Literature DB >> 18522926

Biological switches and clocks.

John J Tyson1, Reka Albert, Albert Goldbeter, Peter Ruoff, Jill Sible.   

Abstract

To introduce this special issue on biological switches and clocks, we review the historical development of mathematical models of bistability and oscillations in chemical reaction networks. In the 1960s and 1970s, these models were limited to well-studied biochemical examples, such as glycolytic oscillations and cyclic AMP signalling. After the molecular genetics revolution of the 1980s, the field of molecular cell biology was thrown wide open to mathematical modellers. We review recent advances in modelling the gene-protein interaction networks that control circadian rhythms, cell cycle progression, signal processing and the design of synthetic gene networks.

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Year:  2008        PMID: 18522926      PMCID: PMC2706456          DOI: 10.1098/rsif.2008.0179.focus

Source DB:  PubMed          Journal:  J R Soc Interface        ISSN: 1742-5662            Impact factor:   4.118


  93 in total

1.  The kinetic origins of the restriction point in the mammalian cell cycle.

Authors:  B D Aguda; Y Tang
Journal:  Cell Prolif       Date:  1999-10       Impact factor: 6.831

2.  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

3.  Classification of biological networks by their qualitative dynamics.

Authors:  L Glass
Journal:  J Theor Biol       Date:  1975-10       Impact factor: 2.691

4.  Robustness and fragility of Boolean models for genetic regulatory networks.

Authors:  Madalena Chaves; Réka Albert; Eduardo D Sontag
Journal:  J Theor Biol       Date:  2005-03-19       Impact factor: 2.691

5.  Design principles underlying circadian clocks.

Authors:  D A Rand; B V Shulgin; D Salazar; A J Millar
Journal:  J R Soc Interface       Date:  2004-11-22       Impact factor: 4.118

6.  Chemosensing in Escherichia coli: two regimes of two-state receptors.

Authors:  Juan E Keymer; Robert G Endres; Monica Skoge; Yigal Meir; Ned S Wingreen
Journal:  Proc Natl Acad Sci U S A       Date:  2006-01-30       Impact factor: 11.205

Review 7.  Quantitative approaches to the study of bistability in the lac operon of Escherichia coli.

Authors:  Moisés Santillán; Michael C Mackey
Journal:  J R Soc Interface       Date:  2008-08-06       Impact factor: 4.118

8.  Boolean formalization of genetic control circuits.

Authors:  R Thomas
Journal:  J Theor Biol       Date:  1973-12       Impact factor: 2.691

9.  Mathematics of cellular control processes. I. Negative feedback to one gene.

Authors:  J S Griffith
Journal:  J Theor Biol       Date:  1968-08       Impact factor: 2.691

10.  The relationship between FRQ-protein stability and temperature compensation in the Neurospora circadian clock.

Authors:  Peter Ruoff; Jennifer J Loros; Jay C Dunlap
Journal:  Proc Natl Acad Sci U S A       Date:  2005-11-28       Impact factor: 11.205

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  29 in total

Review 1.  A comparative analysis of synthetic genetic oscillators.

Authors:  Oliver Purcell; Nigel J Savery; Claire S Grierson; Mario di Bernardo
Journal:  J R Soc Interface       Date:  2010-06-30       Impact factor: 4.118

2.  Design principles for robust oscillatory behavior.

Authors:  Sebastian M Castillo-Hair; Elizabeth R Villota; Alberto M Coronado
Journal:  Syst Synth Biol       Date:  2015-08-05

3.  Optimal homeostasis necessitates bistable control.

Authors:  Guanyu Wang
Journal:  J R Soc Interface       Date:  2012-04-25       Impact factor: 4.118

4.  On the impact of the distance between two genes on their interaction curve.

Authors:  Siamak Taati; Enrico Formenti; Jean-Paul Comet; Gilles Bernot
Journal:  J Math Biol       Date:  2011-02-15       Impact factor: 2.259

Review 5.  Dissipative structures in biological systems: bistability, oscillations, spatial patterns and waves.

Authors:  Albert Goldbeter
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2018-07-28       Impact factor: 4.226

6.  On the role of lateral stabilization during early patterning in the pancreas.

Authors:  Walter de Back; Joseph Xu Zhou; Lutz Brusch
Journal:  J R Soc Interface       Date:  2013-02       Impact factor: 4.118

7.  Unraveling the regulatory connections between two controllers of breast cancer cell fate.

Authors:  Jinho Lee; Abhinav Tiwari; Victor Shum; Gordon B Mills; Michael A Mancini; Oleg A Igoshin; Gábor Balázsi
Journal:  Nucleic Acids Res       Date:  2014-05-03       Impact factor: 16.971

8.  Switches induced by quorum sensing in a model of enzyme-loaded microparticles.

Authors:  Tamás Bánsági; Annette F Taylor
Journal:  J R Soc Interface       Date:  2017-03       Impact factor: 4.118

9.  Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation.

Authors:  Andreea Munteanu; Marco Constante; Mark Isalan; Ricard V Solé
Journal:  BMC Syst Biol       Date:  2010-05-17

10.  Mathematical modeling of fission yeast Schizosaccharomyces pombe cell cycle: exploring the role of multiple phosphatases.

Authors:  P Anbumathi; Sharad Bhartiya; K V Venkatesh
Journal:  Syst Synth Biol       Date:  2011-12-08
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