R31W6B last accessed: 2022-11-04

UniProt Reference Clusters (UniRef)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.660724

uniref
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.660724

Other names: UniProt Reference Clusters, UniProt Reference Clusters (UniRef), uniref

The UniProt Reference Clusters are three separate datasets that compress sequence space at different resolutions, achieved by merging sequences and sub-sequences that are 100% (UniRef100), >=90% (UniRef90), or >=50% (UniRef50) identical, regardless of source organism. The UniRef100 database provides the most comprehensive non-redundant coverage of the known protein sequence space including not only all of UniProtKB but also splice variants that are not separated out in these databases, as well as additional active sequences from UniParc. The UniRef90 and UniRef50 databases provide a more even sampling of sequences by reducing the numbers of closely related sequence. This speeds sequence similarity searches while rendering such searches more informative. The compression of UniRef100 into UniRef90 and UniRef50 yields size reductions of approximately 40% and 65%, respectively.

Webpage:

http://www.uniprot.org/uniref/

Licence:

Name: CC
URL: https://creativecommons.org/licenses/by-nd/3.0/

Publications:

Publications
More detailed information about this field from each metasource.

UniRef: comprehensive and non-redundant UniProt reference clusters
PMID: 17379688
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.660724

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
PMID: 25398609
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.660724

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/10/1282
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

UniRef: comprehensive and non-redundant UniProt reference clusters PubMed citations: 504.

504 articles citing: UniRef: comprehensive and non-redundant UniProt reference clusters

Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli. PMID:35680894
Discovery of bioactive microbial gene products in inflammatory bowel disease. PMID:35614211
Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment. PMID:35534620
Analysis of host-pathogen gene association networks reveals patient-specific response to streptococcal and polymicrobial necrotising soft tissue infections. PMID:35505341
Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome. PMID:35484230
Chemotaxis shapes the microscale organization of the ocean's microbiome. PMID:35444277
Predicting the functional impact of KCNQ1 variants with artificial neural networks. PMID:35442947
Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort. PMID:35335664
Human gut bacteria produce ΤΗ17-modulating bile acid metabolites. PMID:35296854
Improved prediction of protein-protein interactions using AlphaFold2. PMID:35273146
Head transcriptome profiling of glossiphoniid leech (Helobdella austinensis) reveals clues about proboscis development. PMID:35232253
Identification and Validation of Ikaros (IKZF1) as a Cancer Driver Gene for Marek's Disease Virus-Induced Lymphomas. PMID:35208856
The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome. PMID:35139923
Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite. PMID:35120663
SPOT-Contact-LM: Improving Single-Sequence-Based Prediction of Protein Contact Map using a Transformer Language Model. PMID:35104320
Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica. PMID:35102143
Evaluating the relevance of sequence conservation in the prediction of pathogenic missense variants. PMID:35098354
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
Using metagenomic data to boost protein structure prediction and discovery. PMID:35070166
Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing. PMID:35022403
A catalogue of 1,167 genomes from the human gut archaeome. PMID:34969981
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. PMID:34953462
PreBINDS: An Interactive Web Tool to Create Appropriate Datasets for Predicting Compound-Protein Interactions. PMID:34938773
Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention. PMID:34890134
Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core. PMID:34836555
Genomic convergence between Akkermansia muciniphila in different mammalian hosts. PMID:34715771
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
FALCON2: a web server for high-quality prediction of protein tertiary structures. PMID:34525939
Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil. PMID:34468166
Coordinated Diel Gene Expression of Cyanobacteria and Their Microbiome. PMID:34442749
Closely related Lak megaphages replicate in the microbiomes of diverse animals. PMID:34386733
Lytic archaeal viruses infect abundant primary producers in Earth's crust. PMID:34330907
Gram-negative outer-membrane proteins with multiple β-barrel domains. PMID:34330833
A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease. PMID:34313538
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints. PMID:34270679
In-Pero: Exploiting Deep Learning Embeddings of Protein Sequences to Predict the Localisation of Peroxisomal Proteins. PMID:34203866
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. PMID:34140026
Learning the protein language: Evolution, structure, and function. PMID:34139171
Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs. PMID:34116726
A global metagenomic map of urban microbiomes and antimicrobial resistance. PMID:34043940
Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators. PMID:34006865
Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil. PMID:34006626
Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities. PMID:33975974
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. PMID:33876751
Sensitive protein alignments at tree-of-life scale using DIAMOND. PMID:33828273
Improving integrative 3D modeling into low- to medium-resolution electron microscopy structures with evolutionary couplings. PMID:33759266
Genome-resolved metagenomics using environmental and clinical samples. PMID:33758906
lncRNADetector: a bioinformatics pipeline for long non-coding RNA identification and MAPslnc: a repository of medicinal and aromatic plant lncRNAs. PMID:33685383
Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages. PMID:33653940
Interaction dynamics and virus-host range for estuarine actinophages captured by epicPCR. PMID:33633401
Family-specific analysis of variant pathogenicity prediction tools. PMID:33575576
The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. PMID:33574608
Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges. PMID:33537022
Physiological Tradeoffs of Immune Response Differs by Infection Type in Pieris napi. PMID:33519499
Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle. PMID:33462272
Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima. PMID:33431961
Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities. PMID:33424787
Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes. PMID:33419955
Predicting the Disease Risk of Protein Mutation Sequences With Pre-training Model. PMID:33408741
The Lung Microbiome of Three Young Brazilian Patients With Cystic Fibrosis Colonized by Fungi. PMID:33262957
Multi-omics examination of Q fever fatigue syndrome identifies similarities with chronic fatigue syndrome. PMID:33243243
Identification of Natural CRISPR Systems and Targets in the Human Microbiome. PMID:33217332
Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. PMID:33208745
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. PMID:33196814
Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants. PMID:33172966
Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. PMID:33127895
Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter. PMID:33066695
Exploring the sequence fitness landscape of a bridge between protein folds. PMID:33048928
Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus. PMID:33012230
Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins. PMID:33006900
Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts. PMID:32994284
Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities. PMID:32849356
Large freshwater phages with the potential to augment aerobic methane oxidation. PMID:32839536
Age- and duration-dependent effects of whey protein on high-fat diet-induced changes in body weight, lipid metabolism, and gut microbiota in mice. PMID:32748559
The search of sequence variants using a constrained protein evolution simulation approach. PMID:32695271
Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay. PMID:32694140
Structural analysis of missense mutations occurring in the DNA-binding domain of HSF4 associated with congenital cataracts. PMID:32647819
SDS-PAGE fractionation to increase metaproteomic insight into the taxonomic and functional composition of microbial communities for biogas plant samples. PMID:32624931
Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae. PMID:32605988
Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome. PMID:32467975
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. PMID:32427907
In Silico Prediction of the Effects of Nonsynonymous Single Nucleotide Polymorphisms in the Human Catechol-O-Methyltransferase (COMT) Gene. PMID:32236879
Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. PMID:32203118
Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments. PMID:32071164
Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification. PMID:32066366
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. PMID:31988473
Mobilizable antibiotic resistance genes are present in dust microbial communities. PMID:31971995
Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice. PMID:31928131
Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus. PMID:31861932
Molecular replacement using structure predictions from databases. PMID:31793899
A common root for coevolution and substitution rate variability in protein sequence evolution. PMID:31792239
Generation of a Comprehensive Transcriptome Atlas and Transcriptome Dynamics in Medicinal Cannabis. PMID:31719627
Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community. PMID:31719174
Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India. PMID:31719139
ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins. PMID:31702846
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families. PMID:31676016
Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures. PMID:31664492
Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species. PMID:31641485
Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients. PMID:31597568
A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes. PMID:31490930
Universal principles of membrane protein assembly, composition and evolution. PMID:31415673
Short- and Long-Term Effects of UVA on Arabidopsis Are Mediated by a Novel cGMP Phosphodiesterase. PMID:31353185
Disorder Atlas: Web-based software for the proteome-based interpretation of intrinsic disorder predictions. PMID:31326853
Unveiling the presence of biosynthetic pathways for bioactive compounds in the Thalassiosira rotula transcriptome. PMID:31289324
De novo design of symmetric ferredoxins that shuttle electrons in vivo. PMID:31262814
Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. PMID:31241222
Evolutionary coupling analysis identifies the impact of disease-associated variants at less-conserved sites. PMID:31199866
Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PMID:31199787
RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. PMID:31195970
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. PMID:31142855
Functional expression and characterization of the envelope glycoprotein E1E2 heterodimer of hepatitis C virus. PMID:31116791
Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface. PMID:31107587
Surface patches on recombinant erythropoietin predict protein solubility: engineering proteins to minimise aggregation. PMID:31072369
Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants. PMID:31029164
Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. PMID:31005411
A novel transcriptome-derived SNPs array for tench (Tinca tinca L.). PMID:30889192
CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes. PMID:30837341
A Portion of the Apomixis Locus of Paspalum Simplex is Microsyntenic with an Unstable Chromosome Segment Highly Conserved Among Poaceae. PMID:30824748
Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network. PMID:30809011
Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler. PMID:30768175
The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. PMID:30732586
The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. PMID:30698687
Megaphages infect Prevotella and variants are widespread in gut microbiomes. PMID:30692672
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. PMID:30692531
Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton. PMID:30619142
Mechanistic Insight into the Catalytic Promiscuity of Amine Dehydrogenases: Asymmetric Synthesis of Secondary and Primary Amines. PMID:30489013
