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From Thermodynamics of Computation
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- David J. Katz, T. Matthew Edwards, Valerie Reinke, William G. Kelly A C. elegans LSD1 Demethylase Contributes to Germline Immortality by Reprogramming Epigenetic Memory Cell 137, 308-320 (2009)
- A Gallavotti Cohen-Type Symmetry in the Large Deviation Functional for Stochastic Dynamics ,
- A Sampling of the Yeast Proteome ,
- Kim Sneppen, Ian B. Dodd A Simple Histone Code Opens Many Paths to Epigenetics PLoS Computational Biology 8, (2012)
- A complexity measure for selective matching of signals by the brain ,
- Daniel T. Gillespie A general method for numerically simulating the stochastic time evolution of coupled chemical reactions Journal of Computational Physics 22, 403-434 (1976)
- Geoffrey B. West, James H. Brown, Brian J. Enquist A general model for ontogenetic growth Nature 413, 628-631 (2001)
- A general model for the origin of allometric scaling laws in biology ,
- Geoffrey B. West, James H. Brown, Brian J. Enquist A general model for the structure and allometry of plant vascular systems Nature 400, 664-667 (1999)
- Ana Raquel Pengelly, Ömer Copur, Herbert Jäckle, Alf Herzig, Jürg Müller A histone mutant reproduces the phenotype caused by loss of histone-modifying factor polycomb Science 339, 698-699 (2013)
- A mathematical theory of communication ,
- A measure for brain complexity: relating functional segregation and integration in the nervous system. ,
- Klaus H. Hansen, Adrian P. Bracken, Diego Pasini, Nikolaj Dietrich, Simmi S. Gehani, Astrid Monrad, Juri Rappsilber, Mads Lerdrup, Kristian Helin A model for transmission of the H3K27me3 epigenetic mark Nature Cell Biology 10, 1291-1300 (2008)
- Pankaj Mehta, Sidhartha Goyal, Ned S. Wingreen A quantitative comparison of sRNA-based and protein-based gene regulation Molecular Systems Biology 4, (2008)
- Tobias von der Haar A quantitative estimation of the global translational activity in logarithmically growing yeast cells BMC Systems Biology 2, (2008)
- Daniel T. Gillespie A rigorous derivation of the chemical master equation Physica A: Statistical Mechanics and its Applications 188, 404-425 (1992)
- Robert G. Endres, Ned S. Wingreen Accuracy of direct gradient sensing by cell-surface receptors Progress in Biophysics and Molecular Biology 100, 33-39 (2009)
- W. H. Zurek Algorithmic randomness and physical entropy Physical Review A 40, 4731-4751 (1989)
- Xin Wang, Gene O. Bryant, Monique Floer, Dan Spagna, Mark Ptashne An effect of DNA sequence on nucleosome occupancy and removal Nature Structural and Molecular Biology 18, 507-509 (2011)
- Hanna K.E. Landenmark, Duncan H. Forgan, Charles S. Cockell An estimate of the total DNA in the biosphere PLoS Biology 13, 1-10 (2015)
- Giulio Tononi An information integration theory of consciousness BMC Neuroscience 5, (2004)
- Edward Fredkin An informational process based on reversible universal cellular automata Physica D: Nonlinear Phenomena 45, 254-270 (1990)
- Maya Ameyar-Zazoua, Christophe Rachez, Mouloud Souidi, Philippe Robin, Lauriane Fritsch, Robert Young, Nadya Morozova, Romain Fenouil, Nicolas Descostes, Jean Christophe Andrau, Jacques Mathieu, Ali Hamiche, Slimane Ait-Si-Ali, Christian Muchardt, Eric Batsché, Annick Harel-Bellan Argonaute proteins couple chromatin silencing to alternative splicing Nature Structural and Molecular Biology 19, 998-1005 (2012)
