R32K7X last accessed: 2022-11-04

metacyc
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.287250

Other names: Metabolic Pathway Database, a member of the BioCyc database collection, metacyc

MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways, and are curated from the primary scientific literature. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations.

Webpage:

http://metacyc.org/

Licence:

Name: BioCyc Database License
URL: https://biocyc.org/download-flatfiles.shtml

Publications:

Publications
More detailed information about this field from each metasource.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
PMID: 24225315
metasource: Fairsharing.org
version: FAIRsharing.org: MetaCyc; MetaCyc; DOI: https://doi.org/10.25504/FAIRsharing.yytevr; Last edited: Oct. 23, 2019, 11:57 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
PMID: 26527732
metasource: Fairsharing.org
version: FAIRsharing.org: MetaCyc; MetaCyc; DOI: https://doi.org/10.25504/FAIRsharing.yytevr; Last edited: Oct. 23, 2019, 11:57 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
PMID: 22102576
metasource: Fairsharing.org
version: FAIRsharing.org: MetaCyc; MetaCyc; DOI: https://doi.org/10.25504/FAIRsharing.yytevr; Last edited: Oct. 23, 2019, 11:57 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.287250

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
PMID: 19850718
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.287250

http://dx.doi.org/10.1093/nar/gkx935
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases PubMed citations: 478.

