Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and Biomedical Applications

[1]  T. Cao,et al.  The conceptual foundations and the philosophical aspects of renormalization theory , 1993, Synthese.

[2]  M. Gerstein,et al.  What is a gene, post-ENCODE? History and updated definition. , 2007, Genome research.

[3]  S. Counce The Strategy of the Genes , 1958, The Yale Journal of Biology and Medicine.

[4]  S. Fernberger The language and thought of the child. , 1927 .

[5]  C. Benham,et al.  Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. , 1996, Journal of molecular biology.

[6]  Andrei Zinovyev,et al.  How much non-coding DNA do eukaryotes require? , 2006, Journal of theoretical biology.

[7]  Jean-Marie Lehn,et al.  Supramolecular Chemistry / Science , 1999 .

[8]  H. Haken Synergetics: an Introduction, Nonequilibrium Phase Transitions and Self-organization in Physics, Chemistry, and Biology , 1977 .

[9]  Craig J. Benham,et al.  Computation of DNA structural variability - a new predictor of DNA regulatory regions , 1996, Comput. Appl. Biosci..

[10]  A. Pasquinelli,et al.  Genes and Mechanisms Related to RNA Interference Regulate Expression of the Small Temporal RNAs that Control C. elegans Developmental Timing , 2001, Cell.

[11]  H. Stanley,et al.  Scaling, Universality, and Renormalization: Three Pillars of Modern Critical Phenomena , 1999 .

[12]  Ali Nahvi,et al.  Genetic control by a metabolite binding mRNA. , 2002, Chemistry & biology.

[13]  Gabriel Ciobanu,et al.  Conformon-driven biopolymer shape changes in cell modeling. , 2003, Bio Systems.

[14]  Shu-Kun Lin,et al.  Modern Thermodynamics: From Heat Engines to Dissipative , 1999 .

[15]  E. Nudler,et al.  The riboswitch control of bacterial metabolism. , 2004, Trends in biochemical sciences.

[16]  R. Tjian,et al.  Molecular machines that control genes. , 1995, Scientific American.

[17]  K. Rudnick The Essential Peirce: Selected Philosophical Writings , 1993 .

[18]  R. Solé Linked: The New Science of Networks.ByAlbert‐László Barabási.Cambridge (Massachusetts): Perseus Publishing.$26.00. vii + 280 p; ill.; index. ISBN: 0–7382–0667–9. 2002. , 2003 .

[19]  M. Johnston,et al.  Feasting, fasting and fermenting. Glucose sensing in yeast and other cells. , 1999, Trends in genetics : TIG.

[20]  M V Volkenstein,et al.  The conformon. , 1972, Journal of theoretical biology.

[21]  B. Suter,et al.  Interactive proteomics: what lies ahead? , 2008, BioTechniques.

[22]  Scott A. Rifkin,et al.  Microarray analysis of Drosophila development during metamorphosis. , 1999, Science.

[23]  Sungchul Ji,et al.  Microsemiotics of DNA , 2002 .

[24]  C. Benham,et al.  Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[25]  M T Turvey,et al.  A comment on equating information with symbol strings. , 1984, The American journal of physiology.

[26]  Juan G. Roederer On the Concept of Information and Its Role in Nature , 2003, Entropy.

[27]  J. Pérez-Ortín,et al.  Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. , 2004, Molecular cell.

[28]  B. Frieden Science from Fisher Information , 2004 .

[29]  Scott H. Northrup,et al.  The stable states picture of chemical reactions. I. Formulation for rate constants and initial condition effects , 1980 .

[30]  T. Tsuda,et al.  Fibulins in development and heritable disease. , 2004, Birth defects research. Part C, Embryo today : reviews.

[31]  Hong Qian,et al.  Generalized Haldane equation and fluctuation theorem in the steady-state cycle kinetics of single enzymes. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[32]  G. Hannon,et al.  Unlocking the potential of the human genome with RNA interference , 2004, Nature.

[33]  Sungchul Ji A cell linguistic analysis of apoptosis , 1997 .

