R3531R last accessed: 2022-11-04

Other names: NCBITAXON, National Center for Biotechnology Information (NCBI) Organismal Classification, Entrez Taxonomy

The NCBI Taxonomy is a database of taxonomic information. It does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts.

Webpage:

https://www.ncbi.nlm.nih.gov/taxonomy

Licence:

Name: Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
URL: https://creativecommons.org/publicdomain/zero/1.0/

Publications:

Publications
More detailed information about this field from each metasource.

The NCBI Taxonomy database
PMID: 22139910
metasource: Fairsharing.org
version: FAIRsharing.org: NCBITAXON; NCBI Taxonomy; DOI: https://doi.org/10.25504/FAIRsharing.fj07xj; Last edited: Oct. 2, 2020, 12:54 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

GenBank
PMID: 29140468
metasource: Fairsharing.org
version: FAIRsharing.org: NCBITAXON; NCBI Taxonomy; DOI: https://doi.org/10.25504/FAIRsharing.fj07xj; Last edited: Oct. 2, 2020, 12:54 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

NCBI Taxonomy: a comprehensive update on curation, resources and tools
PMID: 32761142
metasource: Fairsharing.org
version: FAIRsharing.org: NCBITAXON; NCBI Taxonomy; DOI: https://doi.org/10.25504/FAIRsharing.fj07xj; Last edited: Oct. 2, 2020, 12:54 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

http://dx.doi.org/10.1093/nar/gku1127
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The NCBI Taxonomy database PubMed citations: 468.