478 articles citing: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

l-Ornithine-N5-monooxygenase (PvdA) Substrate Analogue Inhibitors for Pseudomonas aeruginosa Infections Treatment: Drug Repurposing Computational Studies. PMID:35883443
Organic Connection of Holobiont Components and the Essential Roles of Core Microbes in the Holobiont Formation of Feral Brassica napus. PMID:35875588
Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine. PMID:35789833
Oligofructose restores postprandial short-chain fatty acid levels during high-fat feeding. PMID:35785478
Hurricane Harvey Impacts on Water Quality and Microbial Communities in Houston, TX Waterbodies. PMID:35774461
Escherichia/Shigella, SCFAs, and Metabolic Pathways-The Triad That Orchestrates Intestinal Dysbiosis in Patients with Decompensated Alcoholic Cirrhosis from Western Mexico. PMID:35744749
Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis). PMID:35733110
Child type 1 diabetes associated with mother vaginal bacteriome and mycobiome. PMID:35701558
Metagenomic assessment of gut microbial communities and risk of severe COVID-19. PMID:35677075
Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae. PMID:35642928
Ustilago maydis Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model. PMID:35628779
Exploring the Effects of Six Weeks of Resistance Training on the Fecal Microbiome of Older Adult Males: Secondary Analysis of a Peanut Protein Supplemented Randomized Controlled Trial. PMID:35622473
Individualized discovery of rare cancer drivers in global network context. PMID:35593700
The WalRK Two-Component System Is Essential for Proper Cell Envelope Biogenesis in Clostridioides difficile. PMID:35575581
Survival strategies of an anoxic microbial ecosystem in Lake Untersee, a potential analog for Enceladus. PMID:35513542
Effect of Maternal Catalase Supplementation on Reproductive Performance, Antioxidant Activity and Mineral Transport in Sows and Piglets. PMID:35405818
Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation. PMID:35359727
Application of Transcriptomics for Predicting Protein Interaction Networks, Drug Targets and Drug Candidates. PMID:35356062
Acute and Delayed Effects of Stress Eliciting Post-Traumatic Stress-Like Disorder Differentially Alters Fecal Microbiota Composition in a Male Mouse Model. PMID:35300376
Effect of Magnesium Supplementation on Inflammatory Parameters: A Meta-Analysis of Randomized Controlled Trials. PMID:35277037
Integrated Metabolomics and Lipidomics Reveal High Accumulation of Glycerophospholipids in Human Astrocytes under the Lipotoxic Effect of Palmitic Acid and Tibolone Protection. PMID:35269616
A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets. PMID:35205348
The airway microbiota of non-small cell lung cancer patients and its relationship to tumor stage and EGFR gene mutation. PMID:35142041
GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring. PMID:35087491
Genomic insights into versatile lifestyle of three new bacterial candidate phyla. PMID:35060074
Gut microbes shape microglia and cognitive function during malnutrition. PMID:35019164
Gut Microbiota as a Source of Uremic Toxins. PMID:35008909
Prediction of trehalose-metabolic pathway and comparative analysis of KEGG, MetaCyc, and RAST databases based on complete genome of Variovorax sp. PAMC28711. PMID:34991451
Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation. PMID:34989990
Characterization of the gut microbiota among Veterans with unique military-related exposures and high prevalence of chronic health conditions: A United States-Veteran Microbiome Project (US-VMP) study. PMID:34988495
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome. PMID:34980918
Subgingival Microbiota and Cytokines Profile Changes in Patients with Periodontitis: A Pilot Study Comparing Healthy and Diseased Sites in the Same Oral Cavities. PMID:34835489
Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi. PMID:34777932
Improved Metabolite Prediction Using Microbiome Data-Based Elastic Net Models. PMID:34760716
HumanNet v3: an improved database of human gene networks for disease research. PMID:34747468
Sex-specific relationships of the infant microbiome and early-childhood behavioral outcomes. PMID:34732816
PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes. PMID:34716373
Prolonged Impairment of Short-Chain Fatty Acid and L-Isoleucine Biosynthesis in Gut Microbiome in Patients With COVID-19. PMID:34687739
An orthogonal metabolic framework for one-carbon utilization. PMID:34675440
Ornithine Transcarbamylase - From Structure to Metabolism: An Update. PMID:34658931
Transcriptional Activity of Predominant Streptococcus Species at Multiple Oral Sites Associate With Periodontal Status. PMID:34621696
Periodontitis associates with species-specific gene expression of the oral microbiota. PMID:34556654
Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility. PMID:34499026
Delivery mode and perinatal antibiotics influence the predicted metabolic pathways of the gut microbiome. PMID:34471207
Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities. PMID:34440394
The Role of Metabolic Engineering Technologies for the Production of Fatty Acids in Yeast. PMID:34356487
Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19. PMID:34353886
Data integration uncovers the metabolic bases of phenotypic variation in yeast. PMID:34264947
The LASER database: Formalizing design rules for metabolic engineering. PMID:34150506
Tailoring strain construction strategies for muconic acid production in S. cerevisiae and E. coli. PMID:34150501
Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments. PMID:34127845
WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. PMID:34117752
Decreased Abundance of Akkermansia muciniphila Leads to the Impairment of Insulin Secretion and Glucose Homeostasis in Lean Type 2 Diabetes. PMID:34085773
IDARE2-Simultaneous Visualisation of Multiomics Data in Cytoscape. PMID:34066448
Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production. PMID:34066089
Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling. PMID:33981000
Strategies to Modulate Specialized Metabolism in Mediterranean Crops: From Molecular Aspects to Field. PMID:33809189
Translating insights from the seed metabolome into improved prediction for lipid-composition traits in oat (Avena sativa L.). PMID:33789350
Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance. PMID:33760840
Natural combinatorial genetics and prolific polyamine production enable siderophore diversification in Serratia plymuthica. PMID:33722216
Syntrophic Hydrocarbon Degradation in a Decommissioned Off-Shore Subsea Oil Storage Structure. PMID:33670234
Plant Allelochemicals as Sources of Insecticides. PMID:33668349
Ecosystem engineers drive differing microbial community composition in intertidal estuarine sediments. PMID:33606695
Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem. PMID:33593438
Unveiling the Bovine Epimural Microbiota Composition and Putative Function. PMID:33572291
A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases. PMID:33563976
Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification. PMID:33563788
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. PMID:33539279
Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities. PMID:33424787
Respiratory chain components are required for peptidoglycan recognition protein-induced thiol depletion and killing in Bacillus subtilis and Escherichia coli. PMID:33420211
WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. PMID:33398287
Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease. PMID:33397897
Functional Prediction and Assignment of Methanobrevibacter ruminantium M1 Operome Using a Combined Bioinformatics Approach. PMID:33391347
Integrative characterization of the near-minimal bacterium Mesoplasma florum. PMID:33331123
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species. PMID:33324679
PPAD Activity Promotes Outer Membrane Vesicle Biogenesis and Surface Translocation by Porphyromonas gingivalis. PMID:33257525
Metabolic Flux Analysis-Linking Isotope Labeling and Metabolic Fluxes. PMID:33172051
A practical guide to mechanistic systems modeling in biology using a logic-based approach. PMID:33064138
The Cu(II) Reductase RclA Protects Escherichia coli against the Combination of Hypochlorous Acid and Intracellular Copper. PMID:32994322
A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity. PMID:32977700
Experimental autoimmune encephalomyelitis is associated with changes of the microbiota composition in the gastrointestinal tract. PMID:32938979
Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction. PMID:32932905
Dietary Intervention Reverses Fatty Liver and Altered Gut Microbiota during Early-Life Undernutrition. PMID:32900869
Transcriptomic analysis of a Clostridium thermocellum strain engineered to utilize xylose: responses to xylose versus cellobiose feeding. PMID:32884054
Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4. PMID:32804944
Sex is associated with differences in gut microbial composition and function in hepatic encephalopathy. PMID:32679299
Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis. PMID:32611709
A biochemically-interpretable machine learning classifier for microbial GWAS. PMID:32444610
Assessment of a Potential Role of Dickeya dadantii DSM 18020 as a Pectinase Producer for Utilization in Poultry Diets Based on in silico Analyses. PMID:32390987
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
The relationship between cigarette smoking and the tongue microbiome in an East Asian population. PMID:32341759
Association between oropharyngeal microbiome and weight gain in piglets during pre and post weaning life. PMID:32292932
Persistence of Brucella abortus lineages revealed by genomic characterization and phylodynamic analysis. PMID:32287327
The Saltpan Microbiome is Structured by Sediment Depth and Minimally Influenced by Variable Hydration. PMID:32276533
Study on the Antibreast Cancer Mechanism and Bioactive Components of Si-Wu-Tang by Cell Type-Specific Molecular Network. PMID:32256636
Longitudinal survey of microbiome associated with particulate matter in a megacity. PMID:32127018
Genome-scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae. PMID:32068953
Cultivable, Host-Specific Bacteroidetes Symbionts Exhibit Diverse Polysaccharolytic Strategies. PMID:32060023
Novel Hyperthermophilic Crenarchaeon Thermofilum adornatum sp. nov. Uses GH1, GH3, and Two Novel Glycosidases for Cellulose Hydrolysis. PMID:31998263
Mutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer. PMID:31979117
Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii. PMID:31964928
Oropharyngeal microbiome of a college population following a meningococcal disease outbreak. PMID:31959912
OptFill: A Tool for Infeasible Cycle-Free Gapfilling of Stoichiometric Metabolic Models. PMID:31954977
Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences. PMID:31952477
Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products. PMID:31900122
Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs). PMID:31848398
Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies. PMID:31848305
AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data. PMID:31779604
Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes. PMID:31727954
Production of 5-aminolevulinic acid from glutamate by overexpressing HemA1 and pgr7 from Arabidopsis thaliana in Escherichia coli. PMID:31673852
Computational Identification of Metabolic Pathways of Plasmodium falciparum using the k-Shortest Path Algorithm. PMID:31662957
Whole Genome Sequence of Marinobacter salarius Strain SMR5, Shown to Promote Growth in its Diatom Host. PMID:31588249
Interplay between the human gut microbiome and host metabolism. PMID:31582752
Changes in the metabolic potential of the sponge microbiome under ocean acidification. PMID:31515490
Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster. PMID:31492856
Streptococcus pyogenes Transcriptome Changes in the Inflammatory Environment of Necrotizing Fasciitis. PMID:31471300
Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition. PMID:31399369
Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight. PMID:31399081
Gene Modules Co-regulated with Biosynthetic Gene Clusters for Allelopathy between Rice and Barnyardgrass. PMID:31394718
Contrasting Winter Versus Summer Microbial Communities and Metabolic Functions in a Permafrost Thaw Lake. PMID:31379798
Identification of potential drug targets and vaccine candidates in Clostridium botulinum using subtractive genomics approach. PMID:31359994
Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome. PMID:31333721
Metabolic Model of the Phytophthora infestans-Tomato Interaction Reveals Metabolic Switches during Host Colonization. PMID:31289172
The σB-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in Listeria monocytogenes through a direct interaction with the ilvA transcript. PMID:31242083
AmyloWiki: an integrated database for Bacillus velezensis FZB42, the model strain for plant growth-promoting Bacilli. PMID:31219564
Predicting instances of pathway ontology classes for pathway integration. PMID:31196182
Identification of Resistance Genes and Response to Arsenic in Rhodococcus aetherivorans BCP1. PMID:31133997
Synthetic biology strategies for microbial biosynthesis of plant natural products. PMID:31086174
The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups. PMID:31032842
Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi. PMID:31020039
Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution. PMID:31002734
Metabolic engineering of Bacillus subtilis for production of para-aminobenzoic acid - unexpected importance of carbon source is an advantage for space application. PMID:30980511
MtGA2ox10 encoding C20-GA2-oxidase regulates rhizobial infection and nodule development in Medicago truncatula. PMID:30976084
Defining Dysbiosis in Patients with Urolithiasis. PMID:30932002
Dynamic molecular changes during the first week of human life follow a robust developmental trajectory. PMID:30862783
Liquid Chromatography-Mass Spectrometry-Based Metabolomics of Nonhuman Primates after 4 Gy Total Body Radiation Exposure: Global Effects and Targeted Panels. PMID:30843397
Metabolomic study of the response to cold shock in a strain of Pseudomonas syringae isolated from cloud water. PMID:30830325
Identification of bioactive metabolites using activity metabolomics. PMID:30814649
Amino acids as wetting agents: surface translocation by Porphyromonas gingivalis. PMID:30783212
A Xylose-Inducible Expression System and a CRISPR Interference Plasmid for Targeted Knockdown of Gene Expression in Clostridioides difficile. PMID:30745377
Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1. PMID:30678677
Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children. PMID:30671194
The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges. PMID:30671032
Selection of Fusarium Trichothecene Toxin Genes for Molecular Detection Depends on TRI Gene Cluster Organization and Gene Function. PMID:30646506
Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells. PMID:30609717
A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer. PMID:30568637
A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase. PMID:30564208
Influence of pathway topology and functional class on the molecular evolution of human metabolic genes. PMID:30550546
Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome. PMID:30546118
Coordinated regulation of transcription by CcpA and the Staphylococcus aureus two-component system HptRS. PMID:30540769
Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry. PMID:30504213
Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin. PMID:30498478
The Complete Genome and Physiological Analysis of the Microbialite-Dwelling Agrococcus pavilionensis sp. nov; Reveals Genetic Promiscuity and Predicted Adaptations to Environmental Stress. PMID:30374333
Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities. PMID:30370195
Methionine coordinates a hierarchically organized anabolic program enabling proliferation. PMID:30354837
Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3). PMID:30240424
Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo. PMID:30184095
Secondary metabolite production and the safety of industrially important members of the Bacillus subtilis group. PMID:30053041
CIGene: a literature-based online resource for cancer initiation genes. PMID:30045691
MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions. PMID:30032270
Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes. PMID:29963641
Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. PMID:29959380
Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. PMID:29949965
Discovering variation of secondary metabolite diversity and its relationship with disease resistance in Cornus florida L. PMID:29938079
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. PMID:29914475
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets. PMID:29893885
Pathway based therapeutic targets identification and development of an interactive database CampyNIBase of Campylobacter jejuni RM1221 through non-redundant protein dataset. PMID:29883471
Gene set analysis methods: a systematic comparison. PMID:29881462
Heterotroph Interactions Alter Prochlorococcus Transcriptome Dynamics during Extended Periods of Darkness. PMID:29854954
Characterization of the caprolactam degradation pathway in Pseudomonas jessenii using mass spectrometry-based proteomics. PMID:29850960
Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes. PMID:29788417
Identification of novel drug targets in bovine respiratory disease: an essential step in applying biotechnologic techniques to develop more effective therapeutic treatments. PMID:29765203
High-quality draft genome of the methanotroph Methylovulum psychrotolerans Str. HV10-M2 isolated from plant material at a high-altitude environment. PMID:29686747
Antibiotic Treatment Leads to Fecal Escherichia coli and Coliphage Expansion in Severely Malnourished Diarrhea Patients. PMID:29675461
GROOLS: reactive graph reasoning for genome annotation through biological processes. PMID:29642842
Genome and evolution of the shade-requiring medicinal herb Panax ginseng. PMID:29604169
Complete Genome Sequence of Altererythrobacter sp. Strain B11, an Aromatic Monomer-Degrading Bacterium, Isolated from Deep-Sea Sediment under the Seabed off Kashima, Japan. PMID:29567747
Promises and pitfalls of untargeted metabolomics. PMID:29536203
Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome. PMID:29511180
FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets. PMID:29504895
Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online. PMID:29494574
Quantifying complexity in metabolic engineering using the LASER database. PMID:29468127
Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach. PMID:29460206
Network Analyses in Plant Pathogens. PMID:29441045
Age and fecal microbial strain-specific differences in patients with spondyloarthritis. PMID:29382366
Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation. PMID:29377524
Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149. PMID:29375494
Biosynthesis of Long-Chain N-Acyl Amide by a Truncated Polyketide Synthase-Nonribosomal Peptide Synthetase Hybrid Megasynthase in Fungi. PMID:29343058
Untargeted Metabolomics Approach in Halophiles: Understanding the Biodeterioration Process of Building Materials. PMID:29321766
Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum. PMID:29213318
Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium. PMID:29213256
On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes. PMID:29189888
Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria. PMID:29147021
Characterizing steady states of genome-scale metabolic networks in continuous cell cultures. PMID:29131817
Metabolic Mitigation of Staphylococcus aureus Vancomycin Intermediate-Level Susceptibility. PMID:29109158
A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus. PMID:29062941
Confronting the catalytic dark matter encoded by sequenced genomes. PMID:29059321
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
Unwavering Pathobiology of Volumetric Muscle Loss Injury. PMID:29030619
Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach. PMID:28990716
Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling. PMID:28959251
Strains, functions and dynamics in the expanded Human Microbiome Project. PMID:28953883
Phenotype-driven identification of modules in a hierarchical map of multifluid metabolic correlations. PMID:28948040
Elucidation of complexity and prediction of interactions in microbial communities. PMID:28925555
Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides. PMID:28912798
Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C. PMID:28894932
Brucella Genetic Variability in Wildlife Marine Mammals Populations Relates to Host Preference and Ocean Distribution. PMID:28854602
Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses. PMID:28852182
Fecal concentrations of bacterially derived vitamin K forms are associated with gut microbiota composition but not plasma or fecal cytokine concentrations in healthy adults. PMID:28814395
Identification of Staphylococcus aureus Factors Required for Pathogenicity and Growth in Human Blood. PMID:28808156
Thermodynamic Constraints Improve Metabolic Networks. PMID:28793222
Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils. PMID:28767679
Microbiome and metabolome data integration provides insight into health and disease. PMID:28764956
Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. PMID:28764658
The Association between Cardiorespiratory Fitness and Gut Microbiota Composition in Premenopausal Women. PMID:28757576
Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis. PMID:28752667
Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides. PMID:28744485
Assessment of genome annotation using gene function similarity within the gene neighborhood. PMID:28724412
Yeast longevity promoted by reversing aging-associated decline in heavy isotope content. PMID:28721263