Comparative expression profiling reveals widespread coordinated evolution of gene expression across eukaryotes. PMID:30470754
Computational discovery of direct associations between GO terms and protein domains. PMID:30453875
Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains. PMID:30441862
Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence. PMID:30355302
Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events. PMID:30319674
The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots. PMID:30293092
Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River. PMID:30258036
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property. PMID:30084867
Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon. PMID:29970182
Differences in substrate specificity of V. cholerae FabH enzymes suggest new approaches for the development of novel antibiotics and biofuels. PMID:29917313
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. PMID:29807988
Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome-resolved metagenomics. PMID:29774049
Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations. PMID:29740420
Diapause in a tropical oil-collecting bee: molecular basis unveiled by RNA-Seq. PMID:29703143
Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome. PMID:29690875
A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. PMID:29662147
Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles. PMID:29636439
Genome-reconstruction for eukaryotes from complex natural microbial communities. PMID:29496730
Genome-resolved metagenomics of sugarcane vinasse bacteria. PMID:29483941
Pi-Pi contacts are an overlooked protein feature relevant to phase separation. PMID:29424691
Coordinated gene expression between Trichodesmium and its microbiome over day-night cycles in the North Pacific Subtropical Gyre. PMID:29382945
Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. PMID:29379208
Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of Mutagenized Sorghum. PMID:29378822
Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC). PMID:29343217
Terzyme: a tool for identification and analysis of the plant terpenome. PMID:29339971
Metatranscriptome of human faecal microbial communities in a cohort of adult men. PMID:29335555
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. PMID:29311644
EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species. PMID:29220468
Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. PMID:29180750
Anaerobic degradation of 1-methylnaphthalene by a member of the Thermoanaerobacteraceae contained in an iron-reducing enrichment culture. PMID:29177812
KIXBASE: A comprehensive web resource for identification and exploration of KIX domains. PMID:29097748
Complete Genome of Achalarus lyciades, The First Representative of the Eudaminae Subfamily of Skippers. PMID:29081692
How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis. PMID:29045866
Protein remote homology detection based on bidirectional long short-term memory. PMID:29017445
Strains, functions and dynamics in the expanded Human Microbiome Project. PMID:28953883
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. PMID:28924494
Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment. PMID:28885627
When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. PMID:28882004
De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacus. PMID:28873438
Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients. PMID:28827811
De novo transcriptome assembly for the spiny mouse (Acomys cahirinus). PMID:28827620
Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice. PMID:28808691
Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ. PMID:28806931
De novo assembly and annotation of the retinal transcriptome for the Nile grass rat (Arvicanthis ansorgei). PMID:28759564
The first complete genomes of Metalmarks and the classification of butterfly families. PMID:28757157
Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms. PMID:28754661
A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis. PMID:28751714
BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PMID:28750104
Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment. PMID:28744486
Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. PMID:28652349
Genome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida. PMID:28611758
In silico analyses of deleterious missense SNPs of human apolipoprotein E3. PMID:28559539
Insights from the complete genome sequence of Clostridium tyrobutyricum provide a platform for biotechnological and industrial applications. PMID:28536840
Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean. PMID:28534879
Ethephon induced oxidative stress in the olive leaf abscission zone enables development of a selective abscission compound. PMID:28511694
Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. PMID:28498102
Proteus: a random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins. PMID:28365882
Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. PMID:28350393
Systematic identification of phosphorylation-mediated protein interaction switches. PMID:28346509
Improving prediction of helix-helix packing in membrane proteins using predicted contact numbers as restraints. PMID:28263405
Mixed transmission modes and dynamic genome evolution in an obligate animal-bacterial symbiosis. PMID:28234348
Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller's organ, of the cattle tick, Rhipicephalus australis. PMID:28231302
The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis. PMID:28223457
Dynamic changes in the transcriptome of Populus hopeiensis in response to abscisic acid. PMID:28198429
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. PMID:28193156
Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins. PMID:28163896
Bayesian prediction of RNA translation from ribosome profiling. PMID:28126919
Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information. PMID:28116287
Blind prediction of deleterious amino acid variations with SNPs&GO. PMID:28102005
MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae. PMID:28098242
Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. PMID:28077566
Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. PMID:28073918
Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation. PMID:28067254
Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut. PMID:28057747
Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers. PMID:28028736
Functional proteomics-aided selection of protease inhibitors for herbivore insect control. PMID:27958307
Survey of the green picoalga Bathycoccus genomes in the global ocean. PMID:27901108
UniProt: the universal protein knowledgebase. PMID:27899622
Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods. PMID:27881416
Accelerating Information Retrieval from Profile Hidden Markov Model Databases. PMID:27875548
Size distribution of function-based human gene sets and the split-merge model. PMID:27853602
Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PMID:27843720
Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir. PMID:27822552
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. PMID:27822528
Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse). PMID:27812417
Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus. PMID:27805042
Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. PMID:27803309
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. PMID:27774985
Unique and Universal Features of Epsilonproteobacterial Origins of Chromosome Replication and DnaA-DnaA Box Interactions. PMID:27746772
ProQ3: Improved model quality assessments using Rosetta energy terms. PMID:27698390
Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PMID:27688978
Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics. PMID:27661452
RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae. PMID:27614431
Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57. PMID:27602182
Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. PMID:27462366
FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues. PMID:27383535
HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts. PMID:27375564
Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well. PMID:27375557
NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases. PMID:27373836
ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. PMID:27319297
A Numbering System for MFS Transporter Proteins. PMID:27314000
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. PMID:27224977
Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities. PMID:27199908
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes. PMID:27138088
RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria. PMID:27137126
Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence. PMID:27120974
Correlated rigid modes in protein families. PMID:27063781
Protein Repeats from First Principles. PMID:27044676
The Pokeweed Leaf mRNA Transcriptome and Its Regulation by Jasmonic Acid. PMID:27014307
Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation. PMID:26979958
Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils. PMID:26969694
Speciation in Cloudless Sulphurs Gleaned from Complete Genomes. PMID:26951782
Prediction of G protein-coupled receptor encoding sequences from the synganglion transcriptome of the cattle tick, Rhipicephalus microplus. PMID:26922323
miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria. PMID:26871907
Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. PMID:26844018
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. PMID:26837824
Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins. PMID:26804342
Computational crystallization. PMID:26792536
Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs. PMID:26787827
A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhoei. PMID:26655754
SIFT missense predictions for genomes. PMID:26633127
HMMvar-func: a new method for predicting the functional outcome of genetic variants. PMID:26518340
Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi. PMID:26506000
mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. PMID:26500804
AnABlast: a new in silico strategy for the genome-wide search of novel genes and fossil regions. PMID:26494834
Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity. PMID:26481813
Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia. PMID:26457128
Following the Footsteps of Chlamydial Gene Regulation. PMID:26424812
REC-1 and HIM-5 distribute meiotic crossovers and function redundantly in meiotic double-strand break formation in Caenorhabditis elegans. PMID:26385965
Large-scale determination of previously unsolved protein structures using evolutionary information. PMID:26335199
Skipper genome sheds light on unique phenotypic traits and phylogeny. PMID:26311350
Accurate Ab Initio and Template-Based Prediction of Short Intrinsically-Disordered Regions by Bidirectional Recurrent Neural Networks Trained on Large-Scale Datasets. PMID:26307973
Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. PMID:26228545
Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S. PMID:26203328