468 articles citing: The NCBI Taxonomy database

Source files of the Carbohydrate Structure Database: the way to sophisticated analysis of natural glycans. PMID:35354826
Parallel sequence tagging for concept recognition. PMID:35331131
Structure and biosynthesis of carotenoids produced by a novel Planococcus sp. isolated from South Africa. PMID:35305628
TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets. PMID:35243369
Designing sensitive viral diagnostics with machine learning. PMID:35241837
Biochemical and Molecular Dynamics Study of a Novel GH 43 α-l-Arabinofuranosidase/β-Xylosidase From Caldicellulosiruptor saccharolyticus DSM8903. PMID:35223784
A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets. PMID:35205348
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis. PMID:35191776
A positive correlation between GC content and growth temperature in prokaryotes. PMID:35139824
Isolation of a Dissimilatory Iodate-Reducing Aromatoleum sp. From a Freshwater Creek in the San Francisco Bay Area. PMID:35111143
AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite. PMID:35101114
Seasonal Diversity of Microeukaryotes in the Han River, Korea Through 18S rRNA Gene Metabarcoding. PMID:35095269
ExTaxsI: an exploration tool of biodiversity molecular data. PMID:35077538
Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus. PMID:35056480
Scripting Analyses of Genomes in Ensembl Plants. PMID:35037199
Bovine respiratory microbiota of feedlot cattle and its association with disease. PMID:35022062
SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss. PMID:35021210
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids. PMID:34951622
The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects. PMID:34917063
Cryo-EM structures of human RNA polymerase I. PMID:34887565
An Overview of Biomedical Ontologies for Pandemics and Infectious Diseases Representation. PMID:34868401
The Sequence Read Archive: a decade more of explosive growth. PMID:34850094
The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health. PMID:34838100
A multitask transfer learning framework for the prediction of virus-human protein-protein interactions. PMID:34837942
Gcorn fungi: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi. PMID:34829248
Global Distribution and Richness of Armillaria and Related Species Inferred From Public Databases and Amplicon Sequencing Datasets. PMID:34803949
NP-MRD: the Natural Products Magnetic Resonance Database. PMID:34791429
Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. PMID:34787447
The Human Disease Ontology 2022 update. PMID:34755882
Oral Cyanobacteria and Hepatocellular Carcinoma. PMID:34697061
TAGOPSIN: collating taxa-specific gene and protein functional and structural information. PMID:34688246
Gene Network Analysis of Alzheimer's Disease Based on Network and Statistical Methods. PMID:34682089
Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics. PMID:34681121
Implications of divergence of methionine adenosyltransferase in archaea. PMID:34655277
Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy. PMID:34648558
virusMED: an atlas of hotspots of viral proteins. PMID:34614039
PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems. PMID:34593010
Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi. PMID:34575737
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
Structural characterization of NrnC identifies unifying features of dinucleotidases. PMID:34533457
Examination of the microbiota of normal cow milk using MinIONTM nanopore sequencing. PMID:34526421
Distribution of Denitrification among Haloarchaea: A Comprehensive Study. PMID:34442748
KEGG mapping tools for uncovering hidden features in biological data. PMID:34423492
Mining Natural Products with Anticancer Biological Activity through a Systems Biology Approach. PMID:34422220
Amadis: A Comprehensive Database for Association Between Microbiota and Disease. PMID:34335304
Proteomics, Lipidomics, Metabolomics, and 16S DNA Sequencing of Dental Plaque From Patients With Diabetes and Periodontal Disease. PMID:34332123
Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. PMID:34325658
Forming Consensus To Advance Urobiome Research. PMID:34282932
The Infectious Disease Ontology in the age of COVID-19. PMID:34275487
Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum. PMID:34254817
Evolutionary Origins of Drought Tolerance in Spermatophytes. PMID:34239520
Identification and Characterization of Mycobacterial Species Using Whole-Genome Sequences. PMID:34235665
Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures. PMID:34203511
TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes. PMID:34197621
Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. PMID:34187366
Divide-and-conquer: machine-learning integrates mammalian and viral traits with network features to predict virus-mammal associations. PMID:34172731
Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP. PMID:34168213
A standardized archaeal taxonomy for the Genome Taxonomy Database. PMID:34155373
Screening potential insect vectors in a museum biorepository reveals undiscovered diversity of plant pathogens in natural areas. PMID:34141234
Deciphering the diet of a wandering spider (Phoneutria boliviensis; Araneae: Ctenidae) by DNA metabarcoding of gut contents. PMID:34141195
Simulation study and comparative evaluation of viral contiguous sequence identification tools. PMID:34130621
Functional prediction of environmental variables using metabolic networks. PMID:34108539
An Unsupervised Algorithm for Host Identification in Flaviviruses. PMID:34069049
ML-AdVInfect: A Machine-Learning Based Adenoviral Infection Predictor. PMID:34026828
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. PMID:34021239
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank. PMID:34020714
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
Kokumi taste perception is functional in a model carnivore, the domestic cat (Felis catus). PMID:34006911
Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators. PMID:34006865
DOE JGI Metagenome Workflow. PMID:34006627
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
Learning adaptive representations for entity recognition in the biomedical domain. PMID:34001263
ProteoVision: web server for advanced visualization of ribosomal proteins. PMID:33999189
ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies. PMID:33996287
Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries. PMID:33993214
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life. PMID:33970279
Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient. PMID:33906949
Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi. PMID:33906412
ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis. PMID:33895137
Gut microbiota in Immunoglobulin A Nephropathy: a Malaysian Perspective. PMID:33882859
Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning. PMID:33878118
Near-Complete Genome Sequences of Eight Human Astroviruses Recovered from Diarrheal Stool Samples of Hospitalized Children in Coastal Kenya in 2019. PMID:33858926
Phylogenomic Analyses of Nucleotide-Sugar Biosynthetic and Interconverting Enzymes Illuminate Cell Wall Composition in Fungi. PMID:33849982
Prokaryotic taxonomy and nomenclature in the age of big sequence data. PMID:33824426
Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria. PMID:33815349
Maximum levels of global phylogenetic diversity efficiently capture plant services for humankind. PMID:33782579
animalcules: interactive microbiome analytics and visualization in R. PMID:33775256
An immunologically friendly classification of non-peptidic ligands. PMID:33772585
Analysis of human total antibody repertoires in TIF1γ autoantibody positive dermatomyositis. PMID:33772100
Ancient DNA preserved in small bone fragments from the P.W. Lund collection. PMID:33717442
DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions. PMID:33673098
Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences. PMID:33654096
Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. PMID:33649554
Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage. PMID:33642591
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
Resistome analysis of bloodstream infection bacterial genomes reveals a specific set of proteins involved in antibiotic resistance and drug efflux. PMID:33575606
Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing. PMID:33575567
Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states. PMID:33558764
biotoolsSchema: a formalized schema for bioinformatics software description. PMID:33506265
Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef. PMID:33499977
Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution. PMID:33499799
A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses. PMID:33482803
Oral exposure to environmental cyanobacteria toxins: Implications for cancer risk. PMID:33465665
Review on natural products databases: where to find data in 2020. PMID:33431011
A review on viral data sources and search systems for perspective mitigation of COVID-19. PMID:33348368
Possible Transmission Flow of SARS-CoV-2 Based on ACE2 Features. PMID:33322198
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
New Names for Fungi of Medical Importance: Can We Have Our Cake and Eat It Too? PMID:33268539
Data-Driven Modeling for Species-Level Taxonomic Assignment From 16S rRNA: Application to Human Microbiomes. PMID:33262743
DNA methylation signatures to predict the cervicovaginal microbiome status. PMID:33228781
BRENDA, the ELIXIR core data resource in 2021: new developments and updates. PMID:33211880
Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR. PMID:33211099
Widespread endogenization of giant viruses shapes genomes of green algae. PMID:33208937
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. PMID:33205138
Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads. PMID:33198651
OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836
COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database. PMID:33175089
High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method. PMID:33158461
Searching for target-specific and multi-targeting organics for Covid-19 in the Drugbank database with a double scoring approach. PMID:33154404
Genomes OnLine Database (GOLD) v.8: overview and updates. PMID:33152092
Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata. PMID:33150057
KEGG: integrating viruses and cellular organisms. PMID:33125081
MASI: microbiota-active substance interactions database. PMID:33125077
An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature. PMID:33123100
Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy. PMID:33112882
Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation. PMID:33105659
Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia. PMID:33082403
Peryton: a manual collection of experimentally supported microbe-disease associations. PMID:33080028
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
A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease. PMID:33053371
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics. PMID:33013807
A systematic comparison of chloroplast genome assembly tools. PMID:32988404
When mycologists describe new species, not all relevant information is provided (clearly enough). PMID:32982558
Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction. PMID:32932905
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
Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. PMID:32883995
The Best-Practice Organism for Single-Species Studies of Antimicrobial Efficacy against Biofilms Is Pseudomonas aeruginosa. PMID:32872560
Assembling Reads Improves Taxonomic Classification of Species. PMID:32824429
Metagenomic Studies in Inflammatory Skin Diseases. PMID:32813091
ReDU: a framework to find and reanalyze public mass spectrometry data. PMID:32807955
The diversity of maternal-age effects upon pre-adult survival across animal species. PMID:32781953
NCBI Taxonomy: a comprehensive update on curation, resources and tools. PMID:32761142
The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community. PMID:32756341
Guidelines for human gene nomenclature. PMID:32747822
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
Novel aspects of Cell Division Cycle and Apoptosis Regulator 1 (CCAR1) protein in Morus notabilis: an in silico approach. PMID:32693681
Bacterial chemolithoautotrophy via manganese oxidation. PMID:32669693
Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. PMID:32661357
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. PMID:32657362
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
Data-Driven Inference Reveals Distinct and Conserved Dynamic Pathways of Tool Use Emergence across Animal Taxa. PMID:32629611
MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding. PMID:32620910
LEMMI: a continuous benchmarking platform for metagenomics classifiers. PMID:32616517
Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer. PMID:32611311
COVID-KOP: Integrating Emerging COVID-19 Data with the ROBOKOP Database. PMID:32601612
The Presence of Plant-Associated Bacteria Alters Responses to N-acyl Homoserine Lactone Quorum Sensing Signals that Modulate Nodulation in Medicago Truncatula. PMID:32580337
GTDB: an integrated resource for glycosyltransferase sequences and annotations. PMID:32542364
Comprehensive database and evolutionary dynamics of U12-type introns. PMID:32484558
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads. PMID:32471343
Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians. PMID:32450885
Impact of C-terminal amino acid composition on protein expression in bacteria. PMID:32449593
An Unusual Amino Acid Substitution Within Hummingbird Cytochrome c Oxidase Alters a Key Proton-Conducting Channel. PMID:32444359
Faecal calprotectin and gut microbiota do not predict enteropathy in very preterm infants. PMID:32418251
SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction. PMID:32411695
Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank. PMID:32398145
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. PMID:32392342
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. PMID:32379317
Species Classification for Neuroscience Literature Based on Span of Interest Using Sequence-to-Sequence Learning Model. PMID:32372933
Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities - a proof of concept under laboratory conditions. PMID:32355612
CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data. PMID:32345331
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
Repositories for Taxonomic Data: Where We Are and What is Missing. PMID:32298457
R-loop-forming Sequences Analysis in Thousands of Viral Genomes Identify A New Common Element in Herpesviruses. PMID:32286400
Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts. PMID:32209692
Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA. PMID:32184999
Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV. PMID:32142938
Characteristics of the endometrium in menstruating species: lessons learned from the animal kingdom†. PMID:32129461
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
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
Dead Rhizophagus irregularis biomass mysteriously stimulates plant growth. PMID:32062707
Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping. PMID:31941798
Automatic construction of metabolic models with enzyme constraints. PMID:31937255
CAMITAX: Taxon labels for microbial genomes. PMID:31909794
Emergence and Evolution of ERM Proteins and Merlin in Metazoans. PMID:31851361
GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804
Transcriptome and microbiome of coconut rhinoceros beetle (Oryctes rhinoceros) larvae. PMID:31818246
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PMID:31800571
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. PMID:31792218
New C-Terminal Conserved Regions of Tafazzin, a Catalyst of Cardiolipin Remodeling. PMID:31781330
Improved metagenomic analysis with Kraken 2. PMID:31779668
Myofibril diameter is set by a finely tuned mechanism of protein oligomerization in Drosophila. PMID:31746737
Geography and habitat predominate over climate influences on arbuscular mycorrhizal fungal communities of mid-European meadows. PMID:31724087
In Silico Study of Rett Syndrome Treatment-Related Genes, MECP2, CDKL5, and FOXG1, by Evolutionary Classification and Disordered Region Assessment. PMID:31717404
Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia. PMID:31709051
PlantRegMap: charting functional regulatory maps in plants. PMID:31701126
How the past impacts the future: modelling the performance of evolutionarily distinct mammals through time. PMID:31679492
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. PMID:31667520
Brevibacillus antibioticus sp. nov., with a broad range of antibacterial activity, isolated from soil in the Nakdong River. PMID:31659685
MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PMID:31648227
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. PMID:31640809
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
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
SEAweb: the small RNA Expression Atlas web application. PMID:31598718
gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. PMID:31584099
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. PMID:31584075
Ensemble QSAR Modeling to Predict Multispecies Fish Toxicity Lethal Concentrations and Points of Departure. PMID:31560848
Genetic robustness of let-7 miRNA sequence-structure pairs. PMID:31548338
Gephebase, a database of genotype-phenotype relationships for natural and domesticated variation in Eukaryotes. PMID:31544935
Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis. PMID:31523127
GMrepo: a database of curated and consistently annotated human gut metagenomes. PMID:31504765
Challenges in the construction of knowledge bases for human microbiome-disease associations. PMID:31488215
A Structure-Informed Atlas of Human-Virus Interactions. PMID:31474372
Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life. PMID:31462411
A corpus of plant-disease relations in the biomedical domain. PMID:31461491
ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database. PMID:31412866
Clinical gamasoidosis and antibody response in two patients infested with Ornithonyssus bursa (Acari: Gamasida: Macronyssidae). PMID:31367978
Herb-Induced Liver Injury: Phylogenetic Relationship, Structure-Toxicity Relationship, and Herb-Ingredient Network Analysis. PMID:31349548
JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface. PMID:31331268
geneHummus: an R package to define gene families and their expression in legumes and beyond. PMID:31319791
Multiple origins of reverse transcriptases linked to CRISPR-Cas systems. PMID:31276437
An ontology for representing hematologic malignancies: the cancer cell ontology. PMID:31272372
metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes. PMID:31235611
Metabolic route computation in organism communities. PMID:31174602
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. PMID:31160594
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: 198.