[34]  A. Leggett A Different Universe: Reinventing Physics from the Bottom Down , 2005 .

[35]  Doede Nauta,et al.  meaning of information , 1972 .

[36]  S. Ji,et al.  The bhopalator: a molecular model of the living cell based on the concepts of conformons and dissipative structures. , 1985, Journal of theoretical biology.

[37]  H. Frauenfelder,et al.  Function and Dynamics of Myoglobin a , 1987, Annals of the New York Academy of Sciences.

[38]  Michal Kurzynski The thermodynamic machinery of life , 2006 .

[39]  Vahe G. Gurzadyan,et al.  Concentric circles in WMAP data may provide evidence of violent pre-Big-Bang activity , 2010, 1011.3706.

[40]  Howard Hunt Pattee,et al.  Cell Psychology: An Evolutionary Approach to the Symbol-Matter Problem , 2012 .

[41]  Eugene I Shakhnovich,et al.  Understanding protein evolution: from protein physics to Darwinian selection. , 2008, Annual review of physical chemistry.

[42]  A. Gow,et al.  Macrophages, reactive nitrogen species, and lung injury , 2010, Annals of the New York Academy of Sciences.

[43]  X. Xie,et al.  Single-molecule enzymatic dynamics. , 1998, Science.

[44]  S Ji,et al.  The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics , 1999, Annals of the New York Academy of Sciences.

[45]  Min Chen,et al.  Data, Information, and Knowledge in Visualization , 2009, IEEE Computer Graphics and Applications.

[46]  Julien Gagneur,et al.  Modular decomposition of protein-protein interaction networks , 2004, Genome Biology.

[47]  K. Kwak,et al.  Direct observation of fast protein conformational switching , 2008, Proceedings of the National Academy of Sciences.

[48]  R. Sompallae,et al.  The MAPK Signaling Cascade is a Central Hub in the Regulation of Cell Cycle, Apoptosis and Cytoskeleton Remodeling by Tripeptidyl-Peptidase II , 2008, Gene regulation and systems biology.

[49]  R. Ranganathan,et al.  Evolutionarily conserved pathways of energetic connectivity in protein families. , 1999, Science.

[50]  Hinrich W. H. Göhlmann,et al.  A Diarylquinoline Drug Active on the ATP Synthase of Mycobacterium tuberculosis , 2005, Science.

[51]  Franco Nori,et al.  Colloquium: The physics of Maxwell's demon and information , 2007, 0707.3400.

[52]  Lotfi A. Zadeh,et al.  Fuzzy logic = computing with words , 1996, IEEE Trans. Fuzzy Syst..

[53]  Ian G. Barbour Religion and science : historical and contemporary issues , 1997 .

[54]  Eugenia Mileykovskaya,et al.  Functional Taxonomy of Bacterial Hyperstructures , 2007, Microbiology and Molecular Biology Reviews.

[55]  M. Huynen,et al.  The frequency distribution of gene family sizes in complete genomes. , 1998, Molecular biology and evolution.

[56]  P. Holliger,et al.  Ribozyme-Catalyzed Transcription of an Active Ribozyme , 2011, Science.

[57]  R. Bernards,et al.  Enabling personalized cancer medicine through analysis of gene-expression patterns , 2008, Nature.

[58]  Parviz Moin,et al.  TACKLING TURBULENCE WITH SUPERCOMPUTERS , 1997 .

[59]  T Misteli,et al.  Functional architecture in the cell nucleus. , 2001, The Biochemical journal.

[60]  Jacques Ricard,et al.  Emergent Collective Properties, Networks and Information in Biology , 2006 .

[61]  R. Breaker,et al.  Control of gene expression by a natural metabolite-responsive ribozyme , 2004, Nature.

[62]  S. Newman,et al.  Genes and proteins: Dogmas in decline , 2007, Journal of Biosciences.

[63]  Paul Cobley,et al.  Introduction to Biosemiotics: The New Biological Synthesis , 2008 .