More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes. PMID:28705224
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge. PMID:28690595
Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle. PMID:28687644
Metabolic Engineering of Actinobacillus succinogenes Provides Insights into Succinic Acid Biosynthesis. PMID:28625987
The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization. PMID:28623667
A conserved coiled-coil protein pair focuses the cytokinetic Z-ring in Caulobacter crescentus. PMID:28613431
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome. PMID:28595639
Distinct Biological Potential of Streptococcus gordonii and Streptococcus sanguinis Revealed by Comparative Genome Analysis. PMID:28592797
AGeNNT: annotation of enzyme families by means of refined neighborhood networks. PMID:28545394
Unique identifiers for small molecules enable rigorous labeling of their atoms. PMID:28534867
Pathview Web: user friendly pathway visualization and data integration. PMID:28482075
Plasma metabolomics reveals a diagnostic metabolic fingerprint for mitochondrial aconitase (ACO2) deficiency. PMID:28463998
Systems biology guided by XCMS Online metabolomics. PMID:28448069
ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network. PMID:28442501
The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions. PMID:28439458
Staphylococcus aureus nitric oxide synthase (saNOS) modulates aerobic respiratory metabolism and cell physiology. PMID:28431199
Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation. PMID:28424673
SSER: Species specific essential reactions database. PMID:28420402
NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. PMID:28415074
Multi-Omics of Tomato Glandular Trichomes Reveals Distinct Features of Central Carbon Metabolism Supporting High Productivity of Specialized Metabolites. PMID:28408661
A geographically-diverse collection of 418 human gut microbiome pathway genome databases. PMID:28398290
Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium. PMID:28337181
Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. PMID:28333345
metaX: a flexible and comprehensive software for processing metabolomics data. PMID:28327092
Listeriomics: an Interactive Web Platform for Systems Biology of Listeria. PMID:28317029
Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis. PMID:28266498
Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. PMID:28265262
Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells. PMID:28240279
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. PMID:28228535
Streptococcus mitis and S. oralis Lack a Requirement for CdsA, the Enzyme Required for Synthesis of Major Membrane Phospholipids in Bacteria. PMID:28223392
A Lipidomic and Metabolomic Serum Signature from Nonhuman Primates Exposed to Ionizing Radiation. PMID:28220056
Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism. PMID:28212377
Metabolomic and Metagenomic Analysis of Two Crude Oil Production Pipelines Experiencing Differential Rates of Corrosion. PMID:28197141
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis. PMID:28189581
A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems. PMID:28187207
Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions. PMID:28176778
Comparative analysis of sterol acquisition in the oomycetes Saprolegnia parasitica and Phytophthora infestans. PMID:28152045
Protein Bioinformatics Databases and Resources. PMID:28150231
Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy. PMID:28149702
Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function. PMID:28133437
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PMID:28129330
High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond. PMID:28116042
Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age. PMID:28095919
Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes. PMID:28070515
A Method for Finding Metabolic Pathways Using Atomic Group Tracking. PMID:28068354
The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. PMID:28066333
Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges. PMID:28049838
Considerations when choosing a genetic model organism for metabolomics studies. PMID:28025166
Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology. PMID:27989793
Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota. PMID:27984592
Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes. PMID:27939572
BRENDA in 2017: new perspectives and new tools in BRENDA. PMID:27924025
The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. PMID:27899149
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. PMID:27895706
Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity. PMID:27866838
In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075. PMID:27834373
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
Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes. PMID:27820856
Systems-level analysis of mechanisms regulating yeast metabolic flux. PMID:27789812
Metabolic Complementation in Bacterial Communities: Necessary Conditions and Optimality. PMID:27774085
Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks. PMID:27716045
Genome-wide survey and phylogeny of S-Ribosylhomocysteinase (LuxS) enzyme in bacterial genomes. PMID:27650568
Ubiquitous marine bacterium inhibits diatom cell division. PMID:27623332
Modeling biochemical pathways in the gene ontology. PMID:27589964
Species-function relationships shape ecological properties of the human gut microbiome. PMID:27573110
Can heavy isotopes increase lifespan? Studies of relative abundance in various organisms reveal chemical perspectives on aging. PMID:27554342
Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding. PMID:27549116
COMAN: a web server for comprehensive metatranscriptomics analysis. PMID:27515514
Determining the mode of action of anti-mycobacterial C17 diyne natural products using expression profiling: evidence for fatty acid biosynthesis inhibition. PMID:27514659
Cell-free Determination of Binary Complexes That Comprise Extended Protein-Protein Interaction Networks of Yersinia pestis. PMID:27489291
Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis. PMID:27489274
(1)H NMR metabolomic study of auxotrophic starvation in yeast using Multivariate Curve Resolution-Alternating Least Squares for Pathway Analysis. PMID:27485935
"Candidatus Propionivibrio aalborgensis": A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants. PMID:27458436
Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principle Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01. PMID:27412985
Diverse Metabolic Capacities of Fungi for Bioremediation. PMID:27407289
Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond. PMID:27383682
From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model. PMID:27379044
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. PMID:27372244
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. PMID:27363390
Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium. PMID:27340073
Literature information in PubChem: associations between PubChem records and scientific articles. PMID:27293485
Bioinformatics resources for pollen. PMID:27271281
Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus. PMID:27258949
Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems. PMID:27252693
Metabolomic Analysis in Brain Research: Opportunities and Challenges. PMID:27252656
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. PMID:27242037
YodL and YisK Possess Shape-Modifying Activities That Are Suppressed by Mutations in Bacillus subtilis mreB and mbl. PMID:27215790
A Type I Signal Peptidase Is Required for Pilus Assembly in the Gram-Positive, Biofilm-Forming Bacterium Actinomyces oris. PMID:27215787
A Caenorhabditis elegans Genome-Scale Metabolic Network Model. PMID:27211857
Trimethylamine and Trimethylamine N-Oxide, a Flavin-Containing Monooxygenase 3 (FMO3)-Mediated Host-Microbiome Metabolic Axis Implicated in Health and Disease. PMID:27190056
Reinventing the Wheel and Making It Round Again: Evolutionary Convergence in Buchnera-Serratia Symbiotic Consortia between the Distantly Related Lachninae Aphids Tuberolachnus salignus and Cinara cedri. PMID:27190007
Metabolic drift in the aging brain. PMID:27182841
MOCAT2: a metagenomic assembly, annotation and profiling framework. PMID:27153620
One step beyond a ribosome: The ancient anaerobic core. PMID:27150504
Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24. PMID:27124467
Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor. PMID:27121083
Learning from Co-expression Networks: Possibilities and Challenges. PMID:27092161
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. PMID:27081850
A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers. PMID:27071721
Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3. PMID:27065955
Direct bioconversion of brown algae into ethanol by thermophilic bacterium Defluviitalea phaphyphila. PMID:27042210
Implications of genotypic differences in the generation of a urinary metabolomics radiation signature. PMID:27040378
Cellular Growth Arrest and Persistence from Enzyme Saturation. PMID:27010473
Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome. PMID:26992093
REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer. PMID:26975833
FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca. PMID:26973684
Draft Genome Sequence of Olsenella scatoligenes SK9K4T, a Producer of 3-Methylindole (Skatole) and 4-Methylphenol (p-Cresol), Isolated from Pig Feces. PMID:26950328
Draft Genome Sequence of Pantoea ananatis GB1, a Plant-Growth-Promoting Hydrocarbonoclastic Root Endophyte, Isolated at a Diesel Fuel Phytoremediation Site Planted with Populus. PMID:26950324
Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions. PMID:26925033
Global metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii. PMID:26924392
Flux Control in Glycolysis Varies Across the Tree of Life. PMID:26920685
Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge. PMID:26905629
The RNA-Binding Chaperone Hfq Is an Important Global Regulator of Gene Expression in Pasteurella multocida and Plays a Crucial Role in Production of a Number of Virulence Factors, Including Hyaluronic Acid Capsule. PMID:26883595
Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA. PMID:26847793
PSAMM: A Portable System for the Analysis of Metabolic Models. PMID:26828591
Rethinking Mass Spectrometry-Based Small Molecule Identification Strategies in Metabolomics. PMID:26819881
A longitudinal analysis of the effects of age on the blood plasma metabolome in the common marmoset, Callithrix jacchus. PMID:26805607
ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts. PMID:26794319
Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations. PMID:26792120
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics. PMID:26734060
Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium. PMID:26701084
ECGene: A Literature-Based Knowledgebase of Endometrial Cancer Genes. PMID:26699919
Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries. PMID:26684897
Understanding Metabolomics in Biomedical Research. PMID:26676338
Vitamin E Content and Composition in Tomato Fruits: Beneficial Roles and Bio-Fortification. PMID:26670232
Challenges of Inversely Estimating Jacobian from Metabolomics Data. PMID:26636075
The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. PMID:26631123
Representation and inference of cellular architecture for metabolic reconstruction and modeling. PMID:26628588
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Defluviitalea phaphyphila sp. nov., a Novel Thermophilic Bacterium That Degrades Brown Algae. PMID:26590273
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. PMID:26590256
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. PMID:26586805
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. PMID:26578601
A new network representation of the metabolism to detect chemical transformation modules. PMID:26573681
The Transporter Classification Database (TCDB): recent advances. PMID:26546518
Changes in protein abundance are observed in bacterial isolates from a natural host. PMID:26528441
Integrative "omic" analysis reveals distinctive cold responses in leaves and roots of strawberry, Fragaria × ananassa 'Korona'. PMID:26528299
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. PMID:26527732
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. PMID:26527726
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. PMID:26527720
Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. PMID:26526746
Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions. PMID:26525894
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). PMID:26512311
The essential gene set of a photosynthetic organism. PMID:26508635
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
A rapid method for profiling of volatile and semi-volatile phytohormones using methyl chloroformate derivatisation and GC-MS. PMID:26491427
Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture. PMID:26482235
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. PMID:26481353
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. PMID:26476456
CauloBrowser: A systems biology resource for Caulobacter crescentus. PMID:26476443
Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. PMID:26467476
Genome-Wide Analysis of Oceanimonas sp. GK1 Isolated from Gavkhouni Wetland (Iran) Demonstrates Presence of Genes for Virulence and Pathogenicity. PMID:26464816
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. PMID:26454094
Solving a Bloody Mess: B-Vitamin Independent Metabolic Convergence among Gammaproteobacterial Obligate Endosymbionts from Blood-Feeding Arthropods and the Leech Haementeria officinalis. PMID:26454017
Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica. PMID:26443104
Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity. PMID:26442281
SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis. PMID:26433225
Genetically and Phenotypically Distinct Pseudomonas aeruginosa Cystic Fibrosis Isolates Share a Core Proteomic Signature. PMID:26431321
The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity. PMID:26420832
Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach. PMID:26411587
Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection. PMID:26395877
Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling. PMID:26394049
Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations. PMID:26393660
Ascaris lumbricoides β carbonic anhydrase: a potential target enzyme for treatment of ascariasis. PMID:26385556
High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. PMID:26380634
Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. PMID:26371554
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
Comparative Genomics of a Plant-Parasitic Nematode Endosymbiont Suggest a Role in Nutritional Symbiosis. PMID:26362082
The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids. PMID:26358192
Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities. PMID:26341214
Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria. PMID:26337258
Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides. PMID:26319874
An Enlarged Profile of Uremic Solutes. PMID:26317986
Screening of potential targets in Plasmodium falciparum using stage-specific metabolic network analysis. PMID:26303382
Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula. PMID:26285202
Draft Genome Sequence of Acinetobacter calcoaceticus Strain GK1, a Hydrocarbon-Degrading Plant Growth-Promoting Rhizospheric Bacterium. PMID:26272576
ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis. PMID:26267116
Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae. PMID:26238567
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. PMID:26221418
CovRS-Regulated Transcriptome Analysis of a Hypervirulent M23 Strain of Group A Streptococcus pyogenes Provides New Insights into Virulence Determinants. PMID:26216843
Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes. PMID:26215861
Macroscopic modeling of mammalian cell growth and metabolism. PMID:26198881
Interaction networks for identifying coupled molecular processes in microbial communities. PMID:26180552
The Role of α-CTD in the Genome-Wide Transcriptional Regulation of the Bacillus subtilis Cells. PMID:26154296
Pathway and network analysis of cancer genomes. PMID:26125594
Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery. PMID:26114876
Systems analysis of gene ontology and biological pathways involved in post-myocardial infarction responses. PMID:26100218
Cross-organism analysis using InterMine. PMID:26097192
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals. PMID:26074880
Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks. PMID:26041773
In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3). PMID:26039074
Defining bacterial regulons using ChIP-seq. PMID:26032817
Databases for Microbiologists. PMID:26013493
Computational Metabolomics Operations at BioCyc.org. PMID:26011592
Biocuration at the Saccharomyces genome database. PMID:25997651
Evolution of the Translocation and Assembly Module (TAM). PMID:25994932
A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. PMID:25977815
Sphingomonas taxi, Isolated from Cucurbita pepo, Proves to Be a DDE-Degrading and Plant Growth-Promoting Strain. PMID:25977415
Draft Genome Sequence of Methylobacterium radiotolerans, a DDE-Degrading and Plant Growth-Promoting Strain Isolated from Cucurbita pepo. PMID:25977414
Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms. PMID:25973143
Inference of Evolutionary Forces Acting on Human Biological Pathways. PMID:25971280
FlyNet: a versatile network prioritization server for the Drosophila community. PMID:25943544
The SwissLipids knowledgebase for lipid biology. PMID:25943471
Pathways with PathWhiz. PMID:25934797
PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. PMID:25925572
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. PMID:25915636
Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. PMID:25900361
Predicting internal cell fluxes at sub-optimal growth. PMID:25890056
Measuring semantic similarities by combining gene ontology annotations and gene co-function networks. PMID:25886899
Draft Genome Sequence of Enterobacter aerogenes, a DDE-Degrading and Plant Growth-Promoting Strain Isolated from Cucurbita pepo. PMID:25883299
Metaproteomics of complex microbial communities in biogas plants. PMID:25874383
Quantifying cellular capacity identifies gene expression designs with reduced burden. PMID:25849635
The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders. PMID:25831060
Phenotypic profiling of Scedosporium aurantiacum, an opportunistic pathogen colonizing human lungs. PMID:25811884
Open-access metabolomics databases for natural product research: present capabilities and future potential. PMID:25789275
Intestinal microbiota composition modulates choline bioavailability from diet and accumulation of the proatherogenic metabolite trimethylamine-N-oxide. PMID:25784704
A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs. PMID:25750602
PathCards: multi-source consolidation of human biological pathways. PMID:25725062
Insights from 20 years of bacterial genome sequencing. PMID:25722247
Biological databases for human research. PMID:25712261
EcoliNet: a database of cofunctional gene network for Escherichia coli. PMID:25650278
Quantitative and logic modelling of molecular and gene networks. PMID:25645874
The transcriptomic response of Acinetobacter baumannii to colistin and doripenem alone and in combination in an in vitro pharmacokinetics/pharmacodynamics model. PMID:25587995
Production of stable isotope-labeled acyl-coenzyme A thioesters by yeast stable isotope labeling by essential nutrients in cell culture. PMID:25572876
Synthetic biology outside the cell: linking computational tools to cell-free systems. PMID:25538941
Improving collaboration by standardization efforts in systems biology. PMID:25538939
VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera). PMID:25538713
Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation. PMID:25520953
Assessment of subnetwork detection methods for breast cancer. PMID:25520555
Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks. PMID:25477348
Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes. PMID:25452698
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
The Sol Genomics Network (SGN)--from genotype to phenotype to breeding. PMID:25428362
Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. PMID:25426110
BioModels: ten-year anniversary. PMID:25414348
Beyond protein expression, MOPED goes multi-omics. PMID:25404128
Identifying feasible metabolic routes in Mycobacterium smegmatis and possible alterations under diverse nutrient conditions. PMID:25403821
CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics. PMID:25392417
BRENDA in 2015: exciting developments in its 25th year of existence. PMID:25378310
AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. PMID:25355510
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors. PMID:25315994
Computational approaches for microalgal biofuel optimization: a review. PMID:25309916
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. PMID:25300491
Super Natural II--a database of natural products. PMID:25300487
Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway. PMID:25210598
Elucidation of primary metabolic pathways in Aspergillus species: orphaned research in characterizing orphan genes. PMID:25114096
An introduction to the analysis of shotgun metagenomic data. PMID:24982662
Automated LC-HRMS(/MS) approach for the annotation of fragment ions derived from stable isotope labeling-assisted untargeted metabolomics. PMID:24965664
The Chlamydomonas genome project: a decade on. PMID:24950814
Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses. PMID:24946036
MIRA: mutual information-based reporter algorithm for metabolic networks. PMID:24931981
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. PMID:24316579
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases PubMed citations: 411.

