PMID:25027299

  ---

  Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. PMID:24980130

  ---

  Genomewide comparison and novel ncRNAs of Aquificales. PMID:24965762

  ---

  Egas: a collaborative and interactive document curation platform. PMID:24923820

  ---

  A comprehensive phylogenetic and structural analysis of the carcinoembryonic antigen (CEA) gene family. PMID:24858421

  ---

  The evolution of human cells in terms of protein innovation. PMID:24692656

  ---

  BCL2DB: database of BCL-2 family members and BH3-only proteins. PMID:24608034

  ---

  Origin and evolution of metal P-type ATPases in Plantae (Archaeplastida). PMID:24575101

  ---

  Evaluating, comparing, and interpreting protein domain hierarchies. PMID:24559108

  ---

  Applications of DNA barcoding to fish landings: authentication and diversity assessment. PMID:24453550

  ---

  Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources. PMID:24377417

  ---

  A comprehensive phylogenetic analysis of deadenylases. PMID:24348009

  ---

  TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. PMID:24330842

  ---

  The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. PMID:24293649

  ---

  PDBe: Protein Data Bank in Europe. PMID:24288376

  ---

  Ribosomal Database Project: data and tools for high throughput rRNA analysis. PMID:24288368

  ---

  ExoLocator--an online view into genetic makeup of vertebrate proteins. PMID:24271393

  ---

  The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. PMID:24267744

  ---

  Database resources of the National Center for Biotechnology Information. PMID:24259429

  ---

  The world bacterial biogeography and biodiversity through databases: a case study of NCBI Nucleotide Database and GBIF Database. PMID:24228241

  ---

  GenBank. PMID:24217914

  ---

  The evolution of microRNA pathway protein components in Cnidaria. PMID:24030553

  ---

  Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. PMID:23975157

  ---

  Design and development of portal for biological database in agriculture. PMID:23888101

  ---

  Romance of the three domains: how cladistics transformed the classification of cellular organisms. PMID:23873078

  ---

  Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates. PMID:23871937

  ---

  A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia. PMID:23834245

  ---

  A daily-updated tree of (sequenced) life as a reference for genome research. PMID:23778980

  ---

  The comprehensive antibiotic resistance database. PMID:23650175

  ---

  Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831

  ---

  RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. PMID:23547897

  ---

  A systematic comparison of the MetaCyc and KEGG pathway databases. PMID:23530693

  ---

  search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information. PMID:23452691

  ---

  Metagenomic profile of gut microbiota in children during cholera and recovery. PMID:23369162

  ---

  SyntTax: a web server linking synteny to prokaryotic taxonomy. PMID:23323735

  ---

  A universal trend among proteomes indicates an oily last common ancestor. PMID:23300421

  ---

  BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. PMID:23203881

  ---

  The cell: an image library-CCDB: a curated repository of microscopy data. PMID:23203874

  ---

  SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869

  ---

  GenBank. PMID:23193287

  ---

  Database resources of the National Center for Biotechnology Information. PMID:23193264

  ---

  DDBJ new system and service refactoring. PMID:23180790

  ---

  MetaSee: an interactive and extendable visualization toolbox for metagenomic sample analysis and comparison. PMID:23145044

  ---

  MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. PMID:23118485

  ---

  ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs. PMID:22958836

  ---

  Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. PMID:22882546

  ---

  A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. PMID:22759449

  ---

  Identification of a third osmoprotectant transport system, the osmU system, in Salmonella enterica. PMID:22609924

  ---

  Recurrent horizontal transfer of bacterial toxin genes to eukaryotes. PMID:22411854

  ---

  Dissecting plant genomes with the PLAZA comparative genomics platform. PMID:22198273

  ---

  The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
• GenBank PubMed citations: 246.

  246 articles citing: GenBank

  ×

  A Fast-Growing Oleaginous Strain of Coelastrella Capable of Astaxanthin and Canthaxanthin Accumulation in Phototrophy and Heterotrophy. PMID:35330084

  ---

  Data on the diets of Salish Sea harbour seals from DNA metabarcoding. PMID:35236843

  ---

  LuxT Is a Global Regulator of Low-Cell-Density Behaviors, Including Type III Secretion, Siderophore Production, and Aerolysin Production, in Vibrio harveyi. PMID:35038896

  ---

  What's left in the tank? Identification of non-ascribed aquarium's coral collections with DNA barcodes as part of an integrated diagnostic approach. PMID:35035629

  ---

  Complete mitochondrial genomes of three reef forming Acropora corals (Acroporidae, Scleractinia) from Chagos Archipelago, Indian Ocean. PMID:34707458

  ---

  Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota. PMID:34489402

  ---

  Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex. PMID:34460306

  ---

  Novel and emerging mutations of SARS-CoV-2: Biomedical implications. PMID:33915502

  ---

  Lytic Bacteriophage EFA1 Modulates HCT116 Colon Cancer Cell Growth and Upregulates ROS Production in an Enterococcus faecalis Co-culture System. PMID:33868210

  ---

  LuxT controls specific quorum-sensing-regulated behaviors in Vibrionaceae spp. via repression of qrr1, encoding a small regulatory RNA. PMID:33793568

  ---

  Ancient plant DNA reveals High Arctic greening during the Last Interglacial. PMID:33723011

  ---

  Genome-wide in silico identification and characterization of Simple Sequence Repeats in diverse completed SARS-CoV-2 genomes. PMID:33521382

