Literature DB >> 24922112

Cellular noise and information transmission.

Andre Levchenko1, Ilya Nemenman2.   

Abstract

The technological revolution in biological research, and in particular the use of molecular fluorescent labels, has allowed investigation of heterogeneity of cellular responses to stimuli on the single cell level. Computational, theoretical, and synthetic biology advances have allowed predicting and manipulating this heterogeneity with an exquisite precision previously reserved only for physical sciences. Functionally, this cell-to-cell variability can compromise cellular responses to environmental signals, and it can also enlarge the repertoire of possible cellular responses and hence increase the adaptive nature of cellular behaviors. And yet quantification of the functional importance of this response heterogeneity remained elusive. Recently the mathematical language of information theory has been proposed to address this problem. This opinion reviews the recent advances and discusses the broader implications of using information-theoretic tools to characterize heterogeneity of cellular behaviors.
Copyright © 2014. Published by Elsevier Ltd.

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Year:  2014        PMID: 24922112      PMCID: PMC5561739          DOI: 10.1016/j.copbio.2014.05.002

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  64 in total

1.  Regulation of noise in the expression of a single gene.

Authors:  Ertugrul M Ozbudak; Mukund Thattai; Iren Kurtser; Alan D Grossman; Alexander van Oudenaarden
Journal:  Nat Genet       Date:  2002-04-22       Impact factor: 38.330

2.  Estimating mutual information.

Authors:  Alexander Kraskov; Harald Stögbauer; Peter Grassberger
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2004-06-23

3.  Bacterial persistence as a phenotypic switch.

Authors:  Nathalie Q Balaban; Jack Merrin; Remy Chait; Lukasz Kowalik; Stanislas Leibler
Journal:  Science       Date:  2004-08-12       Impact factor: 47.728

4.  Multivariate dependence and genetic networks inference.

Authors:  A A Margolin; K Wang; A Califano; I Nemenman
Journal:  IET Syst Biol       Date:  2010-11       Impact factor: 1.615

5.  Phenotypic diversity, population growth, and information in fluctuating environments.

Authors:  Edo Kussell; Stanislas Leibler
Journal:  Science       Date:  2005-08-25       Impact factor: 47.728

6.  The finite state projection algorithm for the solution of the chemical master equation.

Authors:  Brian Munsky; Mustafa Khammash
Journal:  J Chem Phys       Date:  2006-01-28       Impact factor: 3.488

7.  A stochastic spectral analysis of transcriptional regulatory cascades.

Authors:  Aleksandra M Walczak; Andrew Mugler; Chris H Wiggins
Journal:  Proc Natl Acad Sci U S A       Date:  2009-04-07       Impact factor: 11.205

8.  Information flow and optimization in transcriptional regulation.

Authors:  Gasper Tkacik; Curtis G Callan; William Bialek
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-21       Impact factor: 11.205

Review 9.  Nature, nurture, or chance: stochastic gene expression and its consequences.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Cell       Date:  2008-10-17       Impact factor: 41.582

10.  Pharmacodynamics, population dynamics, and the evolution of persistence in Staphylococcus aureus.

Authors:  Paul J T Johnson; Bruce R Levin
Journal:  PLoS Genet       Date:  2013-01-03       Impact factor: 5.917

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  42 in total

Review 1.  Signal Transduction at the Single-Cell Level: Approaches to Study the Dynamic Nature of Signaling Networks.

Authors:  L Naomi Handly; Jason Yao; Roy Wollman
Journal:  J Mol Biol       Date:  2016-07-16       Impact factor: 5.469

2.  Embracing Systems Toxicology at Single-Cell Resolution.

Authors:  Qiang Zhang; W Michael Caudle; Jingbo Pi; Sudin Bhattacharya; Melvin E Andersen; Norbert E Kaminski; Rory B Conolly
Journal:  Curr Opin Toxicol       Date:  2019-04-19

3.  Robustness, Accuracy, and Cell State Heterogeneity in Biological Systems.

Authors:  Roy Wollman
Journal:  Curr Opin Syst Biol       Date:  2017-12-15

4.  Dynamic Sampling and Information Encoding in Biochemical Networks.

Authors:  Garrett D Potter; Tommy A Byrd; Andrew Mugler; Bo Sun
Journal:  Biophys J       Date:  2017-02-28       Impact factor: 4.033

5.  Fundamental trade-offs between information flow in single cells and cellular populations.

Authors:  Ryan Suderman; John A Bachman; Adam Smith; Peter K Sorger; Eric J Deeds
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-12       Impact factor: 11.205

6.  Process Information and Evolution.

Authors:  Erick Chastain; Cameron Smith
Journal:  IEEE Trans Mol Biol Multiscale Commun       Date:  2016-12

7.  NF-κB Dynamics Discriminate between TNF Doses in Single Cells.

Authors:  Qiuhong Zhang; Sanjana Gupta; David L Schipper; Gabriel J Kowalczyk; Allison E Mancini; James R Faeder; Robin E C Lee
Journal:  Cell Syst       Date:  2017-11-08       Impact factor: 10.304

8.  Personalized disease signatures through information-theoretic compaction of big cancer data.

Authors:  Swetha Vasudevan; Efrat Flashner-Abramson; F Remacle; R D Levine; Nataly Kravchenko-Balasha
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-05       Impact factor: 11.205

9.  Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis.

Authors:  David Ellison; Andrew Mugler; Matthew D Brennan; Sung Hoon Lee; Robert J Huebner; Eliah R Shamir; Laura A Woo; Joseph Kim; Patrick Amar; Ilya Nemenman; Andrew J Ewald; Andre Levchenko
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-20       Impact factor: 11.205

Review 10.  Engineering cell-based therapies to interface robustly with host physiology.

Authors:  Kelly A Schwarz; Joshua N Leonard
Journal:  Adv Drug Deliv Rev       Date:  2016-06-03       Impact factor: 15.470

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