411 articles citing: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Impact of Quorum Sensing and Tropodithietic Acid Production on the Exometabolome of Phaeobacter inhibens. PMID:35801100
Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation. PMID:35685924
Temporal relationship among adiposity, gut microbiota, and insulin resistance in a longitudinal human cohort. PMID:35585555
The WalRK Two-Component System Is Essential for Proper Cell Envelope Biogenesis in Clostridioides difficile. PMID:35575581
Exploring synergies between plant metabolic modelling and machine learning. PMID:35521559
Tissue remodeling by an opportunistic pathogen triggers allergic inflammation. PMID:35483356
A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility. PMID:35448501
Rhizosphere microbiome dataset of Robusta coffee (Coffea canephora L.) grown in the Central Highlands, Vietnam, based on 16S rRNA metagenomics analysis. PMID:35434233
A Two-Time Point Analysis of Gut Microbiota in the General Population of Buenos Aires and Its Variation Due to Preventive and Compulsory Social Isolation During the COVID-19 Pandemic. PMID:35401432
Integration of the Human Gut Microbiome and Serum Metabolome Reveals Novel Biological Factors Involved in the Regulation of Bone Mineral Density. PMID:35372129
Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome. PMID:35350985
Bacterial community structure and metabolic potential in microbialite-forming mats from South Australian saline lakes. PMID:35312212
Mapping bacterial diversity and metabolic functionality of the human respiratory tract microbiome. PMID:35309410
Bacterial Communities in the Rhizosphere at Different Growth Stages of Maize Cultivated in Soil Under Conventional and Conservation Agricultural Practices. PMID:35254138
Identifying individualized risk subpathways reveals pan-cancer molecular classification based on multi-omics data. PMID:35222843
Pathway Driven Target Selection in Klebsiella pneumoniae: Insights Into Carbapenem Exposure. PMID:35174104
A Similarity-Based Method for Predicting Enzymatic Functions in Yeast Uncovers a New AMP Hydrolase. PMID:35123996
Dissecting the Mycobacterium bovis BCG Response to Macrophage Infection to Help Prioritize Targets for Anti-Tuberculosis Drug and Vaccine Discovery. PMID:35062774
Soil microbiome dataset from Yok Don national park in the Central Highlands region of Vietnam. PMID:35036494
Maternal regulation of biliary disease in neonates via gut microbial metabolites. PMID:35013245
The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain. PMID:34993013
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
Modeling approaches for probing cross-feeding interactions in the human gut microbiome. PMID:34976313
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. PMID:34971560
Not All That Glitters Is Gold: The Paradox of CO-dependent Hydrogenogenesis in Parageobacillus thermoglucosidasius. PMID:34956151
Assessment of Changes in the Oral Microbiome That Occur in Dogs with Periodontal Disease. PMID:34941818
Differential analysis of the bacterial community in colostrum samples from women with gestational diabetes mellitus and obesity. PMID:34934118
A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations. PMID:34907432
Whole-Genome Sequencing of Acer catalpifolium Reveals Evolutionary History of Endangered Species. PMID:34878129
Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers. PMID:34873013
Establishment of quantitative RNAi-based forward genetics in Entamoeba histolytica and identification of genes required for growth. PMID:34843592
Synthetic Biology Advanced Natural Product Discovery. PMID:34822443
Overview of Metabolomic Analysis and the Integration with Multi-Omics for Economic Traits in Cattle. PMID:34822411
The Effects of Moderate Alcohol Consumption on Circulating Metabolites and Gut Microbiota in Patients With Coronary Artery Disease. PMID:34796220
The Concentration of Organic Acids in Cranberry Juice Modulates the Gut Microbiota in Mice. PMID:34768966
Microbial Diversity Analysis Using 16S rRNA Gene Amplicon Sequencing of Rhizosphere Soils from Double-Cropping Rice and Rice-Shrimp Farming Systems in Soc Trang, Vietnam. PMID:34734766
Unraveling the Microbiome of Necrotizing Enterocolitis: Insights in Novel Microbial and Metabolomic Biomarkers. PMID:34704805
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. PMID:34676984
Plasma Metabolome Profiling by High-Performance Chemical Isotope-Labelling LC-MS after Acute and Medium-Term Intervention with Golden Berry Fruit (Physalis peruviana L.), Confirming Its Impact on Insulin-Associated Signaling Pathways. PMID:34579001
Path to improving the life cycle and quality of genome-scale models of metabolism. PMID:34555324
Herbaspirillum seropedicae expresses non-phosphorylative pathways for D-xylose catabolism. PMID:34499201
Associations of the gut microbiome with hepatic adiposity in the Multiethnic Cohort Adiposity Phenotype Study. PMID:34491886
Gut microbiome is associated with multiple sclerosis activity in children. PMID:34409759
Composition and Functions of the Gut Microbiome in Pediatric Obesity: Relationships with Markers of Insulin Resistance. PMID:34361925
Enforcing ATP hydrolysis enhanced anaerobic glycolysis and promoted solvent production in Clostridium acetobutylicum. PMID:34325704
Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy. PMID:34248876
METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses. PMID:34184911
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. PMID:34140026
Deficits in Prenatal Serine Biosynthesis Underlie the Mitochondrial Dysfunction Associated with the Autism-Linked FMR1 Gene. PMID:34070950
Oral Microbiome in Relation to Periodontitis Severity and Systemic Inflammation. PMID:34070915
Gaining Insights Into Metabolic Networks Using Chemometrics and Bioinformatics: Chronic Kidney Disease as a Clinical Model. PMID:34055893
Usnic Acid Treatment Changes the Composition of Mycobacterium tuberculosis Cell Envelope and Alters Bacterial Redox Status. PMID:33947802
A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria. PMID:33931420
Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome. PMID:33897881
History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications. PMID:33841175
Multiple concurrent and convergent stages of genome reduction in bacterial symbionts across a stink bug family. PMID:33833268
Gut Microbiota of Chinese Obese Children and Adolescents With and Without Insulin Resistance. PMID:33815293
The Impact of Migration on the Gut Metagenome of South Asian Canadians. PMID:33794735
Genome-resolved metagenomics using environmental and clinical samples. PMID:33758906
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome. PMID:33692487
Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917. PMID:33672760
Gut Microbiomes of Freshwater Mussels (Unionidae) Are Taxonomically and Phylogenetically Variable across Years but Remain Functionally Stable. PMID:33669471
Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages. PMID:33653940
Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria. PMID:33650078
Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities. PMID:33644024
Cross-species RNA-seq for deciphering host-microbe interactions. PMID:33597744
The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. PMID:33574608
Wolbachia and Virus Alter the Host Transcriptome at the Interface of Nucleotide Metabolism Pathways. PMID:33563832
Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort. PMID:33563781
Guild-based analysis for understanding gut microbiome in human health and diseases. PMID:33563315
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. PMID:33553808
Finding branched pathways in metabolic network via atom group tracking. PMID:33529200
Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation. PMID:33519737
A Mitochondrial Polymorphism Alters Immune Cell Metabolism and Protects Mice from Skin Inflammation. PMID:33498298
Regulator Network Analysis of Rice and Maize Yield-Related Genes. PMID:33425929
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes. PMID:33418085
Production of 10-methyl branched fatty acids in yeast. PMID:33413611
Understanding the unimodal distributions of cancer occurrence rates: it takes two factors for a cancer to occur. PMID:33377150
Atlas: Automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages. PMID:33367504
Usage of Digital Twins Along a Typical Process Development Cycle. PMID:33346864
Integrative characterization of the near-minimal bacterium Mesoplasma florum. PMID:33331123
Comprehensive Transcriptomic Analysis Reveals Dysregulated Competing Endogenous RNA Network in Endocrine Resistant Breast Cancer Cells. PMID:33324567
Leveraging heterogeneous network embedding for metabolic pathway prediction. PMID:33305310
Comprehensive Bioenergetic Evaluation of Microbial Pathway Variants in Syntrophic Propionate Oxidation. PMID:33293404
Bacterial Metabolites of Human Gut Microbiota Correlating with Depression. PMID:33287416
PPAD Activity Promotes Outer Membrane Vesicle Biogenesis and Surface Translocation by Porphyromonas gingivalis. PMID:33257525
The Gut-Muscle Axis in Older Subjects with Low Muscle Mass and Performance: A Proof of Concept Study Exploring Fecal Microbiota Composition and Function with Shotgun Metagenomics Sequencing. PMID:33255677
Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens. PMID:33251208
Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and treatment using microarray dataset and bioinformatics methods. PMID:33251083
Multi-omics integration in biomedical research - A metabolomics-centric review. PMID:33248648
The Transcriptomic Signature of Tigecycline in Acinetobacter baumannii. PMID:33193153
Master curve of boosted diffusion for 10 catalytic enzymes. PMID:33168730
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. PMID:33119741
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. PMID:33084862
Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage. PMID:33073387
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
Metabolic reconstruction of Pseudomonas chlororaphis ATCC 9446 to understand its metabolic potential as a phenazine-1-carboxamide-producing strain. PMID:32984920
Metabolomic Approaches to Study Chemical Exposure-Related Metabolism Alterations in Mammalian Cell Cultures. PMID:32961865
Reconstructing organisms in silico: genome-scale models and their emerging applications. PMID:32958892
Metabolic cooperativity between Porphyromonas gingivalis and Treponema denticola. PMID:32944158
Ancestral state reconstruction of metabolic pathways across pangenome ensembles. PMID:32924924
Warmth Prevents Bone Loss Through the Gut Microbiota. PMID:32916104
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. PMID:32782301
Advances on systems metabolic engineering of Bacillus subtilis as a chassis cell. PMID:32775709
Correlation of host inflammatory cytokines and immune-related metabolites, but not viral NS1 protein, with disease severity of dengue virus infection. PMID:32764789
Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology. PMID:32754171
Lipid A profiling and metabolomics analysis of paired polymyxin-susceptible and -resistant MDR Klebsiella pneumoniae clinical isolates from the same patients before and after colistin treatment. PMID:32696049
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. PMID:32662816
Effects of Housing Types on Cecal Microbiota of Two Different Strains of Laying Hens During the Late Production Phase. PMID:32656252
Investigation of microbial community interactions between Lake Washington methanotrophs using -------genome-scale metabolic modeling. PMID:32655999
Genome-Scale Metabolic Model Driven Design of a Defined Medium for Campylobacter jejuni M1cam. PMID:32636809
Development of a Novel Metagenomic Biomarker for Prediction of Upper Gastrointestinal Tract Involvement in Patients With Crohn's Disease. PMID:32582102
Effect of a Flaxseed Lignan Intervention on Circulating Bile Acids in a Placebo-Controlled Randomized, Crossover Trial. PMID:32575611
NMR and MS-based Stable Isotope-Resolved Metabolomics and Applications in Cancer Metabolism. PMID:32523238
Comprehensive analysis reveals a metabolic ten-gene signature in hepatocellular carcinoma. PMID:32518728
NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. PMID:32503277
The Inactivation of Enzymes Belonging to the Central Carbon Metabolism Is a Novel Mechanism of Developing Antibiotic Resistance. PMID:32487742
PICRUSt2 for prediction of metagenome functions. PMID:32483366
Extracting chemical reactions from text using Snorkel. PMID:32460703
Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens. PMID:32458794
Cannabinomics: Application of Metabolomics in Cannabis (Cannabis sativa L.) Research and Development. PMID:32457786
Reduced Genome of the Gut Symbiotic Bacterium "Candidatus Benitsuchiphilus tojoi" Provides Insight Into Its Possible Roles in Ecology and Adaptation of the Host Insect. PMID:32435239
Metagenomic Analysis of the Gut Microbiome Reveals Enrichment of Menaquinones (Vitamin K2) Pathway in Diabetes Mellitus. PMID:32431114
Eggshell membrane powder lowers plasma triglyceride and liver total cholesterol by modulating gut microbiota and accelerating lipid metabolism in high-fat diet-fed mice. PMID:32405407
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
Biochemical Characteristics and a Genome-Scale Metabolic Model of an Indian Euryhaline Cyanobacterium with High Polyglucan Content. PMID:32365713
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing Megasphaera elsdenii. PMID:32283671
iMM1865: A New Reconstruction of Mouse Genome-Scale Metabolic Model. PMID:32277147
Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. PMID:32240601
Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth. PMID:32234775
Snorkel: rapid training data creation with weak supervision. PMID:32214778
New Therapeutic Candidates for the Treatment of Malassezia pachydermatis -Associated Infections. PMID:32184419
ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data. PMID:32176690
Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of Clostridium drakei. PMID:32170009
Fecal microbiota characteristics of Chinese patients with primary IgA nephropathy: a cross-sectional study. PMID:32169051
Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift. PMID:32058961
Cell-autonomous light sensitivity via Opsin3 regulates fuel utilization in brown adipocytes. PMID:32040503
Initial Transcriptomic Response and Adaption of Listeria monocytogenes to Desiccation on Food Grade Stainless Steel. PMID:32038566
Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss. PMID:32033593
Genome-Based Metabolic Reconstruction Unravels the Key Role of B12 in Methionine Auxotrophy of an Ortho-Phenylphenol-Degrading Sphingomonas haloaromaticamans. PMID:31998277
Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413. PMID:31978122
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
Structure Dependent Determination of Organophosphate Targets in Mammalian Tissues Using Activity-Based Protein Profiling. PMID:31872761
An omics perspective on drug target discovery platforms. PMID:31774113
Transcriptional Profiling and Molecular Characterization of the yccT Mutant Link: A Novel STY1099 Protein with the Peroxide Stress Response and Cell Division of Salmonella enterica Serovar Enteritidis. PMID:31766267
FlySilico: Flux balance modeling of Drosophila larval growth and resource allocation. PMID:31748517
pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species. PMID:31733064
CRISPR interference to interrogate genes that control biofilm formation in Pseudomonas fluorescens. PMID:31685917
Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis support a role in TCA cycle regulation. PMID:31637787
Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs. PMID:31636299
PathBank: a comprehensive pathway database for model organisms. PMID:31602464
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients. PMID:31597568
Complex Oxidation of Apocytochromes c during Bacterial Cytochrome c Maturation. PMID:31585997
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Modeling the Interplay between Photosynthesis, CO2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium. PMID:31477760
LAS: A Lipid Annotation Service Capable of Explaining the Annotations It Generates. PMID:31462967
Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer. PMID:31416420
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
Molecular Basis of Unexpected Specificity of ABC Transporter-Associated Substrate-Binding Protein DppA from Helicobacter pylori. PMID:31358613
FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria. PMID:31333719
Identification of important invasion and proliferation related genes in adrenocortical carcinoma. PMID:31321566
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database. PMID:31319812
Data mining analysis of human gut microbiota links Fusobacterium spp. with colorectal cancer onset. PMID:31312073
Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. PMID:31311202
Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture. PMID:31293529
Patterns of protist diversity associated with raw sewage in New York City. PMID:31289345
Human Systems Biology and Metabolic Modelling: A Review-From Disease Metabolism to Precision Medicine. PMID:31281846
Oxidative stress under low oxygen conditions triggers hyperflagellation and motility in the Antarctic bacterium Pseudomonas extremaustralis. PMID:31250111
Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways. PMID:31239393
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. PMID:31206013
Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks. PMID:31195955
A multidimensional perspective on microbial interactions. PMID:31187139
Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2. PMID:31182796
Elucidation of Akkermansia muciniphila Probiotic Traits Driven by Mucin Depletion. PMID:31178843
Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model. PMID:31175044
Essential Oils as an Intervention Strategy to Reduce Campylobacter in Poultry Production: A Review. PMID:31139172
Identification of functional signatures in the metabolism of the three cellular domains of life. PMID:31136618
Glycoside Hydrolase Genes Are Required for Virulence of Agrobacterium tumefaciens on Bryophyllum daigremontiana and Tomato. PMID:31126942
Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and Virulence. PMID:31117026
Metabolic Remodeling during Biofilm Development of Bacillus subtilis. PMID:31113899
Pseudomonas aeruginosa Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma Patients. PMID:31086830
Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name. PMID:31071451
Anti-inflammatory Gut Microbial Pathways Are Decreased During Crohn's Disease Exacerbations. PMID:31066440
Distinct amino acid and lipid perturbations characterize acute versus chronic malaria. PMID:31045574
The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis. PMID:31032818
Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover. PMID:31023841
The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients. PMID:31001490
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
Metabolic engineering of Bacillus subtilis for production of para-aminobenzoic acid - unexpected importance of carbon source is an advantage for space application. PMID:30980511
Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics. PMID:30970615
Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. PMID:30963208