  ---

  Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance. PMID:33208862

  ---

  Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean - Altiplano. PMID:32760381

  ---

  Uncovering the First Atypical DS-1-like G1P[8] Rotavirus Strains That Circulated during Pre-Rotavirus Vaccine Introduction Era in South Africa. PMID:32443835

  ---

  Salinity-dependent expression of ncc2 in opercular epithelium and gill of mummichog (Fundulus heteroclitus). PMID:31980891

  ---

  SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier. PMID:31648300

  ---

  Towards Sustainable Environmental Quality: Priority Research Questions for the Australasian Region of Oceania. PMID:31273905

  ---

  A new microbial gluten-degrading prolyl endopeptidase: Potential application in celiac disease to reduce gluten immunogenic peptides. PMID:31246975

  ---

  Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding. PMID:31235850

  ---

  Single Core Genome Sequencing for Detection of both Borrelia burgdorferi Sensu Lato and Relapsing Fever Borrelia Species. PMID:31137527

  ---

  An Open Science Approach to Artificial Intelligence in Healthcare. PMID:31022753

  ---

  How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). PMID:30848456

  ---

  Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns. PMID:30655514

  ---

  New species of bone-eating worm Osedax from the abyssal South Atlantic Ocean (Annelida, Siboglinidae). PMID:30651712

  ---

  Structural Patching Fosters Divergence of Mitochondrial Ribosomes. PMID:30517740

  ---

  Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach. PMID:30413726

  ---

  Whole-Genome Alignment and Comparative Annotation. PMID:30379572

  ---

  The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. PMID:29337314

  ---

  The Complete Chloroplast Genome Sequences of Aconitum pseudolaeve and Aconitum longecassidatum, and Development of Molecular Markers for Distinguishing Species in the Aconitum Subgenus Lycoctonum. PMID:29160852

  ---

  Comparative Genome Analysis of Rathayibacter tritici NCPPB 1953 with Rathayibacter toxicus Strains Can Facilitate Studies on Mechanisms of Nematode Association and Host Infection. PMID:28811754

  ---

  Deciphering functional diversification within the lichen microbiota by meta-omics. PMID:28724401

  ---

  A Hybrid Human-Computer Approach to the Extraction of Scientific Facts from the Literature. PMID:28649288

  ---

  The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species. PMID:28608849

  ---

  Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade. PMID:28453569

  ---

  vanA-targeted oligonucleotide DNA probe designed to monitor vancomycin- and teicoplanin-resistant bacteria in surface waters. PMID:27640164

  ---

  The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales. PMID:27602181

  ---

  RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease. PMID:27583836

  ---

  Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method. PMID:27478829

  ---

  Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. PMID:27192708

  ---

  Circular sequence comparison: algorithms and applications. PMID:27168761

  ---

  De Novo Centromere Formation and Centromeric Sequence Expansion in Wheat and its Wide Hybrids. PMID:27110907

  ---

  Isolation and Characterization of DkPK Genes Associated with Natural Deastringency in C-PCNA Persimmon. PMID:26925075

  ---

  Homology modeling and assigned functional annotation of an uncharacterized antitoxin protein from Streptomyces xinghaiensis. PMID:26912949

  ---

  Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America. PMID:26653183

  ---

  Design a cadA-targeted DNA probe for screening of potential bacterial cadmium biosorbents. PMID:26585451

  ---

  Data integration in biological research: an overview. PMID:26336651

  ---

  Complete Genome Sequence of Bifidobacterium longum GT15: Identification and Characterization of Unique and Global Regulatory Genes. PMID:25894918

  ---

  ISOB: A Database of Indigenous Snake Species of Bangladesh with respective known venom composition. PMID:25848172

  ---

  Transposable elements in a clade of three tetraploids and a diploid relative, focusing on Gypsy amplification. PMID:25834645

  ---

  Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data. PMID:25258679

  ---

  DNA sequencing diagnosis of off-season spirochetemia with low bacterial density in Borrelia burgdorferi and Borrelia miyamotoi infections. PMID:24968274

  ---

  Local similarity search to find gene indicators in mitochondrial genomes. PMID:24833343

  ---

  Computational protein structure modeling and analysis of UV-B stress protein in Synechocystis PCC 6803. PMID:23904742

  ---

  Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction. PMID:23675487

  ---

  Computational identification and analysis of arsenate reductase protein in Cronobacter sakazakii ATCC BAA-894 suggests potential microorganism for reducing arsenate. PMID:23666632

  ---

  Comparative genomic analyses of Mycoplasma hyopneumoniae pathogenic 168 strain and its high-passaged attenuated strain. PMID:23384176

  ---

  Defining mycobacteria: Shared and specific genome features for different lifestyles. PMID:23100749

  ---

  Characterization of lead-resistant river isolate Enterococcus faecalis and assessment of its multiple metal and antibiotic resistance. PMID:23079796

  ---

  Genome-wide metabolic (re-) annotation of Kluyveromyces lactis. PMID:23025710

  ---

  Bacteriophage ecology in a commercial cucumber fermentation. PMID:23023756

  ---

  Complete genome sequence of Bacillus anthracis H9401, an isolate from a Korean patient with anthrax. PMID:22815438

  ---

  Bacteriostatic anti-Vibrio parahaemolyticus activity of Pseudoalteromonas sp. strains DIT09, DIT44 and DIT46 isolated from Southern Chilean intertidal Perumytilus purpuratus. PMID:22806110