198 articles citing: GenBank

Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection. PMID:35787252
CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices. PMID:35758788
Target capture sequencing reveals a monoclonal outbreak of respiratory syncytial virus B infections among adult hematologic patients. PMID:35729671
Comparative Analysis of the Chloroplast Genomes of Quercus × morehus and the Presumptive Parents Q. wislizeni and Q. kelloggii (Fagaceae) from California. PMID:35695497
Pan-cancer analyses reveal the genetic and pharmacogenomic landscape of transient receptor potential channels. PMID:35614079
T-G-A Deficiency Pattern in Protein-Coding Genes and Its Potential Reason. PMID:35602045
Six New Species of Tomentella (Thelephorales, Basidiomycota) From Tropical Pine Forests in Central Vietnam. PMID:35547107
Morphological and molecular characterization of a new autochthonous Trichoderma sp. isolate and its biocontrol efficacy against Alternaria sp. PMID:35531149
First two mitochondrial genomes for the order Filobasidiales reveal novel gene rearrangements and intron dynamics of Tremellomycetes. PMID:35501936
Urban Wildlife Crisis: Australian Silver Gull Is a Bystander Host to Widespread Clinical Antibiotic Resistance. PMID:35469421
Comparing protein-protein interaction networks of SARS-CoV-2 and (H1N1) influenza using topological features. PMID:35393450
The Microbiome in Osteoarthritis: a Narrative Review of Recent Human and Animal Model Literature. PMID:35389162
Next-generation sequencing: insights to advance clinical investigations of the microbiome. PMID:35362479
Expanding the Universe of Hemoplasmas: Multi-Locus Sequencing Reveals Putative Novel Hemoplasmas in Lowland Tapirs (Tapirus terrestris), the Largest Land Mammals in Brazil. PMID:35336189
Comparative Genome Analysis of 'Candidatus Phytoplasma luffae' Reveals the Influential Roles of Potential Mobile Units in Phytoplasma Evolution. PMID:35300489
Changes in the Mitochondrial Dynamics and Functions Together with the mRNA/miRNA Network in the Heart Tissue Contribute to Hypoxia Adaptation in Tibetan Sheep. PMID:35268153
Complete Chloroplast Genome of Topotype Material of the Coast Live Oak Quercus agrifolia Née var. agrifolia (Fagaceae) from California. PMID:35254126
Chromosome-scale Echinococcus granulosus (genotype G1) genome reveals the Eg95 gene family and conservation of the EG95-vaccine molecule. PMID:35241789
The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes. PMID:35216360
Phosphate Solubilizing Microorganism Bacillus sp. MVY-004 and Its Significance for Biomineral Fertilizers' Development in Agrobiotechnology. PMID:35205120
Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential. PMID:35049133
Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. PMID:35022048
On six African species of Lyomyces and Xylodon. PMID:35005580
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. PMID:34876495
piRBase: integrating piRNA annotation in all aspects. PMID:34871445
Genetic Diversity and Characteristics of bla NDM-Positive Plasmids in Escherichia coli. PMID:34867846
Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses. PMID:34858377
The evolution of cheating in viruses. PMID:34836945
First report of mitochondrial COI in foraminifera and implications for DNA barcoding. PMID:34772985
RESCRIPt: Reproducible sequence taxonomy reference database management. PMID:34748542
Combination of Pseudo-LC-NMR and HRMS/MS-Based Molecular Networking for the Rapid Identification of Antimicrobial Metabolites From Fusarium petroliphilum. PMID:34746230
Occurrence of south- and north-seeking multicellular magnetotactic prokaryotes in a coastal lagoon in the South Hemisphere. PMID:34738176
Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade. PMID:34677568
Mitochondrial genomes of five Hyphessobrycon tetras and their phylogenetic implications. PMID:34594536
Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank. PMID:34594153
PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems. PMID:34593010
Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas. PMID:34588691
In Silico Analysis of Fungal and Chloride-Dependent α-Amylases within the Family GH13 with Identification of Possible Secondary Surface-Binding Sites. PMID:34577174
Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions. PMID:34549988
DNA-based taxonomy of a mangrove-associated community of fishes in Southeast Asia. PMID:34493747
Molecular Epidemiology and Characterization of Picobirnavirus in Wild Deer and Cattle from Australia: Evidence of Genogroup I and II in the Upper Respiratory Tract. PMID:34452357
Development of two loop-mediated isothermal amplification (LAMP) genomics-informed diagnostic protocols for rapid detection of Pantoea species on rice. PMID:34434739
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. PMID:34417604
Study of the Langat virus RNA-dependent RNA polymerase through homology modeling. PMID:34316455
Evolution of Toll, Spatzle and MyD88 in insects: the problem of the Diptera bias. PMID:34289811
In Silico Identification and Functional Characterization of Conserved miRNAs in the Genome of Cryptosporidium parvum. PMID:34262265
Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes. PMID:34253028
Wide Distribution and Specific Resistance Pattern to Third-Generation Cephalosporins of Enterobacter cloacae Complex Members in Humans and in the Environment in Guadeloupe (French West Indies). PMID:34248862
Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples. PMID:34247601
EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains. PMID:34196123
Landscape and selection of vaccine epitopes in SARS-CoV-2. PMID:34127050
GUNC: detection of chimerism and contamination in prokaryotic genomes. PMID:34120611
Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of AtENO2 Regulating Seed Germination. PMID:34065034
Endophytic Bacterial Isolates From Halophytes Demonstrate Phytopathogen Biocontrol and Plant Growth Promotion Under High Salinity. PMID:34017321
PhyloPrimer: a taxon-specific oligonucleotide design platform. PMID:33986979
A putative novel starch-binding domain revealed by in silico analysis of the N-terminal domain in bacterial amylomaltases from the family GH77. PMID:33968573
Weed-infecting viruses in a tropical agroecosystem present different threats to crops and evolutionary histories. PMID:33909644
A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia. PMID:33906963
iBLAST: Incremental BLAST of new sequences via automated e-value correction. PMID:33886589
Reproduction of East-African bats may guide risk mitigation for coronavirus spillover. PMID:33824945
isa4j: a scalable Java library for creating ISA-Tab metadata. PMID:33728038
Catalase impairs Leishmania mexicana development and virulence. PMID:33724149
Unification and extensive diversification of M/Orf3-related ion channel proteins in coronaviruses and other nidoviruses. PMID:33692906
