Literature DB >> 26584768

Theory in Biology: Figure 1 or Figure 7?

Rob Phillips1.   

Abstract

The pace of modern science is staggering. The quantities of data now flowing from DNA sequencers, fluorescence and electron microscopes, mass spectrometers, and other mind-blowing instruments leave us faced with information overload. This explosion in data has brought on its heels a concomitant need for efforts at the kinds of synthesis and unification we see in theoretical physics. Often in cell biology, when theoretical modeling takes place, it is as a figure 7 reflection on experiments that have already been done, with data fitting providing a metric of success. Figure 1 theory, by way of contrast, is about living dangerously by turning our thinking into formal mathematical predictions and confronting that math with experiments that have not yet been done.
Copyright © 2015 Elsevier Ltd. All rights reserved.

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Year:  2015        PMID: 26584768      PMCID: PMC4666001          DOI: 10.1016/j.tcb.2015.10.007

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


  32 in total

1.  ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.

Authors:  J MONOD; J WYMAN; J P CHANGEUX
Journal:  J Mol Biol       Date:  1965-05       Impact factor: 5.469

2.  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 3.  50 years of allosteric interactions: the twists and turns of the models.

Authors:  Jean-Pierre Changeux
Journal:  Nat Rev Mol Cell Biol       Date:  2013-10-23       Impact factor: 94.444

4.  Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator.

Authors:  J Müller; S Oehler; B Müller-Hill
Journal:  J Mol Biol       Date:  1996-03-22       Impact factor: 5.469

5.  Robustness in simple biochemical networks.

Authors:  N Barkai; S Leibler
Journal:  Nature       Date:  1997-06-26       Impact factor: 49.962

6.  Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration.

Authors:  Mattias Rydenfelt; Robert Sidney Cox; Hernan Garcia; Rob Phillips
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2014-01-06

7.  Single-RNA counting reveals alternative modes of gene expression in yeast.

Authors:  Daniel Zenklusen; Daniel R Larson; Robert H Singer
Journal:  Nat Struct Mol Biol       Date:  2008-11-16       Impact factor: 15.369

8.  Quantitative modeling of sensitivity in bacterial chemotaxis: the role of coupling among different chemoreceptor species.

Authors:  Bernardo A Mello; Yuhai Tu
Journal:  Proc Natl Acad Sci U S A       Date:  2003-06-25       Impact factor: 12.779

9.  Trade-offs and constraints in allosteric sensing.

Authors:  Bruno M C Martins; Peter S Swain
Journal:  PLoS Comput Biol       Date:  2011-11-03       Impact factor: 4.475

10.  Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi.

Authors:  Lee R Swem; Danielle L Swem; Ned S Wingreen; Bonnie L Bassler
Journal:  Cell       Date:  2008-08-08       Impact factor: 41.582

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  11 in total

1.  Negative reciprocity, not ordered assembly, underlies the interaction of Sox2 and Oct4 on DNA.

Authors:  John W Biddle; Maximilian Nguyen; Jeremy Gunawardena
Journal:  Elife       Date:  2019-02-14       Impact factor: 8.140

2.  Understanding the evolution of interspecies interactions in microbial communities.

Authors:  Florien A Gorter; Michael Manhart; Martin Ackermann
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-03-23       Impact factor: 6.237

3.  Finding your inner modeler: An NSF-sponsored workshop to introduce cell biologists to modeling/computational approaches.

Authors:  David E Stone; Elizabeth S Haswell; Elizabeth Sztul
Journal:  Cell Logist       Date:  2017-09-25

4.  Arnold tongue entrainment reveals dynamical principles of the embryonic segmentation clock.

Authors:  Paul Gerald Layague Sanchez; Victoria Mochulska; Christian Mauffette Denis; Gregor Mönke; Takehito Tomita; Nobuko Tsuchida-Straeten; Yvonne Petersen; Katharina Sonnen; Paul François; Alexander Aulehla
Journal:  Elife       Date:  2022-10-12       Impact factor: 8.713

5.  Information Integration and Energy Expenditure in Gene Regulation.

Authors:  Javier Estrada; Felix Wong; Angela DePace; Jeremy Gunawardena
Journal:  Cell       Date:  2016-06-30       Impact factor: 41.582

Review 6.  Communication in Neural Circuits: Tools, Opportunities, and Challenges.

Authors:  Talia N Lerner; Li Ye; Karl Deisseroth
Journal:  Cell       Date:  2016-03-10       Impact factor: 41.582

7.  The paradox of longer sperm telomeres in older men's testes: a birth-cohort effect caused by transgenerational telomere erosion in the female germline.

Authors:  Reinhard Stindl
Journal:  Mol Cytogenet       Date:  2016-02-08       Impact factor: 2.009

Review 8.  Transcriptional precision and accuracy in development: from measurements to models and mechanisms.

Authors:  Lital Bentovim; Timothy T Harden; Angela H DePace
Journal:  Development       Date:  2017-11-01       Impact factor: 6.868

Review 9.  Enhancer grammar in development, evolution, and disease: dependencies and interplay.

Authors:  Granton A Jindal; Emma K Farley
Journal:  Dev Cell       Date:  2021-03-08       Impact factor: 12.270

Review 10.  The biology and polymer physics underlying large-scale chromosome organization.

Authors:  Shelley Sazer; Helmut Schiessel
Journal:  Traffic       Date:  2017-12-03       Impact factor: 6.215

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