  ---

  Genetic analysis of the Cronobacter sakazakii O4 to O7 O-antigen gene clusters and development of a PCR assay for identification of all C. sakazakii O serotypes. PMID:22447597

  ---

  Spatial heterogeneity of bacterial communities in sediments from an infiltration basin receiving highway runoff. PMID:22391798

  ---

  Data ontology and an information system realization for web-based management of image measurements. PMID:22275893

  ---

  Characteristics of spoilage-associated secondary cucumber fermentation. PMID:22179234

  ---

  Global distribution of Polaromonas phylotypes--evidence for a highly successful dispersal capacity. PMID:21897856

  ---

  Bacteriophage-encoded shiga toxin gene in atypical bacterial host. PMID:21733190

  ---

  The two tryptophans of β2-microglobulin have distinct roles in function and folding and might represent two independent responses to evolutionary pressure. PMID:21663612

  ---

  Natural attenuation is enhanced in previously contaminated and coniferous forest soils. PMID:21660637

  ---

  3-(2,4-Dichloro-phen-yl)-2-oxo-1-oxaspiro-[4.5]dec-3-en-4-yl acetate. PMID:21580092

  ---

  Poly[[tetra-aquadi-μ(3)-oxalato-μ(2)-oxalato-diprasedymium(III)] dihydrate]. PMID:21579975

  ---

  3-(2,4-Dichloro-phen-yl)-2-oxo-1-oxa-spiro-[4.5]dec-3-en-4-yl 4-chloro-benzoate. PMID:21578732

  ---

  Abundance and diversity of archaeal ammonia oxidizers in a coastal groundwater system. PMID:20971859

  ---

  Extracellular and mixotrophic symbiosis in the whale-fall mussel Adipicola pacifica: a trend in evolution from extra- to intracellular symbiosis. PMID:20676405

  ---

  The catalytic and protein-protein interaction domains are required for APM1 function. PMID:20154099

  ---

  Comparative genomics reveals selective distribution and domain organization of FYVE and PX domain proteins across eukaryotic lineages. PMID:20122178

  ---

  Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen. PMID:20118375

  ---

  Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PMID:20090843

  ---

  Phylogenetic comparative assembly. PMID:20047659

  ---

  Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs. PMID:19955230

  ---

  BioDEAL: community generation of biological annotations. PMID:19891799

  ---

  Identification of novel retroid agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis. PMID:19461980

  ---

  Analysis of the complement and molecular evolution of tRNA genes in cow. PMID:19393063

  ---

  Homology modelling: a review about the method on hand of the diabetic antigen GAD 65 structure prediction. PMID:19343288

  ---

  Systematic prediction of control proteins and their DNA binding sites. PMID:19056824

  ---

  Mutational analysis of the mitochondrial tRNA genes and flanking regions in umbilical cord tissue from uninfected infants receiving AZT-based therapies for prophylaxis of HIV-1. PMID:19031409

  ---

  The protein structure initiative structural genomics knowledgebase. PMID:19010965

  ---

  Environmental and anthropogenic controls over bacterial communities in wetland soils. PMID:19004771

  ---

  Quantifying nonspecific TEM beta-lactamase (blaTEM) genes in a wastewater stream. PMID:18997031

  ---

  Substrate-specific clades of active marine methylotrophs associated with a phytoplankton bloom in a temperate coastal environment. PMID:18849453

  ---

  Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role. PMID:18825305

  ---

  POEM, A 3-dimensional exon taxonomy and patterns in untranslated exons. PMID:18803852

  ---

  CBESW: sequence alignment on the Playstation 3. PMID:18798993

  ---

  A functional gene array for detection of bacterial virulence elements. PMID:18478124

  ---

  Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages. PMID:18318913

  ---

  Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. PMID:18215291

  ---

  Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. PMID:18192411

  ---

  The influence of gene-environment interactions on GHR and IGF-1 expression and their association with growth in brook charr, Salvelinus fontinalis (Mitchill). PMID:18154679

  ---

  A quantitative synthesis of the medicinal ethnobotany of the Malinké of Mali and the Asháninka of Peru, with a new theoretical framework. PMID:18053260

  ---

  Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in Sporothrix schenckii. PMID:18047672

  ---

  Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. PMID:17586664

  ---

  MyHits: improvements to an interactive resource for analyzing protein sequences. PMID:17545200

  ---

  HitKeeper, a generic software package for hit list management. PMID:17391514

  ---

  Molecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization. PMID:17307877

  ---

  Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level. PMID:17090320

  ---

  Diversity of tRNA genes in eukaryotes. PMID:17088292

  ---

  New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. PMID:16957188

  ---

  Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway. PMID:16901339

  ---

  Podocyte-associated proteins FAT, alpha-actinin-4 and filtrin are expressed in Langerhans islets of the pancreas. PMID:16841182

  ---

  Evaluating the near-term infant for early onset sepsis: progress and challenges to consider with 16S rDNA polymerase chain reaction testing. PMID:16825509

  ---

  The effect of varying levels of sodium bicarbonate on polychlorinated biphenyl dechlorination in Hudson River sediment cultures. PMID:16817937

  ---

  Coupled photochemical and enzymatic Mn(II) oxidation pathways of a planktonic Roseobacter-Like bacterium. PMID:16672501

  ---

  BioWarehouse: a bioinformatics database warehouse toolkit. PMID:16556315

  ---

  Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. PMID:16542435

  ---

  A reliable method to display authentic DNase I hypersensitive sites at long-ranges in single-copy genes from large genomes. PMID:16510851

