Signaling pathways have an inherent need for noise to acquire information
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Andreas Wagner | Eugenio P. Balanzario | Eugenio Azpeitia | A. Wagner | E. Azpeitia | E. Balanzario | Eugenio Azpeitia | Eugenio P. Balanzario | Andreas Wagner
[1] Brian Munsky,et al. Transcription Factors Modulate c-Fos Transcriptional Bursts , 2014, Cell reports.
[2] Signaling by nuclear receptors. , 2013, Cold Spring Harbor perspectives in biology.
[3] C. Furusawa,et al. Theory of robustness of irreversible differentiation in a stem cell system: chaos hypothesis. , 2000, Journal of theoretical biology.
[4] L. Aravind,et al. Interplay between gene expression noise and regulatory network architecture. , 2012, Trends in genetics : TIG.
[5] A. Wagner,et al. Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits , 2011, BMC Evolutionary Biology.
[6] J. Stamatoyannopoulos,et al. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding , 2011, Genome Biology.
[7] N. Stocks,et al. Suprathreshold stochastic resonance in multilevel threshold systems , 2000, Physical review letters.
[8] O. Rissland,et al. Determining mRNA half-lives on a transcriptome-wide scale. , 2017, Methods.
[9] J. Corzo. Time, the forgotten dimension of ligand binding teaching , 2006, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.
[10] Gašper Tkačik,et al. Noise and information transmission in promoters with multiple internal States. , 2013, Biophysical journal.
[11] C Jayaprakash,et al. The role of dimerization in noise reduction of simple genetic networks. , 2003, Journal of theoretical biology.
[12] Carla Bosia,et al. The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering , 2010, PLoS Comput. Biol..
[13] James B. Brown,et al. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila , 2012, Proceedings of the National Academy of Sciences.
[14] Daniel B. Forger,et al. Stochastic simulation of the mammalian circadian clock. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[15] J. Hillston,et al. Stochastic properties of the plant circadian clock , 2012, Journal of The Royal Society Interface.
[16] Thomas M. Cover,et al. Elements of Information Theory , 2005 .
[17] O. Berg,et al. Quantification of transcription factor-DNA binding affinity in a living cell , 2015, Nucleic acids research.
[18] Johannes Berg,et al. What makes the lac-pathway switch: identifying the fluctuations that trigger phenotype switching in gene regulatory systems , 2013, Nucleic acids research.
[19] T. Kepler,et al. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. , 2001, Biophysical journal.
[20] P. R. ten Wolde,et al. Fundamental Limits to Cellular Sensing , 2015, 1505.06577.
[21] J. Starrfelt,et al. Bet‐hedging—a triple trade‐off between means, variances and correlations , 2012, Biological reviews of the Cambridge Philosophical Society.
[22] M. Selbach,et al. Global quantification of mammalian gene expression control , 2011, Nature.
[23] L. Tsimring,et al. Accurate information transmission through dynamic biochemical signaling networks , 2014, Science.
[24] Sarah A Teichmann,et al. Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells. , 2012, Current opinion in cell biology.
[25] Jeroen S. van Zon,et al. Direct cell reprogramming is a stochastic process amenable to acceleration , 2009, Nature.
[26] Alexei A. Sharov,et al. Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells , 2008, DNA research : an international journal for rapid publication of reports on genes and genomes.
[27] Eric J. Deeds,et al. Fundamental trade-offs between information flow in single cells and cellular populations , 2017, Proceedings of the National Academy of Sciences.
[28] Guillermo Rodrigo,et al. Insights about collective decision-making at the genetic level , 2019, Biophysical Reviews.
[29] W. Bialek,et al. Information flow and optimization in transcriptional regulation , 2007, Proceedings of the National Academy of Sciences.
[30] Richard W. Lusk,et al. Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers , 2010, PLoS genetics.
[31] Albert Goldbeter,et al. Modeling-Based Investigation of the Effect of Noise in Cellular Systems , 2018, Front. Mol. Biosci..
[32] J. McNally,et al. Quantifying transcription factor kinetics: At work or at play? , 2013, Critical reviews in biochemistry and molecular biology.
[33] G. Vinnicombe,et al. Fundamental limits on the suppression of molecular fluctuations , 2010, Nature.
[34] U. Rant,et al. Polymerase/DNA interactions and enzymatic activity: multi-parameter analysis with electro-switchable biosurfaces , 2015, Scientific Reports.