The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding. PMID:33664667
KIR2DL4 genetic diversity in a Brazilian population sample: implications for transcription regulation and protein diversity in samples with different ancestry backgrounds. PMID:33595694
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences. PMID:33507271
CE16 acetylesterases: in silico analysis, catalytic machinery prediction and comparison with related SGNH hydrolases. PMID:33505839
Deciphering the Subtype Differentiation History of SARS-CoV-2 Based on a New Breadth-First Searching Optimized Alignment Method Over a Global Data Set of 24,768 Sequences. PMID:33505425
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads. PMID:33503026
Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. PMID:33444546
Functional refolding of the penetration protein on a non-enveloped virus. PMID:33442061
Intra- and Inter-Host Assessment of Bartonella Diversity with Focus on Non-Hematophagous Bats and Associated Ectoparasites from Brazil. PMID:33227996
Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data. PMID:33219685
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. PMID:33196801
Platinum-Quality Mitogenome Haplotypes from United States Populations. PMID:33138247
An Earliest Endosymbiont, Wolbachia massiliensis sp. nov., Strain PL13 from the Bed Bug (Cimex hemipterus), Type Strain of a New Supergroup T. PMID:33138055
Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes. PMID:33125315
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. PMID:33119741
PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs. PMID:33079992
Fruit host-dependent fungal communities in the microbiome of wild Queensland fruit fly larvae. PMID:33024226
Continental-scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria. PMID:33014636
Application of whole genome sequencing to query a potential outbreak of Elizabethkingia anophelis in Ontario, Canada. PMID:32974512
Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks. PMID:32973219
Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-catalytic terminal domains. PMID:32953382
Unlocking COVID therapeutic targets: A structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV Spike. PMID:32913581
Applied Barcoding: The Practicalities of DNA Testing for Herbals. PMID:32899738
Communities of Fungi in Black Cherry Stumps and Effects of Herbicide. PMID:32878134
Complete Genome Sequence of "Candidatus Phytoplasma asteris" RP166, a Plant Pathogen Associated with Rapeseed Phyllody Disease in Poland. PMID:32855252
Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty. PMID:32798768
Interpretation of psychiatric genome-wide association studies with multispecies heterogeneous functional genomic data integration. PMID:32791514
Advancing biodiversity assessments with environmental DNA: Long-read technologies help reveal the drivers of Amazonian fungal diversity. PMID:32760545
Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis. PMID:32754131
Thinning Partially Mitigates the Impact of Atlantic Forest Replacement by Pine Monocultures on the Soil Microbiome. PMID:32719665
GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography. PMID:32683454
Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. PMID:32676598
Hygrophorus subsection Hygrophorus (Hygrophoraceae, Agaricales) in China. PMID:32675938
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. PMID:32657362
Metachromatic leukodystrophy genotypes in The Netherlands reveal novel pathogenic ARSA variants in non-Caucasian patients. PMID:32632536
Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics? PMID:32596311
Diverse and unique viruses discovered in the surface water of the East China Sea. PMID:32590932
Characterization of the Phenanthrene-Degrading Sphingobium yanoikuyae SJTF8 in Heavy Metal Co-Existing Liquid Medium and Analysis of Its Metabolic Pathway. PMID:32586023
Landscape and Selection of Vaccine Epitopes in SARS-CoV-2. PMID:32577654
Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ. PMID:32563153
Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence. PMID:32528034
Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity. PMID:32518251
Global distribution of a chlorophyll f cyanobacterial marker. PMID:32457503
Biochemical Characteristics and a Genome-Scale Metabolic Model of an Indian Euryhaline Cyanobacterium with High Polyglucan Content. PMID:32365713
Catalase and Ascorbate Peroxidase in Euglenozoan Protists. PMID:32344595
Genome-Wide Identification and Characterization of Drought Stress Responsive microRNAs in Tibetan Wild Barley. PMID:32316632
Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics. PMID:32265950
MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. PMID:32245390
Single-Nucleotide Polymorphism-Based Genetic Diversity Analysis of Clinical Pseudomonas aeruginosa Isolates. PMID:32196089
Safety Considerations for Malaria Volunteer Infection Studies: A Mini-Review. PMID:32189610
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes. PMID:32161947
On the complementarity of DNA barcoding and morphology to distinguish benign endemic insects from possible pests: the case of Dirioxa pornia and the tribe Acanthonevrini (Diptera: Tephritidae: Phytalmiinae) in Australia. PMID:32096585
Comparative Genomic Analysis of a Novel Strain of Taiwan Hot-Spring Cyanobacterium Thermosynechococcus sp. CL-1. PMID:32082292
The genus Catathelasma (Catathelasmataceae, Basidiomycota) in China. PMID:32076385
Contents, Construction Methods, Data Resources, and Functions Comparative Analysis of Bacteria Databases. PMID:32071553
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data. PMID:32053657
Structure of the prefusion-locking broadly neutralizing antibody RVC20 bound to the rabies virus glycoprotein. PMID:32001700
Genomic Analysis of Wolbachia from Laodelphax striatellus (Delphacidae, Hemiptera) Reveals Insights into Its "Jekyll and Hyde" Mode of Infection Pattern. PMID:31958110
Diffuse capillary malformation with overgrowth contains somatic PIK3CA variants. PMID:31909475
Characterizing the ribosomal tandem repeat and its utility as a DNA barcode in lichen-forming fungi. PMID:31906844
LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation. PMID:31888452
From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach. PMID:31866739
Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum. PMID:31861401
The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia. PMID:31844092
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
A recombinase polymerase amplification-lateral flow dipstick assay for rapid detection of the quarantine citrus pathogen in China, Phytophthora hibernalis. PMID:31763074
Swordfish or Shark Slice? A Rapid Response by COIBar-RFLP. PMID:31683903