- Vuong Tran, Cindy Lim, Jing Xie, Xin Chen Asymmetric division of Drosophila male germline stem cell shows asymmetric histone distribution Science 338, 679-682 (2012)
- Philipp Voigt, Gary LeRoy, William J. Drury, Barry M. Zee, Jinsook Son, David B. Beck, Nicolas L. Young, Benjamin A. Garcia, Danny Reinberg Asymmetrically modified nucleosomes Cell 151, 181-193 (2012)
- Bacterial computing with engineered populations ,
- Ian B. Dodd, Kim Sneppen Barriers and silencers: A theoretical toolkit for control and containment of nucleosome-based epigenetic states Journal of Molecular Biology 414, 624-637 (2011)
- Body size and metabolic rate. ,
- Winston Timp, Andrew P. Feinberg Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host Nature Reviews Cancer 13, 497-510 (2013)
- Gunnar Schotta, Anja Ebert, Veiko Krauss, Andreas Fischer, Jan Hoffmann, Stephen Rea, Thomas Jenuwein, Rainer Dorn, Gunter Reuter Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing EMBO Journal 21, 1121-1131 (2002)
- Matthew D. Young, Tracy A. Willson, Matthew J. Wakefield, Evelyn Trounson, Douglas J. Hilton, Marnie E. Blewitt, Alicia Oshlack, Ian J. Majewski ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity Nucleic Acids Research 39, 7415-7427 (2011)
- Jessica C. Flack, David C. Krakauer Challenges for complexity measures: A perspective from social dynamics and collective social computation Chaos 21, (2011)
- Tanmoy Mondal, Markus Rasmussen, Gaurav Kumar Pandey, Anders Isaksson, Chandrasekhar Kanduri Characterization of the RNA content of chromatin Genome Research 20, 899-907 (2010)
- Linus Pauling, Emile Zuckerkandl, Thormod Henriksen, Rolf Lövstad Chemical Paleogenetics. Molecular "Restoration Studies" of Extinct Forms of Life. Acta Chemica Scandinavica 17 supl., 9-16 (1963)
- Marcelo O. Magnasco Chemical kinetics is turing universal Physical Review Letters 78, 1190-1193 (1997)
- Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription ,
- Seth J. Brown, Peter Stoilov, Yi Xing Chromatin and epigenetic regulation of pre-mrna processing Human Molecular Genetics 21, (2012)
- Barbara Bryant Chromatin computation PLoS ONE 7, (2012)
- Sylvia C. Tippmann, Robert Ivanek, Dimos Gaidatzis, Anne Schöler, Leslie Hoerner, Erik Van Nimwegen, Michael B. Stadler, Dirk Schübeler, Peter Stadler Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels Molecular Systems Biology 8, (2012)
- Schraga Schwartz, Eran Meshorer, Gil Ast Chromatin organization marks exon-intron structure Nature Structural and Molecular Biology 16, 990-995 (2009)
- Karen T. Smith, Jerry L. Workman Chromatin proteins: Key responders to stress PLoS Biology 10, 7 (2012)
- Raphaël Margueron, Danny Reinberg Chromatin structure and the inheritance of epigenetic information Nature Reviews Genetics 11, 285-296 (2010)
- Oliver J. Rando Combinatorial complexity in chromatin structure and function: Revisiting the histone code Current Opinion in Genetics and Development 22, 148-155 (2012)
- Zhanxin Wang, Dinshaw J. Patel Combinatorial readout of dual histone modifications by paired chromatin-associated modules Journal of Biological Chemistry 286, 18363-18368 (2011)
- Computational limits to binary genes. ,
- Giulio Tononi Consciousness as integrated information: A provisional manifesto Biological Bulletin 215, 216-242 (2008)
- Edward Fredkin, Tommaso Toffoli Conservative logic International Journal of Theoretical Physics 21, 219-253 (1982)