[64]  J C Vincent,et al.  Hypothesis: hyperstructures regulate bacterial structure and the cell cycle. , 1999, Biochimie.

[65]  Robert L. Perlman The Plausibility of Life: Resolving Darwin's Dilemma (review) , 2007 .

[66]  E. Robinson Cybernetics, or Control and Communication in the Animal and the Machine , 1963 .

[67]  D E Green,et al.  Electromechanochemical model of mitochondrial structure and function. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Eugene I. Shakhnovich,et al.  Protein stability imposes limits on organism complexity and speed of molecular evolution , 2007, Proceedings of the National Academy of Sciences.

[69]  Su Lin,et al.  Protein Dynamics Control the Kinetics of Initial Electron Transfer in Photosynthesis , 2007, Science.

[70]  Martin Jähnert Quantum Theory at the Crossroads: Reconsidering the 1927 Solvay Conference Quantum theory at the Crossroads: Reconsidering the 1927 Solvay Conference , Guido Bacciagaluppi and Antony Valentini Cambridge U. Press, New York, 2009. $126.00 (530 pp.). ISBN 978-0-521-81421-8 , 2010 .

[71]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[72]  J. Spudich,et al.  Single myosin molecule mechanics: piconewton forces and nanometre steps , 1994, Nature.

[73]  M. Hisakado Breather trapping mechanism in piecewise homogeneous DNA , 1997 .

[74]  C. F. Hockett The origin of speech. , 1960, Scientific American.

[75]  Charles Sanders Peirce,et al.  On a New List of Categories , 2006 .

[76]  J. Pérez-Ortín,et al.  Mechanism-based clustering of genome-wide RNA levels: Roles of transcription and transcript-degradation rates , 2009 .

[77]  M. V. Volkenstein,et al.  Electronic-conformational interactions in biopolymers , 1979 .

[78]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[79]  Jessica L. Cundiff Center for Discrete Mathematics and Theoretical , 2012 .

[80]  B. Spinoza A Spinoza Reader: The Ethics and Other Works , 2020 .

[81]  Adrian Bejan,et al.  The constructal law of design and evolution in nature , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[82]  A. Kudlicki,et al.  Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes , 2005, Science.

[83]  J. Onuchic,et al.  Protein folding funnels: a kinetic approach to the sequence-structure relationship. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[84]  Helena Brentani,et al.  Gene Expression Profile Associated with Response to Doxorubicin-Based Therapy in Breast Cancer , 2005, Clinical Cancer Research.

[85]  P. Davies,et al.  Special relativity , 1975, Nature.

[86]  David G. Nicholls,et al.  Bioenergetics an Introduction to the Chemiosmotic Theory , 1982 .

[87]  M. Magnasco,et al.  Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. , 2003, Genome research.

[88]  S. Volkov Conformational breather in a DNA macromolecule , 1996 .

[89]  T. Cech,et al.  Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena , 1982, Cell.

[90]  Adrian Be Jan Constructal-theory network of conducting paths for cooling a heat generating volume , 1997 .

[91]  Peter J. Beek,et al.  Dynamical Models of Movement Coordination , 1995 .

[92]  Kerson Huang Fundamental Forces of Nature: The Story of Gauge Fields , 2007 .

[93]  J. Trosko Gap Junctional Intercellular Communication as a Biological “Rosetta Stone” in Understanding, in a Systems Biological Manner, Stem Cell Behavior, Mechanisms of Epigenetic Toxicology, Chemoprevention and Chemotherapy , 2007, Journal of Membrane Biology.

[94]  V. Colapietro,et al.  Glossary of semiotics , 1993 .

[95]  Neal S. Holter,et al.  Fundamental patterns underlying gene expression profiles: simplicity from complexity. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[96]  E. Gould Mechanism and Structure in Organic Chemistry , 1969 .

[97]  G. R. Welch,et al.  On the Field Structure of Metabolic Space-Time , 1990 .

[98]  C. B. Pickett,et al.  The Nrf2-Antioxidant Response Element Signaling Pathway and Its Activation by Oxidative Stress* , 2009, Journal of Biological Chemistry.

