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Title: KBase: The United States Department of Energy Systems Biology Knowledgebase

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3]; ORCiD logo [4];  [5];  [6];  [4]; ORCiD logo [7]; ORCiD logo [8];  [9];  [4];  [4];  [4];  [3];  [4];  [4];  [7]; ORCiD logo [2];  [10];  [3] more »;  [4];  [11]; ORCiD logo [2];  [2];  [4];  [12];  [4];  [13];  [3];  [4];  [7];  [3];  [10];  [10]; ORCiD logo [2];  [14];  [3];  [10];  [4];  [15];  [16]; ORCiD logo [3];  [3];  [3]; ORCiD logo [17];  [9];  [7];  [2]; ORCiD logo [18];  [19];  [4];  [3];  [14];  [7]; ORCiD logo [2]; ORCiD logo [3];  [2];  [4]; ORCiD logo [20];  [21];  [3];  [3];  [7];  [4];  [11];  [4];  [22];  [23];  [19]; ORCiD logo [22];  [3];  [10];  [4];  [24];  [7];  [25]; ORCiD logo [26];  [10];  [10];  [27];  [28] « less
+ Show Author Affiliations
  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
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1471834
Alternate Identifier(s):
OSTI ID: 1526533
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231; AC02-06CH11357; AC02-98CH10886
Resource Type:
Accepted Manuscript
Journal Name:
Nature Biotechnology
Additional Journal Information:
Journal Volume: 36; Journal Issue: 7; Journal ID: ISSN 1087-0156
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Arkin, Adam P., Cottingham, Robert W., Henry, Christopher S., Harris, Nomi L., Stevens, Rick L., Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W., Henderson, Matthew L., Riehl, William J., Murphy-Olson, Dan, Chan, Stephen Y., Kamimura, Roy T., Kumari, Sunita, Drake, Meghan M., Brettin, Thomas S., Glass, Elizabeth M., Chivian, Dylan, Gunter, Dan, Weston, David J., Allen, Benjamin H., Baumohl, Jason, Best, Aaron A., Bowen, Ben, Brenner, Steven E., Bun, Christopher C., Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J., Davison, Brian H., DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N., Fang, Gang, Faria, José P., Frybarger, Paul M., Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L., He, Fei, Jain, Rashmi, Joachimiak, Marcin P., Keegan, Kevin P., Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L., Meyer, Folker, Mills, Marissa, Novichkov, Pavel S., Oh, Taeyun, Olsen, Gary J., Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S., Price, Gavin A., Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C., Schatz, Michael C., Seaver, Samuel M. D., Shukla, Maulik, Sutormin, Roman A., Syed, Mustafa H., Thomason, James, Tintle, Nathan L., Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, and Yu, Dantong. KBase: The United States Department of Energy Systems Biology Knowledgebase. United States: N. p., 2018. Web. doi:10.1038/nbt.4163.
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Arkin, Adam P., Cottingham, Robert W., Henry, Christopher S., Harris, Nomi L., Stevens, Rick L., Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W., Henderson, Matthew L., Riehl, William J., Murphy-Olson, Dan, Chan, Stephen Y., Kamimura, Roy T., Kumari, Sunita, Drake, Meghan M., Brettin, Thomas S., Glass, Elizabeth M., Chivian, Dylan, Gunter, Dan, Weston, David J., Allen, Benjamin H., Baumohl, Jason, Best, Aaron A., Bowen, Ben, Brenner, Steven E., Bun, Christopher C., Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J., Davison, Brian H., DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N., Fang, Gang, Faria, José P., Frybarger, Paul M., Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L., He, Fei, Jain, Rashmi, Joachimiak, Marcin P., Keegan, Kevin P., Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L., Meyer, Folker, Mills, Marissa, Novichkov, Pavel S., Oh, Taeyun, Olsen, Gary J., Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S., Price, Gavin A., Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C., Schatz, Michael C., Seaver, Samuel M. D., Shukla, Maulik, Sutormin, Roman A., Syed, Mustafa H., Thomason, James, Tintle, Nathan L., Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, & Yu, Dantong. KBase: The United States Department of Energy Systems Biology Knowledgebase. United States. https://doi.org/10.1038/nbt.4163