Elucidation of Novel Therapeutic Targets for Acute Myeloid Leukemias with RUNX1-RUNX1T1 Fusion. PMID:30959925
Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics. PMID:30944337
Intestinal Epithelial Cells and the Microbiome Undergo Swift Reprogramming at the Inception of Colonic Citrobacter rodentium Infection. PMID:30940698
Saccharibacteria (TM7) in the Human Oral Microbiome. PMID:30894042
Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery. PMID:30866765
A Comparison of Microbial Genome Web Portals. PMID:30853946
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. PMID:30845144
The Evolution of SlyA/RovA Transcription Factors from Repressors to Countersilencers in Enterobacteriaceae. PMID:30837332
Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). PMID:30804569
Analysis of core protein clusters identifies candidate variable sites conferring metronidazole resistance in Helicobacter pylori. PMID:30792865
Physiological and Transcriptional Responses in Weaned Piglets Fed Diets with Varying Phosphorus and Calcium Levels. PMID:30791512
Amino acids as wetting agents: surface translocation by Porphyromonas gingivalis. PMID:30783212
Metabolomics Approaches for the Diagnosis and Understanding of Kidney Diseases. PMID:30769897
A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems. PMID:30759970
Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling. PMID:30746493
A Xylose-Inducible Expression System and a CRISPR Interference Plasmid for Targeted Knockdown of Gene Expression in Clostridioides difficile. PMID:30745377
Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations. PMID:30715293
Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose. PMID:30709823
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview. PMID:30695998
Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase. PMID:30689844
Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation. PMID:30680888
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. PMID:30664679
Involving community in genes and pathway curation. PMID:30649295
Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways. PMID:30647083
BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. PMID:30612223
Random Forest Analysis of Untargeted Metabolomics Data Suggests Increased Use of Omega Fatty Acid Oxidation Pathway in Drosophila Melanogaster Larvae Fed a Medium Chain Fatty Acid Rich High-Fat Diet. PMID:30602659
In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production. PMID:30588397
Combining multiple functional annotation tools increases coverage of metabolic annotation. PMID:30567498
Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment. PMID:30563853
Circadian Proteomic Analysis Uncovers Mechanisms of Post-Transcriptional Regulation in Metabolic Pathways. PMID:30553726
A genome-scale metabolic model of potato late blight suggests a photosynthesis suppression mechanism. PMID:30537923
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. PMID:30531987
Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. PMID:30488036
Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales). PMID:30487804
An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction. PMID:30486288
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. PMID:30476243
From sequencing data to gene functions: co-functional network approaches. PMID:30460054
Functional analysis of Salmonella Typhi adaptation to survival in water. PMID:30450829
The development of a new parameter for tracking post-transcriptional regulation allows the detailed map of the Pseudomonas aeruginosa Crc regulon. PMID:30429516
Increased sporulation underpins adaptation of Clostridium difficile strain 630 to a biologically-relevant faecal environment, with implications for pathogenicity. PMID:30420658
Metabolic pathways synthesis based on ant colony optimization. PMID:30401873
Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria. PMID:30397005
Proteomics based analysis of the nicotine catabolism in Paenarthrobacter nicotinovorans pAO1. PMID:30390017
Species-level functional profiling of metagenomes and metatranscriptomes. PMID:30377376
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. PMID:30364992
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. PMID:30356183
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PMID:30335785
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future. PMID:30319557
Assessment of flux through oleoresin biosynthesis in epithelial cells of loblolly pine resin ducts. PMID:30312429
Whole-Genome Sequence of the Novel Antarctobacter heliothermus Strain SMS3, Found in Association with the Marine Diatom Skeletonema marinoi. PMID:30310524
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. PMID:30289528
Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages. PMID:30270525
A Requirement for Global Transcription Factor Lrp in Licensing Replication of Vibrio cholerae Chromosome 2. PMID:30250457
Essential Nucleoid Associated Protein mIHF (Rv1388) Controls Virulence and Housekeeping Genes in Mycobacterium tuberculosis. PMID:30242166
Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3). PMID:30240424
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. PMID:30152809
Main Human Urinary Metabolites after Genipap (Genipa americana L.) Juice Intake. PMID:30149503
Synthesis versus degradation: directions of amino acid metabolism during Arabidopsis abiotic stress response. PMID:30143990
In silico Identification of the Indispensable Quorum Sensing Proteins of Multidrug Resistant Proteus mirabilis. PMID:30131943
The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling. PMID:30131500
Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX. PMID:30126456
The marine bacterium Phaeobacter inhibens secures external ammonium by rapid buildup of intracellular nitrogen stocks. PMID:30124819
A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk. PMID:30071832
Functional profiles of coronal and dentin caries in children. PMID:30034639
Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus. PMID:30018396
A Dynamic Multi-Tissue Flux Balance Model Captures Carbon and Nitrogen Metabolism and Optimal Resource Partitioning During Arabidopsis Growth. PMID:29997643
Genome analysis of new Blattabacterium spp., obligatory endosymbionts of Periplaneta fuliginosa and P. japonica. PMID:29990378
Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production. PMID:29988523
Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism. PMID:29973148
SimCAL: a flexible tool to compute biochemical reaction similarity. PMID:29969981
Endospore forming bacteria may be associated with maintenance of surgically-induced remission in Crohn's disease. PMID:29950676
Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface. PMID:29937754
Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches. PMID:29915565
How accurate is automated gap filling of metabolic models? PMID:29914471
Expression and regulation of the Pseudomonas aeruginosa hibernation promoting factor. PMID:29885070
Partnering With a Pest: Genomes of Hemlock Woolly Adelgid Symbionts Reveal Atypical Nutritional Provisioning Patterns in Dual-Obligate Bacteria. PMID:29860412
Phylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates. PMID:29850855
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z. PMID:29843739
Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models. PMID:29791443
In Silico Knockout Screening of Plasmodium falciparum Reactions and Prediction of Novel Essential Reactions by Analysing the Metabolic Network. PMID:29789805
SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis. PMID:29788229
A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species. PMID:29785196
Snorkel: Rapid Training Data Creation with Weak Supervision. PMID:29770249
Mutant phenotypes for thousands of bacterial genes of unknown function. PMID:29769716
SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases. PMID:29762652
EuPathDB: The Eukaryotic Pathogen Genomics Database Resource. PMID:29761457
Benzoxaborole treatment perturbs S-adenosyl-L-methionine metabolism in Trypanosoma brucei. PMID:29758036
Current Challenges in Plant Eco-Metabolomics. PMID:29734799
Metabolic pathways and immunometabolism in rare kidney diseases. PMID:29724730
MetExplore: collaborative edition and exploration of metabolic networks. PMID:29718355
Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. PMID:29713790
Comparative Genomic Analysis of Holospora spp., Intranuclear Symbionts of Paramecia. PMID:29713316
Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa. PMID:29688451
YummyData: providing high-quality open life science data. PMID:29688370
The role of the Human Metabolome Database in inborn errors of metabolism. PMID:29663269
The Genome Sequence of "Candidatus Fokinia solitaria": Insights on Reductive Evolution in Rickettsiales. PMID:29659807
The anti-fecundity effect of 5-azacytidine (5-AzaC) on Schistosoma mansoni is linked to dis-regulated transcription, translation and stem cell activities. PMID:29649665
Exploring Linkages between Taxonomic and Functional Profiles of the Human Microbiome. PMID:29629420
A review of computational tools for design and reconstruction of metabolic pathways. PMID:29552648
From correlation to causation: analysis of metabolomics data using systems biology approaches. PMID:29503602
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. PMID:29499714
Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation. PMID:29468197
The BioCyc collection of microbial genomes and metabolic pathways. PMID:29447345
FindPrimaryPairs: An efficient algorithm for predicting element-transferring reactant/product pairs in metabolic networks. PMID:29447218
Evaluation of reaction gap-filling accuracy by randomization. PMID:29444634
Determination of the small RNA GcvB regulon in the Gram-negative bacterial pathogen Pasteurella multocida and identification of the GcvB seed binding region. PMID:29440476
Expression of Pyridoxal 5'-Phosphate-Independent Racemases Can Reduce 2-Aminoacrylate Stress in Salmonella enterica. PMID:29440254
Cladogenesis and Genomic Streamlining in Extracellular Endosymbionts of Tropical Stink Bugs. PMID:29420776
Host genetic variation and its microbiome interactions within the Human Microbiome Project. PMID:29378630
Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov. PMID:29375512
Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria. PMID:29351192
Metatranscriptome of human faecal microbial communities in a cohort of adult men. PMID:29335555
Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio. PMID:29319806
Exopolysaccharide production in Caulobacter crescentus: A resource allocation trade-off between protection and proliferation. PMID:29293585
Emerging whole-cell modeling principles and methods. PMID:29275251
Prebiotic Oligosaccharides Potentiate Host Protective Responses against L. Monocytogenes Infection. PMID:29257110
Severe infections emerge from commensal bacteria by adaptive evolution. PMID:29256859
Update notifications for the BioCyc collection of databases. PMID:29220477
Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome. PMID:29218869
Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia. PMID:29208119
Integrative analysis to identify oncogenic gene expression changes associated with copy number variations of enhancer in ovarian cancer. PMID:29207666
Utilization of Host Polyamines in Alternatively Activated Macrophages Promotes Chronic Infection by Brucella abortus. PMID:29203548
Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci. PMID:29178959
The Reactome Pathway Knowledgebase. PMID:29145629
HMDB 4.0: the human metabolome database for 2018. PMID:29140435
Automated visualization of rule-based models. PMID:29131816
Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets. PMID:29109515
PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. PMID:29106626
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. PMID:29106569
A review of parameters and heuristics for guiding metabolic pathfinding. PMID:29086092
A Global Survey of ATPase Activity in Plasmodium falciparum Asexual Blood Stages and Gametocytes. PMID:29079720
The MetaCyc database of metabolic pathways and enzymes. PMID:29059334
The fate of lysine: Non-targeted stable isotope analysis reveals parallel ways for lysine catabolization in Phaeobacter inhibens. PMID:29059219
The Omics Dashboard for interactive exploration of gene-expression data. PMID:29040755
Annotation: A Computational Solution for Streamlining Metabolomics Analysis. PMID:29039932
Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon. PMID:28989970
Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo. PMID:28988824
Illumina Sequencing Approach to Characterize Thiamine Metabolism Related Bacteria and the Impacts of Thiamine Supplementation on Ruminal Microbiota in Dairy Cows Fed High-Grain Diets. PMID:28979254
MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data. PMID:28968784
MetExploreViz: web component for interactive metabolic network visualization. PMID:28968733
Strains, functions and dynamics in the expanded Human Microbiome Project. PMID:28953883
Assessing and Resolving Model Misspecifications in Metabolic Flux Analysis. PMID:28952528
Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach. PMID:28934286
Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway. PMID:28910500
Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. PMID:28903046
Navigating freely-available software tools for metabolomics analysis. PMID:28890673
Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery. PMID:28842777
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. PMID:28839072
Bioenergetics of Monoterpenoid Essential Oil Biosynthesis in Nonphotosynthetic Glandular Trichomes. PMID:28838953
Crosstalk between the tricarboxylic acid cycle and peptidoglycan synthesis in Caulobacter crescentus through the homeostatic control of α-ketoglutarate. PMID:28827812
MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis. PMID:28819315
Transcriptional Profiling of Midguts Prepared from Trypanosoma/T. congolense-Positive Glossina palpalis palpalis Collected from Two Distinct Cameroonian Foci: Coordinated Signatures of the Midguts' Remodeling As T. congolense-Supportive Niches. PMID:28804485
New frontiers in metabolomics: from measurement to insight. PMID:28781759
Aspergillus Secondary Metabolite Database, a resource to understand the Secondary metabolome of Aspergillus genus. PMID:28779078
Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides. PMID:28744485
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Metabolite Transporter PEG344 Is Required for Full Virulence of Hypervirulent Klebsiella pneumoniae Strain hvKP1 after Pulmonary but Not Subcutaneous Challenge. PMID:28717029
Metabolomic Studies in Drosophila. PMID:28684601
Perspectives and Challenges in Microbial Communities Metabolic Modeling. PMID:28680442
Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes. PMID:28662112
Investigation of simulated microgravity effects on Streptococcus mutans physiology and global gene expression. PMID:28649626
Coenzyme B12 synthesis as a baseline to study metabolite contribution of animal microbiota. PMID:28612402
A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials. PMID:28604819
Bactericidal potential of silver nanoparticles synthesized using cell-free extract of Comamonas acidovorans: in vitro and in silico approaches. PMID:28555428
Malonate degradation in Acinetobacter baylyi ADP1: operon organization and regulation by MdcR. PMID:28537542
A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants. PMID:28408660
A geographically-diverse collection of 418 human gut microbiome pathway genome databases. PMID:28398290
A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation. PMID:28382331
Measurements of translation initiation from all 64 codons in E. coli. PMID:28334756
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. PMID:28321234
Transcriptomic Analyses Elucidate Adaptive Differences of Closely Related Strains of Pseudomonas aeruginosa in Fuel. PMID:28314727
Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum "Latescibacteria" (WS3). PMID:28314726
Growth Trade-Offs Accompany the Emergence of Glycolytic Metabolism in Shewanella oneidensis MR-1. PMID:28289083
Non-enzymatic molecular damage as a prototypic driver of aging. PMID:28264930
Regulation of Stomatal Immunity by Interdependent Functions of a Pathogen-Responsive MPK3/MPK6 Cascade and Abscisic Acid. PMID:28254778
Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization. PMID:28209199
Resolving host-pathogen interactions by dual RNA-seq. PMID:28207848
Understanding the interplay of carbon and nitrogen supply for ectoines production and metabolic overflow in high density cultures of Chromohalobacter salexigens. PMID:28179004
Mixing omics: combining genetics and metabolomics to study rheumatic diseases. PMID:28148918
Tracing a fat or sweet lifestyle - New insights on catabolic paths of intracellular Salmonella. PMID:28112570
Enhancement of Microbial Biodesulfurization via Genetic Engineering and Adaptive Evolution. PMID:28060828
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Coping with inevitable accidents in metabolism. PMID:28032445
Human exposure to organic arsenic species from seafood. PMID:28024743
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains. PMID:27996047
Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology. PMID:27989793
Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis. PMID:27924274
EuPathDB: the eukaryotic pathogen genomics database resource. PMID:27903906
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. PMID:27899624
YMDB 2.0: a significantly expanded version of the yeast metabolome database. PMID:27899612
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. PMID:27899573
Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes. PMID:27822530
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
Draft Genome Sequence of Terasakiispira papahanaumokuakeensis PH27AT, a Spiral Bacterium from the Northwestern Hawaiian Islands. PMID:27795280
Updates in Rhea - an expert curated resource of biochemical reactions. PMID:27789701
A Nonsense Mutation in Mycobacterium marinum That Is Suppressible by a Novel Mechanism. PMID:27789543
IMG/M: integrated genome and metagenome comparative data analysis system. PMID:27738135
Genome Sequence Variability Predicts Drug Precautions and Withdrawals from the Market. PMID:27690231
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). PMID:27679477
The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae. PMID:27653669
Computational Metabolomics: A Framework for the Million Metabolome. PMID:27629808
Untargeted Metabolomics Strategies-Challenges and Emerging Directions. PMID:27624161
PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants. PMID:27515999
Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era. PMID:27447622
Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach. PMID:27379244
Genome wide analysis of protein production load in Trichoderma reesei. PMID:27354857
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
Cytochrome P450 metabolism of the post-lanosterol intermediates explains enigmas of cholesterol synthesis. PMID:27334049
SensiPath: computer-aided design of sensing-enabling metabolic pathways. PMID:27106061
MBROLE 2.0-functional enrichment of chemical compounds. PMID:27084944
Cancer Metabolomics and the Human Metabolome Database. PMID:26950159
The Time Is Right to Focus on Model Organism Metabolomes. PMID:26891337
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases PubMed citations: 274.

