US Department of Energy Systems Biology Knowledgebase
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US Department of Energy Systems Biology Knowledgebase
metasource: Fairsharing.org
version: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
KBase
metasource: Fairsharing.org
version: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
KBase: The U.S. Department of Energy Systems Biology Knowledgebase
metasource: re3data.org
version: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
Names
More detailed information about this field from each metasource.
US Department of Energy Systems Biology Knowledgebase
metasource: Fairsharing.orgversion: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
KBase
metasource: Fairsharing.orgversion: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
KBase: The U.S. Department of Energy Systems Biology Knowledgebase
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
Other names: KBase, KBase: The U.S. Department of Energy Systems Biology Knowledgebase
Names
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US Department of Energy Systems Biology Knowledgebase
metasource: Fairsharing.orgversion: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
KBase
metasource: Fairsharing.orgversion: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
KBase: The U.S. Department of Energy Systems Biology Knowledgebase
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
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KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.
Description
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KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.
metasource: Fairsharing.orgversion: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics. KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
Webpage:
https://www.kbase.usWebpage
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https://www.kbase.us
metasource: Fairsharing.orgversion: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
https://www.kbase.us/
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
Licence:
Name: KBase Terms and ConditionLicence name
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KBase Terms and Condition
metasource: Fairsharing.orgversion: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Public Domain
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
Licence URL
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https://www.kbase.us/terms-and-conditions/
metasource: Fairsharing.orgversion: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
https://www.kbase.us/data-policy-and-sources/
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
Publications:
Publications
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KBase: The United States Department of Energy Systems Biology Knowledgebase
PMID: 29979655
metasource: Fairsharing.org
version: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications
More detailed information about this field from each metasource.
KBase: The United States Department of Energy Systems Biology Knowledgebase
PMID: 29979655
metasource: Fairsharing.org
version: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
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KBase: The United States Department of Energy Systems Biology Knowledgebase
PubMed citations: 306.
306 articles citing: KBase: The United States Department of Energy Systems Biology Knowledgebase
Metagenomic views on taxonomic and functional profiles of the Himalayan Tsomgo cold lake and unveiling its deterzome potential. PMID:35927361
Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities. PMID:35795346
Metabolic modeling of the International Space Station microbiome reveals key microbial interactions. PMID:35791019
The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction. PMID:35773344
Cross-feeding niches among commensal leaf bacteria are shaped by the interaction of strain-level diversity and resource availability. PMID:35768644
Draft Genome Sequences of Five Putatively Novel Saccharibacteria Species Assembled from the Human Oral Metagenome. PMID:35758687
Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies. PMID:35756023
Coastal Microbial Communities Disrupted During the 2018 Hurricane Season in Outer Banks, North Carolina. PMID:35756005
Genome-scale metabolic modelling of the human gut microbiome reveals changes in the glyoxylate and dicarboxylate metabolism in metabolic disorders. PMID:35754734
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. PMID:35710409
Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil. PMID:35705700
merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. PMID:35694833