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Arkin, Adam P., Cottingham, Robert W., Henry, Christopher S., Harris, Nomi L., Stevens, Rick L., Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W., Henderson, Matthew L., Riehl, William J., Murphy-Olson, Dan, Chan, Stephen Y., Kamimura, Roy T., Kumari, Sunita, Drake, Meghan M., Brettin, Thomas S., Glass, Elizabeth M., Chivian, Dylan, Gunter, Dan, Weston, David J., Allen, Benjamin H., Baumohl, Jason, Best, Aaron A., Bowen, Ben, Brenner, Steven E., Bun, Christopher C., Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J., Davison, Brian H., DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N., Fang, Gang, Faria, José P., Frybarger, Paul M., Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L., He, Fei, Jain, Rashmi, Joachimiak, Marcin P., Keegan, Kevin P., Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L., Meyer, Folker, Mills, Marissa, Novichkov, Pavel S., Oh, Taeyun, Olsen, Gary J., Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S., Price, Gavin A., Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C., Schatz, Michael C., Seaver, Samuel M. D., Shukla, Maulik, Sutormin, Roman A., Syed, Mustafa H., Thomason, James, Tintle, Nathan L., Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, and Yu, Dantong. Fri . "KBase: The United States Department of Energy Systems Biology Knowledgebase". United States. https://doi.org/10.1038/nbt.4163. https://www.osti.gov/servlets/purl/1471834.
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@article{osti_1471834,
title = {KBase: The United States Department of Energy Systems Biology Knowledgebase},
author = {Arkin, Adam P. and Cottingham, Robert W. and Henry, Christopher S. and Harris, Nomi L. and Stevens, Rick L. and Maslov, Sergei and Dehal, Paramvir and Ware, Doreen and Perez, Fernando and Canon, Shane and Sneddon, Michael W. and Henderson, Matthew L. and Riehl, William J. and Murphy-Olson, Dan and Chan, Stephen Y. and Kamimura, Roy T. and Kumari, Sunita and Drake, Meghan M. and Brettin, Thomas S. and Glass, Elizabeth M. and Chivian, Dylan and Gunter, Dan and Weston, David J. and Allen, Benjamin H. and Baumohl, Jason and Best, Aaron A. and Bowen, Ben and Brenner, Steven E. and Bun, Christopher C. and Chandonia, John-Marc and Chia, Jer-Ming and Colasanti, Ric and Conrad, Neal and Davis, James J. and Davison, Brian H. and DeJongh, Matthew and Devoid, Scott and Dietrich, Emily and Dubchak, Inna and Edirisinghe, Janaka N. and Fang, Gang and Faria, José P. and Frybarger, Paul M. and Gerlach, Wolfgang and Gerstein, Mark and Greiner, Annette and Gurtowski, James and Haun, Holly L. and He, Fei and Jain, Rashmi and Joachimiak, Marcin P. and Keegan, Kevin P. and Kondo, Shinnosuke and Kumar, Vivek and Land, Miriam L. and Meyer, Folker and Mills, Marissa and Novichkov, Pavel S. and Oh, Taeyun and Olsen, Gary J. and Olson, Robert and Parrello, Bruce and Pasternak, Shiran and Pearson, Erik and Poon, Sarah S. and Price, Gavin A. and Ramakrishnan, Srividya and Ranjan, Priya and Ronald, Pamela C. and Schatz, Michael C. and Seaver, Samuel M. D. and Shukla, Maulik and Sutormin, Roman A. and Syed, Mustafa H. and Thomason, James and Tintle, Nathan L. and Wang, Daifeng and Xia, Fangfang and Yoo, Hyunseung and Yoo, Shinjae and Yu, Dantong},
abstractNote = {},
doi = {10.1038/nbt.4163},
journal = {Nature Biotechnology},
number = 7,
volume = 36,
place = {United States},
year = {Fri Jul 06 00:00:00 EDT 2018},
month = {Fri Jul 06 00:00:00 EDT 2018}
}
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https://doi.org/10.1038/nbt.4163
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    Genomic Characterization of a Coxsackievirus A20 Strain Recovered from a Child with Acute Flaccid Paralysis in Nigeria
    journal, October 2019

