Literature DB >> 23175606

WholeCellKB: model organism databases for comprehensive whole-cell models.

Jonathan R Karr1, Jayodita C Sanghvi, Derek N Macklin, Abhishek Arora, Markus W Covert.   

Abstract

Whole-cell models promise to greatly facilitate the analysis of complex biological behaviors. Whole-cell model development requires comprehensive model organism databases. WholeCellKB (http://wholecellkb.stanford.edu) is an open-source web-based software program for constructing model organism databases. WholeCellKB provides an extensive and fully customizable data model that fully describes individual species including the structure and function of each gene, protein, reaction and pathway. We used WholeCellKB to create WholeCellKB-MG, a comprehensive database of the Gram-positive bacterium Mycoplasma genitalium using over 900 sources. WholeCellKB-MG is extensively cross-referenced to existing resources including BioCyc, KEGG and UniProt. WholeCellKB-MG is freely accessible through a web-based user interface as well as through a RESTful web service.

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Year:  2012        PMID： 23175606      PMCID： PMC3531061          DOI： 10.1093/nar/gks1108

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  22 in total

1.  The chemical composition and submicroscopic morphology of Mycoplasma gallisepticum, avian PPLO 5969.

Authors:  H J MOROWITZ; M E TOURTELLOTTE; W R GUILD; E CASTRO; C WOESE
Journal:  J Mol Biol       Date:  1962-02       Impact factor: 5.469

2.  Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.

Authors:  Peter D Karp; Suzanne M Paley; Markus Krummenacker; Mario Latendresse; Joseph M Dale; Thomas J Lee; Pallavi Kaipa; Fred Gilham; Aaron Spaulding; Liviu Popescu; Tomer Altman; Ian Paulsen; Ingrid M Keseler; Ron Caspi
Journal:  Brief Bioinform       Date:  2009-12-02       Impact factor: 11.622

3.  Transcriptome complexity in a genome-reduced bacterium.

Authors:  Marc Güell; Vera van Noort; Eva Yus; Wei-Hua Chen; Justine Leigh-Bell; Konstantinos Michalodimitrakis; Takuji Yamada; Manimozhiyan Arumugam; Tobias Doerks; Sebastian Kühner; Michaela Rode; Mikita Suyama; Sabine Schmidt; Anne-Claude Gavin; Peer Bork; Luis Serrano
Journal:  Science       Date:  2009-11-27       Impact factor: 47.728

4.  Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.

Authors:  Bryson D Bennett; Elizabeth H Kimball; Melissa Gao; Robin Osterhout; Stephen J Van Dien; Joshua D Rabinowitz
Journal:  Nat Chem Biol       Date:  2009-06-28       Impact factor: 15.040

5.  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.

Authors:  Jan Schellenberger; Junyoung O Park; Tom M Conrad; Bernhard Ø Palsson
Journal:  BMC Bioinformatics       Date:  2010-04-29       Impact factor: 3.169

6.  DrugBank 3.0: a comprehensive resource for 'omics' research on drugs.

Authors:  Craig Knox; Vivian Law; Timothy Jewison; Philip Liu; Son Ly; Alex Frolkis; Allison Pon; Kelly Banco; Christine Mak; Vanessa Neveu; Yannick Djoumbou; Roman Eisner; An Chi Guo; David S Wishart
Journal:  Nucleic Acids Res       Date:  2010-11-08       Impact factor: 16.971

7.  A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189.

Authors:  Patrick F Suthers; Madhukar S Dasika; Vinay Satish Kumar; Gennady Denisov; John I Glass; Costas D Maranas
Journal:  PLoS Comput Biol       Date:  2009-02-13       Impact factor: 4.475

