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Journal Article · · Nature Biotechnology
DOI:https://doi.org/10.1038/nbt.4163· OSTI ID:1471834
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  1. Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  3. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  5. Univ. of Chicago, IL (United States). Computer Science Dept. and Computation Inst.; Argonne National Lab. (ANL), Argonne, IL (United States). Computing, Environment, and Life Sciences Directorate
  6. Brookhaven National Lab. (BNL), Upton, NY (United States). Biology Dept.; Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Bioengineering and Carl R. Woese Inst. for Genomic Biology
  7. Cold Spring Harbor Lab. (CSHL), Cold Spring Harbor, NY (United States)
  8. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division; Univ. of California, Berkeley, CA (United States). Berkeley Inst. for Data Science and Dept. of Statistics
  9. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
  10. Argonne National Lab. (ANL), Argonne, IL (United States). Computing, Environment, and Life Sciences Directorate
  11. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division
  12. Hope College, Holland, MI (United States). Dept. of Biology
  13. Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  14. Hope College, Holland, MI (United States). Dept. of Computer Science
  15. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division; Univ. of Chicago, IL (United States). Computation Inst.
  16. Yale Univ., New Haven, CT (United States). Program in Computational Biology and Bioinformatics; New York Univ. (NYU) Shanghai Campus, Shanghai (China)
  17. Yale Univ., New Haven, CT (United States). Program in Computational Biology and Bioinformatics
  18. Brookhaven National Lab. (BNL), Upton, NY (United States). Biology Dept.; Kansas State Univ., Manhattan, KS (United States). Dept. of Plant Pathology
  19. Univ. of California, Davis, CA (United States). Dept. of Plant Pathology and Genome Center; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst. (JBEI)
  20. Univ. of California, Davis, CA (United States). Dept. of Plant Pathology and Genome Center; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst. (JBEI); Insilicogen. Inc., Yongin (Korea, Republic of)
  21. Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Microbiology
  22. Cold Spring Harbor Lab. (CSHL), Cold Spring Harbor, NY (United States); Johns Hopkins Univ., Baltimore, MD (United States). Dept. of Computer Science
  23. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Plant Sciences
  24. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Memorial Sloan Kettering Cancer Center (MSKCC), New York City, NY (United States)
  25. Hope College, Holland, MI (United States). Dept. of Mathematics; Dordt College, Sioux Center, IA (United States)
  26. Yale Univ., New Haven, CT (United States). Program in Computational Biology and Bioinformatics; Stony Brook Univ., NY (United States). Dept. of Biomedical Informatics
  27. Brookhaven National Lab. (BNL), Upton, NY (United States). Computer Science and Mathematics and Computational Science Initiative (CSI)
  28. Brookhaven National Lab. (BNL), Upton, NY (United States). Computer Science and Mathematics and Computational Science Initiative (CSI); New Jersey Inst. of Technology, Newark, NJ (United States). Martin Tuchman School of Management
+ Show Author Affiliations

The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) is an open-source software and data platform designed to tackle the grand challenge of systems biology—predicting and designing biological function at scales ranging from the biomolecular to the ecological. KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large analyses on scalable computing infrastructure; and combine experimental evidence and conclusions to model plant and microbial physiology and community dynamics. The KBase platform has extensible analytical capabilities that currently include (meta)genome assembly, annotation, comparative genomics, transcriptomics, and metabolic modeling; a web-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; and a software development kit that enables the community to add functionality to the system.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231; AC02-06CH11357; AC02-98CH10886
OSTI ID:
1471834
Alternate ID(s):
OSTI ID: 1526533
OSTI ID: 1474150
Journal Information:
Nature Biotechnology, Journal Name: Nature Biotechnology Journal Issue: 7 Vol. 36; ISSN 1087-0156
Publisher:
Springer NatureCopyright Statement
Country of Publication:
United States
Language:
English

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Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota journal November 2016
Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes journal February 2020
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MetaCyc: a multiorganism database of metabolic pathways and enzymes journal January 2006
Phytozome: a comparative platform for green plant genomics journal November 2011
Global phenotypic characterization of bacteria journal January 2009
Enhancing reproducibility for computational methods journal December 2016
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions journal January 2010
Modeling central metabolism and energy biosynthesis across microbial life journal August 2016
Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions
  • St. James, Andrew; Crockett, Zachary
  • Cornell Univ., Ithaca, NY (United States);Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States) https://doi.org/10.25982/51077.6/1637903
dataset January 2020
Viral Annotation Pipeline in KBase
  • Bolduc, Benjamin; Wood-Charlson, Elisha; Dehal, Paramvir
  • Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); The Ohio State University; U.S. Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States) https://doi.org/10.25982/59912.37/1635154
dataset January 2020
Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation journal November 2016
Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction: COMMUNITY DATA-DRIVEN METABOLIC NETWORK MODELING journal June 2016
KEGG: Kyoto Encyclopedia of Genes and Genomes journal January 2000
MetaCyc: a multiorganism database of metabolic pathways and enzymes journal January 2004
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins journal January 2007
IPython: A System for Interactive Scientific Computing journal January 2007