    • Faleye, T. O. C.; Adewumi, O. M.; Olayinka, O. T.
    • Microbiology Resource Announcements, Vol. 8, Issue 42
    • DOI: 10.1128/mra.00849-19

    Complete Genome Sequence of Terriglobus albidus Strain ORNL, an Acidobacterium Isolated from the Populus deltoides Rhizosphere
    journal, November 2019

    • Podar, Mircea; Turner, Joel; Burdick, Leah H.
    • Microbiology Resource Announcements, Vol. 8, Issue 46
    • DOI: 10.1128/mra.01065-19

    Draft Genome Sequence of Acidobacteria Group 1 Acidipila sp. Strain EB88, Isolated from Forest Soil
    journal, January 2019

    • Domeignoz-Horta, Luiz A.; DeAngelis, Kristen M.; Pold, Grace
    • Microbiology Resource Announcements, Vol. 8, Issue 1
    • DOI: 10.1128/mra.01464-18

    Draft Genome Sequences of Seven Chryseobacterium Type Strains
    journal, January 2019

    • Matu, Andisiwe; Lum Nde, Adeline; Oosthuizen, Lize
    • Microbiology Resource Announcements, Vol. 8, Issue 1
    • DOI: 10.1128/mra.01518-18

    Draft Genome Sequence of Heavy Metal-Resistant Bacillus cereus NWUAB01
    journal, February 2019

    • Babalola, Olubukola Oluranti; Aremu, Bukola Rhoda; Ayangbenro, Ayansina Segun
    • Microbiology Resource Announcements, Vol. 8, Issue 7
    • DOI: 10.1128/mra.01706-18

    Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen
    journal, October 2019

    Saccharibacteria (TM7) in the Human Oral Microbiome
    journal, February 2019

    Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens)
    journal, December 2019

    • Silva-Pereira, Taiana T.; Ikuta, Cássia Y.; Zimpel, Cristina K.
    • BMC Genomics, Vol. 20, Issue 1
    • DOI: 10.1186/s12864-019-6407-5

    Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site
    journal, May 2020

    • Grettenberger, Christen L.; Havig, Jeff R.; Hamilton, Trinity L.
    • BMC Microbiology, Vol. 20, Issue 1
    • DOI: 10.1186/s12866-020-01768-w

    Current status and applications of genome-scale metabolic models
    journal, June 2019

    Machine learning framework for assessment of microbial factory performance
    journal, January 2019

    Mobilizable antibiotic resistance genes are present in dust microbial communities
    journal, January 2020

    Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica
    journal, August 2019

    Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14
    journal, July 2018

    • diCenzo, George C.; Debiec, Klaudia; Krzysztoforski, Jan
    • Genes, Vol. 9, Issue 8
    • DOI: 10.3390/genes9080379

    Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome
    journal, June 2019

    • Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel
    • eLife, Vol. 8
    • DOI: 10.7554/elife.39733

    Osur_paper
    dataset, January 2021

    JGI QC impact on assembly, binning, phylogenomics, and functional analysis
    dataset, January 2021

    Substrate-explicit Modeling Tutorial
    dataset, January 2020

    • Song, Hyun-Seob; Lee, Joon-Yong
    • Pacific Northwest National Laboratory (PNNL), Richland, WA (United States) University of Nebraska-Lincoln, Lincoln, NE (United States)
    • DOI: 10.25982/65526.69/1755438

    Case Study: Can you find Delftia?
    August 2020

    Avocado_Bark_Diversity
    dataset, January 2020

    • 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
    • DOI: 10.25982/69195.32/1647032

    Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in MOPS Medium
    dataset, January 2021

    Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium
    dataset, January 2021

    Impact of BBDuk metagenomic read trimming and decontamination
    dataset, January 2021

    Biopython: freely available Python tools for computational molecular biology and bioinformatics
    journal, March 2009

    Conditional Filamentation of Paraburkholderia elongata 5N - Data Container
    dataset, January 2021

    Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica
    text, January 2019

    A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum
    dataset, January 2021

    A systematic assessment of current genome-scale metabolic reconstruction tools
    journal, August 2019