[35] Clive G. Bowsher,et al. Environmental sensing, information transfer, and cellular decision-making. , 2014, Current opinion in biotechnology.
[36] A. Wagner,et al. Short Residence Times of DNA-Bound Transcription Factors Can Reduce Gene Expression Noise and Increase the Transmission of Information in a Gene Regulation System , 2020, Frontiers in Molecular Biosciences.
[37] Anastasia Baryshnikova,et al. Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome. , 2018, Cell systems.
[38] Jerome T. Mettetal,et al. Stochastic switching as a survival strategy in fluctuating environments , 2008, Nature Genetics.
[39] Andre Levchenko,et al. The application of information theory to biochemical signaling systems , 2012, Physical biology.
[40] Hannah H. Chang,et al. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells , 2008, Nature.
[41] Ursula Kummer,et al. Information transfer in signaling pathways: A study using coupled simulated and experimental data , 2008, BMC Bioinformatics.
[42] L. Cantley. Signal transduction : principles, pathways, and processes , 2014 .
[43] Mads Kærn,et al. A chance at survival: gene expression noise and phenotypic diversification strategies , 2009, Molecular microbiology.
[44] Derek Abbott,et al. What Is Stochastic Resonance? Definitions, Misconceptions, Debates, and Its Relevance to Biology , 2009, PLoS Comput. Biol..
[45] L. M. Ward,et al. Stochastic resonance and sensory information processing: a tutorial and review of application , 2004, Clinical Neurophysiology.
[46] A. van Oudenaarden,et al. Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos. , 2012, WormBook : the online review of C. elegans biology.
[47] D. Gillespie. Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .
[48] Juan F. Poyatos,et al. Genetic Redundancies Enhance Information Transfer in Noisy Regulatory Circuits , 2016, bioRxiv.
[49] Nicholas A. DeLateur,et al. Stochastic Turing patterns in a synthetic bacterial population , 2018, Proceedings of the National Academy of Sciences.
[50] A. Arkin,et al. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.
[51] Naama Barkai,et al. The design of transcription-factor binding sites is affected by combinatorial regulation , 2005, Genome Biology.
[52] John M. McNamara,et al. Information is a fitness enhancing resource , 2010 .
[53] A. Arkin,et al. Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[54] Martin Falcke,et al. Reliable Encoding of Stimulus Intensities Within Random Sequences of Intracellular Ca2+ Spikes , 2014, Science Signaling.
[55] Carl T. Bergstrom,et al. The fitness value of information , 2005, Oikos.
[56] L. Serrano,et al. Engineering stability in gene networks by autoregulation , 2000, Nature.
[57] M. Elowitz,et al. Functional roles for noise in genetic circuits , 2010, Nature.
[58] H. Westerhoff,et al. Recurrent design patterns in the feedback regulation of the mammalian signalling network , 2008, Molecular systems biology.
[59] A. E. Hirsh,et al. Noise Minimization in Eukaryotic Gene Expression , 2004, PLoS biology.
[60] Shinya Kuroda,et al. Robustness and Compensation of Information Transmission of Signaling Pathways , 2013, Science.
[61] M. Hetzer,et al. Protein homeostasis: live long, won't prosper , 2012, Nature Reviews Molecular Cell Biology.
[62] Ryan A. Kellogg,et al. Noise Facilitates Transcriptional Control under Dynamic Inputs , 2015, Cell.
[63] I. Nemenman,et al. Information Transduction Capacity of Noisy Biochemical Signaling Networks , 2011, Science.
[64] Peter S. Swain,et al. The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks , 2013, PLoS Comput. Biol..
[65] A. Vazquez,et al. Cell population heterogeneity driven by stochastic partition and growth optimality , 2018, Scientific Reports.
[66] L. Tsimring. Noise in biology , 2014, Reports on progress in physics. Physical Society.
[67] H. Putzer,et al. Initiation of mRNA decay in bacteria , 2013, Cellular and Molecular Life Sciences.
[68] M. Thattai,et al. Intrinsic noise in gene regulatory networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[69] Alfonso Martinez Arias,et al. Filtering transcriptional noise during development: concepts and mechanisms , 2006, Nature Reviews Genetics.
[70] W. Bialek,et al. Physical limits to biochemical signaling. , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[71] M. Biggin. Animal transcription networks as highly connected, quantitative continua. , 2011, Developmental cell.
[72] C. Rao,et al. Control, exploitation and tolerance of intracellular noise , 2002, Nature.