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Comparative Genomics of Wild Bee and Flower Isolated Lactobacillus Reveals Potential Adaptation to the Bee Host journal July 2019
iMicrobe: Tools and data-driven discovery platform for the microbiome sciences journal July 2019
Modelling microbial communities using biochemical resource allocation analysis journal November 2019
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Metagenome-Assembled Genome Sequences of Three Uncultured Planktomarina sp. Strains from the Northeast Atlantic Ocean journal March 2020
Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16 journal November 2019
Draft Genome Sequence of Enterobacter sp. Strain A8, a Carbazole-Degrading Bacterium journal May 2019
Genomic Characterization of a Coxsackievirus A20 Strain Recovered from a Child with Acute Flaccid Paralysis in Nigeria journal October 2019
Draft Genome Sequence of Heavy Metal-Resistant Bacillus cereus NWUAB01 journal February 2019
Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling journal February 2020
Current status and applications of genome-scale metabolic models journal June 2019
Machine learning framework for assessment of microbial factory performance journal January 2019
MEMOTE for standardized genome-scale metabolic model testing text January 2020
A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum dataset January 2021
KBase Narrative - natrialba dataset January 2023
Metagenomes from Eastern Brazilian Amazonian floodplains in the wet and dry seasons
  • Gontijo, Júlia; Venturini, Andressa; Da França, Aline
  • Center for Nuclear Energy in Agriculture, University of São Paulo, Brazil; Princeton Institute for International and Regional Studies, USA. https://doi.org/10.25982/113717.182/1864845
dataset January 2022
KBase Narrative - Mse_Genome_Assembly dataset January 2022
KBase Narrative - Metagenome-assembled genomes from Amazonian soil microbial consortia dataset January 2022
KBase Narrative - O'Toole et al Citricoccus MRA Genome Announcement Analysis Narrative dataset January 2022
KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Decontamination through Metagenomic Fractionation and analysis of Metabolic Potential- dataset January 2024
KBase Narrative - Timberlake Metagenomes dataset January 2024
KBase Narrative - 13 draft genomes of Bacillus from HLB-impacted citrus trees dataset January 2024
Metabacillus indicus EGFCL74 dataset January 2023
KBase Narrative - Metabolically diverse Miscanthus x giganteus microbiome isolates with tremendous growth-promoting potential - Copy dataset January 2024
KBase Narrative - Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures dataset January 2024
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KBase Narrative - Genomes of nine cultured microbes from two hydrologically connected freshwater sites in Wellesley MA dataset January 2024
Conditional Filamentation of Paraburkholderia elongata 5N - Data Container dataset January 2021
Genome Extraction from Shotgun Metagenome Sequence Data dataset January 2021
Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions
  • St. James, Andrew; Crockett, Zachary
  • Cornell Univ., Ithaca, NY (United States);Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States) https://doi.org/10.25982/51077.6/1637903
dataset January 2020
Análisis de la secuencia de un aislamiento de coronavirus Covid-19 dataset January 2020
Osur_paper dataset January 2021
Viral Annotation Pipeline in KBase
  • Bolduc, Benjamin; Wood-Charlson, Elisha; Dehal, Paramvir
  • Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); The Ohio State University; U.S. Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States) https://doi.org/10.25982/59912.37/1635154
dataset January 2020
Moab Desert Crust - Sample 4E dataset January 2021
JGI QC impact on assembly, binning, phylogenomics, and functional analysis dataset January 2021
Substrate-explicit Modeling Tutorial
  • Song, Hyun-Seob; Lee, Joon-Yong
  • Pacific Northwest National Laboratory (PNNL), Richland, WA (United States) University of Nebraska-Lincoln, Lincoln, NE (United States) https://doi.org/10.25982/65526.69/1755438
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KBase Silver Case Study: Determining Media Formulation Requirements for Isolation of Microbiome Constituents dataset January 2021
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  • Aguirre Von Wobeser, Eneas; Alfonso-Sánchez, Alexandro; Méndez-Bravo, Alfonso
  • CONACYT – Centro de Investigación y Desarrollo en Agrobiotecnología Alimentaria, Centro de Investigación y Desarrollo, A.C., Blvd. Sta. Catarina s/n, Col. Santiago Tlapacoya, 42110, San Agustín Tlaxiaca, Hidalgo, Mexico https://doi.org/10.25982/69195.32/1647032
dataset January 2020
Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in MOPS Medium dataset January 2021
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KBase Narrative - Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils dataset January 2022
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The moderately defficient enzyme: Catalysis-related damage in vivo and its repair
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  • U.S. Department of Energy Systems Biology Knowledgebase; Argonne National Laboratory (ANL), Argonne, IL (United States); US Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/95771.20/1828591
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A Comparison of Microbial Genome Web Portals journal February 2019
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation journal December 2019
Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14 journal July 2018
Additional file 1 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila dataset January 2021
Additional file 3 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila dataset January 2021
Additional file 4 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila dataset January 2021
Additional file 5 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila dataset January 2021
Additional file 6 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila dataset January 2021
Additional file 7 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila dataset January 2021
Additional file 8 of Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila dataset January 2021
Additional file 1 of Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics dataset January 2024
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59 BASIC BIOLOGICAL SCIENCES
96 KNOWLEDGE MANAGEMENT AND PRESERVATION
97 MATHEMATICS AND COMPUTING