Organelle 16S rRNA amplicon sequencing enables profiling of active gut microbiota in murine model.
PMID:35896837
In Vitro Growth-Inhibitory Synergistic Effect of Zinc Pyrithione in Combination with Gentamicin against Bacterial Skin Pathogens of Livestock.
PMID:35884214
Deep embeddings to comprehend and visualize microbiome protein space.
PMID:35725732
Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies.
PMID:35612752
Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain.
PMID:35581640
Nuclear Magnetic Resonance-Measured Ionized Magnesium Is Inversely Associated with Type 2 Diabetes in the Insulin Resistance Atherosclerosis Study.
PMID:35565760
LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation.
PMID:35420129
Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa.
PMID:35384379
Considerations for constructing a protein sequence database for metaproteomics.
PMID:35242286
The crewed journey to Mars and its implications for the human microbiome.
PMID:35125119
Bacterial Communities in Lanna Phak-Gard-Dong (Pickled Mustard Green) from Three Different Ethnolinguistic Groups in Northern Thailand.
PMID:35053147
Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer.
PMID:35030025
Impact of intensive lifestyle intervention on gut microbiota composition in type 2 diabetes: a post-hoc analysis of a randomized clinical trial.
PMID:34965188
Systems biology and machine learning approaches identify drug targets in diabetic nephropathy.
PMID:34873190
The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools.
PMID:34828362
Rhea, the reaction knowledgebase in 2022.
PMID:34755880
CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria.
PMID:34614159
Discovering and Summarizing Relationships Between Chemicals, Genes, Proteins, and Diseases in PubChem.
PMID:34322655
Annotating Putative D. discoideum Proteins Using I-TASSER.
PMID:34278246
Analysis and application of a suite of recombinant endo-β(1,3)-D-glucanases for studying fungal cell walls.
PMID:34217291
Machine learning differentiates enzymatic and non-enzymatic metals in proteins.
PMID:34140507
Structure-based protein function prediction using graph convolutional networks.
PMID:34039967
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.
PMID:33944776
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users.
PMID:33849055
Magnesium: Biochemistry, Nutrition, Detection, and Social Impact of Diseases Linked to Its Deficiency.
PMID:33808247
Extracellular Vesicles and Preeclampsia: Current Knowledge and Future Research Directions.
PMID:33779928
The evolution of oxygen-utilizing enzymes suggests early biosphere oxygenation.
PMID:33633374
The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes.
PMID:33563959
Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding.
PMID:33239700
Repositioned Drugs for Chagas Disease Unveiled via Structure-Based Drug Repositioning.
PMID:33233837
A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain.
PMID:33181823
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
PMID:33147627
Magnesium Absorption in Intestinal Cells: Evidence of Cross-Talk between EGF and TRPM6 and Novel Implications for Cetuximab Therapy.
PMID:33114586
A Need for Improved Cellulase Identification from Metagenomic Sequence Data.
PMID:33067195
Metabolic pathway inference using multi-label classification with rich pathway features.
PMID:33001968
Novel variant in the CNNM2 gene associated with dominant hypomagnesemia.
PMID:32997713
Molecular Mechanisms of Metal Toxicity in the Pathogenesis of Alzheimer's Disease.
PMID:32889653
Phenotypic and molecular spectrum of pyridoxamine-5'-phosphate oxidase deficiency: A scoping review of 87 cases of pyridoxamine-5'-phosphate oxidase deficiency.
PMID:32888189
The Flavoproteome of the Model Plant Arabidopsis thaliana.
PMID:32731628
Birth of a pathway for sulfur metabolism in early amniote evolution.
PMID:32601391
Circulating Ionized Magnesium as a Measure of Supplement Bioavailability: Results from a Pilot Study for Randomized Clinical Trial.
PMID:32353962
DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving understudied kinases.
PMID:32044914
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes.
PMID:32034905
Compartment and hub definitions tune metabolic networks for metabolomic interpretations.
PMID:31972021
Modeling aspects of the language of life through transfer-learning protein sequences.
PMID:31847804
The human DEPhOsphorylation Database DEPOD: 2019 update.
PMID:31836896
Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model.