  ---

  The reductive dechlorination of 2,3,4,5-tetrachlorobiphenyl in three different sediment cultures: evidence for the involvement of phylogenetically similar Dehalococcoides-like bacterial populations. PMID:16420633

  ---

  Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples. PMID:16391035

  ---

  The tmRDB and SRPDB resources. PMID:16381838

  ---

  At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. PMID:16332745

  ---

  AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. PMID:16305757

  ---

  An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. PMID:16305755

  ---

  Endosperm-preferred expression of maize genes as revealed by transcriptome-wide analysis of expressed sequence tags. PMID:16247562

  ---

  Draft versus finished sequence data for DNA and protein diagnostic signature development. PMID:16243783

  ---

  Indole alkaloid marine natural products: an established source of cancer drug leads with considerable promise for the control of parasitic, neurological and other diseases. PMID:16236327

  ---

  Gene expression profiling of jejunal Peyer's patches in juvenile and adult pigs. PMID:16180142

  ---

  An expression and bioinformatics analysis of the Arabidopsis serine carboxypeptidase-like gene family. PMID:15908604

  ---

  Structural and functional characterization of AtPTR3, a stress-induced peptide transporter of Arabidopsis. PMID:15889294

  ---

  Requirement of the receiver and phosphotransfer domains of ArcB for efficient dephosphorylation of phosphorylated ArcA in vivo. PMID:15838055

  ---

  System to assess genome sequencing needs for viral protein diagnostics and therapeutics. PMID:15815002

  ---

  Use of pyrosequencing of 16S rRNA fragments to differentiate between bacteria responsible for neonatal sepsis. PMID:15681481

  ---

  Development and validation of PCR primers to assess the diversity of Clostridium spp. in cheese by temporal temperature gradient gel electrophoresis. PMID:15640166

  ---

  PSORTdb: a protein subcellular localization database for bacteria. PMID:15608169

  ---

  Visualizing information across multidimensional post-genomic structured and textual databases. PMID:15598839

  ---

  Sequencing needs for viral diagnostics. PMID:15583268

  ---

  A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase. PMID:15557261

  ---

  Evolutionary relatedness between glycolytic enzymes most frequently occurring in genomes. PMID:15259764

  ---

  Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. PMID:15215334

  ---

  Specificity of cellular expression of C. variopedatus polychaete innexin in the developing embryo: evolutionary aspects of innexins' heterogeneous gene structures. PMID:15008413

  ---

  Possible association of GroES and antigen 85 proteins with heat resistance of Mycobacterium paratuberculosis. PMID:15006794

  ---

  Functional prediction of a T-DNA tagged gene of Arabidopsis thaliana by in silico analysis. PMID:14767695

  ---

  Bifunctional aldehyde/alcohol dehydrogenase (ADHE) in chlorophyte algal mitochondria. PMID:14756315

  ---

  Molecular evolution of FtsZ protein sequences encoded within the genomes of archaea, bacteria, and eukaryota. PMID:14743312

  ---

  EyeSite: a semi-automated database of protein families in the eye. PMID:14681381

  ---

  RIDOM: comprehensive and public sequence database for identification of Mycobacterium species. PMID:14611664

  ---

  Capnocytophaga sp. isolated from a cat with chronic sinusitis and rhinitis. PMID:14605195

  ---

  Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species, Robinia pseudoacacia. PMID:14558656

  ---

  Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution x-ray crystallographic, molecular modeling, and sequence-based methods. PMID:12915569

  ---

  Identification of long intergenic repeat sequences associated with DNA methylation sites in Caulobacter crescentus and other alpha-proteobacteria. PMID:12897020

  ---

  Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase. PMID:12877744

  ---

  Molecular identification of bacteria and Eukarya inhabiting an Antarctic cryoconite hole. PMID:12768448

  ---

  Conservation of human alternative splice events in mouse. PMID:12736303

  ---

  MHC class I-like genes in cattle, MHCLA, with similarity to genes encoding NK cell stimulatory ligands. PMID:12679856

  ---

  Cloning and characterization of dipeptidyl peptidase 10, a new member of an emerging subgroup of serine proteases. PMID:12662155

  ---

  Binding mode of ecdysone agonists to the receptor: comparative modeling and docking studies. PMID:12638012

  ---

  The EMBL Nucleotide Sequence Database: major new developments. PMID:12519939

  ---

  Comparison of whole genome assemblies of the human genome. PMID:12434005

  ---

  Thermoconditional modulation of the pleiotropic sensitivity phenotype by the Saccharomyces cerevisiae PRP19 mutant allele pso4-1. PMID:12434004

  ---

  Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. PMID:12368242

  ---

  Detection of Helicobacter colonization of the murine lower bowel by genus-specific PCR-denaturing gradient gel electrophoresis. PMID:12324369

  ---

  Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. PMID:12213775

  ---

  Pervasive properties of the genomic signature. PMID:12171605

  ---

  Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. PMID:12147470

  ---

  The Phage Proteomic Tree: a genome-based taxonomy for phage. PMID:12142423

  ---

  Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. PMID:12136103

  ---

  Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. PMID:12136096

  ---

  Novel human ZAKI-4 isoforms: hormonal and tissue-specific regulation and function as calcineurin inhibitors. PMID:12102656

