Literature DB >> 29806041

A blueprint for human whole-cell modeling.

Balázs Szigeti1,2, Yosef D Roth1,2, John A P Sekar1,2, Arthur P Goldberg1,2, Saahith C Pochiraju1,2, Jonathan R Karr1,2.   

Abstract

Whole-cell dynamical models of human cells are a central goal of systems biology. Such models could help researchers understand cell biology and help physicians treat disease. Despite significant challenges, we believe that human whole-cell models are rapidly becoming feasible. To develop a plan for achieving human whole-cell models, we analyzed the existing models of individual cellular pathways, surveyed the biomodeling community, and reflected on our experience developing whole-cell models of bacteria. Based on these analyses, we propose a plan for a project, termed the Human Whole-Cell Modeling Project, to achieve human whole-cell models. The foundations of the plan include technology development, standards development, and interdisciplinary collaboration.

Entities:  

Year:  2017        PMID: 29806041      PMCID: PMC5966287          DOI: 10.1016/j.coisb.2017.10.005

Source DB:  PubMed          Journal:  Curr Opin Syst Biol        ISSN: 2452-3100


  47 in total

1.  Integrating high-throughput and computational data elucidates bacterial networks.

Authors:  Markus W Covert; Eric M Knight; Jennifer L Reed; Markus J Herrgard; Bernhard O Palsson
Journal:  Nature       Date:  2004-05-06       Impact factor: 49.962

2.  Systems biology and new technologies enable predictive and preventative medicine.

Authors:  Leroy Hood; James R Heath; Michael E Phelps; Biaoyang Lin
Journal:  Science       Date:  2004-10-22       Impact factor: 47.728

Review 3.  Modeling single-neuron dynamics and computations: a balance of detail and abstraction.

Authors:  Andreas V M Herz; Tim Gollisch; Christian K Machens; Dieter Jaeger
Journal:  Science       Date:  2006-10-06       Impact factor: 47.728

4.  Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis.

Authors:  Sriram Chandrasekaran; Nathan D Price
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-27       Impact factor: 11.205

Review 5.  The principles of whole-cell modeling.

Authors:  Jonathan R Karr; Koichi Takahashi; Akira Funahashi
Journal:  Curr Opin Microbiol       Date:  2015-06-24       Impact factor: 7.934

6.  A whole-cell computational model predicts phenotype from genotype.

Authors:  Jonathan R Karr; Jayodita C Sanghvi; Derek N Macklin; Miriam V Gutschow; Jared M Jacobs; Benjamin Bolival; Nacyra Assad-Garcia; John I Glass; Markus W Covert
Journal:  Cell       Date:  2012-07-20       Impact factor: 41.582

7.  A pathology atlas of the human cancer transcriptome.

Authors:  Mathias Uhlen; Cheng Zhang; Sunjae Lee; Evelina Sjöstedt; Linn Fagerberg; Gholamreza Bidkhori; Rui Benfeitas; Muhammad Arif; Zhengtao Liu; Fredrik Edfors; Kemal Sanli; Kalle von Feilitzen; Per Oksvold; Emma Lundberg; Sophia Hober; Peter Nilsson; Johanna Mattsson; Jochen M Schwenk; Hans Brunnström; Bengt Glimelius; Tobias Sjöblom; Per-Henrik Edqvist; Dijana Djureinovic; Patrick Micke; Cecilia Lindskog; Adil Mardinoglu; Fredrik Ponten
Journal:  Science       Date:  2017-08-18       Impact factor: 47.728