- Jeanne Morinière, Sophie Rousseaux, Ulrich Steuerwald, Montserrat Soler-López, Sandrine Curtet, Anne Laure Vitte, Jérme Govin, Jonathan Gaucher, Karin Sadoul, Darren J. Hart, Jeroen Krijgsveld, Saadi Khochbin, Christoph W. Müller, Carlo Petosa Cooperative binding of two acetylation marks on a histone tail by a single bromodomain Nature 461, 664-668 (2009)
- William Bialek, Sima Setayeshgar Cooperativity, sensitivity, and noise in biochemical signaling Physical Review Letters 100, (2008)
- Benjamin Callahan, Richard A. Neher, Doris Bachtrog, Peter Andolfatto, Boris I. Shraiman Correlated evolution of nearby residues in drosophilid proteins PLoS Genetics 7, (2011)
- E. R. Weibel, W. Stäubli, H. R. Gnägi, F. A. Hess Correlated morphometric and biochemical studies on the liver cell. I. Morphometric model, stereologic methods, and normal morphometric data for rat liver. The Journal of cell biology 42, 68-91 (1969)
- Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis ,
- Dazhong Xu, Jingxiang Bai, Qing Duan, Max Costa, Wei Dai Covalent modifications of histones during mitosis and meiosis Cell Cycle 8, 3688-3694 (2009)
- Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. ,
- Neil D. Clarke Covariation of residues in the homeodomain sequence family Protein Science 4, 2269-2278 (1995)
- Cybernetics : Control and Communication in the Animal and the Machine --2nd. ed ,
- David C. Krakauer Darwinian demons, evolutionary complexity, and information maximization Chaos 21, (2011)
- Sonja J. Prohaska, Christian V. Forst, David C. Krakauer, Peter Stadler Defining genes: A computational framework Theory in Biosciences 128, 165-170 (2009)
- Martin Billeter, Yan Qiu Qian, Gottfried Otting, Martin Müller, Walter Gehring, Kurt Wüthrich Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex Journal of Molecular Biology 234, 1084-1097 (1993)
- Christoph Adami Digital genetics: Unravelling the genetic basis of evolution Nature Reviews Genetics 7, 109-118 (2006)
- Kenjiro Adachi, Hans R. Schöler Directing reprogramming to pluripotency by transcription factors Current Opinion in Genetics and Development 22, 416-422 (2012)
- Jason Ernst, Manolis Kellis Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 6577 LNBI, 53 (2011)
- Charles H. Bennett Dissipation-error tradeoff in proofreading BioSystems 11, 85-91 (1979)
- Nathaniel D. Heintzman, Rhona K. Stuart, Gary Hon, Yutao Fu, Christina W. Ching, R. David Hawkins, Leah O. Barrera, Sara Van Calcar, Chunxu Qu, Keith A. Ching, Wei Wang, Zhiping Weng, Roland D. Green, Gregory E. Crawford, Bing Ren Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nature Genetics 39, 311-318 (2007)
- Distinctive features of dinoflagellate chromatin. Absence of nucleosomes in a primitive species Prorocentrum micans E. ,
- Qi Wang, Christopher Lee Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase PLoS ONE 2, (2007)
- Peter M. van Bodegom, David Wolpert, Eric Libby, Jan Amend, Tori Hoehler, Chris Kempes Drivers of bacterial maintenance and minimal energy requirements Frontiers in Microbiology 8, (2017)
- Anders M. Lindroth, David Shultis, Zuzana Jasencakova, Jörg Fuchs, Lianna Johnson, Daniel Schubert, Debasis Patnaik, Sriharsa Pradhan, Justin Goodrich, Ingo Schubert, Thomas Jenuwein, Sepideh Khorasanizadeh, Steven E. Jacobsen Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMENTHYLASE3 EMBO Journal 23, 4286-4296 (2004)
- Nathaniel A. Hathaway, Oliver Bell, Courtney Hodges, Erik L. Miller, Dana S. Neel, Gerald R. Crabtree Dynamics and memory of heterochromatin in living cells Cell 149, 1447-1460 (2012)
- Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. ,
- Dynamics of inherently bounded histone modification domains ,