PMID:31694544
Enzyme annotation in UniProtKB using Rhea.
PMID:31688925
Unraveling allosteric landscapes of allosterome with ASD.
PMID:31665428
Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook.
PMID:31656120
ProCarbDB: a database of carbohydrate-binding proteins.
PMID:31598690
Genus for biomolecules.
PMID:31584078
Pseudomonas spp. are key players in agricultural biogas substrate degradation.
PMID:31492882
A Structure-Informed Atlas of Human-Virus Interactions.
PMID:31474372
I-TASSER gateway: A protein structure and function prediction server powered by XSEDE.
PMID:31427836
The Landscape of Genetic Content in the Gut and Oral Human Microbiome.
PMID:31415755
Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.
PMID:31399369
FunFam protein families improve residue level molecular function prediction.
PMID:31319797
Unveiling the presence of biosynthetic pathways for bioactive compounds in the Thalassiosira rotula transcriptome.
PMID:31289324
iMet: A graphical user interface software tool to merge metabolic networks.
PMID:31286073
Integrated analysis of microRNA regulation and its interaction with mechanisms of epigenetic regulation in the etiology of systemic lupus erythematosus.
PMID:31237906
metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes.
PMID:31235611
Recent trends in molecular diagnostics of yeast infections: from PCR to NGS.
PMID:31158289
The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions.
PMID:31149898
Secretion of DNases by Marine Bacteria: A Culture Based and Bioinformatics Approach.
PMID:31134017
Substrate inhibition imposes fitness penalty at high protein stability.
PMID:31097595
LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins.
PMID:31081035
Marek's Disease Virus Regulates the Ubiquitylome of Chicken CD4+ T Cells to Promote Tumorigenesis.
PMID:31035338
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments.
PMID:30902113
Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus.
PMID:30285612
Binding site matching in rational drug design: algorithms and applications.
PMID:30169563
Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns.
PMID:30086708
Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes.
PMID:29980796
HFSP: high speed homology-driven function annotation of proteins.
PMID:29950013
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources.
PMID:29931155
Tissue-Specific Analysis of Pharmacological Pathways.
PMID:29920991
Improved enzyme annotation with EC-specific cutoffs using DETECT v2.
PMID:29722785
Evidence That Speciation of Oxovanadium Complexes Does Not Solely Account for Inhibition of Leishmania Acid Phosphatases.
PMID:29707535
Systematic characterization of pan-cancer mutation clusters.
PMID:29572294
Phylogeny of Vibrio vulnificus from the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy.
PMID:29358930
Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains.
PMID:29310579
Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus.
PMID:29270219
Comparative Genome Analysis Reveals Adaptation to the Ectophytic Lifestyle of Sooty Blotch and Flyspeck Fungi.
PMID:29126189
Biometal Dyshomeostasis and Toxic Metal Accumulations in the Development of Alzheimer's Disease.
PMID:29114205
Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens.
PMID:29106651
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.
PMID:29106569
Human microbiome signatures of differential colorectal cancer drug metabolism.
PMID:29104759
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics.
PMID:29092055
Software-aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry.
PMID:29091918
A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication.
PMID:28981525
Molecular Imaging of Hydrolytic Enzymes Using PET and SPECT.
PMID:28927325
De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacus.
PMID:28873438
Genomic analysis of methanogenic archaea reveals a shift towards energy conservation.
PMID:28826405
Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone.
PMID:28732462
DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species.
PMID:28729549
Structural properties of genotype-phenotype maps.
PMID:28679667
ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network.
PMID:28442501
Exploring the differences in metabolic behavior of astrocyte and glioblastoma: a flux balance analysis approach.
PMID:28392849
DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.
PMID:28387604
Comparative analysis of sterol acquisition in the oomycetes Saprolegnia parasitica and Phytophthora infestans.
PMID:28152045
Protein Bioinformatics Databases and Resources.
PMID:28150231
Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science.
PMID:27929431
InterPro in 2017-beyond protein family and domain annotations.
PMID:27899635
The Human Kinome Targeted by FDA Approved Multi-Target Drugs and Combination Products: A Comparative Study from the Drug-Target Interaction Network Perspective.