8.  Architecture of the human regulatory network derived from ENCODE data.

Authors:  Mark B Gerstein; Anshul Kundaje; Manoj Hariharan; Stephen G Landt; Koon-Kiu Yan; Chao Cheng; Xinmeng Jasmine Mu; Ekta Khurana; Joel Rozowsky; Roger Alexander; Renqiang Min; Pedro Alves; Alexej Abyzov; Nick Addleman; Nitin Bhardwaj; Alan P Boyle; Philip Cayting; Alexandra Charos; David Z Chen; Yong Cheng; Declan Clarke; Catharine Eastman; Ghia Euskirchen; Seth Frietze; Yao Fu; Jason Gertz; Fabian Grubert; Arif Harmanci; Preti Jain; Maya Kasowski; Phil Lacroute; Jing Jane Leng; Jin Lian; Hannah Monahan; Henriette O'Geen; Zhengqing Ouyang; E Christopher Partridge; Dorrelyn Patacsil; Florencia Pauli; Debasish Raha; Lucia Ramirez; Timothy E Reddy; Brian Reed; Minyi Shi; Teri Slifer; Jing Wang; Linfeng Wu; Xinqiong Yang; Kevin Y Yip; Gili Zilberman-Schapira; Serafim Batzoglou; Arend Sidow; Peggy J Farnham; Richard M Myers; Sherman M Weissman; Michael Snyder
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

9.  Europe PMC: a full-text literature database for the life sciences and platform for innovation.

Authors: 
Journal:  Nucleic Acids Res       Date:  2014-11-06       Impact factor: 16.971

10.  Recon 2.2: from reconstruction to model of human metabolism.

Authors:  Neil Swainston; Kieran Smallbone; Hooman Hefzi; Paul D Dobson; Judy Brewer; Michael Hanscho; Daniel C Zielinski; Kok Siong Ang; Natalie J Gardiner; Jahir M Gutierrez; Sarantos Kyriakopoulos; Meiyappan Lakshmanan; Shangzhong Li; Joanne K Liu; Veronica S Martínez; Camila A Orellana; Lake-Ee Quek; Alex Thomas; Juergen Zanghellini; Nicole Borth; Dong-Yup Lee; Lars K Nielsen; Douglas B Kell; Nathan E Lewis; Pedro Mendes
Journal:  Metabolomics       Date:  2016-06-07       Impact factor: 4.290

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  26 in total

Review 1.  Whole-Cell Models and Simulations in Molecular Detail.

Authors:  Michael Feig; Yuji Sugita
Journal:  Annu Rev Cell Dev Biol       Date:  2019-07-12       Impact factor: 13.827

Review 2.  Challenges in protein docking.

Authors:  Ilya A Vakser
Journal:  Curr Opin Struct Biol       Date:  2020-08-21       Impact factor: 6.809

Review 3.  Computational approaches to macromolecular interactions in the cell.

Authors:  Ilya A Vakser; Eric J Deeds
Journal:  Curr Opin Struct Biol       Date:  2019-04-15       Impact factor: 6.809

4.  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

5.  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

6.  Programmatic modeling for biological systems.

Authors:  Alexander L R Lubbock; Carlos F Lopez
Journal:  Curr Opin Syst Biol       Date:  2021-05-24

Review 7.  Best Practices for Making Reproducible Biochemical Models.

Authors:  Veronica L Porubsky; Arthur P Goldberg; Anand K Rampadarath; David P Nickerson; Jonathan R Karr; Herbert M Sauro
Journal:  Cell Syst       Date:  2020-08-26       Impact factor: 10.304

8.  When Is an In Silico Representation a Digital Twin? A Biopharmaceutical Industry Approach to the Digital Twin Concept.

Authors:  Rui M C Portela; Christos Varsakelis; Anne Richelle; Nikolaos Giannelos; Julia Pence; Sandrine Dessoy; Moritz von Stosch
Journal:  Adv Biochem Eng Biotechnol       Date:  2021       Impact factor: 2.635

9.  RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.

Authors:  Bilal Shaikh; Gnaneswara Marupilla; Mike Wilson; Michael L Blinov; Ion I Moraru; Jonathan R Karr
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

10.  BiPSim: a flexible and generic stochastic simulator for polymerization processes.

Authors:  Stephan Fischer; Marc Dinh; Vincent Henry; Philippe Robert; Anne Goelzer; Vincent Fromion
Journal:  Sci Rep       Date:  2021-07-08       Impact factor: 4.379

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