Complete Genome Sequences of Rhizobium gallicum M101 and Two Potential New Rhizobium Species Isolated from Soils in Central Canada. PMID:35670609
Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction. PMID:35630399
Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges. PMID:35625648
Development of Phage Cocktails to Treat E. coli Catheter-Associated Urinary Tract Infection and Associated Biofilms. PMID:35620093
Genomic, morphological, and biochemical analyses of a multi-metal resistant but multi-drug susceptible strain of Bordetella petrii from hospital soil. PMID:35589928
Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium. PMID:35579457
Draft Genome Sequences of 10 Pseudomonas sp. Isolates from the Active Layer of Permafrost in Ny Ålesund, Svalbard, Norway. PMID:35575557
Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations. PMID:35547121
Metabolic Synergy between Human Symbionts Bacteroides and Methanobrevibacter. PMID:35536023
Integrated analysis of microbe-host interactions in Crohn's disease reveals potential mechanisms of microbial proteins on host gene expression. PMID:35479407
Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface Environment. PMID:35475637
A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility. PMID:35448501
Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas. PMID:35404785
A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. PMID:35402883
Deciphering Genomes: Genetic Signatures of Plant-Associated Micromonospora. PMID:35401599
Hyperaccumulation of Gadolinium by Methylorubrum extorquens AM1 Reveals Impacts of Lanthanides on Cellular Processes Beyond Methylotrophy. PMID:35369483
Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork. PMID:35362895
A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications. PMID:35328559
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PMID:35320266
Structure and biosynthesis of carotenoids produced by a novel Planococcus sp. isolated from South Africa. PMID:35305628
Comparative Genomics on Cultivated and Uncultivated Freshwater and Marine "Candidatus Manganitrophaceae" Species Implies Their Worldwide Reach in Manganese Chemolithoautotrophy. PMID:35285693
The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut. PMID:35266814
Integrative Genome-Scale Metabolic Modeling Reveals Versatile Metabolic Strategies for Methane Utilization in Methylomicrobium album BG8. PMID:35258342
Whole-Genome Analysis of Escherichia Phage vB_EcoM-S1P5QW, Isolated from Manures Collected from Cattle Farms in Maine. PMID:35254108
Comparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains. PMID:35196120
Permafrost Active Layer Microbes From Ny Ålesund, Svalbard (79°N) Show Autotrophic and Heterotrophic Metabolisms With Diverse Carbon-Degrading Enzymes. PMID:35185810
Complete Genome Sequence of Luteitalea sp. Strain TBR-22. PMID:35175120
Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov. PMID:35173698
Draft Genome Sequence of Sweet Pepper Fruit Epiphyte-Associated Bacillus cereus HRT7.7. PMID:35142557
Complete Genome Sequence of Human Oral Saccharibacterium "Candidatus Nanosynbacter sp. HMT352" Strain KC1. PMID:35142548
Draft Genome Sequence of a Methanogenic Archaeon from West Spitsbergen Permafrost. PMID:35142547
Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts. PMID:35107338
Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan Valley. PMID:35095268
Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis. PMID:35076269
Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns. PMID:35052488
Whole-Genome Sequence of Paenibacillus polymyxa Strain SRT9.1, a Promising Plant Growth-Promoting Bacterium. PMID:35049350
Integrating Bioinformatics Tools Into Inquiry-Based Molecular Biology Laboratory Education Modules. PMID:35036827
Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study. PMID:35027090
Draft Genome Sequence of Bryobacteraceae Strain F-183. PMID:35023779
A quantitative framework reveals traditional laboratory growth is a highly accurate model of human oral infection. PMID:34992142
Ten simple rules for researchers who want to develop web apps. PMID:34990469
Draft Genome Sequence of Leifsonia poae Strain BS71, Isolated from a Drought Microcosm. PMID:34989599
Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PMID:34986141
Three Novel Bacteria Associated with Two Centric Diatom Species from the Mediterranean Sea, Thalassiosira rotula and Skeletonema marinoi. PMID:34947994
Metagenome-Scale Metabolic Network Suggests Folate Produced by Bifidobacterium longum Might Contribute to High-Fiber-Diet-Induced Weight Loss in a Prader-Willi Syndrome Child. PMID:34946095