- Early metazoan life: divergence, environment and ecology ,
- Thomas M. Cover, Joy A. Thomas Elements of Information Theory Elements of Information Theory , 1-748 (2005)
- Elements of Information Theory 2nd Edition ,
- Energy Balance for Analysis of Complex Metabolic Networks ,
- S. B. Laughlin Energy as a constraint on the coding and processing of sensory information Current Opinion in Neurobiology 11, 475-480 (2001)
- Eric J. Chaisson Energy flows in low-entropy complex systems Entropy 17, 8007-8018 (2015)
- Peter B. Detwiler, Sharad Ramanathan, Anirvan Sengupta, Boris I. Shraiman Engineering aspects of enzymatic signal transduction: Photoreceptors in the retina Biophysical Journal 79, 2801-2817 (2000)
- Udo Seifert Entropy production along a stochastic trajectory and an integral fluctuation theorem Physical Review Letters 95, (2005)
- Gavin Crooks Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 60, 2721-2726 (1999)
- Georg Seelig, David Soloveichik, David Yu Zhang, Erik Winfree Enzyme-free nucleic acid logic circuits Science 314, 1585-1588 (2006)
- Epigenetic regulation by long noncoding RNAs. ,
- Epigenetic regulation in pluripotent stem cells: a key to breaking the epigenetic barrier ,
- Reini F. Luco, Mariano Allo, Ignacio E. Schor, Alberto R. Kornblihtt, Tom Misteli Epigenetics in alternative pre-mRNA splicing Cell 144, 16-26 (2011)
- Eukaryotic organisms in Proterozoic oceans ,
- Matthew S. Dodd, Dominic Papineau, Tor Grenne, John F. Slack, Martin Rittner, Franco Pirajno, Jonathan O'Neil, Crispin T.S. Little Evidence for early life in Earth's oldest hydrothermal vent precipitates Nature 543, 60-64 (2017)
- Lawrence Wang, Jan P. Amend, John Doyle, Tori Hoehler, Chris Kempes Evolutionary tradeoffs in cellular composition across diverse bacteria ISME Journal 10, 2145-2157 (2016)
- Olaf Sporns, Max Lungarella Evolving Coordinated Behavior by Maximizing Information Structure Complexity 2, 323-329 (2006)
- Exact stochastic simulation of coupled chemical reactions ,
- J. V. Koski, V. F. Maisi, T. Sagawa, J. P. Pekola Experimental observation of the role of mutual information in the nonequilibrium dynamics of a Maxwell demon Physical Review Letters 113, (2014)
- Antoine Bérut, Artak Arakelyan, Artyom Petrosyan, Sergio Ciliberto, Raoul Dillenschneider, Eric Lutz Experimental verification of Landauer's principle linking information and thermodynamics Nature 483, 187-189 (2012)
- Teresa K. Barth, Axel Imhof Fast signals and slow marks: the dynamics of histone modifications Trends in Biochemical Sciences 35, 618-626 (2010)
- Takahiro Sagawa, Masahito Ueda Fluctuation theorem with information exchange: Role of correlations in stochastic thermodynamics Physical Review Letters 109, (2012)
- Thomas E. Ouldridge, Pieter Rein ten Wolde Fundamental Costs in the Production and Destruction of Persistent Polymer Copies Physical Review Letters 118, (2017)
- H. H. Hasegawa, J. Ishikawa, K. Takara, D. J. Driebe Generalization of the second law for a nonequilibrium initial state Physics Letters, Section A: General, Atomic and Solid State Physics 374, 1001-1004 (2010)
- K. Takara, H. H. Hasegawa, D. J. Driebe Generalization of the second law for a transition between nonequilibrium states Physics Letters, Section A: General, Atomic and Solid State Physics 375, 88-92 (2010)
- O. J.E. Maroney Generalizing Landauer's principle Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 79, (2009)
- Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection ,