    MEMOTE for standardized genome-scale metabolic model testing
    text, January 2020

    Corrigendum: Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica
    journal, January 2021

    Genome Extraction from Shotgun Metagenome Sequence Data
    dataset, January 2021

    • Chivian, Dylan; Jungbluth, Sean; Dehal, Paramvir
    • U.S. Department of Energy Systems Biology Knowledgebase
    • DOI: 10.25982/33233.606/1831502

    Moab Desert Crust - Sample 4E
    dataset, January 2021

    • Chivian, Dylan; Jungbluth, Sean; Dehal, Paramvir
    • U.S. Department of Energy Systems Biology Knowledgebase
    • DOI: 10.25982/62384.253/1831503

    Metagenomes from Eastern Brazilian Amazonian floodplains in the wet and dry seasons
    dataset, January 2022

    • 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.
    • DOI: 10.25982/113717.182/1864845

    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

    • McGivern, Bridget; O'Toole, Paul; Wrighton, Kelly
    • U.S. Department of Energy Systems Biology Knowledgebase
    • DOI: 10.25982/130581.14/1897514

    Análisis de la secuencia de un aislamiento de coronavirus Covid-19
    dataset, January 2020

    KBase Narrative - Viral Analysis End-to-End
    dataset, January 2022

    KBase Narrative - Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils
    dataset, January 2022

    • Venturini, Andressa; Gontijo, Júlia; Mandro, Jéssica
    • U.S. Department of Energy Systems Biology Knowledgebase
    • DOI: 10.25982/91640.61/1870603

    KBase Narrative - Mse_Genome_Assembly
    dataset, January 2022

    Metagenomes from Eastern Brazilian Amazonian floodplains in the wet and dry seasons
    dataset, January 2022

    • 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.
    • DOI: 10.25982/113717.182/1864845

    Conditional Filamentation of Paraburkholderia elongata 5N - Data Container
    dataset, January 2021

    Genome Extraction from Shotgun Metagenome Sequence Data
    dataset, January 2021

    • Chivian, Dylan; Jungbluth, Sean; Dehal, Paramvir
    • U.S. Department of Energy Systems Biology Knowledgebase
    • DOI: 10.25982/33233.606/1831502

    Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions
    dataset, January 2020

    • 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)
    • DOI: 10.25982/51077.6/1637903

    Osur_paper
    dataset, January 2021

    Viral Annotation Pipeline in KBase
    dataset, January 2020

    • 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)
    • DOI: 10.25982/59912.37/1635154

    Moab Desert Crust - Sample 4E
    dataset, January 2021

    • Chivian, Dylan; Jungbluth, Sean; Dehal, Paramvir
    • U.S. Department of Energy Systems Biology Knowledgebase
    • DOI: 10.25982/62384.253/1831503

    JGI QC impact on assembly, binning, phylogenomics, and functional analysis
    dataset, January 2021

    Substrate-explicit Modeling Tutorial
    dataset, January 2020

    • Song, Hyun-Seob; Lee, Joon-Yong
    • Pacific Northwest National Laboratory (PNNL), Richland, WA (United States) University of Nebraska-Lincoln, Lincoln, NE (United States)
    • DOI: 10.25982/65526.69/1755438

    Case Study: Can you find Delftia?
    August 2020

    Avocado_Bark_Diversity
    dataset, January 2020

    • 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
    • DOI: 10.25982/69195.32/1647032

    Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in MOPS Medium
    dataset, January 2021

    Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium
    dataset, January 2021

    Impact of BBDuk metagenomic read trimming and decontamination
    dataset, January 2021

    KBase Narrative - Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils
    dataset, January 2022

    • Venturini, Andressa; Gontijo, Júlia; Mandro, Jéssica
    • U.S. Department of Energy Systems Biology Knowledgebase
    • DOI: 10.25982/91640.61/1870603

    Genomic resources for energy cane breeding in the post genomics era
    journal, January 2019

    • Diniz, Augusto L.; Ferreira, Sávio S.; ten-Caten, Felipe
    • Computational and Structural Biotechnology Journal, Vol. 17
    • DOI: 10.1016/j.csbj.2019.10.006