274 articles citing: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Nuclear Magnetic Resonance-Measured Ionized Magnesium Is Inversely Associated with Type 2 Diabetes in the Insulin Resistance Atherosclerosis Study. PMID:35565760
Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome. PMID:35456791
Alzheimer's disease as an autoimmune disorder of innate immunity endogenously modulated by tryptophan metabolites. PMID:35415204
Magnesium Nutritional Status, Risk Factors, and the Associations with Glucose Parameters of Childbearing Women in the China Adult Chronic Disease and Nutrition Surveillance (2015). PMID:35215497
Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen Staphylococcus epidermidis RP62A. PMID:35208211
Analogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic Growth. PMID:34903058
Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance. PMID:34413843
DTYMK Expression Predicts Prognosis and Chemotherapeutic Response and Correlates with Immune Infiltration in Hepatocellular Carcinoma. PMID:34377684
METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses. PMID:34184911
Gut lactate-producing bacteria promote CD4 T cell recovery on Anti-retroviral therapy in HIV-infected patients. PMID:34141131
Genome analysis to decipher syntrophy in the bacterial consortium 'SCP' for azo dye degradation. PMID:34116639
Tobacco Smoking and the Fecal Microbiome in a Large, Multi-ethnic Cohort. PMID:34020999
Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate. PMID:33970538
Magnesium: Biochemistry, Nutrition, Detection, and Social Impact of Diseases Linked to Its Deficiency. PMID:33808247
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. PMID:33691770
Magnesium in Infectious Diseases in Older People. PMID:33435521
Enhancement of polyhydroxyalkanoate production by co-feeding lignin derivatives with glycerol in Pseudomonas putida KT2440. PMID:33413621
Magnesium and Hypertension in Old Age. PMID:33396570
A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data. PMID:33343536
A comparative UHPLC-Q/TOF-MS-based eco-metabolomics approach reveals temperature adaptation of four Nepenthes species. PMID:33318532
Evidence Regarding Vitamin D and Risk of COVID-19 and Its Severity. PMID:33142828
Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments. PMID:32994326
Functional Disassociation Between the Protein Domains of MSMEG_4305 of Mycolicibacterium smegmatis (Mycobacterium smegmatis) in vivo. PMID:32973726
Multi-omics Approaches To Decipher the Impact of Diet and Host Physiology on the Mammalian Gut Microbiome. PMID:32948523
Ecological insights into assembly processes and network structures of bacterial biofilms in full-scale biologically active carbon filters under ozone implementation. PMID:32882545
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. PMID:32662816
In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes. PMID:32605102
Circulating Ionized Magnesium as a Measure of Supplement Bioavailability: Results from a Pilot Study for Randomized Clinical Trial. PMID:32353962
Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose. PMID:32313551
Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria. PMID:32296121
Linoleic acid induces metabolic stress in the intestinal microorganism Bifidobacterium breve DSM 20213. PMID:32265475
Lolium perenne apoplast metabolomics for identification of novel metabolites produced by the symbiotic fungus Epichloë festucae. PMID:32155669
Relationship between gut microbiota and circulating metabolites in population-based cohorts. PMID:31862950
Stable Isotope-Assisted Plant Metabolomics: Combination of Global and Tracer-Based Labeling for Enhanced Untargeted Profiling and Compound Annotation. PMID:31708958
INDISIM-Denitrification, an individual-based model for study the denitrification process. PMID:31691030
The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury. PMID:31654639
Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities. PMID:31653790
Arcobacter peruensis sp. nov., a Chemolithoheterotroph Isolated from Sulfide- and Organic-Rich Coastal Waters off Peru. PMID:31585991
Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate. PMID:31583016
A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome. PMID:31554820
High-resolution 13C metabolic flux analysis. PMID:31471597
Genomic Prediction Including SNP-Specific Variance Predictors. PMID:31467030
Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome. PMID:31275260
The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile. PMID:31272480
Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. PMID:31005411
Temporal proteomic profiling reveals changes that support Burkholderia biofilms. PMID:30759239
BioReader: a text mining tool for performing classification of biomedical literature. PMID:30717659
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. PMID:30707687
Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase. PMID:30577795
Flux Connections Between Gluconate Pathway, Glycolysis, and Pentose-Phosphate Pathway During Carbohydrate Metabolism in Bacillus megaterium QM B1551. PMID:30524402
Magnesium: Are We Consuming Enough? PMID:30513803
Interpretation of an individual functional genomics experiment guided by massive public data. PMID:30478325
Comparative genomics of the major parasitic worms. PMID:30397333
A Cyclic Metabolic Network in Pseudomonas protegens Pf-5 Prioritizes the Entner-Doudoroff Pathway and Exhibits Substrate Hierarchy during Carbohydrate Co-Utilization. PMID:30366991
Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. PMID:30309961
Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community. PMID:30260956
Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome. PMID:30013164
YAMP: a containerized workflow enabling reproducibility in metagenomics research. PMID:29917068
The iron hand of uropathogenic Escherichia coli: the role of transition metal control in virulence. PMID:29870278
In Silico Knockout Screening of Plasmodium falciparum Reactions and Prediction of Novel Essential Reactions by Analysing the Metabolic Network. PMID:29789805
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications. PMID:29468116
Targeted and Untargeted Metabolic Profiling of Wild Grassland Plants identifies Antibiotic and Anthelmintic Compounds Targeting Pathogen Physiology, Metabolism and Reproduction. PMID:29374230
Pathway design using de novo steps through uncharted biochemical spaces. PMID:29330441
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. PMID:29311644
Comparative Histological and Transcriptional Analysis of Maize Kernels Infected with Aspergillus flavus and Fusarium verticillioides. PMID:29270183
Mapping the small RNA interactome in bacteria using RIL-seq. PMID:29215635
A comprehensive evaluation of constraining amino acid biosynthesis in compartmented models for metabolic flux analysis. PMID:29188182
Granzyme B Disrupts Central Metabolism and Protein Synthesis in Bacteria to Promote an Immune Cell Death Program. PMID:29107333
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. PMID:29086112
The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites. PMID:29075248
MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. PMID:29069412
Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis. PMID:29042298
13C metabolic flux analysis of three divergent extremely thermophilic bacteria: Geobacillus sp. LC300, Thermus thermophilus HB8, and Rhodothermus marinus DSM 4252. PMID:29037779
Polyamine is a critical determinant of Pseudomonas chlororaphis O6 for GacS-dependent bacterial cell growth and biocontrol capacity. PMID:28862813
Genomic analysis of methanogenic archaea reveals a shift towards energy conservation. PMID:28826405
Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis. PMID:28752667
Nutrient Acquisition and the Metabolic Potential of Photoferrotrophic Chlorobi. PMID:28729857
Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. PMID:28444480
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. PMID:28228535
Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer. PMID:28179898
Mining pathway associations for disease-related pathway activity analysis based on gene expression and methylation data. PMID:28168005
Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data. PMID:28137712
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia. PMID:28117656
Carbon Sources Tune Antibiotic Susceptibility in Pseudomonas aeruginosa via Tricarboxylic Acid Cycle Control. PMID:28111098
Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. PMID:28106881
Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement. PMID:27965696
A Comprehensively Curated Genome-Scale Two-Cell Model for the Heterocystous Cyanobacterium Anabaena sp. PCC 7120. PMID:27899536
Advances on plant-pathogen interactions from molecular toward systems biology perspectives. PMID:27870294
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. PMID:27867422
Shewanella baltica Ecotypes Have Wide Transcriptional Variation under the Same Growth Conditions. PMID:27777983
A Resource Allocation Trade-Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum. PMID:27732672
In silico structural characterization of protein targets for drug development against Trypanosoma cruzi. PMID:27665464
Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. PMID:27602057
A fast and simple LC-MS-based characterization of the flavonoid biosynthesis pathway for few seed(ling)s. PMID:27586417
Novel small molecule binders of human N-glycanase 1, a key player in the endoplasmic reticulum associated degradation pathway. PMID:27567076
Metabolic requirements for cancer cell proliferation. PMID:27540483
Mapping the patent landscape of synthetic biology for fine chemical production pathways. PMID:27489206
Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study. PMID:27166072
Metabolomics and Its Application to Acute Lung Diseases. PMID:26973643
Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with infectious bovine keratoconjunctivitis versus the deep nasopharynx of asymptomatic cattle. PMID:26872821
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PMID:26812499
Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process. PMID:26807149
Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans. PMID:26776497
Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. PMID:26677108
Metagenome-assembled genomes uncover a global brackish microbiome. PMID:26667648
Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach. PMID:26629901
PPIM: A Protein-Protein Interaction Database for Maize. PMID:26620522
mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. PMID:26500804
Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. PMID:26494363
Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River. PMID:26483785
Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis. PMID:26453433
Dissecting Germ Cell Metabolism through Network Modeling. PMID:26367011
Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways. PMID:26350459
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. PMID:26221418
A novel intracellular mutualistic bacterium in the invasive ant Cardiocondyla obscurior. PMID:26172209
PubChem structure-activity relationship (SAR) clusters. PMID:26150895
Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery. PMID:26114876
Revisiting Protocols for the NMR Analysis of Bacterial Metabolomes. PMID:26078915
MetaPathways v2.5: quantitative functional, taxonomic and usability improvements. PMID:26076725
DksA and (p)ppGpp have unique and overlapping contributions to Haemophilus ducreyi pathogenesis in humans. PMID:26056381
kpath: integration of metabolic pathway linked data. PMID:26055101
Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology. PMID:26041051
Pan-phylum Comparison of Nematode Metabolic Potential. PMID:26000881
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists. PMID:25983554
MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data. PMID:25972773
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
Reconstructing genome-scale metabolic models with merlin. PMID:25845595
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. PMID:25806041
Personal genomes, quantitative dynamic omics and personalized medicine. PMID:25798291
Genetic basis and detection of unintended effects in genetically modified crop plants. PMID:25716164
Metabolomics and diabetes: analytical and computational approaches. PMID:25713200
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. PMID:25501486
Computational strategies for a system-level understanding of metabolism. PMID:25427076
Predicting the functional repertoire of an organism from unassembled RNA-seq data. PMID:25409897
Integrated network analysis and effective tools in plant systems biology. PMID:25408696
Plasma metabolomic profiles of breast cancer patients after short-term limonene intervention. PMID:25388013
Computational approaches for microalgal biofuel optimization: a review. PMID:25309916
Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam. PMID:25293379
MetaProx: the database of metagenomic proximons. PMID:25288655
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis. PMID:25279447
Metabolic network prediction through pairwise rational kernels. PMID:25260372
L-methionase: a therapeutic enzyme to treat malignancies. PMID:25250324
Insilico analysis of hypothetical proteins unveils putative metabolic pathways and essential genes in Leishmania donovani. PMID:25206363
Study of leaf metabolome modifications induced by UV-C radiations in representative Vitis, Cissus and Cannabis species by LC-MS based metabolomics and antioxidant assays. PMID:25197936
Genome Sequencing of a Mung Bean Plant Growth Promoting Strain of P. aeruginosa with Biocontrol Ability. PMID:25184130
Metabolite profiling and integrative modeling reveal metabolic constraints for carbon partitioning under nitrogen starvation in the green algae Haematococcus pluvialis. PMID:25183014
Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides. PMID:25164283
Comparative analysis of functional metagenomic annotation and the mappability of short reads. PMID:25148512
Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models. PMID:25148472
Physiological and genomic features of a novel sulfur-oxidizing gammaproteobacterium belonging to a previously uncultivated symbiotic lineage isolated from a hydrothermal vent. PMID:25133584
Evolution of a genome-encoded bias in amino acid biosynthetic pathways is a potential indicator of amino acid dynamics in the environment. PMID:25118252
Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. PMID:25071821
Elucidating how the saprophytic fungus Aspergillus nidulans uses the plant polyester suberin as carbon source. PMID:25043916
Text-mining-assisted biocuration workflows in Argo. PMID:25037308
Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. PMID:24998033
Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. PMID:24980702
GABA from reactive astrocytes impairs memory in mouse models of Alzheimer's disease. PMID:24973918
Efficiently gap-filling reaction networks. PMID:24972703
Current understanding of the formation and adaptation of metabolic systems based on network theory. PMID:24957641
Application of stable isotope-assisted metabolomics for cell metabolism studies. PMID:24957020
Settling down: the genome of Serratia symbiotica from the aphid Cinara tujafilina zooms in on the process of accommodation to a cooperative intracellular life. PMID:24951564
Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data. PMID:24949426
The S-layer proteins of Tannerella forsythia are secreted via a type IX secretion system that is decoupled from protein O-glycosylation. PMID:24943676
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. PMID:24927599
Profiling the orphan enzymes. PMID:24906382
Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, a member of the marine roseobacter clade. PMID:24858085
Finding sequences for over 270 orphan enzymes. PMID:24826896
Phylogenomic reconstruction of archaeal fatty acid metabolism. PMID:24818264
Integration of bioinformatics to biodegradation. PMID:24808763
Prediction of substrates for glutathione transferases by covalent docking. PMID:24802635
XTMS: pathway design in an eXTended metabolic space. PMID:24792156
Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing. PMID:24781900
Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27. PMID:24774833
Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens. PMID:24762737
MetDisease--connecting metabolites to diseases via literature. PMID:24713438
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. PMID:24708835
Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software. PMID:24688832
Integrated LC-MS/MS system for plant metabolomics. PMID:24688692
Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. PMID:24684742
Effects of age, sex, and genotype on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster. PMID:24636523
New hydrocarbon degradation pathways in the microbial metagenome from Brazilian petroleum reservoirs. PMID:24587220
Meta-analysis of pathway enrichment: combining independent and dependent omics data sets. PMID:24586671
Nutrient salvaging and metabolism by the intracellular pathogen Legionella pneumophila. PMID:24575391
PathNER: a tool for systematic identification of biological pathway mentions in the literature. PMID:24555844
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. PMID:24495517
Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don. PMID:24482265
Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces. PMID:24478124
Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes. PMID:24477196
Pseudomonas putida CSV86: a candidate genome for genetic bioaugmentation. PMID:24475028
An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. PMID:24448676
A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. PMID:24280345
WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. PMID:24280312
The Structure-Function Linkage Database. PMID:24271399
Formiminoglutamase from Trypanosoma cruzi is an arginase-like manganese metalloenzyme. PMID:24261485
Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses. PMID:24260300
FireDB: a compendium of biological and pharmacologically relevant ligands. PMID:24243844
Revealing the hidden functional diversity of an enzyme family. PMID:24240508
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. PMID:24225315
Gramene 2013: comparative plant genomics resources. PMID:24217918
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. PMID:24214998
SMPDB 2.0: big improvements to the Small Molecule Pathway Database. PMID:24203708
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti. PMID:24176055
IMG 4 version of the integrated microbial genomes comparative analysis system. PMID:24165883
Metabolic adaptation and trophic strategies of soil bacteria-C1- metabolism and sulfur chemolithotrophy in Starkeya novella. PMID:24146664
Analytical tools and databases for metagenomics in the next-generation sequencing era. PMID:24124405
Swimming in light: a large-scale computational analysis of the metabolism of Dinoroseobacter shibae. PMID:24098096
Functional genomics of novel secondary metabolites from diverse cyanobacteria using untargeted metabolomics. PMID:24084783
QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. PMID:24064420
Topology of molecular interaction networks. PMID:24041013
Groups: knowledge spreadsheets for symbolic biocomputing. PMID:24037025
Experimental approaches for defining functional roles of microbes in the human gut. PMID:24024637
The COMBREX project: design, methodology, and initial results. PMID:24013487
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. PMID:23953132
Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PMID:23935467
Metagenome survey of a multispecies and alga-associated biofilm revealed key elements of bacterial-algal interactions in photobioreactors. PMID:23913425
Functional profiling of the gut microbiome in disease-associated inflammation. PMID:23906180
Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. PMID:23902988
Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PMID:23894306
Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii. PMID:23872562
Predicting network activity from high throughput metabolomics. PMID:23861661
Integrative variable selection via Bayesian model uncertainty. PMID:23824835
MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. PMID:23800136
Members of the Sinorhizobium meliloti ChvI regulon identified by a DNA binding screen. PMID:23758731
Elucidating rice cell metabolism under flooding and drought stresses using flux-based modeling and analysis. PMID:23753178
The challenge of constructing, classifying, and representing metabolic pathways. PMID:23746312
Activation of CpxRA in Haemophilus ducreyi primarily inhibits the expression of its targets, including major virulence determinants. PMID:23729647
Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria. PMID:23716574
Computational meta'omics for microbial community studies. PMID:23670539
Role of central metabolism in the osmoadaptation of the halophilic bacterium Chromohalobacter salexigens. PMID:23615905
Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. PMID:23612296
Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas. PMID:23607266
Does habitat variability really promote metabolic network modularity? PMID:23593470
Protein engineering for metabolic engineering: current and next-generation tools. PMID:23589443
A systematic comparison of the MetaCyc and KEGG pathway databases. PMID:23530693
The complete genome and phenome of a community-acquired Acinetobacter baumannii. PMID:23527001
Genomics of Loa loa, a Wolbachia-free filarial parasite of humans. PMID:23525074
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PMID:23516347
Regulation of reductive dehalogenase gene transcription in Dehalococcoides mccartyi. PMID:23479747
QM/MM calculations suggest a novel intermediate following the proton abstraction catalyzed by thymidylate synthase. PMID:23464672
Genome-scale reconstruction and in silico analysis of Klebsiella oxytoca for 2,3-butanediol production. PMID:23432904
Linking genome-scale metabolic modeling and genome annotation. PMID:23417799
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Subcellular compartmentation of sugar signaling: links among carbon cellular status, route of sucrolysis, sink-source allocation, and metabolic partitioning. PMID:23346090
CINPER: an interactive web system for pathway prediction for prokaryotes. PMID:23236458
Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium. PMID:23226010
From essential to persistent genes: a functional approach to constructing synthetic life. PMID:23219343
Bioinformatics for the Human Microbiome Project. PMID:23209389
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. PMID:23203881
LUCApedia: a database for the study of ancient life. PMID:23193296
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. PMID:23193289
MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. PMID:23193269
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. PMID:23180789
HMDB 3.0--The Human Metabolome Database in 2013. PMID:23161693
RNApathwaysDB--a database of RNA maturation and decay pathways. PMID:23155061
RNA-seq and microarray complement each other in transcriptome profiling. PMID:23153100
EcoCyc: fusing model organism databases with systems biology. PMID:23143106
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. PMID:23110892
TSGene: a web resource for tumor suppressor genes. PMID:23066107
A constraint-based model of Scheffersomyces stipitis for improved ethanol production. PMID:22998943
Role of trehalose in heat and desiccation tolerance in the soil bacterium Rhizobium etli. PMID:22985230
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment. PMID:22923307
Qualitative translation of relations from BioPAX to SBML qual. PMID:22923304
Metagenomic annotation networks: construction and applications. PMID:22879885
State of the art in silico tools for the study of signaling pathways in cancer. PMID:22837650
Parasites, proteomes and systems: has Descartes' clock run out of time? PMID:22828391
Vitamin B(12) synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales. PMID:22798452
Engineering ecosystems and synthetic ecologies. PMID:22722235
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). PMID:22719821
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. PMID:22700702
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:22684505
Phenotypic and transcriptomic response of auxotrophic Mycobacterium avium subsp. paratuberculosis leuD mutant under environmental stress. PMID:22675497
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases PubMed citations: 211.