- Jeffrey E. Barrick, Dong Su Yu, Sung Ho Yoon, Haeyoung Jeong, Tae Kwang Oh, Dominique Schneider, Richard E. Lenski, Jihyun F. Kim Genome evolution and adaptation in a long-term experiment with Escherichia coli Nature 461, 1243-1247 (2009)
- James L. Friar, Terrance Goldman, Juan Pérez-Mercader Genome sizes and the benford distribution PLoS ONE 7, (2012)
- Catherine B. Millar, Michael Grunstein Genome-wide patterns of histone modifications in yeast Nature Reviews Molecular Cell Biology 7, 657-666 (2006)
- Growth, metabolic partitioning, and the size of microorganisms ,
- Kousuke Shizume Heat generation required by information erasure Physical Review E 52, 3495-3499 (1995)
- Yael Katan-Khaykovich, Kevin Struhl Heterochromatin formation involves changes in histone modifications over multiple cell generations EMBO Journal 24, 2138-2149 (2005)
- Desiree Tillo, Noam Kaplan, Irene K. Moore, Yvonne Fondufe-Mittendorf, Andrea J. Gossett, Yair Field, Jason D. Lieb, Jonathan Widom, Eran Segal, Timothy R. Hughes High nucleosome occupancy is encoded at human regulatory sequences PLoS ONE 5, (2010)
- Yonggun Jun, Momčilo Gavrilov, John Bechhoefer High-precision test of Landauer's principle in a feedback trap Physical Review Letters 113, (2014)
- Keyan Zahedi, Nihat Ay, Ralf Der Higher coordination with less control-a result of information maximization in the sensorimotor loop Adaptive Behavior 18, 338-355 (2010)
- Helena Santos-Rosa, Antonis Kirmizis, Christopher Nelson, Till Bartke, Nehme Saksouk, Jacques Cote, Tony Kouzarides Histone H3 tail clipping regulates gene expression Nature Structural and Molecular Biology 16, 17-22 (2009)
- Vaughn Jackson, Roger Chalkley Histone Segregation on Replicating Chromatinâ Biochemistry 24, 6930-6938 (1985)
- Vaughn Jackson, Roger Chalkley Histone Segregation on Replicating Chromatin† Biochemistry 24, 6930-6938 (1985)
- B. M. Turner Histone acetylation as an epigenetic determinant of long-term transcriptional competence Cellular and Molecular Life Sciences 54, 21-31 (1998)
- Histone marks: repairing DNA breaks within the context of chromatin ,
- Nathaniel D. Heintzman, Gary C. Hon, R. David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F. Harp, Zhen Ye, Leonard K. Lee, Rhona K. Stuart, Christina W. Ching, Keith A. Ching, Jessica E. Antosiewicz-Bourget, Hui Liu, Xinmin Zhang, Roland D. Green, Victor V. Lobanenkov, Ron Stewart, James A. Thomson, Gregory E. Crawford, Manolis Kellis, Bing Ren Histone modifications at human enhancers reflect global cell-type-specific gene expression Nature 459, 108-112 (2009)
- Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli ,
- Sebastian E. Ahnert, Andrei Zinovyev, Thomas M.A. Fink How much non-coding DNA do eukaryotes require? Journal of Theoretical Biology 252, 587-592 (2008)
- Human cytochrome c oxidase: structure, function, and deficiency ,
- Human cytochrome oxidase deficiency. ,
- Minjia Tan, Hao Luo, Sangkyu Lee, Fulai Jin, Jeong Soo Yang, Emilie Montellier, Thierry Buchou, Zhongyi Cheng, Sophie Rousseaux, Nisha Rajagopal, Zhike Lu, Zhen Ye, Qin Zhu, Joanna Wysocka, Yang Ye, Saadi Khochbin, Bing Ren, Yingming Zhao Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification Cell 146, 1016-1028 (2011)
- Dominique F. Chu In silico evolution of diauxic growth BMC Evolutionary Biology 15, (2015)
- Stephen M. Fuchs, Krzysztof Krajewski, Richard W. Baker, Victoria L. Miller, Brian D. Strahl Influence of combinatorial histone modifications on antibody and effector protein recognition Current Biology 21, 53-58 (2011)