In silico Screening and Heterologous Expression of a Polyethylene Terephthalate Hydrolase (PETase)-Like Enzyme (SM14est) With Polycaprolactone (PCL)-Degrading Activity, From the Marine Sponge-Derived Strain Streptomyces sp. SM14. PMID:31632361
Genomic Characterization of the Periwinkle Leaf Yellowing (PLY) Phytoplasmas in Taiwan. PMID:31608032
Genome-wide Identification and Characterization of a Superfamily of Bacterial Extracellular Contractile Injection Systems. PMID:31597107
Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. PMID:31584084
Genome Mining Coupled with OSMAC-Based Cultivation Reveal Differential Production of Surugamide A by the Marine Sponge Isolate Streptomyces sp. SM17 When Compared to Its Terrestrial Relative S. albidoflavus J1074. PMID:31561472
Ice Nucleation Properties of Ice-binding Proteins from Snow Fleas. PMID:31557956
Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. PMID:31510914
Comparative Evaluation of a Novel Recombinase Polymerase Amplification-Lateral Flow Dipstick (RPA-LFD) Assay, LAMP, Conventional PCR, and Leaf-Disc Baiting Methods for Detection of Phytophthora sojae. PMID:31447827
The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations. PMID:31405380
Analysis of Vibrio cholerae genomes identifies new type VI secretion system gene clusters. PMID:31405375
Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential. PMID:31404169
In Silico Phylogenetic and Structural Analyses of Plant Endogenous Danger Signaling Molecules upon Stress. PMID:31396307
Weighted Fused Pathway Graphical Lasso for Joint Estimation of Multiple Gene Networks. PMID:31396259
Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. PMID:31363753
Differentiations in Gene Content and Expression Response to Virulence Induction Between Two Agrobacterium Strains. PMID:31354658
Influenza passaging annotations: what they tell us and why we should listen. PMID:31275610
Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials. PMID:31216285
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
Four new East Asian species of Aleurodiscus with echinulate basidiospores. PMID:31139010
DiVenn: An Interactive and Integrated Web-Based Visualization Tool for Comparing Gene Lists. PMID:31130993
β-Aminopeptidases: Insight into Enzymes without a Known Natural Substrate. PMID:31126950
Contraction of the ROS Scavenging Enzyme Glutathione S-Transferase Gene Family in Cetaceans. PMID:31092607
Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. PMID:31092555
In silico Approach for Unveiling the Glycoside Hydrolase Activities in Faecalibacterium prausnitzii Through a Systematic and Integrative Large-Scale Analysis. PMID:31024464
Complete Genome Sequence of Spiroplasma alleghenense PLHS-1T (ATCC 51752), a Bacterium Isolated from Scorpion Fly (Panorpa helena). PMID:31023800
Prunus genetics and applications after de novo genome sequencing: achievements and prospects. PMID:30962943
OsNAC-like transcription factor involved in regulating seed-storage protein content at different stages of grain filling in rice under aerobic conditions. PMID:30945674
Development of Phytomonas lipae sp. n. (Kinetoplastea: Trypanosomatidae) in the true bug Coreus marginatus (Heteroptera: Coreidae) and insights into the evolution of life cycles in the genus Phytomonas. PMID:30943229
Four new corticioid species in Trechisporales (Basidiomycota) from East Asia and notes on phylogeny of the order. PMID:30930653
Phylogenetic and morphological studies in Xylodon (Hymenochaetales, Basidiomycota) with the addition of four new species. PMID:30858753
The Pathogenic Neisseria Use a Streamlined Set of Peptidoglycan Degradation Proteins for Peptidoglycan Remodeling, Recycling, and Toxic Fragment Release. PMID:30766523
The plastid and mitochondrial genomes of Eucalyptus grandis. PMID:30760198
Transcriptomic Analysis of the Spider Venom Gland Reveals Venom Diversity and Species Consanguinity. PMID:30682870
Gypsy moth genome provides insights into flight capability and virus-host interactions. PMID:30642971
Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels. PMID:30631317
EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA. PMID:30629718
Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences. PMID:30535314
Genetic assessment of a bighorn sheep population expansion in the Silver Bell Mountains, Arizona. PMID:30533296
Origins and Evolution of the Global RNA Virome. PMID:30482837
Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq. PMID:30479362
Characterization and Genomic Analyses of Pseudomonas aeruginosa Podovirus TC6: Establishment of Genus Pa11virus. PMID:30410478
Database resources of the National Center for Biotechnology Information. PMID:30395293
The European Nucleotide Archive in 2018. PMID:30395270
Additions to the taxonomy of Lagarobasidium and Xylodon (Hymenochaetales, Basidiomycota). PMID:30386167
GenBank. PMID:30365038
Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human. PMID:30357418
DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data. PMID:30357349
Taxonomy and phylogeny of Dichostereum (Russulales), with descriptions of three new species from southern China. PMID:30344439
Differential Usefulness of Nine Commonly Used Genetic Markers for Identifying Phytophthora Species. PMID:30337915
Growing and cultivating the forest genomics database, TreeGenes. PMID:30239664
Insights into the life strategy of the common marine diatom Chaetoceros peruvianus Brightwell. PMID:30208090
Attack of the clones: whole genome-based characterization of two closely related enterohemorrhagic Escherichia coli O26 epidemic lineages. PMID:30170539
The scale-free nature of protein sequence space. PMID:30067815
ChemDIS 2: an update of chemical-disease inference system. PMID:30053236
Comparative genomic analysis of eutherian adiponectin genes. PMID:30003153
In silico analysis of the α-amylase family GH57: eventual subfamilies reflecting enzyme specificities. PMID:29998051
Horizontal transfer of BovB and L1 retrotransposons in eukaryotes. PMID:29983116
Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation. PMID:29970463
Plasmids of Psychrotolerant Polaromonas spp. Isolated From Arctic and Antarctic Glaciers - Diversity and Role in Adaptation to Polar Environments. PMID:29967598
Escherichia coli ItaT is a type II toxin that inhibits translation by acetylating isoleucyl-tRNAIle. PMID:29931259
MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis. PMID:29927748
Biological meaning of "habitable zone" in nucleotide composition space. PMID:29892513
In silico Phylogenetic Analysis of hAT Transposable Elements in Plants. PMID:29882803
No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects. PMID:29806194
The NCBI BioCollections Database. PMID:29688360
A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes. PMID:29643938
ProtaBank: A repository for protein design and engineering data. PMID:29575358
NCBI Taxonomy: a comprehensive update on curation, resources and tools PubMed citations: 110.