  ---

  Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. PMID:12089052

  ---

  The fibril_one on-line database: mutations, experimental conditions, and trends associated with amyloid fibril formation. PMID:12070339

  ---

  Streptococcus-zebrafish model of bacterial pathogenesis. PMID:12065534

  ---

  Tandem repeats in protein coding regions of primate genes. PMID:12045144

  ---

  Multiplex three-dimensional brain gene expression mapping in a mouse model of Parkinson's disease. PMID:12045141

  ---

  The diversity of microorganisms associated with Acromyrmex leafcutter ants. PMID:12019020

  ---

  Multiple database coverage of structural biology. PMID:11999187

  ---

  Sequence similarities and evolutionary relationships of influenza virus A hemagglutinins. PMID:11928990

  ---

  Molecular biological detection and characterization of Clostridium populations in municipal landfill sites. PMID:11916731

  ---

  Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. PMID:11875040

  ---

  The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. PMID:11869452

  ---

  Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems. PMID:11860214

  ---

  Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. PMID:11827946

  ---

  Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. PMID:11823182

  ---

  Comparative analysis of FUR regulons in gamma-proteobacteria. PMID:11812853

  ---

  The CATH extended protein-family database: providing structural annotations for genome sequences. PMID:11790833

  ---

  RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database. PMID:11752353

  ---

  MEROPS: the protease database. PMID:11752332

  ---

  MODBASE, a database of annotated comparative protein structure models. PMID:11752309

  ---

  The Protein Data Bank: unifying the archive. PMID:11752306

  ---

  FIMM, a database of functional molecular immunology: update 2002. PMID:11752300

  ---

  JSNP: a database of common gene variations in the Japanese population. PMID:11752280

  ---

  HOWDY: an integrated database system for human genome research. PMID:11752279

  ---

  The EMBL Nucleotide Sequence Database. PMID:11752244

  ---

  GenBank. PMID:11752243

  ---

  Database resources of the National Center for Biotechnology Information: 2002 update. PMID:11752242

  ---

  Phylogenetic analysis reveals multiple lateral transfers of adenosine-5'-phosphosulfate reductase genes among sulfate-reducing microorganisms. PMID:11741869

  ---

  Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. PMID:11731496

  ---

  Archaeal diversity in waters from deep South African gold mines. PMID:11722932

  ---

  Redox signal transduction by the ArcB sensor kinase of Haemophilus influenzae lacking the PAS domain. PMID:11717280

  ---

  Mosaic structure of the DNA molecules of the human chromosomes 21 and 22. PMID:11710567

  ---

  Having a BLAST with bioinformatics (and avoiding BLASTphemy). PMID:11597340

  ---

  On the species of origin: diagnosing the source of symbiotic transcripts. PMID:11574056

  ---

  Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria. PMID:11571178

  ---

  Comparing function and structure between entire proteomes. PMID:11567088

  ---

  Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. PMID:11544196

  ---

  HIV-1 LTR C/EBP binding site sequence configurations preferentially encountered in brain lead to enhanced C/EBP factor binding and increased LTR-specific activity. PMID:11517398

  ---

  EBI databases and services. PMID:11503515

  ---

  Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. PMID:11472932

  ---

  Identification and characterization of the STIM (stromal interaction molecule) gene family: coding for a novel class of transmembrane proteins. PMID:11463338

  ---

  SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. PMID:11433035

  ---

  Photosynthetic and phylogenetic primers for detection of anoxygenic phototrophs in natural environments. PMID:11425703

  ---

  Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions. PMID:11410667

  ---

  Evaluation of gene-finding programs on mammalian sequences. PMID:11337477

  ---

  PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. PMID:11292848

  ---

  Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5. PMID:11239002

  ---

  Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics. PMID:11206052

  ---

  Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). PMID:11178258

  ---

  Dissimilatory sulfite reductase (desulfoviridin) of the taurine-degrading, non-sulfate-reducing bacterium Bilophila wadsworthia RZATAU contains a fused DsrB-DsrD subunit. PMID:11160104

  ---

  Coinfection with three Ehrlichia species in dogs from Thailand and Venezuela with emphasis on consideration of 16S ribosomal DNA secondary structure. PMID:11136754

  ---

  Characterization of a novel spirochete associated with the hydrothermal vent polychaete annelid, Alvinella pompejana. PMID:11133434

  ---

  ICB database: the gyrB database for identification and classification of bacteria. PMID:11125132

  ---

  GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources. PMID:11125129

  ---

  AsMamDB: an alternative splice database of mammals. PMID:11125106

  ---

  The PDB data uniformity project. PMID:11125095

  ---

  The RDP-II (Ribosomal Database Project). PMID:11125082

  ---

  tmRDB (tmRNA database). PMID:11125081

  ---

  SRPDB (Signal Recognition Particle Database). PMID:11125080

  ---

  RHdb: the Radiation Hybrid database. PMID:11125078

  ---

  RefSeq and LocusLink: NCBI gene-centered resources. PMID:11125071

  ---

  VIDA: a virus database system for the organization of animal virus genome open reading frames. PMID:11125070

  ---

  GOBASE: the organelle genome database. PMID:11125069

  ---

  The Mouse Gene Expression Database (GXD). PMID:11125060

  ---

  The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments. PMID:11125049

  ---

  The MetaFam Server: a comprehensive protein family resource. PMID:11125046

  ---

  The EMBL nucleotide sequence database. PMID:11125039

  ---

  Database resources of the National Center for Biotechnology Information. PMID:11125038