- G. Tononi Information integration: Its relevance to brain function and consciousness Archives Italiennes de Biologie 148, 299-322 (2010)
- Information measures for conscious experience ,
- Christoph Adami Information theory in molecular biology Physics of Life Reviews 1, 3-22 (2004)
- Information theory, evolution, and the origin of life ,
- Mikhail Prokopenko, Itai Einav Information thermodynamics of near-equilibrium computation Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 91, (2015)
- Hugo Touchette, Seth Lloyd Information-theoretic approach to the study of control systems Physica A: Statistical Mechanics and its Applications 331, 140-172 (2004)
- Information-theoretic lower bound on energy cost of stochastic computation ,
- Sonja J. Prohaska, David C. Krakauer, Peter Stadler Innovation in gene regulation: The case of chromatin computation Journal of Theoretical Biology 265, 27-44 (2010)
- David Balduzzi, Giulio Tononi Integrated information in discrete dynamical systems: Motivation and theoretical framework PLoS Computational Biology 4, (2008)
- Jeffrey A. Edlund, Nicolas Chaumont, Arend Hintze, Christof Koch, Giulio Tononi, Christoph Adami Integrated information increases with fitness in the evolution of animats PLoS Computational Biology 7, (2011)
- Tommaso Toffoli, Norman H. Margolus Invertible cellular automata: A review Physica D: Nonlinear Phenomena 45, 229-253 (1990)
- Rolf Landauer Irreversibility and Heat Generation in the Computing Process 5, 183-191 (1961)
- Jens Przybilla, Joerg Galle, Thimo Rohlf Is adult stem cell aging driven by conflicting modes of chromatin remodeling? BioEssays 34, 841-848 (2012)
- I. Bena, C. Van Den Broeck, R. Kawai Jarzynski equality for the Jepsen gas Europhysics Letters 71, 879-885 (2005)
- Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity ,
- Jacques Ninio Kinetic amplification of enzyme discrimination Biochimie 57, 587-595 (1975)
- Pablo Sartori, Simone Pigolotti Kinetic versus energetic discrimination in biological copying Physical Review Letters 110, (2013)
- Mark A. Lever, Karyn L. Rogers, Karen G. Lloyd, Jörg Overmann, Bernhard Schink, Rudolf K. Thauer, Tori M. Hoehler, Bo Barker Jørgensen Life under extreme energy limitation: A synthesis of laboratory- and field-based investigations FEMS Microbiology Reviews 39, 688-728 (2015)
- Dominique Chu Limited by sensing - A minimal stochastic model of the lag-phase during diauxic growth Journal of Theoretical Biology 414, 137-146 (2017)
- Thierry Mora, Ned S. Wingreen Limits of sensing temporal concentration changes by single cells Physical Review Letters 104, (2010)
- Logical Reversibility of Computation ,
- Armelle Corpet, Geneviève Almouzni Making copies of chromatin: the challenge of nucleosomal organization and epigenetic information Trends in Cell Biology 19, 29-41 (2009)
- Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression ,
- Max Lungarella, Olaf Sporns Mapping information flow in sensorimotor networks PLoS Computational Biology 2, 1301-1312 (2006)
- Robert G. Endres, Ned S. Wingreen Maximum likelihood and the single receptor Physical Review Letters 103, (2009)
- Giulio Tononi, Olaf Sporns Measuring information integration BMC Neuroscience 4, (2003)
- Danesh Moazed Mechanisms for the inheritance of chromatin states Cell 146, 510-518 (2011)
- Metabolically efficient information processing. ,
- Max Lungarella, Teresa Pegors, Daniel Bulwinkle, Olaf Sporns Methods for quantifying the informational structure of sensory and motor data Neuroinformatics 3, 243-262 (2005)
