Literature DB >> 32472051

Predictive biology: modelling, understanding and harnessing microbial complexity.

Allison J Lopatkin1,2,3,4, James J Collins5,6,7.   

Abstract

Predictive biology is the next great chapter in synthetic and systems biology, particularly for microorganisms. Tasks that once seemed infeasible are increasingly being realized such as designing and implementing intricate synthetic gene circuits that perform complex sensing and actuation functions, and assembling multi-species bacterial communities with specific, predefined compositions. These achievements have been made possible by the integration of diverse expertise across biology, physics and engineering, resulting in an emerging, quantitative understanding of biological design. As ever-expanding multi-omic data sets become available, their potential utility in transforming theory into practice remains firmly rooted in the underlying quantitative principles that govern biological systems. In this Review, we discuss key areas of predictive biology that are of growing interest to microbiology, the challenges associated with the innate complexity of microorganisms and the value of quantitative methods in making microbiology more predictable.

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Year:  2020        PMID: 32472051     DOI: 10.1038/s41579-020-0372-5

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN: 1740-1526            Impact factor:   60.633


  165 in total

1.  Construction of a genetic toggle switch in Escherichia coli.

Authors:  T S Gardner; C R Cantor; J J Collins
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

2.  A synthetic oscillatory network of transcriptional regulators.

Authors:  M B Elowitz; S Leibler
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

3.  Programmable cells: interfacing natural and engineered gene networks.

Authors:  Hideki Kobayashi; Mads Kaern; Michihiro Araki; Kristy Chung; Timothy S Gardner; Charles R Cantor; James J Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2004-05-24       Impact factor: 11.205

4.  The challenges of integrating multi-omic data sets.

Authors:  Bernhard Palsson; Karsten Zengler
Journal:  Nat Chem Biol       Date:  2010-11       Impact factor: 15.040

5.  Engineering of regulated stochastic cell fate determination.

Authors:  Min Wu; Ri-Qi Su; Xiaohui Li; Tom Ellis; Ying-Cheng Lai; Xiao Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-10       Impact factor: 11.205

6.  The complete genome sequence of Escherichia coli K-12.

Authors:  F R Blattner; G Plunkett; C A Bloch; N T Perna; V Burland; M Riley; J Collado-Vides; J D Glasner; C K Rode; G F Mayhew; J Gregor; N W Davis; H A Kirkpatrick; M A Goeden; D J Rose; B Mau; Y Shao
Journal:  Science       Date:  1997-09-05       Impact factor: 47.728

Review 7.  Cellular decision making and biological noise: from microbes to mammals.

Authors:  Gábor Balázsi; Alexander van Oudenaarden; James J Collins
Journal:  Cell       Date:  2011-03-18       Impact factor: 41.582

8.  Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.

Authors:  Ahmad A Mannan; Yoshihiro Toya; Kazuyuki Shimizu; Johnjoe McFadden; Andrzej M Kierzek; Andrea Rocco
Journal:  PLoS One       Date:  2015-10-15       Impact factor: 3.240

9.  The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function.

Authors:  Sankha Ghatak; Zachary A King; Anand Sastry; Bernhard O Palsson
Journal:  Nucleic Acids Res       Date:  2019-03-18       Impact factor: 16.971

10.  Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota.

Authors:  Richard R Stein; Vanni Bucci; Nora C Toussaint; Charlie G Buffie; Gunnar Rätsch; Eric G Pamer; Chris Sander; João B Xavier
Journal:  PLoS Comput Biol       Date:  2013-12-12       Impact factor: 4.475

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  15 in total

1.  Observation of universal ageing dynamics in antibiotic persistence.

Authors:  Yoav Kaplan; Shaked Reich; Elyaqim Oster; Shani Maoz; Irit Levin-Reisman; Irine Ronin; Orit Gefen; Oded Agam; Nathalie Q Balaban
Journal:  Nature       Date:  2021-11-17       Impact factor: 49.962

2.  Energetic scaling in microbial growth.

Authors:  Salvatore Calabrese; Arjun Chakrawal; Stefano Manzoni; Philippe Van Cappellen
Journal:  Proc Natl Acad Sci U S A       Date:  2021-11-23       Impact factor: 11.205

Review 3.  Towards an ecosystem model of infectious disease.

Authors:  James M Hassell; Tim Newbold; Andrew P Dobson; Yvonne-Marie Linton; Lydia H V Franklinos; Dawn Zimmerman; Katrina M Pagenkopp Lohan
Journal:  Nat Ecol Evol       Date:  2021-05-17       Impact factor: 15.460

4.  Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities.

Authors:  Aida Alonso-Del Valle; Ricardo León-Sampedro; Jerónimo Rodríguez-Beltrán; Javier DelaFuente; Marta Hernández-García; Patricia Ruiz-Garbajosa; Rafael Cantón; Rafael Peña-Miller; Alvaro San Millán
Journal:  Nat Commun       Date:  2021-05-11       Impact factor: 14.919

5.  A Framework for Investigating Rules of Life by Establishing Zones of Influence.

Authors:  A Michelle Lawing; Michael McCoy; Beth A Reinke; Susanta K Sarkar; Felisa A Smith; Derek Wright
Journal:  Integr Comp Biol       Date:  2022-02-05       Impact factor: 3.392

6.  Yeast optimizes metal utilization based on metabolic network and enzyme kinetics.

Authors:  Yu Chen; Feiran Li; Jiwei Mao; Yun Chen; Jens Nielsen
Journal:  Proc Natl Acad Sci U S A       Date:  2021-03-23       Impact factor: 12.779

7.  Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism.

Authors:  Pierre Salvy; Vassily Hatzimanikatis
Journal:  Proc Natl Acad Sci U S A       Date:  2021-02-23       Impact factor: 11.205

8.  Spurious regulatory connections dictate the expression-fitness landscape of translation factors.

Authors:  Jean-Benoît Lalanne; Darren J Parker; Gene-Wei Li
Journal:  Mol Syst Biol       Date:  2021-04       Impact factor: 11.429

9.  Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.

Authors:  Lauren M Lui; Erica L-W Majumder; Heidi J Smith; Hans K Carlson; Frederick von Netzer; Matthew W Fields; David A Stahl; Jizhong Zhou; Terry C Hazen; Nitin S Baliga; Paul D Adams; Adam P Arkin
Journal:  Front Microbiol       Date:  2021-03-24       Impact factor: 5.640

10.  Stability and Robustness of Unbalanced Genetic Toggle Switches in the Presence of Scarce Resources.

Authors:  Chentao Yong; Andras Gyorgy
Journal:  Life (Basel)       Date:  2021-03-24
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