  ---

  Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene. PMID:11076860

  ---

  Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools. PMID:11071948

  ---

  Links from genome proteins to known 3-D structures. PMID:11042161

  ---

  Human immunodeficiency virus on the web: a guided tour. PMID:10987723

  ---

  Mutations in the protein kinase A R1alpha regulatory subunit cause familial cardiac myxomas and Carney complex. PMID:10974026

  ---

  Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. PMID:10908680

  ---

  Archaeal population dynamics during sequential reduction processes in rice field soil. PMID:10877762

  ---

  EB1 proteins regulate microtubule dynamics, cell polarity, and chromosome stability. PMID:10811817

  ---

  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. PMID:10802651

  ---

  Molecular phylogenetic evidence for noninvasive zoonotic transmission of Staphylococcus intermedius from a canine pet to a human. PMID:10747154

  ---

  Database resources of the National Center for Biotechnology Information. PMID:10592169
• Database resources of the National Center for Biotechnology Information PubMed citations: 173.

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

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  Computational Design of a Multi-Epitope Vaccine Against Porphyromonas gingivalis. PMID:35250977

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  A deep learning ensemble approach to prioritize antiviral drugs against novel coronavirus SARS-CoV-2 for COVID-19 drug repurposing. PMID:34630000

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  Epitope-based universal vaccine for Human T-lymphotropic virus-1 (HTLV-1). PMID:33798232

  ---

  Comprehensive in silico analysis and molecular dynamics of the superoxide dismutase 1 (SOD1) variants related to amyotrophic lateral sclerosis. PMID:33630959

  ---

  Functional screening of a Caatinga goat (Capra hircus) rumen metagenomic library reveals a novel GH3 β-xylosidase. PMID:33449963

  ---

  Identification and computational analysis of mutations in SARS-CoV-2. PMID:33383528

  ---

  Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery. PMID:33206037

  ---

  Informing epidemic (research) responses in a timely fashion by knowledge management - a Zika virus use case. PMID:33148605

  ---

  Transcriptome sequencing and screening of genes related to sex determination of Trichosanthes kirilowii Maxim. PMID:33057394

  ---

  Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study. PMID:32776991

  ---

  Scoring functions for drug-effect similarity. PMID:32484516

  ---

  A lipophilicity-based energy function for membrane-protein modelling and design. PMID:31461441

  ---

  Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum. PMID:31304854

  ---

  FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration. PMID:31304272

  ---

  In silico analysis of the V66M variant of human BDNF in psychiatric disorders: An approach to precision medicine. PMID:30998730

  ---

  Analysis Tools for Large Connectomes. PMID:30374293

  ---

  Functional Characterization of Soybean Glyma04g39610 as a Brassinosteroid Receptor Gene and Evolutionary Analysis of Soybean Brassinosteroid Receptors. PMID:27338344

  ---

  The Association between Gene-Environment Interactions and Diseases Involving the Human GST Superfamily with SNP Variants. PMID:27043589

  ---

  Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PMID:26335687

  ---

  Identification and Characterization of 40 Isolated Rehmannia glutinosa MYB Family Genes and Their Expression Profiles in Response to Shading and Continuous Cropping. PMID:26147429

  ---

  GlycoRDF: an ontology to standardize glycomics data in RDF. PMID:25388145

  ---

  Metagenomic analysis reveals presence of Treponema denticola in a tissue biopsy of the Iceman. PMID:24941044

  ---

  A pilot study using next-generation sequencing in advanced cancers: feasibility and challenges. PMID:24204627

  ---

  Characterization of regulatory features of housekeeping and tissue-specific regulators within tissue regulatory networks. PMID:24172660

  ---

  Analysis of 953 human proteins from a mitochondrial HEK293 fraction by complexome profiling. PMID:23935861

  ---

  Defining mycobacteria: Shared and specific genome features for different lifestyles. PMID:23100749

  ---

  Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing. PMID:23071490

  ---

  Rananos expression pattern during oogenesis and early embryonic development in Rhynchosciara americana. PMID:22526873

  ---

  De novo identification of viral pathogens from cell culture hologenomes. PMID:22226071

  ---

  The two tryptophans of β2-microglobulin have distinct roles in function and folding and might represent two independent responses to evolutionary pressure. PMID:21663612

  ---

  Natural attenuation is enhanced in previously contaminated and coniferous forest soils. PMID:21660637

  ---

  Flexible taxonomic assignment of ambiguous sequencing reads. PMID:21211059

  ---

  Analyses of an expressed sequence tag library from Taenia solium, Cysticerca. PMID:21200421

  ---

  3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes. PMID:21143789

  ---

  Combining target enrichment with barcode multiplexing for high throughput SNP discovery. PMID:21083938

  ---

  Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. PMID:20624743

  ---

  The transcriptome of the early life history stages of the California Sea Hare Aplysia californica. PMID:20434970

  ---

  High-throughput knockout screen in Schizosaccharomyces pombe identifies a novel gene required for efficient homolog disjunction during meiosis I. PMID:20404563

  ---

  Comparative genomics reveals selective distribution and domain organization of FYVE and PX domain proteins across eukaryotic lineages. PMID:20122178

  ---

  Phylogenetic comparative assembly. PMID:20047659

  ---

  The evolutionary history of protein domains viewed by species phylogeny. PMID:20041107

  ---

  The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PMID:20011103

  ---

  Eukaryotic transcriptomics in silico: optimizing cDNA-AFLP efficiency. PMID:19948029