Transcriptome sequencing of three Pseudo-nitzschia species reveals comparable gene sets and the presence of Nitric Oxide Synthase genes in diatoms. PMID:26189990
A reproducible approach to high-throughput biological data acquisition and integration. PMID:26157642
TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool. PMID:26123059
Unusual biology across a group comprising more than 15% of domain Bacteria. PMID:26083755
Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus. PMID:26038723
Lifestyle evolution in cyanobacterial symbionts of sponges. PMID:26037118
Functional consequences of transferrin receptor-2 mutations causing hereditary hemochromatosis type 3. PMID:26029709
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. PMID:25969446
Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. PMID:25954263
Novel insights into the insect trancriptome response to a natural DNA virus. PMID:25924671
RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements. PMID:25917918
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. PMID:25915636
JPred4: a protein secondary structure prediction server. PMID:25883141
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii. PMID:25880642
Metaproteomics of complex microbial communities in biogas plants. PMID:25874383
Quantitative proteogenomic profiling of epidermal barrier formation in vitro. PMID:25862149
The role of monovalent cations in the ATPase reaction of DNA gyrase. PMID:25849408
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis. PMID:25833954
Plastid establishment did not require a chlamydial partner. PMID:25758953
Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite. PMID:25723966
The interaction of RNA helicase DDX3 with HIV-1 Rev-CRM1-RanGTP complex during the HIV replication cycle. PMID:25723178
Protein docking with predicted constraints. PMID:25722738
Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. PMID:25689026
Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense. PMID:25683714
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PMID:25650158
Aquifer environment selects for microbial species cohorts in sediment and groundwater. PMID:25647349
Conserved residues of the Pro103-Arg115 loop are involved in triggering the allosteric response of the Escherichia coli ADP-glucose pyrophosphorylase. PMID:25620658
Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm. PMID:25573960
Div-BLAST: diversification of sequence search results. PMID:25531115
Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. PMID:25511286
Grouping of large populations into few CTL immune 'response-types' from influenza H1N1 genome analysis. PMID:25505972
Flavonoid supplementation affects the expression of genes involved in cell wall formation and lignification metabolism and increases sugar content and saccharification in the fast-growing eucalyptus hybrid E. urophylla x E. grandis. PMID:25407319
A structured loop modulates coupling between the substrate-binding and dimerization domains in the multidrug resistance transporter EmrE. PMID:25406320
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. PMID:25398609
DISOPRED3: precise disordered region predictions with annotated protein-binding activity. PMID:25391399
Interspecific and host-related gene expression patterns in nematode-trapping fungi. PMID:25384908
UniProt: a hub for protein information. PMID:25348405
The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. PMID:25342549
New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. PMID:25323955
Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses. PMID:25313075
Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs. PMID:25307852
Analysis of the tryptic search space in UniProt databases. PMID:25307260
NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. PMID:25262355
Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus. PMID:25260963
A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna. PMID:25228340
A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness. PMID:25217195
Frameshift alignment: statistics and post-genomic applications. PMID:25172925
Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. PMID:25168586
STATdb: a specialised resource for the STATome. PMID:25157689
GPCRsort-responding to the next generation sequencing data challenge: prediction of G protein-coupled receptor classes using only structural region lengths. PMID:25133496
De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms. PMID:25104951
Evidence for loss of a partial flagellar glycolytic pathway during trypanosomatid evolution. PMID:25050549
Establishing an in vivo assay system to identify components involved in environmental RNA interference in the western corn rootworm. PMID:25003334
Prediction of membrane transport proteins and their substrate specificities using primary sequence information. PMID:24968309
Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase. PMID:24938123
Primary sequence contribution to the optical function of the eye lens. PMID:24903231
The midgut of Aedes albopictus females expresses active trypsin-like serine peptidases. PMID:24886160
Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern. PMID:24884518
SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. PMID:24860169
Differential effects of CSF-1R D802V and KIT D816V homologous mutations on receptor tertiary structure and allosteric communication. PMID:24828813
Prediction and prioritization of rare oncogenic mutations in the cancer Kinome using novel features and multiple classifiers. PMID:24743239
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Fruit load induces changes in global gene expression and in abscisic acid (ABA) and indole acetic acid (IAA) homeostasis in citrus buds. PMID:24706719
The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). PMID:24699266
A novel regio‑specific cyclosporin hydroxylase gene revealed through the genome mining of Pseudonocardia autotrophica. PMID:24659179
Identification of microRNAs in the coral Stylophora pistillata. PMID:24658574
Genome profiling of sterol synthesis shows convergent evolution in parasites and guides chemotherapeutic attack. PMID:24627128
Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana. PMID:24614631
Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases. PMID:24571091
HMPAS: Human Membrane Protein Analysis System. PMID:24564858
Insights into the maize pan-genome and pan-transcriptome. PMID:24488960
Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications. PMID:24465857
Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. PMID:24451181
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. PMID:24450983
Microarray analysis of genes and gene functions in disc degeneration. PMID:24396401
A metagenomic framework for the study of airborne microbial communities. PMID:24349140
The basic leucine zipper transcription factor ABSCISIC ACID RESPONSE ELEMENT-BINDING FACTOR2 is an important transcriptional regulator of abscisic acid-dependent grape berry ripening processes. PMID:24276949
Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses. PMID:24260300
Activities at the Universal Protein Resource (UniProt). PMID:24253303
MetaRef: a pan-genomic database for comparative and community microbial genomics. PMID:24203705
Expression of the mevalonate pathway enzymes in the Lutzomyia longipalpis (Diptera: Psychodidae) sex pheromone gland demonstrated by an integrated proteomic approach. PMID:24185139
PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. PMID:24170408
Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. PMID:24149512
Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations. PMID:24146760
SCLpredT: Ab initio and homology-based prediction of subcellular localization by N-to-1 neural networks. PMID:24133649
Discovery of a new genetic variant of methionine aminopeptidase from Streptococci with possible post-translational modifications: biochemical and structural characterization. PMID:24124477
GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. PMID:24096415
Origins of Myc proteins--using intrinsic protein disorder to trace distant relatives. PMID:24086436
Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PMID:24023625
Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers. PMID:24015778
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. PMID:23979677
A fast Peptide Match service for UniProt Knowledgebase. PMID:23958731
Characterisation and analysis of the Aegilops sharonensis transcriptome, a wild relative of wheat in the Sitopsis section. PMID:23951332
kClust: fast and sensitive clustering of large protein sequence databases. PMID:23945046
Functional profiling of the gut microbiome in disease-associated inflammation. PMID:23906180
The genome sequence of Leishmania (Leishmania) amazonensis: functional annotation and extended analysis of gene models. PMID:23857904
Collective judgment predicts disease-associated single nucleotide variants. PMID:23819846
Minireview: Toward the establishment of a link between melatonin and glucose homeostasis: association of melatonin MT2 receptor variants with type 2 diabetes. PMID:23798576
Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins. PMID:23766289
Gut transcriptome of replete adult female cattle ticks, Rhipicephalus (Boophilus) microplus, feeding upon a Babesia bovis-infected bovine host. PMID:23749091
BeEP Server: Using evolutionary information for quality assessment of protein structure models. PMID:23729471
Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. PMID:23674305
Protein clustering and RNA phylogenetic reconstruction of the influenza A [corrected] virus NS1 protein allow an update in classification and identification of motif conservation. PMID:23667580
Memoir: template-based structure prediction for membrane proteins. PMID:23640332
Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona. PMID:23637636
The architecture of Trypanosoma brucei tubulin-binding cofactor B and implications for function. PMID:23627368
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. PMID:23575371
Clustering evolving proteins into homologous families. PMID:23566217
De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana. PMID:23555698
Analyses of the general rule on residue pair frequencies in local amino acid sequences of soluble, ordered proteins. PMID:23526551
Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species. PMID:23521840
Protein function prediction by massive integration of evolutionary analyses and multiple data sources. PMID:23514099
Transcriptional analysis of genes involved in nodulation in soybean roots inoculated with Bradyrhizobium japonicum strain CPAC 15. PMID:23497193
Uncovering hidden duplicated content in public transcriptomics data. PMID:23487185
Increasing sequence search sensitivity with transitive alignments. PMID:23457449
iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. PMID:23445546
A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. PMID:23445355
Protein structure based prediction of catalytic residues. PMID:23433045
Comparative transcriptomics of early dipteran development. PMID:23432914