- M. Lachner, D. O'Carroll, S. Rea, K. Mechtler, T. Jenuwein Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins Nature 410, 116-120 (2001)
- Tori M. Hoehler, Bo Barker Jørgensen Microbial life under extreme energy limitation Nature Reviews Microbiology 11, 83-94 (2013)
- Takahiro Sagawa, Masahito Ueda Minimal energy cost for thermodynamic information processing: Measurement and information erasure Physical Review Letters 102, (2009)
- Rolf Landauer Minimal energy requirements in communication Science 272, 1914-1918 (1996)
- Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin ,
- Matthew R. Lakin, Andrew Phillips Modelling, simulating and verifying Turing-powerful strand displacement systems Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 6937 LNCS, 130-144 (2011)
- Hans Bremer, Patrick P Dennis Modulation of Chemical Composition and Other Parameters of the Cell by Growth Rate Escherichia coli and Salmonella: cellular and molecular biology 2, 1527-1542 (1987)
- Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora and molecular clocks. ,
- William J. McGill Multivariate information transmission IRE Professional Group on Information Theory 4, 93-111 (1954)
- Natural Selection ,
- Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems ,
- C. Jarzynski Nonequilibrium equality for free energy differences Physical Review Letters 78, 2690-2693 (1997)
- Nonequilibrium generation of information in copolymerization processes. ,
- Hong Qian, Timothy C. Reluga Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling switch Physical Review Letters 94, (2005)
- Charles H. Bennett Notes on Landauer's principle, reversible computation, and Maxwell's Demon Studies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics 34, 501-510 (2003)
- Nucleosome Structure(s) and Stability: Variations on a Theme ,
- Travis N. Mavrich, Cizhong Jiang, Ilya P. Ioshikhes, Xiaoyong Li, Bryan J. Venters, Sara J. Zanton, Lynn P. Tomsho, Ji Qi, Robert L. Glaser, Stephan C. Schuster, David S. Gilmour, Istvan Albert, B. Franklin Pugh Nucleosome organization in the Drosophila genome Nature 453, 358-362 (2008)
- Cizhong Jiang, B. Franklin Pugh Nucleosome positioning and gene regulation: Advances through genomics Nature Reviews Genetics 10, 161-172 (2009)
- Robin Andersson, Stefan Enroth, Alvaro Rada-Iglesias, Claes Wadelius, Jan Komorowski Nucleosomes are well positioned in exons and carry characteristic histone modifications Genome Research 19, 1732-1741 (2009)
- On a Statistical Estimate for the Entropy of a Sequence of Independent Random Variables ,
- Eric R. Pianka On r- and K-Selection The American Naturalist 104, 592-597 (1970)
- On the decrease of entropy in a thermodynamic system by the intervention of intelligent beings ,
- Prajwal Raj Kafle, Sanjib Sharma, Geraint F. Lewis, Joss Bland-Hawthorn On the shoulders of giants: Properties of the stellar halo and the milky way mass distribution Astrophysical Journal 794, (2014)
- Mikhail Prokopenko, Joseph T. Lizier, Don C. Price On thermodynamic interpretation of transfer entropy Entropy 15, 524-543 (2013)
- Open Markov Processes and Open Reaction Networks ,
- Kathryn E. Gardner, C. David Allis, Brian D. Strahl Operating on chromatin, a colorful language where context matters Journal of Molecular Biology 409, 36-46 (2011)
- Optimal parameter settings for information processing in gene regulatory networks. ,
- Optimal resource allocation in cellular sensing systems ,
- PRISM : Probabilistic Symbolic Model Checker ,