  ---

  EGAN: exploratory gene association networks. PMID:19933825

  ---

  An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PMID:19851441

  ---

  Chinese bellflower root anaphylaxis: IgE-binding components and cross-reactivity with mugwort and birch. PMID:19721867

  ---

  A proposed syntax for Minimotif Semantics, version 1. PMID:19656396

  ---

  Rodent and nonrodent malaria parasites differ in their phospholipid metabolic pathways. PMID:19561325

  ---

  Identification of novel retroid agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis. PMID:19461980

  ---

  PhyloExplorer: a web server to validate, explore and query phylogenetic trees. PMID:19450253

  ---

  iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences. PMID:19443442

  ---

  The R2 mobile element of Rhynchosciara americana: molecular, cytological and dynamic aspects. PMID:19350401

  ---

  Homology modelling: a review about the method on hand of the diabetic antigen GAD 65 structure prediction. PMID:19343288

  ---

  PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. PMID:19208196

  ---

  Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PMID:19190775

  ---

  CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge. PMID:19091025

  ---

  WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding. PMID:19091012

  ---

  Data deposition and annotation at the worldwide protein data bank. PMID:19082769

  ---

  A survey of visualization tools for biological network analysis. PMID:19040716

  ---

  [Virtual tissue. Quaoaring]. PMID:19039616

  ---

  Minimotif miner 2nd release: a database and web system for motif search. PMID:18978024

  ---

  A computational screen for type I polyketide synthases in metagenomics shotgun data. PMID:18953415

  ---

  PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood. PMID:18832367

  ---

  Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role. PMID:18825305

  ---

  GlycomeDB - integration of open-access carbohydrate structure databases. PMID:18803830

  ---

  Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans. PMID:18694500

  ---

  An upper-level ontology for the biomedical domain. PMID:18629109

  ---

  The MGED ontology: a framework for describing functional genomics experiments. PMID:18629093

  ---

  Molecular characterization of a retrotransposon in the Rhynchosciara americana genome and its association with telomere. PMID:18528768

  ---

  Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. PMID:18460183

  ---

  Large-scale analysis of gene clustering in bacteria. PMID:18390694

  ---

  Dynamics of Recognition between tRNA and elongation factor Tu. PMID:18336835

  ---

  Evolution of exceptionally large genes in prokaryotes. PMID:18322635

  ---

  Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history. PMID:18320058

  ---

  Towards ontology-driven navigation of the lipid bibliosphere. PMID:18315858

  ---

  DBMLoc: a Database of proteins with multiple subcellular localizations. PMID:18304364

  ---

  Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. PMID:18215291

  ---

  A quantitative synthesis of the medicinal ethnobotany of the Malinké of Mali and the Asháninka of Peru, with a new theoretical framework. PMID:18053260

  ---

  Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in Sporothrix schenckii. PMID:18047672

  ---

  Data growth and its impact on the SCOP database: new developments. PMID:18000004

  ---

  Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets. PMID:17963508

  ---

  Metagenomic characterization of Chesapeake Bay virioplankton. PMID:17921274

  ---

  Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. PMID:17868481

  ---

  DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data. PMID:17868443

  ---

  Evolution of protein families: is it possible to distinguish between domains of life? PMID:17826006

  ---

  Functional characterization of pathogenic human MSH2 missense mutations in Saccharomyces cerevisiae. PMID:17720936

  ---

  Multiple domain insertions and losses in the evolution of the Rab prenylation complex. PMID:17705859

  ---

  Mariner-like elements in Rhynchosciara americana (Sciaridae) genome: molecular and cytological aspects. PMID:17705057

  ---

  Information theory applied to the sparse gene ontology annotation network to predict novel gene function. PMID:17646340

  ---

  Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment. PMID:17629909

  ---

  Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. PMID:17586664

  ---

  Distinct profiles of expressed sequence tags during intestinal regeneration in the sea cucumber Holothuria glaberrima. PMID:17579180

  ---

  MyHits: improvements to an interactive resource for analyzing protein sequences. PMID:17545200

  ---

  BLASTO: a tool for searching orthologous groups. PMID:17483516

  ---

  Semantic classification of biomedical concepts using distributional similarity. PMID:17460124

  ---

  The genopolis microarray database. PMID:17430566

  ---

  HitKeeper, a generic software package for hit list management. PMID:17391514

  ---

  Long-term trends in evolution of indels in protein sequences. PMID:17298668

  ---

  CYCLONET--an integrated database on cell cycle regulation and carcinogenesis. PMID:17202170

  ---

  EVEREST: a collection of evolutionary conserved protein domains. PMID:17099230

  ---

  PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing. PMID:17094228

  ---

  Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level. PMID:17090320

  ---

  Diversity of tRNA genes in eukaryotes. PMID:17088292

  ---

  Meta-All: a system for managing metabolic pathway information. PMID:17059592

  ---

  ORENZA: a web resource for studying ORphan ENZyme activities. PMID:17026747

  ---

  PhyloPat: phylogenetic pattern analysis of eukaryotic genes. PMID:16948844

  ---

  Comparative analysis and "expression space" coverage of the production of prokaryotic membrane proteins for structural genomics. PMID:16943447

  ---

  MultiSeq: unifying sequence and structure data for evolutionary analysis. PMID:16914055

  ---

  Virtual Ribosome--a comprehensive DNA translation tool with support for integration of sequence feature annotation. PMID:16845033