Ancient Metabolisms of a Thermophilic Subseafloor Bacterium. PMID:34925271
The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella. PMID:34910616
Comparative Genomics Reveals Insights into Induction of Violacein Biosynthesis and Adaptive Evolution in Janthinobacterium. PMID:34908429
Analogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic Growth. PMID:34903058
Long-Range PCR Reveals the Genetic Cargo of IncP-1 Plasmids in the Complex Microbial Community of an On-Farm Biopurification System Treating Pesticide-Contaminated Wastewater. PMID:34878814
Complete Genome Analysis of Undecylprodigiosin Pigment Biosynthesizing Marine Streptomyces Species Displaying Potential Bioactive Applications. PMID:34835376
Characterization of Komagataeibacter Isolate Reveals New Prospects in Waste Stream Valorization for Bacterial Cellulose Production. PMID:34835356
Synthetic Biology Advanced Natural Product Discovery. PMID:34822443
Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics. PMID:34795375
Unraveling Fe(II)-Oxidizing Mechanisms in a Facultative Fe(II) Oxidizer, Sideroxydans lithotrophicus Strain ES-1, via Culturing, Transcriptomics, and Reverse Transcription-Quantitative PCR. PMID:34788064
TRIMER: Transcription Regulation Integrated with Metabolic Regulation. PMID:34761179
Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance. PMID:34749649
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PMID:34748537
Draft Genome Sequence of Schaalia odontolytica Strain ORNL0103, a Basibiont of "Candidatus Saccharibacteria" HMT352. PMID:34734770
The Moderately (D)efficient Enzyme: Catalysis-Related Damage In Vivo and Its Repair. PMID:34729986
A gap-filling algorithm for prediction of metabolic interactions in microbial communities. PMID:34723959
A Beginner's Guide to the COBRA Toolbox. PMID:34719002
Curating COBRA Models of Microbial Metabolism. PMID:34719001
Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome. PMID:34719000
Using Genome Scale Mutant Libraries to Identify Essential Genes. PMID:34709619
Characterization of a highly xylose tolerant β-xylosidase isolated from high temperature horse manure compost. PMID:34689773
Rubber Degrading Strains: Microtetraspora and Dactylosporangium. PMID:34685283
Genomic Characterization of a Prophage, Smhb1, That Infects Salinivibrio kushneri BNH Isolated from a Namib Desert Saline Spring. PMID:34683373
Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. PMID:34681003
Functional attractors in microbial community assembly. PMID:34653368
Advancing Equity and Inclusion in Microbiome Research and Training. PMID:34636663
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS). PMID:34635859
metaGEM: reconstruction of genome scale metabolic models directly from metagenomes. PMID:34614189
Three Draft Single-Cell Genome Sequences of Novel SAR324 Strains Isolated from the Abyssopelagic Southern Ocean. PMID:34591681
Modelling microbial communities: Harnessing consortia for biotechnological applications. PMID:34584635
Periodically Disturbing the Spatial Structure of Biofilms Can Affect the Production of an Essential Virulence Factor in Pseudomonas aeruginosa. PMID:34581603
Genomic Analysis of Endophytic Bacillus cereus T4S and Its Plant Growth-Promoting Traits. PMID:34579311
Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa. PMID:34576823
Stimulation of Nicotiana tabacum L. In Vitro Shoot Growth by Endophytic Bacillus cereus Group Bacteria. PMID:34576789
Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment. PMID:34572839
Description of Ornithinimicrobium ciconiae sp. nov., and Ornithinimicrobium avium sp. nov., isolated from the faeces of the endangered and near-threatened birds. PMID:34570338
Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila. PMID:34565363
Path to improving the life cycle and quality of genome-scale models of metabolism. PMID:34555324
Metagenome-Assembled Genome Sequences Recovered from Epilithic River Biofilm in the Tama River, Japan. PMID:34554005
Frigoriflavimonas asaccharolytica gen. nov., sp. nov., a novel psychrophilic esterase and protease producing bacterium isolated from Antarctica. PMID:34541621
Draft Genome Sequences of Three Shewanella sp. Strains Isolated from Urban Freshwaters in the Ohio River Valley, USA. PMID:34528821
Identification of essential β-oxidation genes and corresponding metabolites for oestrogen degradation by actinobacteria. PMID:34523795
Pathways of thymidine hypermodification. PMID:34522950
Flavobacterium erciyesense sp. nov., a putative non-pathogenic fish symbiont. PMID:34515811
Characterization of Erwinia gerundensis A4, an Almond-Derived Plant Growth-Promoting Endophyte. PMID:34512566
Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. PMID:34507539
Draft Genome Sequence of Salegentibacter sp. Strain BDJ18, a Plankton-Associated Bacterium in the Northeast Atlantic Ocean. PMID:34498925
Draft Genome Sequence of Pseudoalteromonas sp. Strain JC3. PMID:34498923
Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera. PMID:34484138
DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations. PMID:34473240
Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models. PMID:34455914
Combining OSMAC Approach and Untargeted Metabolomics for the Identification of New Glycolipids with Potent Antiviral Activity Produced by a Marine Rhodococcus. PMID:34445761
Whole Genome Sequencing of Sunflower Root-Associated Bacillus cereus. PMID:34421294
Investigating the Chemolithoautotrophic and Formate Metabolism of Nitrospira moscoviensis by Constraint-Based Metabolic Modeling and 13C-Tracer Analysis. PMID:34402644
Use of hemagglutinin and neuraminidase amplicon-based high-throughput sequencing with variant analysis to detect co-infection and resolve identical consensus sequences of seasonal influenza in a university setting. PMID:34388979
Characterization of plant growth-promoting rhizobacterial isolates associated with food plants in South Africa. PMID:34387781
SiGMoiD: A super-statistical generative model for binary data. PMID:34358223
An extended reconstruction of human gut microbiota metabolism of dietary compounds. PMID:34354065
Draft Genome Sequences of Clinical Respiratory Isolates of Mycobacterium goodii Recovered in Ireland. PMID:34351236
Metabolic control of nitrogen fixation in rhizobium-legume symbioses. PMID:34330708
309 metagenome assembled microbial genomes from deep sediment samples in the Gulfs of Kathiawar Peninsula. PMID:34321485
The Potential of OMICs Technologies for the Treatment of Immune-Mediated Inflammatory Diseases. PMID:34299122
Chryseobacterium pennae sp. nov., isolated from poultry feather waste. PMID:34292147
Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost. PMID:34288700
Draft Genome Sequencing of Stenotrophomonas indicatrix BOVIS40 and Stenotrophomonas maltophilia JVB5, Two Strains with Identifiable Genes Involved in Plant Growth Promotion. PMID:34264096
Draft Genome Sequence of Staphylococcus succinus Strain GN1, Isolated from a Basement Floor in Milwaukee, WI. PMID:34236223
Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil. PMID:34211102
Genomic assessment of Stenotrophomonas indicatrix for improved sunflower plant. PMID:34195871
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains. PMID:34180992
An ecophysiological explanation for manganese enrichment in rock varnish. PMID:34161271
Metagenome-Assembled Genomes of Novel Taxa from an Acid Mine Drainage Environment. PMID:34161177
Barks from avocado trees of different geographic locations have consistent microbial communities. PMID:34160629
High-quality draft genome sequence data of six Lactiplantibacillus plantarum subsp. argentoratensis strains isolated from various Greek wheat sourdoughs. PMID:34150961
Complete Genome Sequences of Two Rhodococcus sp. Strains with Large and Linear Chromosomes, Isolated from Apple Rhizosphere. PMID:34137630
In situ microcosms deployed at the coast of British Columbia (Canada) to study dilbit weathering and associated microbial communities under marine conditions. PMID:34124756
Complete Genome Sequence of Human Oral Actinomyces sp. HMT175 Strain ORNL0102, a Host of the Saccharibacterium (TM7) HMT957. PMID:34110241
A conserved rhizobial peptidase that interacts with host-derived symbiotic peptides. PMID:34083727
Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. PMID:34046017
Analysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven Heterogeneity. PMID:34025805
Formation, characterization and modeling of emergent synthetic microbial communities. PMID:33995895
Type II Photosynthetic Reaction Center Genes of Avocado (Persea americana Mill.) Bark Microbial Communities are Dominated by Aerobic Anoxygenic Alphaproteobacteria. PMID:33990868
Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling. PMID:33981000
Inhibition of a nutritional endosymbiont by glyphosate abolishes mutualistic benefit on cuticle synthesis in Oryzaephilus surinamensis. PMID:33976379
A method for achieving complete microbial genomes and improving bins from metagenomics data. PMID:33961626
Structural genomics and the Protein Data Bank. PMID:33957120
Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas. PMID:33936009
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont. PMID:33883280
Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions. PMID:33869975
Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. PMID:33841364
Complete Genome Sequence of Human Oral Actinomyces sp. HMT897 Strain ORNL0104, a Host of the Saccharibacterium (TM7) HMT351. PMID:33833021
Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile. PMID:33828081
Genomes of Gut Bacteria from Nasonia Wasps Shed Light on Phylosymbiosis and Microbe-Assisted Hybrid Breakdown. PMID:33824199
Metabolic Capacity of the Antarctic Cyanobacterium Phormidium pseudopriestleyi That Sustains Oxygenic Photosynthesis in the Presence of Hydrogen Sulfide. PMID:33809699
Draft Genome Sequences of Dysgonomonas sp. Strains GY75 and GY617, Isolated from the Hindgut of Reticulitermes flavipes. PMID:33766898
Functional Analysis of Phenazine Biosynthesis Genes in Burkholderia spp. PMID:33741619
Draft Genome Sequences of Nine Environmental Bacterial Isolates Colonizing Plastic. PMID:33737371
Genome Sequence of Clostridium sp. Strain P21, a CO-Fermenting Acetogen Isolated from Old Hay. PMID:33737364
Draft Genomic Analysis of Pseudomonas sp. Strain OA3, a Potential Plant Growth-Promoting Rhizospheric Bacterium. PMID:33737350
Genomic Characterization of Two Shiga Toxin-Converting Bacteriophages Induced From Environmental Shiga Toxin-Producing Escherichia coli. PMID:33716997
Deep-sea microbes as tools to refine the rules of innate immune pattern recognition. PMID:33712473
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. PMID:33691770
Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen-limited methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments. PMID:33650794
Genome Sequence of Streptomyces sp. Strain HB-N217, Isolated from the Marine Sponge Forcepia sp. PMID:33632867
Metagenome Assembly and Metagenome-Assembled Genome Sequences from the Rhizosphere of Maize Plants in Mafikeng, South Africa. PMID:33632860
Metagenomes and Assembled Genomes from Diarrhea-Affected Cattle (Bos taurus). PMID:33602735
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis. PMID:33602294
MetNet: A two-level approach to reconstructing and comparing metabolic networks. PMID:33577575
Complete Genome Sequence of Desulfobulbus oligotrophicus Prop6, an Anaerobic Deltabacterota Strain That Lacks Mercury Methylation Capability. PMID:33541869
Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota. PMID:33517907
Draft Genome Sequences of Dysgonomonas sp. Strains BGC7 and HGC4, Isolated from the Hindgut of a Lower Termite. PMID:33509995
Understanding the host-microbe interactions using metabolic modeling. PMID:33472685
Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations. PMID:33467644
Metagenome-Assembled Genome Sequences of Raphidiopsis raciborskii and Planktothrix agardhii from a Cyanobacterial Bloom in Kissena Lake, New York, USA. PMID:33446598
Comparative genomics and metabolomics analysis of Riemerella anatipestifer strain CH-1 and CH-2. PMID:33436670
Pan-Enterovirus Amplicon-Based High-Throughput Sequencing Detects the Complete Capsid of a EVA71 Genotype C1 Variant via Wastewater-Based Epidemiology in Arizona. PMID:33430521
Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species. PMID:33428734
Metabolic modelling approaches for describing and engineering microbial communities. PMID:33425254
Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA. PMID:33410936
Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil. PMID:33402535
Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. PMID:33372654
Atlas: Automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages. PMID:33367504
Community-led, integrated, reproducible multi-omics with anvi'o. PMID:33349678
Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease. PMID:33330572
Draft Genome Sequence of a Terrestrial Planctomycete, Singulisphaera sp. Strain GP187, Isolated from Forest Soil. PMID:33303655
carP, encoding a Ca2+-regulated putative phytase, is evolutionarily conserved in Pseudomonas aeruginosa and has potential as a biomarker. PMID:33295862
Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community. PMID:33273721
Draft Genome Sequence of the Antimony-Oxidizing Pseudomonas sp. Strain SbOxS1, Isolated from Stibnite Mine Tailing Soil. PMID:33273005
Metagenome-Assembled Genome Sequence of Aphanizomenon flos-aquae Strain Clear-A1, Assembled from an Enrichment Culture. PMID:33272999
Metagenome-Assembled Genome Sequence of Dolichospermum circinale Strain Clear-D4, Assembled from a Harmful Cyanobacterial Bloom Enrichment Culture. PMID:33272998
Metagenome-Assembled Genome Sequence of Vulcanococcus sp. Strain Clear-D1, Assembled from a Cyanobacterial Enrichment Culture. PMID:33272997