VIROME: a standard operating procedure for analysis of viral metagenome sequences. PMID:23407591
Accurate prediction of protein enzymatic class by N-to-1 Neural Networks. PMID:23368876
Identification of a cyclosporine-specific P450 hydroxylase gene through targeted cytochrome P450 complement (CYPome) disruption in Sebekia benihana. PMID:23354713
Genome evolution and phylogenomic analysis of Candidatus Kinetoplastibacterium, the betaproteobacterial endosymbionts of Strigomonas and Angomonas. PMID:23345457
Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species. PMID:23300689
Genomic sequence analysis and characterization of Sneathia amnii sp. nov. PMID:23281612
Functional identification of valerena-1,10-diene synthase, a terpene synthase catalyzing a unique chemical cascade in the biosynthesis of biologically active sesquiterpenes in Valeriana officinalis. PMID:23243312
Is chemically dispersed oil more toxic to Atlantic cod (Gadus morhua) larvae than mechanically dispersed oil? A transcriptional evaluation. PMID:23241080
UniProtKB amid the turmoil of plant proteomics research. PMID:23230445
Pyrosequencing-based transcriptome analysis of the asian rice gall midge reveals differential response during compatible and incompatible interaction. PMID:23202939
Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. PMID:23190730
Update on activities at the Universal Protein Resource (UniProt) in 2013. PMID:23161681
Draft genome sequence of Actinobacillus pleuropneumoniae serotype 7 strain S-8. PMID:23144372
MonarchBase: the monarch butterfly genome database. PMID:23143105
Genomic approaches for interrogating the biochemistry of medicinal plant species. PMID:23084937
The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential. PMID:23083487
CD-HIT: accelerated for clustering the next-generation sequencing data. PMID:23060610
Structure and flexibility of the C-ring in the electromotor of rotary F(0)F(1)-ATPase of pea chloroplasts. PMID:23049735
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. PMID:23033316
Improved model quality assessment using ProQ2. PMID:22963006
A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. PMID:22958331
Pentamers not found in the universal proteome can enhance antigen specific immune responses and adjuvant vaccines. PMID:22937099
Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective. PMID:22900718
Analysis of Babesia bovis infection-induced gene expression changes in larvae from the cattle tick, Rhipicephalus (Boophilus) microplus. PMID:22871314
Phylogenomic and domain analysis of iterative polyketide synthases in Aspergillus species. PMID:22844193
Complete genome sequence of Bacillus anthracis H9401, an isolate from a Korean patient with anthrax. PMID:22815438
A web-based bioinformatics interface applied to the GENOSOJA Project: Databases and pipelines. PMID:22802706
Ultrafast clustering algorithms for metagenomic sequence analysis. PMID:22772836
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). PMID:22719821
Labellum transcriptome reveals alkene biosynthetic genes involved in orchid sexual deception and pollination-induced senescence. PMID:22706647
A structural model of the copper ATPase ATP7B to facilitate analysis of Wilson disease-causing mutations and studies of the transport mechanism. PMID:22692182
Genomic characterization of the Bacillus cereus sensu lato species: backdrop to the evolution of Bacillus anthracis. PMID:22645259
Extent of structural asymmetry in homodimeric proteins: prevalence and relevance. PMID:22629324
Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. PMID:22554255
mRNA-Seq analysis of the Pseudoperonospora cubensis transcriptome during cucumber (Cucumis sativus L.) infection. PMID:22545137
Expression profiling of Cucumis sativus in response to infection by Pseudoperonospora cubensis. PMID:22545095
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. PMID:22536955
MSV3d: database of human MisSense Variants mapped to 3D protein structure. PMID:22491796
Roles of residues in the interface of transient protein-protein complexes before complexation. PMID:22451863
Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing. PMID:22438891
Proteome-wide discovery of evolutionary conserved sequences in disordered regions. PMID:22416277
Functional characterization of protein domains common to animal viruses and mouse. PMID:22369715
Preimplantation development regulatory pathway construction through a text-mining approach. PMID:22369103
Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution. PMID:22369087
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. PMID:22335941
Complete genome sequence of the thermophilic bacterium Thermus sp. strain CCB_US3_UF1. PMID:22328745
Complete genome sequence of the thermophilic bacterium Geobacillus thermoleovorans CCB_US3_UF5. PMID:22328744
Viral proteins acquired from a host converge to simplified domain architectures. PMID:22319434
Bioinformatics for personal genome interpretation. PMID:22247263
Cultivar-specific kinetics of gene induction during downy mildew early infection in grapevine. PMID:22246600
Gentle masking of low-complexity sequences improves homology search. PMID:22205972
Novel search method for the discovery of functional relationships. PMID:22180409
The Pfam protein families database. PMID:22127870
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. PMID:22120664
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. PMID:22120661
Reorganizing the protein space at the Universal Protein Resource (UniProt). PMID:22102590
Targeted RNA sequencing reveals the deep complexity of the human transcriptome. PMID:22081020
Structural requirements for interaction of peroxisomal targeting signal 2 and its receptor PEX7. PMID:22057399
Assembly, gene annotation and marker development using 454 floral transcriptome sequences in Ziziphus celata (Rhamnaceae), a highly endangered, Florida endemic plant. PMID:22039173
Complete genome sequence of multidrug-resistant Acinetobacter baumannii strain 1656-2, which forms sturdy biofilm. PMID:22038960
Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone. PMID:21901122
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. PMID:21878105
Structural and functional analysis of the tandem β-zipper interaction of a Streptococcal protein with human fibronectin. PMID:21840989
New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins. PMID:21720552
Crystal structure of the C17/25 subcomplex from Schizosaccharomyces pombe RNA polymerase III. PMID:21714024
The IGS Standard Operating Procedure for Automated Prokaryotic Annotation. PMID:21677861
MarkUs: a server to navigate sequence-structure-function space. PMID:21672961
Single nucleotide polymorphism discovery in elite North American potato germplasm. PMID:21658273
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PMID:21556138
Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PMID:21541297
Gene duplication and divergence of long wavelength-sensitive opsin genes in the guppy, Poecilia reticulata. PMID:21170644
Concept and application of a computational vaccinology workflow. PMID:21067549
Ongoing and future developments at the Universal Protein Resource. PMID:21051339
M-ORBIS: mapping of molecular binding sites and surfaces. PMID:20813758
Comparative genomic characterization of Actinobacillus pleuropneumoniae. PMID:20802045
Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. PMID:20688752
Diterpene cyclases and the nature of the isoprene fold. PMID:20602361
MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane. PMID:20565847
Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies. PMID:20540756
Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins. PMID:20537180
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PMID:20498836
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. PMID:20478830
Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003. PMID:20418398
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica. PMID:20353604
Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri. PMID:20353595
Evolutionary constraints acting on DDX3X protein potentially interferes with Rev-mediated nuclear export of HIV-1 RNA. PMID:20300618
Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. PMID:20233449
A large and accurate collection of peptidase cleavages in the MEROPS database. PMID:20157488
Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system. PMID:20147619
Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications. PMID:20137074
CD-HIT Suite: a web server for clustering and comparing biological sequences. PMID:20053844
Genomic characterization of the Yersinia genus. PMID:20047673
Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175. PMID:19927321
The MiST2 database: a comprehensive genomics resource on microbial signal transduction. PMID:19900966
The Universal Protein Resource (UniProt) in 2010. PMID:19843607
Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae. PMID:19843335
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. PMID:19779614
SmCL3, a gastrodermal cysteine protease of the human blood fluke Schistosoma mansoni. PMID:19488406
Bioinformatic approaches to identifying orthologs and assessing evolutionary relationships. PMID:19467333
PEP-FOLD: an online resource for de novo peptide structure prediction. PMID:19433514
Candidate effector gene identification in the ascomycete fungal phytopathogen Venturia inaequalis by expressed sequence tag analysis. PMID:19400844
A nitrile hydratase in the eukaryote Monosiga brevicollis. PMID:19096720
Complete genome sequence of Rhodobacter sphaeroides KD131. PMID:19028901
Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. PMID:19014603
FastBLAST: homology relationships for millions of proteins. PMID:18974889
A computational screen for type I polyketide synthases in metagenomics shotgun data. PMID:18953415
Probing metagenomics by rapid cluster analysis of very large datasets. PMID:18846219
PMAP: databases for analyzing proteolytic events and pathways. PMID:18842634
The Universal Protein Resource (UniProt) 2009. PMID:18836194
Translational integrity and continuity: personalized biomedical data integration. PMID:18760382
Development of ChillPeach genomic tools and identification of cold-responsive genes in peach fruit. PMID:18661259
A genome-wide 20 K citrus microarray for gene expression analysis. PMID:18598343
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. PMID:18586742
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. PMID:18503088
The Jpred 3 secondary structure prediction server. PMID:18463136
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. PMID:18460207
Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices. PMID:18398479
Prediction of protein function improving sequence remote alignment search by a fuzzy logic algorithm. PMID:18066655
Towards completion of the Earth's proteome. PMID:18059312
The universal protein resource (UniProt). PMID:18045787
The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily. PMID:17996046
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches PubMed citations: 383.