  ---

  Molecular cloning and characterization of a novel human testis-specific gene by use of digital differential display. PMID:16809841

  ---

  A new measure for functional similarity of gene products based on Gene Ontology. PMID:16776819

  ---

  BioWarehouse: a bioinformatics database warehouse toolkit. PMID:16556315

  ---

  Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. PMID:16542435

  ---

  13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA. PMID:16461909

  ---

  MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. PMID:16433928

  ---

  Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples. PMID:16391035

  ---

  The tmRDB and SRPDB resources. PMID:16381838

  ---

  An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. PMID:16305755

  ---

  GeneSeer: a sage for gene names and genomic resources. PMID:16176584

  ---

  Micro-Mar: a database for dynamic representation of marine microbial biodiversity. PMID:16153293

  ---

  Evolution of the genetic triplet code via two types of doublet codons. PMID:16059752

  ---

  Cloning and characterization of hoxH genes from Arthrospira and Spirulina and application in phylogenetic study. PMID:16049666

  ---

  An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. PMID:15960829

  ---

  A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal. PMID:15884978

  ---

  Columba: an integrated database of proteins, structures, and annotations. PMID:15801979

  ---

  The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. PMID:15608200

  ---

  PSORTdb: a protein subcellular localization database for bacteria. PMID:15608169

  ---

  Visualizing information across multidimensional post-genomic structured and textual databases. PMID:15598839

  ---

  High-throughput computational and experimental techniques in structural genomics. PMID:15489337

  ---

  The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. PMID:15170256

  ---

  Phylogenetic position of the Pentastomida and (pan)crustacean relationships. PMID:15129965

  ---

  A guide to building image-centric databases. PMID:15043221

  ---

  Annotation and cross-indexing of array elements on multiple platforms. PMID:15033601

  ---

  Possible association of GroES and antigen 85 proteins with heat resistance of Mycobacterium paratuberculosis. PMID:15006794

  ---

  Assembly properties of the human immunodeficiency virus type 1 CA protein. PMID:14963157

  ---

  Molecular evolution of FtsZ protein sequences encoded within the genomes of archaea, bacteria, and eukaryota. PMID:14743312

  ---

  Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? PMID:14691234

  ---

  IntAct: an open source molecular interaction database. PMID:14681455

  ---

  DNA sequence-based "bar codes" for tracking the origins of expressed sequence tags from a maize cDNA library constructed using multiple mRNA sources. PMID:14555776

  ---

  Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. PMID:14531933

  ---

  Target selection and determination of function in structural genomics. PMID:12880206

  ---

  NEWT, a new taxonomy portal. PMID:12824428

  ---

  Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. PMID:12808149

  ---

  A recombinant beta-1,3-glucanosyltransferase homolog of Coccidioides posadasii protects mice against coccidioidomycosis. PMID:12761077

  ---

  DAVID: Database for Annotation, Visualization, and Integrated Discovery. PMID:12734009

  ---

  Identification of Down's syndrome critical locus gene SIM2-s as a drug therapy target for solid tumors. PMID:12676991

  ---

  On the origin of mitochondria: a genomics perspective. PMID:12594925

  ---

  GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update. PMID:12520065

  ---

  E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. PMID:12520052

  ---

  The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. PMID:12520046

  ---

  ProtoNet: hierarchical classification of the protein space. PMID:12520020

  ---

  MBGD: microbial genome database for comparative analysis. PMID:12519947

  ---

  Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. PMID:12147470

  ---

  The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis. PMID:12068129

  ---

  A filter that prevents the spread of mail-attachment-type Trojan horse computer worms. PMID:12018608

  ---

  The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. PMID:11869452

  ---

  High genetic variability of the agr locus in Staphylococcus species. PMID:11807079

  ---

  Transterm: a database of mRNAs and translational control elements. PMID:11752323

  ---

  A 3D structure model of integrin alpha 4 beta 1 complex: I. Construction of a homology model of beta 1 and ligand binding analysis. PMID:11751331

  ---

  On the species of origin: diagnosing the source of symbiotic transcripts. PMID:11574056

  ---

  Sodium ion cycle in bacterial pathogens: evidence from cross-genome comparisons. PMID:11528000

  ---

  Assessment of clone identity and sequence fidelity for 1189 IMAGE cDNA clones. PMID:11139630

  ---

  The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes. PMID:11125131

  ---

  DBTBS: a database of Bacillus subtilis promoters and transcription factors. PMID:11125112

  ---

  RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression. PMID:11125107

  ---

  AsMamDB: an alternative splice database of mammals. PMID:11125106

  ---

  BIND--The Biomolecular Interaction Network Database. PMID:11125103

  ---

  The PDB data uniformity project. PMID:11125095

  ---

  The European Large Subunit Ribosomal RNA Database. PMID:11125083

  ---

  Mutations affecting the development of the peripheral nervous system in Drosophila: a molecular screen for novel proteins. PMID:11102367

  ---

  Links from genome proteins to known 3-D structures. PMID:11042161

  ---

  MMDB: 3D structure data in Entrez. PMID:10592236

  ---

  GenBank. PMID:10592170
• http://dx.doi.org/10.1093/nar/gki031

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taxonomy

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:33.962827

---

model organisms

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:33.962827

---

genotype and phenotype

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:33.962827

---

mapping

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:33.962827

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taxonomy model organisms genotype and phenotype mapping