PMID:27828998
Updates in Rhea - an expert curated resource of biochemical reactions.
PMID:27789701
Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data.
PMID:27595107
Order, Disorder, and Everything in Between.
PMID:27548131
Comparison of FDA Approved Kinase Targets to Clinical Trial Ones: Insights from Their System Profiles and Drug-Target Interaction Networks.
PMID:27547755
Representing and querying disease networks using graph databases.
PMID:27462371
Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type.
PMID:27462366
Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.
PMID:27434306
Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach.
PMID:27379244
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind.
PMID:27131375
Standardized benchmarking in the quest for orthologs.
PMID:27043882
Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome.
PMID:27030248
CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state.
PMID:27022160
Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning.
PMID:26855674
A network analysis of cofactor-protein interactions for analyzing associations between human nutrition and diseases.
PMID:26777674
Metagenome-assembled genomes uncover a global brackish microbiome.
PMID:26667648
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond.
PMID:26615025
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.
PMID:26559508
SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis.
PMID:26433225
Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective.
PMID:26367006
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View.
PMID:26366735
Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling.
PMID:26332409
De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis.
PMID:26330142
The Immunoreactive Exo-1,3-β-Glucanase from the Pathogenic Oomycete Pythium insidiosum Is Temperature Regulated and Exhibits Glycoside Hydrolase Activity.
PMID:26263509
Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant.
PMID:26191049
Transcriptome sequencing of three Pseudo-nitzschia species reveals comparable gene sets and the presence of Nitric Oxide Synthase genes in diatoms.
PMID:26189990
Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism.
PMID:26099921
Novel systems modeling methodology in comparative microbial metabolomics: identifying key enzymes and metabolites implicated in autism spectrum disorders.
PMID:25913376
Metaproteomics of complex microbial communities in biogas plants.
PMID:25874383
iPathCase(KEGG): An iPad interface for KEGG metabolic pathways.
PMID:25825656
The Listeria monocytogenes strain 10403S BioCyc database.
PMID:25819074
Subsistence strategies in traditional societies distinguish gut microbiomes.
PMID:25807110
Potential inhibitors for isocitrate lyase of Mycobacterium tuberculosis and non-M. tuberculosis: a summary.
PMID:25649791
The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research.
PMID:25522365
Determining microbial products and identifying molecular targets in the human microbiome.
PMID:25440055
Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes.
PMID:25435546
The InterPro protein families database: the classification resource after 15 years.
PMID:25428371
Circulating biomarkers of one-carbon metabolism in relation to renal cell carcinoma incidence and survival.
PMID:25376861
CATH: comprehensive structural and functional annotations for genome sequences.
PMID:25348408
Updates in Rhea--a manually curated resource of biochemical reactions.
PMID:25332395
Comparative genomics of nucleotide metabolism: a tour to the past of the three cellular domains of life.
PMID:25230797
Involvement of PG2212 zinc finger protein in the regulation of oxidative stress resistance in Porphyromonas gingivalis W83.
PMID:25225267
PlantCAZyme: a database for plant carbohydrate-active enzymes.
PMID:25125445
Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility.
PMID:25124718
Metabolome variations in the Porphyromonas gingivalis vimA mutant during hydrogen peroxide-induced oxidative stress.
PMID:25055986
Structural DNA nanotechnology: state of the art and future perspective.
PMID:25029570
The evolution of enzyme function in the isomerases.
PMID:25000289
Fungal Beta-glucosidases: a bottleneck in industrial use of lignocellulosic materials.
PMID:24970184
Functional evolution of PLP-dependent enzymes based on active-site structural similarities.
PMID:24920327
Profiling the orphan enzymes.
PMID:24906382
Coiled-coil proteins facilitated the functional expansion of the centrosome.
PMID:24901223
Finding sequences for over 270 orphan enzymes.
PMID:24826896
Systematic detection of internal symmetry in proteins using CE-Symm.
PMID:24681267
M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations.
PMID:24565382
Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes 'Gramella forsetii' KT0803.
PMID:24522261
InterProScan 5: genome-scale protein function classification.