110 articles citing: NCBI Taxonomy: a comprehensive update on curation, resources and tools

A spectral analysis of stem bark for boreal and temperate tree species. PMID:35342560
Coelastrella terrestris for Adonixanthin Production: Physiological Characterization and Evaluation of Secondary Carotenoid Productivity. PMID:35323473
Bias at the third nucleotide of codon pairs in virus and host genomes. PMID:35296743
TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets. PMID:35243369
In-Silico Detection of Oral Prokaryotic Species With Highly Similar 16S rRNA Sequence Segments Using Different Primer Pairs. PMID:35223533
Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes. PMID:35217859
Viromes of Freshwater Fish with Lacustrine and Diadromous Life Histories Differ in Composition. PMID:35215850
A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs. PMID:35211148
Biodiversity and Physiological Characteristics of Novel Faecalibacterium prausnitzii Strains Isolated from Human Feces. PMID:35208752
PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types. PMID:35208748
BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies. PMID:35194141
Identification of bovine respiratory disease through the nasal microbiome. PMID:35193707
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis. PMID:35191776
Legionella pneumophila regulates host cell motility by targeting Phldb2 with a 14-3-3ζ-dependent protease effector. PMID:35175192
Limitations of Phylogenomic Data Can Drive Inferred Speciation Rate Shifts. PMID:35166841
The curse of the uncultured fungus. PMID:35153529
Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex. PMID:35082828
Petabase-scale sequence alignment catalyses viral discovery. PMID:35082445
Isolation and Characterization of a Novel Temperate Escherichia coli Bacteriophage, Kapi1, Which Modifies the O-Antigen and Contributes to the Competitiveness of Its Host during Colonization of the Murine Gastrointestinal Tract. PMID:35073745
Substrate preferences, phylogenetic and biochemical properties of proteolytic bacteria present in the digestive tract of Nile tilapia (Oreochromis niloticus). PMID:35071947
Phylostat: a web-based tool to analyze paralogous clade divergence in phylogenetic trees. PMID:35068947
Complete chloroplast genome of Campsis grandiflora (Thunb.) schum and systematic and comparative analysis within the family Bignoniaceae. PMID:35059974
The Azurin Coding Gene: Origin and Phylogenetic Distribution. PMID:35056457
A Comprehensive Evaluation of Enterobacteriaceae Primer Sets for Analysis of Host-Associated Microbiota. PMID:35055964
Bacterial Survey in the Guts of Domestic Silkworms, Bombyx mori L. PMID:35055946
Exploring the universal healthy human gut microbiota around the World. PMID:35035791
Genome Sequence of the Early 20th-Century Extreme Halophile Halobacterium sp. Strain NRC-34001. PMID:35023769
The colors of life: an interdisciplinary artist-in-residence project to research fungal pigments as a gateway to empathy and understanding of microbial life. PMID:35012670
Characterization of the complete mitochondrial genome of Haemadipsa tianmushana Song 1977 (Hirudiniformes, Haemadipsidae) and its phylogenetic analysis. PMID:35005228
Using Genomics to Shape the Definition of the Agglutinin-Like Sequence (ALS) Family in the Saccharomycetales. PMID:34970511
Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank. PMID:34966599
Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic. PMID:34956155
Isolation and Characterization of Group III Campylobacter jejuni-Specific Bacteriophages From Germany and Their Suitability for Use in Food Production. PMID:34956123
Bacterial species identification using MALDI-TOF mass spectrometry and machine learning techniques: A large-scale benchmarking study. PMID:34938408
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance. PMID:34908470
Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations. PMID:34889729
Depletion of Lipocalin 2 (LCN2) in Mice Leads to Dysbiosis and Persistent Colonization with Segmented Filamentous Bacteria. PMID:34884961
Genome Sequence of Halobacterium sp. Strain BOL4-2, Isolated and Cultured from Salar de Uyuni, Bolivia. PMID:34854697
Expression Atlas update: gene and protein expression in multiple species. PMID:34850121
The Sequence Read Archive: a decade more of explosive growth. PMID:34850094
Expanded analyses of the functional correlations within structural classifications of glycoside hydrolases. PMID:34849197
Molecular and Clinical Aspects of Chronic Manifestations in Chagas Disease: A State-of-the-Art Review. PMID:34832648
Correcting the Estimation of Viral Taxa Distributions in Next-Generation Sequencing Data after Applying Artificial Neural Networks. PMID:34828361
ORPER: A Workflow for Constrained SSU rRNA Phylogenies. PMID:34828348
Biologically-oriented mud volcano database: muddy_db. PMID:34820191
Customization of a DADA2-based pipeline for fungal internal transcribed spacer 1 (ITS1) amplicon data sets. PMID:34813499
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison. PMID:34788838
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. PMID:34788826
Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences. PMID:34752446
RESCRIPt: Reproducible sequence taxonomy reference database management. PMID:34748542
BioSamples database: FAIRer samples metadata to accelerate research data management. PMID:34747489
Bacterial Communities Present Distinct Co-occurrence Networks in Sediment and Water of the Thermokarst Lakes in the Yellow River Source Area. PMID:34745028
Assessing the Biodegradation of Vulcanised Rubber Particles by Fungi Using Genetic, Molecular and Surface Analysis. PMID:34733834
ViRBase v3.0: a virus and host ncRNA-associated interaction repository with increased coverage and annotation. PMID:34723320
CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. PMID:34718745
BacDive in 2022: the knowledge base for standardized bacterial and archaeal data. PMID:34718743
mBodyMap: a curated database for microbes across human body and their associations with health and diseases. PMID:34718713
The Natural Products Atlas 2.0: a database of microbially-derived natural products. PMID:34718710
MOSGA 2: Comparative genomics and validation tools. PMID:34712396
Nanomaterial-Based Antifungal Therapies to Combat Fungal Diseases Aspergillosis, Coccidioidomycosis, Mucormycosis, and Candidiasis. PMID:34684252
The complete mitochondrial genome of Toxotes chatareus (Toxotes; Toxotidae; Carangaria) assembled by the next-generation sequencing data and phylogenetic analysis of Carangaria. PMID:34676299
