Literature DB >> 26471224

Why Build Whole-Cell Models?

Javier Carrera1, Markus W Covert2.   

Abstract

Our ability to build computational models that account for all known gene functions in a cell has increased dramatically. But why build whole-cell models, and how can they best be used? In this forum, we enumerate several areas in which whole-cell modeling can significantly impact research and technology.
Copyright © 2015 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  model-driven discovery; predictive biology; whole-cell modeling

Mesh：

Year:  2015        PMID： 26471224      PMCID： PMC4663153          DOI： 10.1016/j.tcb.2015.09.004

Source DB:  PubMed          Journal:  Trends Cell Biol        ISSN： 0962-8924            Impact factor:   20.808


  15 in total

1.  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

2.  Computer model for glucose-limited growth of a single cell of Escherichia coli B/r-A.

Authors:  M M Domach; S K Leung; R E Cahn; G G Cocks; M L Shuler
Journal:  Biotechnol Bioeng       Date:  1984-09       Impact factor: 4.530

3.  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

4.  Towards a whole-cell modeling approach for synthetic biology.

Authors:  Oliver Purcell; Bonny Jain; Jonathan R Karr; Markus W Covert; Timothy K Lu
Journal:  Chaos       Date:  2013-06       Impact factor: 3.642

5.  Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers.

Authors:  Yu Kyung Jung; Tae Yong Kim; Si Jae Park; Sang Yup Lee
Journal:  Biotechnol Bioeng       Date:  2010-01-01       Impact factor: 4.530

6.  Three-dimensional structural view of the central metabolic network of Thermotoga maritima.

Authors:  Ying Zhang; Ines Thiele; Dana Weekes; Zhanwen Li; Lukasz Jaroszewski; Krzysztof Ginalski; Ashley M Deacon; John Wooley; Scott A Lesley; Ian A Wilson; Bernhard Palsson; Andrei Osterman; Adam Godzik
Journal:  Science       Date:  2009-09-18       Impact factor: 47.728

7.  Computational design of genomic transcriptional networks with adaptation to varying environments.

Authors:  Javier Carrera; Santiago F Elena; Alfonso Jaramillo
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-27       Impact factor: 11.205

8.  Noise contributions in an inducible genetic switch: a whole-cell simulation study.

Authors:  Elijah Roberts; Andrew Magis; Julio O Ortiz; Wolfgang Baumeister; Zaida Luthey-Schulten
Journal:  PLoS Comput Biol       Date:  2011-03-10       Impact factor: 4.475

9.  CellNet: network biology applied to stem cell engineering.

Authors:  Patrick Cahan; Hu Li; Samantha A Morris; Edroaldo Lummertz da Rocha; George Q Daley; James J Collins
Journal:  Cell       Date:  2014-08-14       Impact factor: 41.582

10.  Accelerated discovery via a whole-cell model.

Authors:  Jayodita C Sanghvi; Sergi Regot; Silvia Carrasco; Jonathan R Karr; Miriam V Gutschow; Benjamin Bolival; Markus W Covert
Journal:  Nat Methods       Date:  2013-11-03       Impact factor: 28.547
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  27 in total

1.  Hybrid modelling of biological systems using fuzzy continuous Petri nets.

Authors:  Fei Liu; Wujie Sun; Monika Heiner; David Gilbert
Journal:  Brief Bioinform       Date:  2021-01-18       Impact factor: 11.622

2.  Prediction of Cellular Burden with Host-Circuit Models.

Authors:  Evangelos-Marios Nikolados; Andrea Y Weiße; Diego A Oyarzún
Journal:  Methods Mol Biol       Date:  2021

Review 3.  Cellular Biophysics.

Authors:  Rick Horwitz
Journal:  Biophys J       Date:  2016-03-08       Impact factor: 4.033

Review 4.  Mathematical modelling of microbes: metabolism, gene expression and growth.

Authors:  Hidde de Jong; Stefano Casagranda; Nils Giordano; Eugenio Cinquemani; Delphine Ropers; Johannes Geiselmann; Jean-Luc Gouzé
Journal:  J R Soc Interface       Date:  2017-11       Impact factor: 4.118

Review 5.  Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell.

Authors:  Jitin Singla; Kyle M McClary; Kate L White; Frank Alber; Andrej Sali; Raymond C Stevens
Journal:  Cell       Date:  2018-03-22       Impact factor: 41.582

6.  A blueprint for human whole-cell modeling.

Authors:  Balázs Szigeti; Yosef D Roth; John A P Sekar; Arthur P Goldberg; Saahith C Pochiraju; Jonathan R Karr
Journal:  Curr Opin Syst Biol       Date:  2017-11-09

7.  A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.

Authors:  Jason H Yang; Sarah N Wright; Meagan Hamblin; Douglas McCloskey; Miguel A Alcantar; Lars Schrübbers; Allison J Lopatkin; Sangeeta Satish; Amir Nili; Bernhard O Palsson; Graham C Walker; James J Collins
Journal:  Cell       Date:  2019-05-09       Impact factor: 41.582

8.  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 9.  Challenges in structural approaches to cell modeling.

Authors:  Wonpil Im; Jie Liang; Arthur Olson; Huan-Xiang Zhou; Sandor Vajda; Ilya A Vakser
Journal:  J Mol Biol       Date:  2016-05-30       Impact factor: 5.469

10.  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
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