PMID:24451626
Motif-directed redesign of enzyme specificity.
PMID:24407908
iEzy-drug: a web server for identifying the interaction between enzymes and drugs in cellular networking.
PMID:24371828
LigSearch: a knowledge-based web server to identify likely ligands for a protein target.
PMID:24311580
ArchDB 2014: structural classification of loops in proteins.
PMID:24265221
MultitaskProtDB: a database of multitasking proteins.
PMID:24253302
MetaRef: a pan-genomic database for comparative and community microbial genomics.
PMID:24203705
Analytical tools and databases for metagenomics in the next-generation sequencing era.
PMID:24124405
A broader view: microbial enzymes and their relevance in industries, medicine, and beyond.
PMID:24106701
Association of vitamin B6, vitamin B12 and methionine with risk of breast cancer: a dose-response meta-analysis.
PMID:23907430
TCW: transcriptome computational workbench.
PMID:23874959
JBioWH: an open-source Java framework for bioinformatics data integration.
PMID:23846595
Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome.
PMID:23815283
Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity.
PMID:23782552
Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction.
PMID:23704901
Identification of mitochondrial coenzyme a transporters from maize and Arabidopsis.
PMID:23590975
Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria.
PMID:23537208
The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4.
PMID:23516524
De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen.
PMID:23349770
FastAnnotator--an efficient transcript annotation web tool.
PMID:23281853
Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases.
PMID:23281650
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
PMID:23203873
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites.
PMID:23193253
Enzyme informatics.
PMID:23116471
Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin.
PMID:23043000
MESSA: MEta-Server for protein Sequence Analysis.
PMID:23031578
Prediagnostic plasma pyridoxal 5'-phosphate (vitamin b6) levels and invasive breast carcinoma risk: the multiethnic cohort.
PMID:22879204
Analysis of Babesia bovis infection-induced gene expression changes in larvae from the cattle tick, Rhipicephalus (Boophilus) microplus.
PMID:22871314
Mining GO annotations for improving annotation consistency.
PMID:22848383
TPX: Biomedical literature search made easy.
PMID:22829734
Template-based protein structure modeling using the RaptorX web server.
PMID:22814390
A global characterization and identification of multifunctional enzymes.
PMID:22723914
Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.
PMID:22712506
An elm EST database for identifying leaf beetle egg-induced defense genes.
PMID:22702658
Quality of computationally inferred gene ontology annotations.
PMID:22693439
A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.
PMID:22651983
The use of evolutionary patterns in protein annotation.
PMID:22633559
The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation.
PMID:22630137
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.
PMID:22615551
An in silico platform for the design of heterologous pathways in nonnative metabolite production.
PMID:22578364
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110.
PMID:22443545
A top-down approach to classify enzyme functional classes and sub-classes using random forest.
PMID:22376768
A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags.
PMID:22281184
KB-Rank: efficient protein structure and functional annotation identification via text query.
PMID:22270457
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases.
PMID:22233419
Modulating protein-protein interactions with small molecules: the importance of binding hotspots.
PMID:22198293
Advanced stoichiometric analysis of metabolic networks of mammalian systems.
PMID:22196224
Novel search method for the discovery of functional relationships.
PMID:22180409
VimA-dependent modulation of acetyl coenzyme A levels and lipid A biosynthesis can alter virulence in Porphyromonas gingivalis.
PMID:22144476
MetaBase--the wiki-database of biological databases.
PMID:22139927
neXtProt: a knowledge platform for human proteins.
PMID:22139911
Rhea--a manually curated resource of biochemical reactions.
PMID:22135291
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree.
PMID:22121228
InterPro in 2011: new developments in the family and domain prediction database.
PMID:22096229
Critical assessment of human metabolic pathway databases: a stepping stone for future integration.
PMID:21999653
Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes.
PMID:21965536
Genomic basis of endosymbiont-conferred protection against an insect parasitoid.
PMID:21948522
Computational methods for Gene Orthology inference.
PMID:21690100
Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context.
PMID:21689481
Mining metabolites: extracting the yeast metabolome from the literature.
PMID:21687783
MarkUs: a server to navigate sequence-structure-function space.