8.  Database resources of the National Center for Biotechnology Information.

Authors:  Eric W Sayers; Tanya Barrett; Dennis A Benson; Evan Bolton; Stephen H Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M Church; Michael Dicuccio; Scott Federhen; Michael Feolo; Lewis Y Geer; Wolfgang Helmberg; Yuri Kapustin; David Landsman; David J Lipman; Zhiyong Lu; Thomas L Madden; Tom Madej; Donna R Maglott; Aron Marchler-Bauer; Vadim Miller; Ilene Mizrachi; James Ostell; Anna Panchenko; Kim D Pruitt; Gregory D Schuler; Edwin Sequeira; Stephen T Sherry; Martin Shumway; Karl Sirotkin; Douglas Slotta; Alexandre Souvorov; Grigory Starchenko; Tatiana A Tatusova; Lukas Wagner; Yanli Wang; W John Wilbur; Eugene Yaschenko; Jian Ye
Journal:  Nucleic Acids Res       Date:  2009-11-12       Impact factor: 16.971

9.  The comprehensive microbial resource.

Authors:  Tanja Davidsen; Erin Beck; Anuradha Ganapathy; Robert Montgomery; Nikhat Zafar; Qi Yang; Ramana Madupu; Phil Goetz; Kevin Galinsky; Owen White; Granger Sutton
Journal:  Nucleic Acids Res       Date:  2009-11-05       Impact factor: 16.971

10.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.

Authors:  Adam M Feist; Christopher S Henry; Jennifer L Reed; Markus Krummenacker; Andrew R Joyce; Peter D Karp; Linda J Broadbelt; Vassily Hatzimanikatis; Bernhard Ø Palsson
Journal:  Mol Syst Biol       Date:  2007-06-26       Impact factor: 11.429
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  19 in total

1.  Building Structural Models of a Whole Mycoplasma Cell.

Authors:  Martina Maritan; Ludovic Autin; Jonathan Karr; Markus W Covert; Arthur J Olson; David S Goodsell
Journal:  J Mol Biol       Date:  2021-11-10       Impact factor: 5.469

2.  Bayesian metamodeling of complex biological systems across varying representations.

Authors:  Barak Raveh; Liping Sun; Kate L White; Tanmoy Sanyal; Jeremy Tempkin; Dongqing Zheng; Kala Bharath; Jitin Singla; Chenxi Wang; Jihui Zhao; Angdi Li; Nicholas A Graham; Carl Kesselman; Raymond C Stevens; Andrej Sali
Journal:  Proc Natl Acad Sci U S A       Date:  2021-08-31       Impact factor: 11.205

3.  Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.

Authors:  Michael Feig; Ryuhei Harada; Takaharu Mori; Isseki Yu; Koichi Takahashi; Yuji Sugita
Journal:  J Mol Graph Model       Date:  2015-02-28       Impact factor: 2.518

Review 4.  The future of whole-cell modeling.

Authors:  Derek N Macklin; Nicholas A Ruggero; Markus W Covert
Journal:  Curr Opin Biotechnol       Date:  2014-02-17       Impact factor: 9.740

Review 5.  Computational approaches for understanding energy metabolism.

Authors:  Alexander A Shestov; Brandon Barker; Zhenglong Gu; Jason W Locasale
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2013-07-29

6.  Guidelines for Reproducibly Building and Simulating Systems Biology Models.

Authors:  J Kyle Medley; Arthur P Goldberg; Jonathan R Karr
Journal:  IEEE Trans Biomed Eng       Date:  2016-07-18       Impact factor: 4.538

Review 7.  Reaching new levels of realism in modeling biological macromolecules in cellular environments.

Authors:  Michael Feig; Yuji Sugita
Journal:  J Mol Graph Model       Date:  2013-08-28       Impact factor: 2.518

Review 8.  Databases for Microbiologists.

Authors:  Igor B Zhulin
Journal:  J Bacteriol       Date:  2015-05-26       Impact factor: 3.490

9.  WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.

Authors:  Jonathan R Karr; Nolan C Phillips; Markus W Covert
Journal:  Database (Oxford)       Date:  2014-09-16       Impact factor: 3.451

10.  WholeCellViz: data visualization for whole-cell models.

Authors:  Ruby Lee; Jonathan R Karr; Markus W Covert
Journal:  BMC Bioinformatics       Date:  2013-08-21       Impact factor: 3.169
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