- Omar Haq, Ronald M. Levy, Alexandre V. Morozov, Michael Andrec Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease BMC Bioinformatics 10, (2009)
- Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli ,
- Jamie A. Hackett, Jan J. Zylicz, M. Azim Surani Parallel mechanisms of epigenetic reprogramming in the germline Trends in Genetics 28, 164-174 (2012)
- Marta Radman-Livaja, Kitty F. Verzijlbergen, Assaf Weiner, Tibor van Welsem, Nir Friedman, Oliver J. Rando, Fred van Leeuwen Patterns and mechanisms of Ancestral Histone protein inheritance in Budding yeast PLoS Biology 9, (2011)
- Catherine A. Musselman, Marie Eve Lalonde, Jacques Côté, Tatiana G. Kutateladze Perceiving the epigenetic landscape through histone readers Nature Structural and Molecular Biology 19, 1218-1227 (2012)
- Pfam ,
- Physical limits on cellular sensing of spatial gradients. ,
- H. C. Berg, E. M. Purcell Physics of chemoreception Biophysical Journal 20, 193-219 (1977)
- Predictability , Complexity , and Learning ,
- N. Ay, N. Bertschinger, R. Der, F. Güttler, E. Olbrich Predictive information and explorative behavior of autonomous robots European Physical Journal B 63, 329-339 (2008)
- Sergey Kryazhimskiy, Jonathan Dushoff, Georgii A. Bazykin, Joshua B. Plotkin Prevalence of epistasis in the evolution of influenza A surface proteins PLoS Genetics 7, (2011)
- R. M. Cormack, D. L. Hartl, A. G. Clark Principles of Population Genetics. Biometrics 46, 546 (1990)
- Thomas Gregor, David W. Tank, Eric F. Wieschaus, William Bialek Probing the Limits to Positional Information Cell 130, 153-164 (2007)
- Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach ,
- Dirk De Vos, Floor Frederiks, Marit Terweij, Tibor Van Welsem, Kitty F. Verzijlbergen, Ekaterina Iachina, Erik L. De Graaf, A. F. Maarten Altelaar, Gideon Oudgenoeg, Albert J.R. Heck, Jeroen Krijgsveld, Barbara M. Bakker, Fred Van Leeuwen Progressive methylation of ageing histones by Dot1 functions as a timer EMBO Reports 12, 956-962 (2011)
- Peter Sarkies, Julian E. Sale Propagation of histone marks and epigenetic memory during normal and interrupted DNA replication Cellular and Molecular Life Sciences 69, 697-716 (2012)
- David Balduzzi, Giulio Tononi Qualia: The geometry of integrated information PLoS Computational Biology 5, (2009)
- Sean R. Eddy, Richard Durbin RNA sequence analysis using covariance models Nucleic Acids Research 22, 2079-2088 (1994)
- Miyong Yun, Jun Wu, Jerry L. Workman, Bing Li Readers of histone modifications Cell Research 21, 564-578 (2011)
- Alexander J. Ruthenburg, Haitao Li, Thomas A. Milne, Scott Dewell, Robert K. McGinty, Melanie Yuen, Beatrix Ueberheide, Yali Dou, Tom W. Muir, Dinshaw J. Patel, C. David Allis Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions Cell 145, 692-706 (2011)
- Regulation of cell size in the yeast Saccharomyces cerevisiae. ,
- Marco Magistri, Mohammad Ali Faghihi, Georges St Laurent, Claes Wahlestedt Regulation of chromatin structure by long noncoding RNAs: Focus on natural antisense transcripts Trends in Genetics 28, 389-396 (2012)
- Representations of Space and Time in the Maximization of Information Flow in the Perception-Action Loop ,
- Joseph W. Thornton Resurrecting ancient genes: Experimental analysis of extinct molecules Nature Reviews Genetics 5, 366-375 (2004)
- Aaron Fluitt, Elsje Pienaar, Hendrik Viljoen Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis Computational Biology and Chemistry 31, 335-346 (2007)
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