PMID:21672961
Common peptides study of aminoacyl-tRNA synthetases.
PMID:21647378
Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome.
PMID:21639913
ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities.
PMID:21541071
A survey of metabolic databases emphasizing the MetaCyc family.
PMID:21523460
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.
PMID:21472436
A new approach to assess and predict the functional roles of proteins across all known structures.
PMID:21445639
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.
PMID:21408081
Mining the soluble chloroplast proteome by affinity chromatography.
PMID:21365755
Genome (re-)annotation and open-source annotation pipelines.
PMID:21255336
1,000 structures and more from the MCSG.
PMID:21219649
Evolutionary innovations and the organization of protein functions in genotype space.
PMID:21152394
BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation.
PMID:21122127
PCDB: a database of protein conformational diversity.
PMID:21097895
Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
PMID:21097779
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium.
PMID:21083885
PCDDB: the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata.
PMID:21071417
Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains.
PMID:20860794
Prototypes of elementary functional loops unravel evolutionary connections between protein functions.
PMID:20823313
Characterizing the metabolism of Dehalococcoides with a constraint-based model.
PMID:20811585
The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.
PMID:20624719
Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement.
PMID:20594333
Fast integration of heterogeneous data sources for predicting gene function with limited annotation.
PMID:20507895
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network.
PMID:20498836
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.
PMID:20433725
Large-scale analyses of glycosylation in cellulases.
PMID:20172492
MicroScope: a platform for microbial genome annotation and comparative genomics.
PMID:20157493
Prediction of functional class of proteins and peptides irrespective of sequence homology by support vector machines.
PMID:20066123
Next generation transcriptomes for next generation genomes using est2assembly.
PMID:20034392
Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency.
PMID:20025723
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets.
PMID:19906710
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
PMID:19850718
EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts.
PMID:19758466
FLORA: a novel method to predict protein function from structure in diverse superfamilies.
PMID:19714201
Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development.
PMID:19709400
Enzyme classification with peptide programs: a comparative study.
PMID:19630945
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development.
PMID:19543979
The energy profiles of atomic conformational transition intermediates of adenylate kinase.
PMID:19507242
Designed human serum hyaluronidase 1 variant, HYAL1DeltaL, exhibits activity up to pH 5.9.
PMID:19478093
Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation.
PMID:19478002
Public databases and software for the pathway analysis of cancer genomes.
PMID:19455256
Phylogenetic and functional assessment of orthologs inference projects and methods.
PMID:19148271
The 2008 update of the Aspergillus nidulans genome annotation: a community effort.
PMID:19146970
Toward understanding the conformational dynamics of RNA ligation.
PMID:19133737
A survey of visualization tools for biological network analysis.
PMID:19040716
OryGenesDB 2008 update: database interoperability for functional genomics of rice.
PMID:19036791
The National Center for Biotechnology Information's Protein Clusters Database.
PMID:18940865
ExplorEnz: the primary source of the IUBMB enzyme list.
PMID:18776214
Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis.
PMID:18767192
Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry.
PMID:18560811
Prediction of enzyme function by combining sequence similarity and protein interactions.
PMID:18505562
Characterization and prediction of residues determining protein functional specificity.
PMID:18450811
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks.
PMID:18440972
annot8r: GO, EC and KEGG annotation of EST datasets.
PMID:18400082
ISOL@: an Italian SOLAnaceae genomics resource.
PMID:18387209
Mining experimental evidence of molecular function claims from the literature.
PMID:17942445
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.
PMID:17933782
MetaCrop: a detailed database of crop plant metabolism.
PMID:17933764
An EST database from saffron stigmas.
PMID:17925031
Linking microarray reporters with protein functions.
PMID:17897448
Integrated network reconstruction, visualization and analysis using YANAsquare.
PMID:17725829
PROCOGNATE: a cognate ligand domain mapping for enzymes.
PMID:17720712
ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature.
PMID:17662133
A survey of orphan enzyme activities.
PMID:17623104
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
PMID:17570147
CORRIE: enzyme sequence annotation with confidence estimates.
PMID:17570146
The 2006 automated function prediction meeting.