383 articles citing: UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

A genome and gene catalog of glacier microbiomes. PMID:35760913
Refined Contact Map Prediction of Peptides Based on GCN and ResNet. PMID:35571037
Identification, diversity and domain structure analysis of mucin and mucin-like genes in sea anemone Actinia tenebrosa. PMID:35539013
Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain. PMID:35501923
Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India. PMID:35495730
Tissue remodeling by an opportunistic pathogen triggers allergic inflammation. PMID:35483356
Machine Learning-driven Protein Library Design: A Path Toward Smarter Libraries. PMID:35482186
An Interpretable Double-Scale Attention Model for Enzyme Protein Class Prediction Based on Transformer Encoders and Multi-Scale Convolutions. PMID:35432476
Deciphering the structure of Arabidopsis thaliana 5-enol-pyruvyl-shikimate-3-phosphate synthase: An essential step toward the discovery of novel inhibitors to supersede glyphosate. PMID:35422967
B-Cell Epitope Mapping of TprC and TprD Variants of Treponema pallidum Subspecies Informs Vaccine Development for Human Treponematoses. PMID:35422800
SSGraphCPI: A Novel Model for Predicting Compound-Protein Interactions Based on Deep Learning. PMID:35409140
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data. PMID:35380623
Correlation Analysis of the Microbiome and Immune Function in the Lung-Gut Axis of Critically Ill Patients in the ICU. PMID:35372413
Integration of the Human Gut Microbiome and Serum Metabolome Reveals Novel Biological Factors Involved in the Regulation of Bone Mineral Density. PMID:35372129
Protein design via deep learning. PMID:35348602
Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT. PMID:35347217
NKX2-5 Variant in Two Siblings with Thyroid Hemiagenesis. PMID:35328834
Human gut bacteria produce ΤΗ17-modulating bile acid metabolites. PMID:35296854
Microbiome Resilience and Health Implications for People in Half-Year Travel. PMID:35281043
Discovery of a Ni2+-dependent guanidine hydrolase in bacteria. PMID:35264792
Host-microbiome protein-protein interactions capture disease-relevant pathways. PMID:35246229
Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing. PMID:35196800
Indole-3-Acetic Acid Alters Intestinal Microbiota and Alleviates Ankylosing Spondylitis in Mice. PMID:35185872
High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. PMID:35156767
Protein sequence design with a learned potential. PMID:35136054
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers. PMID:35134816
Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite. PMID:35120663
The properties of human disease mutations at protein interfaces. PMID:35120134
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
Using metagenomic data to boost protein structure prediction and discovery. PMID:35070166
Learning protein fitness models from evolutionary and assay-labeled data. PMID:35039677
Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes. PMID:35022216
From systems to structure - using genetic data to model protein structures. PMID:35013567
The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:34986604
Decoding Cancer Variants of Unknown Significance for Helicase-Nuclease-RPA Complexes Orchestrating DNA Repair During Transcription and Replication. PMID:34966786
The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host. PMID:34911987
Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention. PMID:34890134
Accurate protein function prediction via graph attention networks with predicted structure information. PMID:34882195
Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. PMID:34873061
Dormant spores sense amino acids through the B subunits of their germination receptors. PMID:34824238
Interspecies variation in hominid gut microbiota controls host gene regulation. PMID:34818542
Neural networks to learn protein sequence-function relationships from deep mutational scanning data. PMID:34815338
Accelerated discovery of novel glycoside hydrolases using targeted functional profiling and selective pressure on the rumen microbiome. PMID:34814938
An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2. PMID:34776222
A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans. PMID:34740326
Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city. PMID:34724986
Disease variant prediction with deep generative models of evolutionary data. PMID:34707284
Prolonged Impairment of Short-Chain Fatty Acid and L-Isoleucine Biosynthesis in Gut Microbiome in Patients With COVID-19. PMID:34687739
Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade. PMID:34677568
Oral and gastric microbiome in relation to gastric intestinal metaplasia. PMID:34664721
Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. PMID:34654884
Performance of Multiple Metagenomics Pipelines in Understanding Microbial Diversity of a Low-Biomass Spacecraft Assembly Facility. PMID:34650522
Navigating the amino acid sequence space between functional proteins using a deep learning framework. PMID:34616884
Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. PMID:34593021
Sulfidogenic Microbial Communities of the Uzen High-Temperature Oil Field in Kazakhstan. PMID:34576714
Maturation of Rhodobacter capsulatus Multicopper Oxidase CutO Depends on the CopA Copper Efflux Pathway and Requires the cutF Product. PMID:34566924
Temporal Transcriptomics of Gut Escherichia coli in Caenorhabditis elegans Models of Aging. PMID:34523995
Improved 3-D Protein Structure Predictions using Deep ResNet Model. PMID:34510309
Associations of the gut microbiome with hepatic adiposity in the Multiethnic Cohort Adiposity Phenotype Study. PMID:34491886
OPUS-X: An Open-Source Toolkit for Protein Torsion Angles, Secondary Structure, Solvent Accessibility, Contact Map Predictions, and 3D Folding. PMID:34478500
LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction. PMID:34466411
SecProCT: In Silico Prediction of Human Secretory Proteins Based on Capsule Network and Transformer. PMID:34445760
Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. PMID:34423306
Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases. PMID:34409984
Synergistic stabilization of a double mutant in chymotrypsin inhibitor 2 from a library screen in E. coli. PMID:34408246
The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs. PMID:34377966
Inhibiting Type VI Secretion System Activity with a Biomimetic Peptide Designed To Target the Baseplate Wedge Complex. PMID:34372705
Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. PMID:34355210
Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14). PMID:34350630
Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba. PMID:34344949
Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis. PMID:34342541
Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14. PMID:34331351
Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction. PMID:34273146
Highly accurate protein structure prediction with AlphaFold. PMID:34265844
Performance of Regression Models as a Function of Experiment Noise. PMID:34262264
Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. PMID:34261503
Metagenomics: a path to understanding the gut microbiome. PMID:34259891
Leri: A web-server for identifying protein functional networks from evolutionary couplings. PMID:34257835
Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy. PMID:34248876
Deep Learning for Protein-Protein Interaction Site Prediction. PMID:34236667
Increasing the Accuracy of Single Sequence Prediction Methods Using a Deep Semi-Supervised Learning Framework. PMID:34213528
Structural characterization of two solute-binding proteins for N,N'-diacetylchitobiose/N,N',N''-triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7. PMID:34195603
Hunting for Beneficial Mutations: Conditioning on SIFT Scores When Estimating the Distribution of Fitness Effect of New Mutations. PMID:34180988
Growth faltering regardless of chronic diarrhea is associated with mucosal immune dysfunction and microbial dysbiosis in the gut lumen. PMID:34158595
Transcriptome Analysis Reveals Putative Target Genes of APETALA3-3 During Early Floral Development in Nigella damascena L. PMID:34149759
Representation learning applications in biological sequence analysis. PMID:34141139
Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction. PMID:34139218
In vitro fermentation test bed for evaluation of engineered probiotics in polymicrobial communities. PMID:34104665
Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers. PMID:34092249
NAD(H)-mediated tetramerization controls the activity of Legionella pneumophila phospholipase PlaB. PMID:34074754
Protein Structure Prediction: Conventional and Deep Learning Perspectives. PMID:34050498
Pretraining model for biological sequence data. PMID:34050350
Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading. PMID:34046429
A global metagenomic map of urban microbiomes and antimicrobial resistance. PMID:34043940
Novel strain-level resolution of Crohn's disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing. PMID:34035441
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. PMID:34021239
ProtCHOIR: a tool for proteome-scale generation of homo-oligomers. PMID:34015821
Biosynthesis and Heterologous Production of Mycosporine-Like Amino Acid Palythines. PMID:34006097
The evolution and changing ecology of the African hominid oral microbiome. PMID:33972424
Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets. PMID:33961221
CopulaNet: Learning residue co-evolution directly from multiple sequence alignment for protein structure prediction. PMID:33953201
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
iT4SE-EP: Accurate Identification of Bacterial Type IV Secreted Effectors by Exploring Evolutionary Features from Two PSI-BLAST Profiles. PMID:33923273
An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies. PMID:33918473
Longitudinal Profiling of the Macaque Vaginal Microbiome Reveals Similarities to Diverse Human Vaginal Communities. PMID:33906914
Infant Feeding Alters the Longitudinal Impact of Birth Mode on the Development of the Gut Microbiota in the First Year of Life. PMID:33897650
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. PMID:33876751
Microbial community structure and composition is associated with host species and sex in Sigmodon cotton rats. PMID:33863395
Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction. PMID:33828153
Distinct transcriptional profiles of Leptospira borgpetersenii serovar Hardjo strains JB197 and HB203 cultured at different temperatures. PMID:33826628
The Impact of Migration on the Gut Metagenome of South Asian Canadians. PMID:33794735
Protein Contact Map Refinement for Improving Structure Prediction Using Generative Adversarial Networks. PMID:33787852
Balancing Data on Deep Learning-Based Proteochemometric Activity Classification. PMID:33779173
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PMID:33770072
A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas. PMID:33764468
Inflammation in children with cystic fibrosis: contribution of bacterial production of long-chain fatty acids. PMID:33654282
Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors. PMID:33636189
Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1). PMID:33630910
RNA-Seq in Nonmodel Organisms. PMID:33606257
Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome. PMID:33597514
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. PMID:33596852
Restructuring the Gut Microbiota by Intermittent Fasting Lowers Blood Pressure. PMID:33596669
RNAsamba: neural network-based assessment of the protein-coding potential of RNA sequences. PMID:33575571
Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees. PMID:33574391
Ammonium Removal in Aquaponics Indicates Participation of Comammox Nitrospira. PMID:33544185
Adherent-invasive E. coli metabolism of propanediol in Crohn's disease regulates phagocytes to drive intestinal inflammation. PMID:33539767
A persistent giant algal virus, with a unique morphology, encodes an unprecedented number of genes involved in energy metabolism. PMID:33536167