    OptFill: A Tool for Infeasible Cycle-Free Gapfilling of Stoichiometric Metabolic Models
    journal, January 2020

    A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data
    journal, December 2019

    • Dinh, Hoang V.; Suthers, Patrick F.; Chan, Siu Hung Joshua
    • Metabolic Engineering Communications, Vol. 9
    • DOI: 10.1016/j.mec.2019.e00101

    Microbial carbon use efficiency predicted from genome-scale metabolic models
    journal, August 2019

    • Saifuddin, Mustafa; Bhatnagar, Jennifer M.; Segrè, Daniel
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-019-11488-z

    Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes
    journal, March 2020

    • Romero Victorica, Matias; Soria, Marcelo A.; Batista-García, Ramón Alberto
    • Scientific Reports, Vol. 10, Issue 1
    • DOI: 10.1038/s41598-020-60850-5

    Comparative Genomics of Wild Bee and Flower Isolated Lactobacillus Reveals Potential Adaptation to the Bee Host
    journal, July 2019

    • Vuong, Hoang Q.; McFrederick, Quinn S.
    • Genome Biology and Evolution, Vol. 11, Issue 8
    • DOI: 10.1093/gbe/evz136

    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

    • Sharma, Suraj; Steuer, Ralf
    • Journal of The Royal Society Interface, Vol. 16, Issue 160
    • DOI: 10.1098/rsif.2019.0474

    Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16
    journal, November 2019

    • Aremu, Bukola Rhoda; Prigent-Combaret, Claire; Babalola, Olubukola Oluranti
    • Microbiology Resource Announcements, Vol. 8, Issue 46
    • DOI: 10.1128/mra.00136-19

    Draft Genome Sequence of Enterobacter sp. Strain A8, a Carbazole-Degrading Bacterium
    journal, May 2019

    • Gupta, Nidhi; Skinner, Kelly A.; Khan, Samiya
    • Microbiology Resource Announcements, Vol. 8, Issue 18
    • DOI: 10.1128/mra.00301-19

    Genomic Characterization of a Coxsackievirus A20 Strain Recovered from a Child with Acute Flaccid Paralysis in Nigeria
    journal, October 2019

    • Faleye, T. O. C.; Adewumi, O. M.; Olayinka, O. T.
    • Microbiology Resource Announcements, Vol. 8, Issue 42
    • DOI: 10.1128/mra.00849-19

    Draft Genome Sequence of Heavy Metal-Resistant Bacillus cereus NWUAB01
    journal, February 2019

    • Babalola, Olubukola Oluranti; Aremu, Bukola Rhoda; Ayangbenro, Ayansina Segun
    • Microbiology Resource Announcements, Vol. 8, Issue 7
    • DOI: 10.1128/mra.01706-18

    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

    KBase Narrative - natrialba
    dataset, January 2023

    DRAM example narrative
    dataset, January 2021

    The moderately defficient enzyme: Catalysis-related damage in vivo and its repair
    dataset, January 2021

    • Henry, Christopher; Wilson, Mark; Hanson, Andrew
    • U.S. Department of Energy Systems Biology Knowledgebase; Argonne National Laboratory (ANL), Argonne, IL (United States); US Department of Energy Systems Biology Knowledgebase
    • DOI: 10.25982/95771.20/1828591

    Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens
    journal, November 2020

    Soil Organic Matter, Soil Structure, and Bacterial Community Structure in a Post-Agricultural Landscape
    journal, February 2021

    Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics
    journal, November 2018

    • Lima, Alex Ranieri Jerônimo; Siqueira, Andrei Santos; Vasconcelos, Janaina Mota de
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.02811

    A Comparison of Microbial Genome Web Portals
    journal, February 2019

    • Karp, Peter D.; Ivanova, Natalia; Krummenacker, Markus
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.00208

    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

    • diCenzo, George C.; Debiec, Klaudia; Krzysztoforski, Jan
    • Genes, Vol. 9, Issue 8
    • DOI: 10.3390/genes9080379

    Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome
    journal, June 2019

    • Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel
    • eLife, Vol. 8
    • DOI: 10.7554/elife.39733
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