PMID:17570143
Advancing translational research with the Semantic Web.
PMID:17493285
Structural and functional insights into Mimivirus ORFans.
PMID:17490476
DBAli tools: mining the protein structure space.
PMID:17478513
HMM-ModE--improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences.
PMID:17389042
Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance.
PMID:17254327
SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas.
PMID:17202169
PATRIC: the VBI PathoSystems Resource Integration Center.
PMID:17142235
TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species.
PMID:17142232
Identification of transcripts associated with cell wall metabolism and development in the stem of sugarcane by Affymetrix GeneChip Sugarcane Genome Array expression profiling.
PMID:17111183
ORENZA: a web resource for studying ORphan ENZyme activities.
PMID:17026747
Accelerating the reconstruction of genome-scale metabolic networks.
PMID:16772023
EVEREST: automatic identification and classification of protein domains in all protein sequences.
PMID:16749920
Structure-based function inference using protein family-specific fingerprints.
PMID:16731985
From the similarity analysis of protein cavities to the functional classification of protein families using cavbase.
PMID:16697007
Functional annotation prediction: all for one and one for all.
PMID:16672244
BioWarehouse: a bioinformatics database warehouse toolkit.
PMID:16556315
VANTED: a system for advanced data analysis and visualization in the context of biological networks.
PMID:16519817
GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins.
PMID:16417636
LMPD: LIPID MAPS proteome database.
PMID:16381922
PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways.
PMID:16381888
DMAPS: a database of multiple alignments for protein structures.
PMID:16381863
Probabilistic annotation of protein sequences based on functional classifications.
PMID:16354297
ParPEST: a pipeline for EST data analysis based on parallel computing.
PMID:16351758
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms.
PMID:16351748
Bioinformatics in microbial biotechnology--a mini review.
PMID:15985162
The bioinformatics resource for oral pathogens.
PMID:15980574
Comparison of substructural epitopes in enzyme active sites using self-organizing maps.
PMID:15865062
Columba: an integrated database of proteins, structures, and annotations.
PMID:15801979
Large scale hierarchical clustering of protein sequences.
PMID:15663796
MetaRouter: bioinformatics for bioremediation.
PMID:15608267
Metagrowth: a new resource for the building of metabolic hypotheses in microbiology.
PMID:15608207
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
PMID:15608193
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
PMID:15608188
The SYSTERS Protein Family Database in 2005.
PMID:15608183
ProtoNet 4.0: a hierarchical classification of one million protein sequences.
PMID:15608180
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.
PMID:15608178
A functional hierarchical organization of the protein sequence space.
PMID:15596019
EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference.
PMID:15576349
Predicting enzyme family class in a hybridization space.
PMID:15498934
Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase.
PMID:15287962
Human cytomegalovirus carries a cell-derived phospholipase A2 required for infectivity.
PMID:15220446
MitoProteome: mitochondrial protein sequence database and annotation system.
PMID:14681458
IntEnz, the integrated relational enzyme database.
PMID:14681451
E-MSD: an integrated data resource for bioinformatics.
PMID:14681397
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.
PMID:14681376
Enzyme-specific profiles for genome annotation: PRIAM.
PMID:14602924
PANDORA: keyword-based analysis of protein sets by integration of annotation sources.
PMID:14500825
The organization of the microbial biodegradation network from a systems-biology perspective.
PMID:12973298
ExPASy: The proteomics server for in-depth protein knowledge and analysis.
PMID:12824418
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.
PMID:12654719
Using binning to maintain confidentiality of medical data.
PMID:12463865
Newly identified cytochrome c oxidase operon in the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 specifically induced in heterocysts.
PMID:11948164
TTD: Therapeutic Target Database.
PMID:11752352
ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro.
PMID:11752292
Annotation transfer for genomics: measuring functional divergence in multi-domain proteins.
PMID:11591640
Functional versatility and molecular diversity of the metabolic map of Escherichia coli.
PMID:11544193
A cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus is actually a broad specificity phosphatase.
PMID:11514674
Divergence of function in sequence-related groups of Escherichia coli proteins.
PMID:11483578
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
PMID:10802651