211 articles citing: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Pharmacoinformatics approaches to identify potential hits against tetraacyldisaccharide 4'-kinase (LpxK) of Pseudomonas aeruginosa. PMID:35516480
Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics. PMID:35417463
Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. PMID:34657989
Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles. PMID:34294881
Four families of folate-independent methionine synthases. PMID:33534785
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data. PMID:33287694
GapMind: Automated Annotation of Amino Acid Biosynthesis. PMID:32576650
Gene-Wise Burden of Coding Variants Correlates to Noncoding Pharmacogenetic Risk Variants. PMID:32349395
Effectiveness of Bacillus pumilus PDSLzg-1, an innovative Hydrocarbon-Degrading Bacterium conferring antifungal and plant growth-promoting function. PMID:31355114
Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism. PMID:31235964
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. PMID:31003499
Curated BLAST for Genomes. PMID:30944879
Transcriptional and Chemical Changes in Soybean Leaves in Response to Long-Term Aphid Colonization. PMID:30930925
The Patchy Distribution of Restriction⁻Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria. PMID:30893937
Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community. PMID:30260956
Acetylenotrophy: a hidden but ubiquitous microbial metabolism? PMID:29933435
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota. PMID:29600286
Identification of cancer biomarkers of prognostic value using specific gene regulatory networks (GRN): a novel role of RAD51AP1 for ovarian and lung cancers. PMID:29126163
PaperBLAST: Text Mining Papers for Information about Homologs. PMID:28845458
Insights into Butyrate Production in a Controlled Fermentation System via Gene Predictions. PMID:28761933
Succession in the petroleum reservoir microbiome through an oil field production lifecycle. PMID:28524866
Analyses of the probiotic property and stress resistance-related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays. PMID:28384209
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA. PMID:28263984
Bioactive Nutrients and Nutrigenomics in Age-Related Diseases. PMID:28075340
Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts. PMID:27983719
Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm. PMID:27742723
Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis. PMID:27736793
Drug Target Identification and Prioritization for Treatment of Ovine Foot Rot: An In Silico Approach. PMID:27379247
LmSmdB: an integrated database for metabolic and gene regulatory network in Leishmania major and Schistosoma mansoni. PMID:26981382
Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. PMID:26617277
Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network. PMID:26480823
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. PMID:26454280
Towards in vivo estimation of reaction kinetics using high-throughput metabolomics data: a maximum likelihood approach. PMID:26437964
Insight into metabolic pathways of the potential biofuel producer, Paenibacillus polymyxa ICGEB2008. PMID:26413158
Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition. PMID:26248853
Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. PMID:26125681
Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant. PMID:26020781
Robust Expansion of Human Pluripotent Stem Cells: Integration of Bioprocess Design With Transcriptomic and Metabolomic Characterization. PMID:25979863
Systems biology of host-microbe metabolomics. PMID:25929487
A new platform for ultra-high density Staphylococcus aureus transposon libraries. PMID:25888466
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. PMID:25887539
The Listeria monocytogenes strain 10403S BioCyc database. PMID:25819074
Personal genomes, quantitative dynamic omics and personalized medicine. PMID:25798291
Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes. PMID:25755651
Selective paired ion contrast analysis: a novel algorithm for analyzing postprocessed LC-MS metabolomics data possessing high experimental noise. PMID:25683158
Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. PMID:25673291
Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. PMID:25573232
Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer. PMID:25555398
Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates. PMID:25536074
Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State. PMID:25477871
Computational strategies for a system-level understanding of metabolism. PMID:25427076
2-Keto acids based biosynthesis pathways for renewable fuels and chemicals. PMID:25424696
Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. PMID:25406383
A genomic and evolutionary approach reveals non-genetic drug resistance in malaria. PMID:25395010
Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models. PMID:25329157
Computational approaches for microalgal biofuel optimization: a review. PMID:25309916
An online system for metabolic network analysis. PMID:25267793
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. PMID:25231498
Functional genomics of Lactobacillus casei establishment in the gut. PMID:25024222
ODE constrained mixture modelling: a method for unraveling subpopulation structures and dynamics. PMID:24992156
Minimal metabolic pathway structure is consistent with associated biomolecular interactions. PMID:24987116
The Metabolic Interplay between Plants and Phytopathogens. PMID:24957887
The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled. PMID:24923325
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
Fetal alcohol syndrome, chemo-biology and OMICS: ethanol effects on vitamin metabolism during neurodevelopment as measured by systems biology analysis. PMID:24816220
Streptococcus pyogenes polymyxin B-resistant mutants display enhanced ExPortal integrity. PMID:24794568
Genomic features of a bumble bee symbiont reflect its host environment. PMID:24747890
Integrated LC-MS/MS system for plant metabolomics. PMID:24688692
Computational tools for the secondary analysis of metabolomics experiments. PMID:24688685
Plant systems biology: insights, advances and challenges. PMID:24671625
Pathogen roid rage: cholesterol utilization by Mycobacterium tuberculosis. PMID:24611808
Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. PMID:24569707
The future of whole-cell modeling. PMID:24556244
Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits. PMID:24529378
Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don. PMID:24482265
Genome degeneration and adaptation in a nascent stage of symbiosis. PMID:24407854
ITEP: an integrated toolkit for exploration of microbial pan-genomes. PMID:24387194
STITCH 4: integration of protein-chemical interactions with user data. PMID:24293645
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. PMID:24167155
Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological databases are incorporated in scientific papers and vice versa. PMID:24107613
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. PMID:24099179
Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease. PMID:24098138
Using biological pathway data with paxtools. PMID:24068901
Network-based approaches in drug discovery and early development. PMID:24025802
Metabolomics and in-silico analysis reveal critical energy deregulations in animal models of Parkinson's disease. PMID:23935941
Helicobacter pylori salvages purines from extracellular host cell DNA utilizing the outer membrane-associated nuclease NucT. PMID:23893109
Quantification of endospore-forming firmicutes by quantitative PCR with the functional gene spo0A. PMID:23811505
Characterization of genes required for the pathogenicity of Pectobacterium carotovorum subsp. carotovorum Pcc21 in Chinese cabbage. PMID:23676432
Parallel exploitation of diverse host nutrients enhances Salmonella virulence. PMID:23633950
Inactivation of the Pta-AckA pathway causes cell death in Staphylococcus aureus. PMID:23625849
Characterization of the biocontrol activity of pseudomonas fluorescens strain X reveals novel genes regulated by glucose. PMID:23596526
Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. PMID:23579629
Finding type 2 diabetes causal single nucleotide polymorphism combinations and functional modules from genome-wide association data. PMID:23566118
A systematic comparison of the MetaCyc and KEGG pathway databases. PMID:23530693
Molecular tools for chemical biotechnology. PMID:23528237
Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics. PMID:23481603
The evolutionary history of amino acid variations mediating increased resistance of S. aureus identifies reversion mutations in metabolic regulators. PMID:23424663
Chapter 8: Biological knowledge assembly and interpretation. PMID:23300429
Chapter 12: Human microbiome analysis. PMID:23300406
DB Dehydrogenase: an online integrated structural database on enzyme dehydrogenase. PMID:23275696
CINPER: an interactive web system for pathway prediction for prokaryotes. PMID:23236458
CcpA regulates arginine biosynthesis in Staphylococcus aureus through repression of proline catabolism. PMID:23209408
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites. PMID:23193253
Data mining in the MetaCyc family of pathway databases. PMID:23192547
The chemical interactome space between the human host and the genetically defined gut metabotypes. PMID:23178670
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. PMID:23175748
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). PMID:23110428
A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). PMID:23020652
Integration of biological networks and pathways with genetic association studies. PMID:22777728
Investigating metabolite-protein interactions: an overview of available techniques. PMID:22750303
Fungal genome resources at NCBI. PMID:22737589
Metabolic reconstruction for metagenomic data and its application to the human microbiome. PMID:22719234
Mass spectrometry-based metabolomics to elucidate functions in marine organisms and ecosystems. PMID:22690147
The pathway tools pathway prediction algorithm. PMID:22675592
Identification of functional differences in metabolic networks using comparative genomics and constraint-based models. PMID:22666308
Analyzing large biological datasets with association networks. PMID:22638576
Computational tools for metabolic engineering. PMID:22629572
Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions. PMID:22629315
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. PMID:22591066
ZINC: a free tool to discover chemistry for biology. PMID:22587354
Nutritional metabolomics: progress in addressing complexity in diet and health. PMID:22540256
BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments. PMID:22536968
Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. PMID:22479625
Quantitative Proteomics of Intracellular Campylobacter jejuni Reveals Metabolic Reprogramming. PMID:22412372
The gpsX gene encoding a glycosyltransferase is important for polysaccharide production and required for full virulence in Xanthomonas citri subsp. citri. PMID:22404966
Microbial metabolomics. PMID:22379393
Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis. PMID:22356827
Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction. PMID:22316246
Construction and completion of flux balance models from pathway databases. PMID:22262672
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. PMID:22233419
A genomic reappraisal of symbiotic function in the aphid/Buchnera symbiosis: reduced transporter sets and variable membrane organisations. PMID:22229056
Advances in omics and bioinformatics tools for systems analyses of plant functions. PMID:22156726
Phosphorylation in protein-protein binding: effect on stability and function. PMID:22153503
Browsing metabolic and regulatory networks with BioCyc. PMID:22144155
IPAVS: Integrated Pathway Resources, Analysis and Visualization System. PMID:22140115
MMMDB: Mouse Multiple Tissue Metabolome Database. PMID:22139941
MOPED: Model Organism Protein Expression Database. PMID:22139914
Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. PMID:22139506
BacMap: an up-to-date electronic atlas of annotated bacterial genomes. PMID:22135301
Rhea--a manually curated resource of biochemical reactions. PMID:22135291
hiPathDB: a human-integrated pathway database with facile visualization. PMID:22123737
Xanthusbase after five years expands to become Openmods. PMID:22116063
DNAtraffic--a new database for systems biology of DNA dynamics during the cell life. PMID:22110027
UniPathway: a resource for the exploration and annotation of metabolic pathways. PMID:22102589
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. PMID:22102576
InterPro in 2011: new developments in the family and domain prediction database. PMID:22096229
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis. PMID:22096228
Databases and bioinformatics tools for the study of DNA repair. PMID:22091405
MetaCrop 2.0: managing and exploring information about crop plant metabolism. PMID:22086948
STITCH 3: zooming in on protein-chemical interactions. PMID:22075997
Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. PMID:22074569
YMDB: the Yeast Metabolome Database. PMID:22064855
Origins of specificity and promiscuity in metabolic networks. PMID:22052908
SegMine workflows for semantic microarray data analysis in Orange4WS. PMID:22029475
BioPAX support in CellDesigner. PMID:22021903
Pathos: a web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry. PMID:22002696
Horizontal and vertical growth of S. cerevisiae metabolic network. PMID:21999464
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. PMID:21995956
Large-scale bi-level strain design approaches and mixed-integer programming solution techniques. PMID:21949695
EnzymeDetector: an integrated enzyme function prediction tool and database. PMID:21943292
Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). PMID:21908640
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. PMID:21896772
The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. PMID:21866182
Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans--Ignicoccus hospitalis relationship. PMID:21826220
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. PMID:21825121
BKM-react, an integrated biochemical reaction database. PMID:21824409
A retrosynthetic biology approach to metabolic pathway design for therapeutic production. PMID:21819595
Colonic contribution to uremic solutes. PMID:21784895
COLOMBOS: access port for cross-platform bacterial expression compendia. PMID:21779320
Genome-wide mutagenesis of Xanthomonas axonopodis pv. citri reveals novel genetic determinants and regulation mechanisms of biofilm formation. PMID:21750733
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. PMID:21749710
Computational approaches for translational clinical research in disease progression. PMID:21712727
General metabolism of Laribacter hongkongensis: a genome-wide analysis. PMID:21711917
NMR analysis of a stress response metabolic signaling network. PMID:21692534
GLAMM: Genome-Linked Application for Metabolic Maps. PMID:21624891
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. PMID:21596990
Web-based metabolic network visualization with a zooming user interface. PMID:21595965
Fosmidomycin uptake into Plasmodium and Babesia-infected erythrocytes is facilitated by parasite-induced new permeability pathways. PMID:21573242
Comparative genomics of cell envelope components in mycobacteria. PMID:21573108
The impact of oxygen on the transcriptome of recombinant S. cerevisiae and P. pastoris - a comparative analysis. PMID:21554735
A survey of metabolic databases emphasizing the MetaCyc family. PMID:21523460
The wxacO gene of Xanthomonas citri ssp. citri encodes a protein with a role in lipopolysaccharide biosynthesis, biofilm formation, stress tolerance and virulence. PMID:21453433
The architecture and conservation pattern of whole-cell control circuitry. PMID:21371478
Protein function prediction: towards integration of similarity metrics. PMID:21353529
Systems biology: the next frontier for bioinformatics. PMID:21331364
Complete genome sequence of Archaeoglobus profundus type strain (AV18). PMID:21304717
Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. PMID:21266540
Genome (re-)annotation and open-source annotation pipelines. PMID:21255336
Core and panmetabolism in Escherichia coli. PMID:21239590
Plasmids with a chromosome-like role in rhizobia. PMID:21217003
The annotation of the asparagine N-linked glycosylation pathway in the Reactome database. PMID:21199820
EcoCyc: a comprehensive database of Escherichia coli biology. PMID:21097882
The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies. PMID:21092328
MetNetAPI: A flexible method to access and manipulate biological network data from MetNet. PMID:21083943
Gramene database in 2010: updates and extensions. PMID:21076153
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
BRENDA, the enzyme information system in 2011. PMID:21062828
Human and chicken TLR pathways: manual curation and computer-based orthology analysis. PMID:21052677
A systematic study of genome context methods: calibration, normalization and combination. PMID:20920312
Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development. PMID:20860850
The BioPAX community standard for pathway data sharing. PMID:20829833
Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies. PMID:20649993
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. PMID:20616194
Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement. PMID:20594333
Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. PMID:20522724
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. PMID:20444866
Improved microarray-based decision support with graph encoded interactome data. PMID:20419106
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766
http://dx.doi.org/10.1093/nar/gkx935

