Literature DB >> 34139161

A forecast for large-scale, predictive biology: Lessons from meteorology.

Markus W Covert1, Taryn E Gillies2, Takamasa Kudo3, Eran Agmon2.   

Abstract

Quantitative systems biology, in which predictive mathematical models are constructed to guide the design of experiments and predict experimental outcomes, is at an exciting transition point, where the foundational scientific principles are becoming established, but the impact is not yet global. The next steps necessary for mathematical modeling to transform biological research and applications, in the same way it has already transformed other fields, is not completely clear. The purpose of this perspective is to forecast possible answers to this question-what needs to happen next-by drawing on the experience gained in another field, specifically meteorology. We review here a number of lessons learned in weather prediction that are directly relevant to biological systems modeling, and that we believe can enable the same kinds of global impact in our field as atmospheric modeling makes today.
Copyright © 2021 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  computational biology; systems biology; whole-cell modeling

Mesh:

Year:  2021        PMID: 34139161      PMCID: PMC8217727          DOI: 10.1016/j.cels.2021.05.014

Source DB:  PubMed          Journal:  Cell Syst        ISSN: 2405-4712            Impact factor:   11.091


  80 in total

Review 1.  Whole-cell simulation: a grand challenge of the 21st century.

Authors:  M Tomita
Journal:  Trends Biotechnol       Date:  2001-06       Impact factor: 19.536

Review 2.  Stochasticity and cell fate.

Authors:  Richard Losick; Claude Desplan
Journal:  Science       Date:  2008-04-04       Impact factor: 47.728

3.  Stochastic mechanisms in gene expression.

Authors:  H H McAdams; A Arkin
Journal:  Proc Natl Acad Sci U S A       Date:  1997-02-04       Impact factor: 11.205

Review 4.  The promise and the challenges of cryo-electron tomography.

Authors:  Martin Turk; Wolfgang Baumeister
Journal:  FEBS Lett       Date:  2020-10-23       Impact factor: 4.124

Review 5.  How to deal with parameters for whole-cell modelling.

Authors:  Ann C Babtie; Michael P H Stumpf
Journal:  J R Soc Interface       Date:  2017-08-02       Impact factor: 4.118

6.  Controlling low rates of cell differentiation through noise and ultrahigh feedback.

Authors:  Robert Ahrends; Asuka Ota; Kyle M Kovary; Takamasa Kudo; Byung Ouk Park; Mary N Teruel
Journal:  Science       Date:  2014-06-20       Impact factor: 47.728

7.  Big Data: Astronomical or Genomical?

Authors:  Zachary D Stephens; Skylar Y Lee; Faraz Faghri; Roy H Campbell; Chengxiang Zhai; Miles J Efron; Ravishankar Iyer; Michael C Schatz; Saurabh Sinha; Gene E Robinson
Journal:  PLoS Biol       Date:  2015-07-07       Impact factor: 8.029

8.  Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli.

Authors:  Nusrat Jahan; Kazuhiro Maeda; Yu Matsuoka; Yurie Sugimoto; Hiroyuki Kurata
Journal:  Microb Cell Fact       Date:  2016-06-21       Impact factor: 5.328

9.  A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains.

Authors:  Ali Khodayari; Costas D Maranas
Journal:  Nat Commun       Date:  2016-12-20       Impact factor: 14.919

Review 10.  OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans.

Authors:  Gopal P Sarma; Chee Wai Lee; Tom Portegys; Vahid Ghayoomie; Travis Jacobs; Bradly Alicea; Matteo Cantarelli; Michael Currie; Richard C Gerkin; Shane Gingell; Padraig Gleeson; Richard Gordon; Ramin M Hasani; Giovanni Idili; Sergey Khayrulin; David Lung; Andrey Palyanov; Mark Watts; Stephen D Larson
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2018-09-10       Impact factor: 6.237

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  1 in total

Review 1.  Fundamentals to function: Quantitative and scalable approaches for measuring protein stability.

Authors:  Beatriz Atsavapranee; Catherine D Stark; Fanny Sunden; Samuel Thompson; Polly M Fordyce
Journal:  Cell Syst       Date:  2021-06-16       Impact factor: 11.091

  1 in total

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