[99]  Pierluigi Frisco,et al.  Conformons-P Systems , 2002, DNA.

[100]  Antoine M. van Oijen,et al.  Single-molecule studies of the replisome. , 2010, Annual review of biophysics.

[101]  L. Darden Reasoning in Biological Discoveries: Essays on Mechanisms, Interfield Relations, and Anomaly Resolution , 2006 .

[102]  J. Fodor,et al.  What Darwin Got Wrong , 2010 .

[103]  Rajeev Ramanath,et al.  Blackbody Radiation , 2014, Computer Vision, A Reference Guide.

[104]  Huda Akil,et al.  Gene chips and arrays revealed: a primer on their power and their uses , 1999, Biological Psychiatry.

[105]  Hyeong Jun An,et al.  Estimating the size of the human interactome , 2008, Proceedings of the National Academy of Sciences.

[106]  S Ji,et al.  The cell as the smallest DNA-based molecular computer. , 1999, Bio Systems.

[107]  W. R. Lieb,et al.  ACTIVE TRANSPORT OF CATIONS ACROSS BIOLOGICAL MEMBRANES , 1974, Annals of the New York Academy of Sciences.

[108]  Lippincott-Schwartz,et al.  Supporting Online Material Materials and Methods Som Text Figs. S1 to S8 Table S1 Movies S1 to S3 a " Silent " Polymorphism in the Mdr1 Gene Changes Substrate Specificity Corrected 30 November 2007; See Last Page , 2022 .

[109]  Enzymatic catalysis as a process controlled by protein conformational relaxation , 1993, FEBS letters.

[110]  U. Alon,et al.  Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[111]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[112]  M. Barbieri The Code Model of Semiosis: The First Steps Toward a Scientific Biosemiotics , 2008 .

[113]  S. Ji,et al.  Free energy and information contents of conformons in proteins and DNA. , 2000, Bio Systems.

[114]  S. Gould,et al.  Punctuated equilibria: an alternative to phyletic gradualism , 1972 .

[115]  Albert-László Barabási,et al.  Scale-Free Networks: A Decade and Beyond , 2009, Science.

[116]  Steven Pinker,et al.  The Blank Slate , 2006 .

[117]  T. Gelder,et al.  Mind as Motion: Explorations in the Dynamics of Cognition , 1995 .

[118]  Dagmar Ringe,et al.  “Sleeping Beauty”: Quiescence in Saccharomyces cerevisiae , 2004, Microbiology and Molecular Biology Reviews.

[119]  Luciano Floridi,et al.  Trends in the Philosophy of Information , 2008 .

[120]  S Ji,et al.  Isomorphism between cell and human languages: molecular biological, bioinformatic and linguistic implications. , 1997, Bio Systems.

[121]  D. Boal Mechanics of the Cell: Membranes , 2012 .

[122]  Nicholas V Swindale Neural Synchrony, Axonal Path Lengths, and General Anesthesia: A Hypothesis , 2003, The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry.

[123]  Wolfgang Fischle,et al.  Binary switches and modification cassettes in histone biology and beyond , 2003, Nature.

[124]  P. Gowaty Developmental Plasticity and Evolution Mary Jane West-Eberhard , 2005, Animal Behaviour.

[125]  S. Mundlos,et al.  Heritable diseases of the skeleton. Part I: Molecular insights into skeletal development‐transcription factors and signaling pathways 1 , 1997, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[126]  D. Ingber The architecture of life. , 1998, Scientific American.

[127]  L. Prescott,et al.  Paracetamol, alcohol and the liver. , 2000, British journal of clinical pharmacology.

[128]  L. Zadeh Discussion: probability theory and fuzzy logic are complementary rather than competitive , 1995 .

[129]  Alexander N. Gorban,et al.  Elastic Principal Graphs and Manifolds and their Practical Applications , 2005, Computing.

[130]  M. Fried Biochemistry, Third Edition (Armstrong, Frank B.) , 1990 .