AncestralClust: Clustering of Divergent Nucleotide Sequences by Ancestral Sequence Reconstruction using Phylogenetic Trees. PMID:34668516
Thylakoid attachment to the plasma membrane in Synechocystis sp. PCC 6803 requires the AncM protein. PMID:34665262
Extracellular Vesicle Proteomes Shed Light on the Evolutionary, Interactive, and Functional Divergence of Their Biogenesis Mechanisms. PMID:34660591
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database. PMID:34643708
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. PMID:34632381
Microbial storage and its implications for soil ecology. PMID:34593996
Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria. PMID:34546073
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. PMID:34520557
The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis. PMID:34516368
gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites. PMID:34500458
Gut Microbiota in Military International Travelers with Doxycycline Malaria Prophylaxis: Towards the Risk of a Simpson Paradox in the Human Microbiome Field. PMID:34451527
The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference? PMID:34440517
Phage Diversity in the Human Gut Microbiome: a Taxonomist's Perspective. PMID:34402650
Genome Characterization of Nocturne116, Novel Lactococcus lactis-Infecting Phage Isolated from Moth. PMID:34361975
Polyclonal antibody-based immunohistochemical detection of intraleukocytic Theileria parasites in roan and sable antelopes. PMID:34333997
An Overview of 24 Years of Molecular Phylogenetic Studies in Phallales (Basidiomycota) With Notes on Systematics, Geographic Distribution, Lifestyle, and Edibility. PMID:34305850
Complete Genome Sequence of an Extremely Halophilic Archaeon from Great Salt Lake, Halobacterium sp. GSL-19. PMID:34264097
Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health. PMID:34196581
Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. PMID:34187366
Rhodobacter sphaeroides CarD Negatively Regulates Its Own Promoter. PMID:34152199
Host-Parasite Interaction of Atlantic salmon (Salmo salar) and the Ectoparasite Neoparamoeba perurans in Amoebic Gill Disease. PMID:34135900
Scaling relation between genome length and particle size of viruses provides insights into viral life history. PMID:34113814
A TonB-Like Protein, SjdR, Is Involved in the Structural Definition of the Intercellular Septa in the Heterocyst-Forming Cyanobacterium Anabaena. PMID:34101487
The critical importance of vouchers in genomics. PMID:34061026
Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models. PMID:34059925
Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants. PMID:34059664
Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments. PMID:34040064
How to publish a new fungal species, or name, version 3.0. PMID:33934723
Genome-wide association analysis of bean fly resistance and agro-morphological traits in common bean. PMID:33914796
Fungal taxonomy and sequence-based nomenclature. PMID:33903746
Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages. PMID:33865444
The Conservation of Low Complexity Regions in Bacterial Proteins Depends on the Pathogenicity of the Strain and Subcellular Location of the Protein. PMID:33809982
Autochthonous Trypanosoma spp. in European Mammals: A Brief Journey amongst the Neglected Trypanosomes. PMID:33805748
Occurrence and diversity of viruses associated with cyanobacterial communities in a Brazilian freshwater reservoir. PMID:33791954
Non-essential ribosomal proteins in bacteria and archaea identified using COGs. PMID:33753464
Recognizing species as a new focus of virus research. PMID:33662033
Characterization and complete genome sequence of Privateer, a highly prolate Proteus mirabilis podophage. PMID:33614267
Molecular Signatures of Inflammatory Profile and B-Cell Function in Patients with Severe Fever with Thrombocytopenia Syndrome. PMID:33593977
Quantifying the taxonomic bias in enzymology. PMID:33583070
Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation. PMID:33536487
Current Evidence on the Role of the Gut Microbiome in ADHD Pathophysiology and Therapeutic Implications. PMID:33467150
Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics. PMID:33441133
The Dfam community resource of transposable element families, sequence models, and genome annotations. PMID:33436076
Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods. PMID:33363701
The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa. PMID:33266327
GenBank. PMID:33196830
SMART: recent updates, new developments and status in 2020. PMID:33104802
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. PMID:32986829
http://dx.doi.org/10.1093/nar/gku1127

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More detailed information about this field from each metasource.

taxonomic classification
metasource: Fairsharing.org
version: FAIRsharing.org: NCBITAXON; NCBI Taxonomy; DOI: https://doi.org/10.25504/FAIRsharing.fj07xj; Last edited: Oct. 2, 2020, 12:54 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

taxonomy and identification
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

archaea
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

bacteria
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

biological classification
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

biological nomenclature
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

cladistics
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

eukaryota
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

genomes
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

nucleotide sequences
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

phylogenetics
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

taxa
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

viroids
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

viruses
metasource: re3data.org
version: re3data.org: NCBI Taxonomy; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3531R last accessed: 2022-11-04

taxonomic classification genomics taxonomy and identification archaea bacteria biological classification biological nomenclature cladistics eukaryota genomes nucleotide sequences phylogenetics taxa viroids viruses

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NCBI Taxonomy Database

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Taxonomic Rank Vocabulary

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