Metagenome-Assembled Genome Sequence of Rhodobacteraceae Bacterium Strain Clear-D3, Assembled from a Dolichospermum Consortium from Clear Lake, California. PMID:33272996
Metagenome-Assembled Genome Sequence of Kapabacteriales Bacterium Strain Clear-D13, Assembled from a Harmful Algal Bloom Enrichment Culture. PMID:33272995
Comparative genomics in "Candidatus Kuenenia stuttgartiensis" reveal high genomic plasticity in the overall genome structure, CRISPR loci and surface proteins. PMID:33261555
Severe Corrosion of Carbon Steel in Oil Field Produced Water Can Be Linked to Methanogenic Archaea Containing a Special Type of [NiFe] Hydrogenase. PMID:33257309
Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens. PMID:33251208
Feces Metagenomes and Metagenome-Assembled Genome Sequences from Two Separate Dogs (Canis lupus familiaris) with Multiple Diarrheal Episodes. PMID:33239463
Whole-Genome Sequence of Brevibacillus borstelensis SDM, Isolated from a Sorghum-Adapted Microbial Community. PMID:33239462
Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. PMID:33193240
Organohalide-Respiring Bacteria at the Heart of Anaerobic Metabolism in Arctic Wet Tundra Soils. PMID:33187999
Modified SHI medium supports growth of a disease-state subgingival polymicrobial community in vitro. PMID:33174294
A genomic catalog of Earth's microbiomes. PMID:33169036
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. PMID:33137183
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment. PMID:33122416
Genome Sequences of Four Strains of Acinetobacter bereziniae Isolated from Human Milk Pumped with a Personal Breast Pump and Hand-Washed Milk Collection Supplies. PMID:33122407
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. PMID:33119741
PhycoCosm, a comparative algal genomics resource. PMID:33104790
Systems biology approaches integrated with artificial intelligence for optimized metabolic engineering. PMID:33072513
High-throughput mapping of the phage resistance landscape in E. coli. PMID:33048924
Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia. PMID:33013780
Ecophysiological Study of Paraburkholderia sp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency. PMID:33008817
Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri. PMID:33004914
Genome Sequence of Campylobacter fetus subsp. venerealis NW_ED23, Isolated from Bovine Sheath Wash. PMID:33004452
Whole-Genome Sequencing of Multidrug-Resistant Campylobacter fetus subsp. fetus NWU_ED24, Isolated from a Bovine Sheath Wash Sample. PMID:33004450
Genomics-enabled analysis of specialized metabolism in bioenergy crops: current progress and challenges. PMID:32995549
Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models. PMID:32994290
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
A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity. PMID:32977700
Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design. PMID:32974289
Reconstructing organisms in silico: genome-scale models and their emerging applications. PMID:32958892
Genome Sequences of Frankineae sp. Strain MT45 and Jatrophihabitans sp. Strain GAS493, Two Actinobacteria Isolated from Forest Soil. PMID:32943557
Draft Genome Sequence of Pseudarthrobacter sp. Strain ATCC 49442 (Formerly Micrococcus luteus), a Pyridine-Degrading Bacterium. PMID:32943555
Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis. PMID:32935086
A carotenoid-deficient mutant of the plant-associated microbe Pantoea sp. YR343 displays an altered membrane proteome. PMID:32917935
Metabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicron. PMID:32873608
Genome Sequence of a Blattabacterium Strain Isolated from the Viviparous Cockroach, Diploptera punctata. PMID:32855240
Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PMID:32853201
Draft Genome Sequence of 2-Methylpyridine-, 2-Ethylpyridine-, and 2-Hydroxypyridine-Degrading Arthrobacter sp. Strain ATCC 49987. PMID:32816982
Draft Genome Sequences of Six Strains Isolated from the Rhizosphere of Wheat Grown in Cadmium-Contaminated Soil. PMID:32816975
Defining the nutritional input for genome-scale metabolic models: A roadmap. PMID:32797084
Publishing reproducible dynamic kinetic models. PMID:32793969
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
Bacterial chemolithoautotrophy via manganese oxidation. PMID:32669693
A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus. PMID:32635563
Complete Genome Sequence of Starkeya sp. Strain ORNL1, a Soil Alphaproteobacterium Isolated from the Rhizosphere of Populus deltoides. PMID:32616649
Complete Genome Sequence of the Novel Roseimicrobium sp. Strain ORNL1, a Verrucomicrobium Isolated from the Populus deltoides Rhizosphere. PMID:32616646
Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species. PMID:32589566
Bacterial symbionts support larval sap feeding and adult folivory in (semi-)aquatic reed beetles. PMID:32528063
MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions. PMID:32455748
Out From the Shadows - Resolution of the Taxonomy of the Family Cryomorphaceae. PMID:32431677
Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site. PMID:32423375
Nitrogen Substrate Utilization in Three Rhizosphere Bacterial Strains Investigated Using Proteomics. PMID:32411116
Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture. PMID:32331293
Extensive transcriptome changes during seasonal leaf senescence in field-grown black cottonwood (Populus trichocarpa Nisqually-1). PMID:32313054
Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost. PMID:32301987
Comparative Metagenome-Assembled Genome Analysis of "Candidatus Lachnocurva vaginae", Formerly Known as Bacterial Vaginosis-Associated Bacterium-1 (BVAB1). PMID:32296647
Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots. PMID:32193238
Metagenome-Assembled Genome Sequences of Three Uncultured Planktomarina sp. Strains from the Northeast Atlantic Ocean. PMID:32193237
Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer. PMID:32156795
MEMOTE for standardized genome-scale metabolic model testing. PMID:32123384
Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes. PMID:32123275
Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery. PMID:32095820
Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling. PMID:32071157
An integrated computational and experimental study to investigate Staphylococcus aureus metabolism. PMID:32001720
Mobilizable antibiotic resistance genes are present in dust microbial communities. PMID:31971995
OptFill: A Tool for Infeasible Cycle-Free Gapfilling of Stoichiometric Metabolic Models. PMID:31954977
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. PMID:31937763
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens). PMID:31888476
Genomic resources for energy cane breeding in the post genomics era. PMID:31871586
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology. PMID:31813964
Antimicrobial Activity of, and Cellular Pathways Targeted by, p-Anisaldehyde and Epigallocatechin Gallate in the Opportunistic Human Pathogen Pseudomonas aeruginosa. PMID:31811038
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. PMID:31730192
Complete Genome Sequence of Terriglobus albidus Strain ORNL, an Acidobacterium Isolated from the Populus deltoides Rhizosphere. PMID:31727704
Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16. PMID:31727695
A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. PMID:31720216
Improved Draft Genome Sequence of Microbacterium sp. Strain LKL04, a Bacterial Endophyte Associated with Switchgrass Plants. PMID:31699756
Modelling microbial communities using biochemical resource allocation analysis. PMID:31690234
Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen. PMID:31662430
Genomic Characterization of a Coxsackievirus A20 Strain Recovered from a Child with Acute Flaccid Paralysis in Nigeria. PMID:31624161
ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models. PMID:31598631
Common principles and best practices for engineering microbiomes. PMID:31548653
Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica. PMID:31543895
Complete Genome Sequence of a Shiga Toxin-Converting Bacteriophage, Escherichia Phage Lys12581Vzw, Induced from an Outbreak Shiga Toxin-Producing Escherichia coli Strain. PMID:31488531
Challenges in the construction of knowledge bases for human microbiome-disease associations. PMID:31488215
Modeling the Interplay between Photosynthesis, CO2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium. PMID:31477760
Microbial carbon use efficiency predicted from genome-scale metabolic models. PMID:31395870
A systematic assessment of current genome-scale metabolic reconstruction tools. PMID:31391098
Genome Sequence of Lipopeptide- and Antioxidant-Producing Strain Bacillus velezensis NWUMFkBS10.5. PMID:31296686
iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences. PMID:31289831
Draft Genome Sequences of Three Rhizospheric Plant Growth-Promoting Bacteria. PMID:31248993
Comparative Genomics of Wild Bee and Flower Isolated Lactobacillus Reveals Potential Adaptation to the Bee Host. PMID:31243442
Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium. PMID:31221646
Whole-Genome Sequence of Lactobacillus acidophilus PNW3, Isolated from Weaned Piglets of the Indigenous South African Windsnyer Pig Breed. PMID:31221645
Current status and applications of genome-scale metabolic models. PMID:31196170
Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome. PMID:31194675
Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. PMID:31092280
Draft Genome Sequence of Enterobacter sp. Strain A8, a Carbazole-Degrading Bacterium. PMID:31048380
Comparative Genomics Analysis Provides New Insight Into Molecular Basis of Stomatal Movement in Kalanchoë fedtschenkoi. PMID:30930922
Saccharibacteria (TM7) in the Human Oral Microbiome. PMID:30894042
Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome. PMID:30866812
A Comparison of Microbial Genome Web Portals. PMID:30853946
Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. PMID:30808697
Draft Genome Sequence of Heavy Metal-Resistant Bacillus cereus NWUAB01. PMID:30801070
Machine learning framework for assessment of microbial factory performance. PMID:30645629
Draft Genome Sequences of Seven Chryseobacterium Type Strains. PMID:30637405
Draft Genome Sequence of Acidobacteria Group 1 Acidipila sp. Strain EB88, Isolated from Forest Soil. PMID:30637399
Genomic and in-situ Transcriptomic Characterization of the Candidate Phylum NPL-UPL2 From Highly Alkaline Highly Reducing Serpentinized Groundwater. PMID:30619209
Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics. PMID:30515147
Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities. PMID:30457843
Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. PMID:30060533
Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction. PMID:29976645
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota. PMID:29600286
Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. PMID:28861526
Draft Genome Sequences of Three β-Lactam-Catabolizing Soil Proteobacteria. PMID:28798166
Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center. PMID:28663297
From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data. PMID:25902288
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metasource: Fairsharing.org
version: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
fair
metasource: re3data.org
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sequence reads and assemblies
metasource: re3data.org
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biochemistry
metasource: re3data.org
version: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
metabolic modeling
metasource: re3data.org
version: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
metabolic pathways
metasource: re3data.org
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metabolite
metasource: re3data.org
version: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
metabolomes
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pangenomes
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plant
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predictive biology
metasource: re3data.org
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prokaryotic genomes
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species trees
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taxonomic profiles
metasource: re3data.org
version: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
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workflow
metasource: Fairsharing.orgversion: FAIRsharing.org: KBase; US Department of Energy Systems Biology Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.jsxqrk; Last edited: Oct. 12, 2020, 11:28 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
fair
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
sequence reads and assemblies
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
biochemistry
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
metabolic modeling
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
metabolic pathways
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
metabolite
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
metabolomes
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
pangenomes
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
plant
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
predictive biology
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
prokaryotic genomes
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
species trees
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
taxonomic profiles
metasource: re3data.orgversion: re3data.org: KBase; editing status 2021-09-10; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MB8V last accessed: 2022-11-04
workflow sequence reads and assemblies biochemistry metabolic modeling metabolic and signaling pathways metabolite metabolomes pangenomes plant predictive biology prokaryotic genomes species trees taxonomic profiles
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