Tags:

Tags
More detailed information about this field from each metasource.

annotation
metasource: Fairsharing.org
version: FAIRsharing.org: MetaCyc; MetaCyc; DOI: https://doi.org/10.25504/FAIRsharing.yytevr; Last edited: Oct. 23, 2019, 11:57 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

enzyme
metasource: Fairsharing.org
version: FAIRsharing.org: MetaCyc; MetaCyc; DOI: https://doi.org/10.25504/FAIRsharing.yytevr; Last edited: Oct. 23, 2019, 11:57 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: MetaCyc; MetaCyc; DOI: https://doi.org/10.25504/FAIRsharing.yytevr; Last edited: Oct. 23, 2019, 11:57 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: MetaCyc; MetaCyc; DOI: https://doi.org/10.25504/FAIRsharing.yytevr; Last edited: Oct. 23, 2019, 11:57 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

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

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

genomics
metasource: re3data.org
version: re3data.org: MetaCyc; editing status 2021-10-11; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R32K7X last accessed: 2022-11-04

life sciences
metasource: re3data.org
version: re3data.org: MetaCyc; editing status 2021-10-11; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R32K7X last accessed: 2022-11-04

metabolic engineering
metasource: re3data.org
version: re3data.org: MetaCyc; editing status 2021-10-11; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R32K7X last accessed: 2022-11-04

molecular biology
metasource: re3data.org
version: re3data.org: MetaCyc; editing status 2021-10-11; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R32K7X last accessed: 2022-11-04

systems biology
metasource: re3data.org
version: re3data.org: MetaCyc; editing status 2021-10-11; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R32K7X last accessed: 2022-11-04

endocrinology and metabolism
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.287250

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.287250

enzymes
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.287250

literature and language
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:00.287250

enzyme pathway model small molecule protein sequence protein family genomics life sciences metabolic engineering molecular biology systems biology endocrinology and metabolism molecular interactions, pathways and networks enzyme literature and language

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BioCyc

Small Molecule Pathway Database

MetaCrop 2.0

BioCarta Pathways

Reactome - a curated knowledgebase of biological pathways

Unipathway

Enzyme Portal

BsubCyc

BRENDA

HumanCyc

RNApathwaysDB

PMN

GlycoPathDB

MANET

Pathway Ontology

Pathway Commons

PathBank

LAMP

BioSilico

Pathguide