A Transcriptomic Approach to the Recruitment of Venom Proteins in a Marine Annelid. PMID:33525375
A Conserved Motif in Intracellular Loop 1 Stabilizes the Outward-Facing Conformation of TmrAB. PMID:33524413
Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota. PMID:33517907
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems. PMID:33495623
Transcriptomic analysis of s-methoprene resistance in the lesser grain borer, Rhyzopertha dominica, and evaluation of piperonyl butoxide as a resistance breaker. PMID:33472593
Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons. PMID:33468056
Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins. PMID:33446856
Specific Antiproliferative Properties of Proteinaceous Toxin Secretions from the Marine Annelid Eulalia sp. onto Ovarian Cancer Cells. PMID:33445445
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes. PMID:33418085
Crystal structure of bacterial cytotoxic necrotizing factor CNFY reveals molecular building blocks for intoxication. PMID:33410511
Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease. PMID:33397897
Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. PMID:33393786
RNA-Seq used to identify ipsdienone reductase (IDONER): A novel monoterpene carbon-carbon double bond reductase central to Ips confusus pheromone production. PMID:33388375
DeepNOG: Fast and accurate protein orthologous group assignment. PMID:33367584
A Metagenome-Wide Association Study of Gut Microbiome in Patients With Multiple Sclerosis Revealed Novel Disease Pathology. PMID:33363050
Metabolic Reconstruction Elucidates the Lifestyle of the Last Diplomonadida Common Ancestor. PMID:33361320
The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins. PMID:33347434
DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction. PMID:33325500
Immunoproteomic Analysis Reveals Novel Candidate Antigens for the Diagnosis of Paracoccidioidomycosis Due to Paracoccidioides lutzii. PMID:33322269
Dysbiotic Lesional Microbiome With Filaggrin Missense Variants Associate With Atopic Dermatitis in India. PMID:33282748
Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos. PMID:33246412
Comparative Genomics of Strictly Vertically Transmitted, Feminizing Microsporidia Endosymbionts of Amphipod Crustaceans. PMID:33216144
Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning. PMID:33212013
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. PMID:33199808
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. PMID:33196814
Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2. PMID:33158276
Genomics and metatranscriptomics of biogeochemical cycling and degradation of lignin-derived aromatic compounds in thermal swamp sediment. PMID:33139871
From sequence to information. PMID:33131436
Structure of human steroid 5α-reductase 2 with the anti-androgen drug finasteride. PMID:33110062
In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision. PMID:33059593
Stabilizing AqdC, a Pseudomonas Quinolone Signal-Cleaving Dioxygenase from Mycobacteria, by FRESCO-Based Protein Engineering. PMID:33058333
Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins. PMID:33006900
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. PMID:32986834
Genomic Features of Parthenogenetic Animals. PMID:32985658
De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks. PMID:32945673
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora. PMID:32932872
SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity. PMID:32866236
DRAM for distilling microbial metabolism to automate the curation of microbiome function. PMID:32766782
CerealsDB-new tools for the analysis of the wheat genome: update 2020. PMID:32754757
Sequencing effort dictates gene discovery in marine microbial metagenomes. PMID:32743860
QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks. PMID:32657397
Adaptation of Carbon Source Utilization Patterns of Geobacter metallireducens During Sessile Growth. PMID:32655526
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules. PMID:32636252
Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms. PMID:32587239
Effect of a Flaxseed Lignan Intervention on Circulating Bile Acids in a Placebo-Controlled Randomized, Crossover Trial. PMID:32575611
Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate. PMID:32571930
Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation. PMID:32561885
Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. PMID:32544460
CapsNet-SSP: multilane capsule network for predicting human saliva-secretory proteins. PMID:32517646
Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination. PMID:32515539
Transcriptomes reveal expression of hemoglobins throughout insects and other Hexapoda. PMID:32502196
Antibiotic Substrate Selectivity of Pseudomonas aeruginosa MexY and MexB Efflux Systems Is Determined by a Goldilocks Affinity. PMID:32457110
Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium. PMID:32424245
Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps. PMID:32422044
Extreme Viral Partitioning in a Marine-Derived High Arctic Lake. PMID:32404515
Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. PMID:32327732
Rapid Reconstitution of the Fecal Microbiome after Extended Diet-Induced Changes Indicates a Stable Gut Microbiome in Healthy Adult Dogs. PMID:32303546
Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica. PMID:32282803
Novel application of normalized pointwise mutual information (NPMI) to mine biomedical literature for gene sets associated with disease: use case in breast carcinogenesis. PMID:32274464
Exploring Evolutionary Constraints in the Proteomes of Zika, Dengue, and Other Flaviviruses to Find Fitness-Critical Sites. PMID:32266427
Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics. PMID:32205368
The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography. PMID:32203121
Physiological, Biochemical, and Transcriptional Responses to Single and Combined Abiotic Stress in Stress-Tolerant and Stress-Sensitive Potato Genotypes. PMID:32184796
Learning supervised embeddings for large scale sequence comparisons. PMID:32168338
Ancient evolutionary signals of protein-coding sequences allow the discovery of new genes in the Drosophila melanogaster genome. PMID:32138644
Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing. PMID:32135388
A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia. PMID:32123704
A transcriptomic and proteomic atlas of expression in the Nezara viridula (Heteroptera: Pentatomidae) midgut suggests the compartmentalization of xenobiotic metabolism and nutrient digestion. PMID:32028881
Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. PMID:31972239
A Pathway for Degradation of Uracil to Acetyl Coenzyme A in Bacillus megaterium. PMID:31953335
Fam151b, the mouse homologue of C.elegans menorin gene, is essential for retinal function. PMID:31949211
Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling. PMID:31924745
A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation. PMID:31862382
Modeling aspects of the language of life through transfer-learning protein sequences. PMID:31847804
Cotrimoxazole Prophylaxis Increases Resistance Gene Prevalence and α-Diversity but Decreases β-Diversity in the Gut Microbiome of Human Immunodeficiency Virus-Exposed, Uninfected Infants. PMID:31832638
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. PMID:31782791
The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations. PMID:31778187
Novel redox-active enzymes for ligninolytic applications revealed from multiomics analyses of Peniophora sp. CBMAI 1063, a laccase hyper-producer strain. PMID:31772294
DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. PMID:31738385
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. PMID:31730850
Groundwater cable bacteria conserve energy by sulfur disproportionation. PMID:31728021
ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins. PMID:31702846
Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population. PMID:31699813
MGnify: the microbiome analysis resource in 2020. PMID:31696235
Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization. PMID:31694351
Unified rational protein engineering with sequence-based deep representation learning. PMID:31636460
pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes. PMID:31504173
Sibe: a computation tool to apply protein sequence statistics to predict folding and design in silico. PMID:31492097
Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages. PMID:31490939
A Three-Dimensional Model of Human Lysyl Oxidase, a Cross-Linking Enzyme. PMID:31459939
Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion. PMID:31459527
An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine. PMID:31455636
Molecular profiling of tissue biopsies reveals unique signatures associated with streptococcal necrotizing soft tissue infections. PMID:31451691
Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease. PMID:31451108
Universal principles of membrane protein assembly, composition and evolution. PMID:31415673
Estimating statistical significance of local protein profile-profile alignments. PMID:31409275
Progress in data interoperability to support computational toxicology and chemical safety evaluation. PMID:31404555
Metagenomic Functional Shifts to Plant Induced Environmental Changes. PMID:31404278
Distance-based protein folding powered by deep learning. PMID:31399549
The Oral Mouse Microbiome Promotes Tumorigenesis in Oral Squamous Cell Carcinoma. PMID:31387932
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. PMID:31375809
Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease. PMID:31370880
Deep-learning contact-map guided protein structure prediction in CASP13. PMID:31365149
Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance. PMID:31332384
CAGI5: Objective performance assessments of predictions based on the Evolutionary Action equation. PMID:31317604
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. PMID:31316056
Patterns of protist diversity associated with raw sewage in New York City. PMID:31289345
Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential. PMID:31248378
Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. PMID:31241222
Genes functioned in kleptoplastids of Dinophysis are derived from haptophytes rather than from cryptophytes. PMID:31227737
BCScreen: A gene panel to test for breast carcinogenesis in chemical safety screening. PMID:31218268
Combining learning and constraints for genome-wide protein annotation. PMID:31208327
RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. PMID:31195970
Comparative genomics and genome biology of Campylobacter showae. PMID:31169073
Mapping human microbiome drug metabolism by gut bacteria and their genes. PMID:31158845
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. PMID:31142855
Identification and characterization of a new sulfoacetaldehyde reductase from the human gut bacterium Bifidobacterium kashiwanohense. PMID:31123167
Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles. PMID:31101123
AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. PMID:31081040
LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. PMID:31081035
Structural prerequisites for CRM1-dependent nuclear export signaling peptides: accessibility, adapting conformation, and the stability at the binding site. PMID:31036839
Marine DNA Viral Macro- and Microdiversity from Pole to Pole. PMID:31031001
Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes. PMID:30961590
New insights into the structures and interactions of bacterial Y-family DNA polymerases. PMID:30916324
Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome. PMID:30901843
Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population. PMID:30894435
In Silico Analysis of the Subtype Selective Blockage of KCNA Ion Channels through the µ-Conotoxins PIIIA, SIIIA, and GIIIA. PMID:30893914
Microbial abundance, activity and population genomic profiling with mOTUs2. PMID:30833550
Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease. PMID:30801026
DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. PMID:30768156
Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant Ferula assafoetida. PMID:30679248
Genomic and metagenomic insights into the microbial community of a thermal spring. PMID:30674352
Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children. PMID:30671194
The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics. PMID:30619779
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. PMID:30602777
Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors. PMID:30574558
A resource of variant effect predictions of single nucleotide variants in model organisms. PMID:30573687
Gut microbiome structure and metabolic activity in inflammatory bowel disease. PMID:30531976
Genomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan. PMID:30510597
De novo protein structure prediction using ultra-fast molecular dynamics simulation. PMID:30458007
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
Evidence that regulation of intramembrane proteolysis is mediated by substrate gating during sporulation in Bacillus subtilis. PMID:30403663
UniProt: a worldwide hub of protein knowledge. PMID:30395287
US Immigration Westernizes the Human Gut Microbiome. PMID:30388453
Species-level functional profiling of metagenomes and metatranscriptomes. PMID:30377376
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. PMID:30356183
RaftProt V2: understanding membrane microdomain function through lipid raft proteomes. PMID:30329070
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). PMID:30323263
Using transcriptomics to enable a plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research. PMID:30253734
Deep generative models of genetic variation capture the effects of mutations. PMID:30250057
Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments. PMID:30244836
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. PMID:30241466
Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments. PMID:30228802
Characterization of ML-005, a Novel Metaproteomics-Derived Esterase. PMID:30210461
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. PMID:30165572
In situ development of a methanotrophic microbiome in deep-sea sediments. PMID:30154496
Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature. PMID:30152871
TMC1 Forms the Pore of Mechanosensory Transduction Channels in Vertebrate Inner Ear Hair Cells. PMID:30138589
Conducting metagenomic studies in microbiology and clinical research. PMID:30078138
Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids. PMID:30060184
Functional profiles of coronal and dentin caries in children. PMID:30034639
An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets. PMID:30018343
Crystal Structure of an Unusual Single-Stranded DNA-Binding Protein Encoded by Staphylococcal Cassette Chromosome Elements. PMID:30017563
Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes. PMID:29963641
Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid Anglerfishes. PMID:29946051
A distinct abundant group of microbial rhodopsins discovered using functional metagenomics. PMID:29925949
Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota. PMID:29906449
Structure and mutagenic analysis of the lipid II flippase MurJ from Escherichia coli. PMID:29891673
Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes darwiniensis and Cryptocercus Wood Roaches. PMID:29860278
AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. PMID:29762724
Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome. PMID:29690875
Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species. PMID:29689044
Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis. PMID:29590088
The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature. PMID:29560829
Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms. PMID:29556065
Species classifier choice is a key consideration when analysing low-complexity food microbiome data. PMID:29554948
Strong phenotypic plasticity limits potential for evolutionary responses to climate change. PMID:29520061
Biochemical Properties of α-Amylase from Midgut of Alphitobius diaperinus (Panzer) (Coleoptera: Tenebrionidae) Larvae. PMID:29484545
The genomes of two Eutrema species provide insight into plant adaptation to high altitudes. PMID:29394339
Host genetic variation and its microbiome interactions within the Human Microbiome Project. PMID:29378630
A global ocean atlas of eukaryotic genes. PMID:29371626
Prediction of Metal Ion Binding Sites in Proteins from Amino Acid Sequences by Using Simplified Amino Acid Alphabets and Random Forest Model. PMID:29307143
Improving pairwise comparison of protein sequences with domain co-occurrence. PMID:29293498
Genetic variation in human drug-related genes. PMID:29273096
3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures. PMID:29244774
Role of cis-trans proline isomerization in the function of pathogenic enterobacterial Periplasmic Binding Proteins. PMID:29190818
PDB-wide identification of biological assemblies from conserved quaternary structure geometry. PMID:29155427
Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling. PMID:29152585
Draft Genome Sequence and Annotation of the Apicomplexan Parasite Besnoitia besnoiti. PMID:29146849
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice. PMID:29123534
The MAR databases: development and implementation of databases specific for marine metagenomics. PMID:29106641
The sea cucumber genome provides insights into morphological evolution and visceral regeneration. PMID:29023486
Protein-protein interactions leave evolutionary footprints: High molecular coevolution at the core of interfaces. PMID:28980349
Strains, functions and dynamics in the expanded Human Microbiome Project. PMID:28953883
Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities. PMID:28865481
Metabolic Reconstruction and Modeling Microbial Electrosynthesis. PMID:28827682
De novo transcriptome assembly for the spiny mouse (Acomys cahirinus). PMID:28827620
Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. PMID:28821012
Development of pathogenicity predictors specific for variants that do not comply with clinical guidelines for the use of computational evidence. PMID:28812538
Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae. PMID:28769884
Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule". PMID:28738801
A TALE-inspired computational screen for proteins that contain approximate tandem repeats. PMID:28617832
Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance. PMID:28578660
Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA. PMID:28548659
Contrasting patterns of nucleotide polymorphism suggest different selective regimes within different parts of the PgiC1 gene in Festuca ovina L. PMID:28529468
COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. PMID:28472402
Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range. PMID:28464870
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. PMID:28453653
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. PMID:28453649
FireProt: web server for automated design of thermostable proteins. PMID:28449074
EigenTHREADER: analogous protein fold recognition by efficient contact map threading. PMID:28419258
Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions. PMID:28393904
Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PMID:28384184
Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling. PMID:28230923
An Extra Amino Acid Residue in Transmembrane Domain 10 of the γ-Aminobutyric Acid (GABA) Transporter GAT-1 Is Required for Efficient Ion-coupled Transport. PMID:28213519
RNA-Seq of Guar (Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources. PMID:28210265
A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. PMID:28183913
Protein Bioinformatics Databases and Resources. PMID:28150231
Identification and evolutionary analysis of long non-coding RNAs in zebra finch. PMID:28143393
Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders. PMID:28137743
Protein structure determination using metagenome sequence data. PMID:28104891
Mutation effects predicted from sequence co-variation. PMID:28092658
Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix. PMID:28083762
Minimizing proteome redundancy in the UniProt Knowledgebase. PMID:28025334
Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus. PMID:27977800
UniProt: the universal protein knowledgebase. PMID:27899622
ECOD: new developments in the evolutionary classification of domains. PMID:27899594
Uniclust databases of clustered and deeply annotated protein sequences and alignments. PMID:27899574
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. PMID:27822528
Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse). PMID:27812417
Insights into the innate immunome of actiniarians using a comparative genomic approach. PMID:27806695
GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features. PMID:27708373
FFPred 3: feature-based function prediction for all Gene Ontology domains. PMID:27561554
De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure. PMID:27527578
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. PMID:27503221
SAR11 bacteria linked to ocean anoxia and nitrogen loss. PMID:27487207
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
Discovery of a Natural Microsporidian Pathogen with a Broad Tissue Tropism in Caenorhabditis elegans. PMID:27362540
A Plasma Membrane Association Module in Yeast Amino Acid Transporters. PMID:27226538
HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. PMID:27174934
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. PMID:27166375
Computational clustering for viral reference proteomes. PMID:27153712
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes. PMID:27138088
CABRA: Cluster and Annotate Blast Results Algorithm. PMID:27129717
PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. PMID:27106060
Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. PMID:26945779
Structural basis of outer membrane protein insertion by the BAM complex. PMID:26901871
Natural protein sequences are more intrinsically disordered than random sequences. PMID:26801222
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. PMID:26682918
Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta. PMID:26677056
Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors. PMID:26527717
Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation. PMID:26455268
The Apis mellifera Filamentous Virus Genome. PMID:26184284
Identification, Functional Characterization, and Evolution of Terpene Synthases from a Basal Dicot. PMID:26157114
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/10/1282

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

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

biological process
metasource: re3data.org
version: re3data.org: UniRef; editing status 2020-01-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31W6B last accessed: 2022-11-04

cellular component
metasource: re3data.org
version: re3data.org: UniRef; editing status 2020-01-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31W6B last accessed: 2022-11-04

coding sequence diversity
metasource: re3data.org
version: re3data.org: UniRef; editing status 2020-01-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31W6B last accessed: 2022-11-04

disease
metasource: re3data.org
version: re3data.org: UniRef; editing status 2020-01-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31W6B last accessed: 2022-11-04

protein sequences
metasource: re3data.org
version: re3data.org: UniRef; editing status 2020-01-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31W6B last accessed: 2022-11-04

sequence clusters
metasource: re3data.org
version: re3data.org: UniRef; editing status 2020-01-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31W6B last accessed: 2022-11-04

sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.660724

gene structure
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.660724

protein sequence general sequence biological process cellular component coding sequence diversity disease protein sequences sequence clusters sequence analysis gene structure

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