[131]  S Ji ENERGY AND NEGENTROPY IN ENZYMIC CATALYSIS * , 1974, Annals of the New York Academy of Sciences.

[132]  R. Raghow Regulation of messenger RNA turnover in eukaryotes , 1987 .

[133]  M. Barbieri Biosemiotics: a new understanding of life , 2008, Naturwissenschaften.

[134]  Craig R. White,et al.  Allometric scaling of mammalian metabolism , 2005, Journal of Experimental Biology.

[135]  K. Okamoto DNA microarrays in cancer diagnosis and prognosis , 2006 .

[136]  D. Long Networks of the Brain , 2011 .

[137]  T. L. Short Peirce's Theory of Signs , 2007 .

[138]  A. Corney,et al.  Atomic and laser spectroscopy , 1977 .

[139]  Rodrigo Lopez,et al.  Multiple sequence alignment with the Clustal series of programs , 2003, Nucleic Acids Res..

[140]  S. Grewal,et al.  Heterochromatin revisited , 2007, Nature Reviews Genetics.

[141]  J. Dubochet,et al.  Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. , 1995, Journal of molecular biology.

[142]  Rama Ranganathan,et al.  Knowledge-based potentials in protein design. , 2006, Current opinion in structural biology.

[143]  G. Storz An Expanding Universe of Noncoding RNAs , 2002, Science.

[144]  Michael T. Turvey,et al.  Control parameters, equilibria, and coordination dynamics , 1995, Behavioral and Brain Sciences.

[145]  J. Rowlinson The critical point: A historical introduction to the modern theory of critical phenomena , 1997 .

[146]  E. Katayama,et al.  Higher plant myosin XI moves processively on actin with 35 nm steps at high velocity , 2003, The EMBO journal.

[147]  John A. Gowan Introduction to Information , 2014 .

[148]  M. Fisher Renormalization group theory: Its basis and formulation in statistical physics , 1998 .

[149]  Hong Qian,et al.  Open-system nonequilibrium steady state: statistical thermodynamics, fluctuations, and chemical oscillations. , 2006, The journal of physical chemistry. B.

[150]  K. Peeva,et al.  Computing behavior of finite fuzzy machines - Algorithm and its application to reduction and minimization , 2008, Inf. Sci..

[151]  H. Frauenfelder,et al.  Proteins are paradigms of stochastic complexity , 2005 .

[152]  J. Vilardell,et al.  The quest for a message: budding yeast, a model organism to study the control of pre-mRNA splicing. , 2008, Briefings in functional genomics & proteomics.

[153]  Ned S Wingreen,et al.  Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression , 2003, The EMBO journal.

[154]  M. Volkenstein,et al.  Entropy and Information , 2009 .

[155]  Eugene I. Shakhnovich,et al.  A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds , 2007, PLoS Comput. Biol..

[156]  G. Vogel,et al.  A Seismic Shift for Stem Cell Research , 2008, Science.

[157]  Jirí Wiedermann,et al.  Characterizing the super-Turing computing power and efficiency of classical fuzzy Turing machines , 2004, Theor. Comput. Sci..

[158]  P. W. Anderson,et al.  Suggested model for prebiotic evolution: the use of chaos. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[159]  Howard Hunt Pattee,et al.  Evolving Self-reference: Matter, Symbols, and Semantic Closure , 2012 .

[160]  Grégoire Nicolis,et al.  Self-Organization in nonequilibrium systems , 1977 .

[161]  A. Chinnaiyan,et al.  Bioinformatics Strategies for Translating Genome‐Wide Expression Analyses into Clinically Useful Cancer Markers , 2004, Annals of the New York Academy of Sciences.

[162]  William M. Lee,et al.  Acetaminophen‐induced acute liver failure: Results of a United States multicenter, prospective study , 2005, Hepatology.

[163]  Guo-Ping Zhao,et al.  Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux , 2010, Science.

[164]  G. Jona,et al.  Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast. , 2000, Biochimica et biophysica acta.

[165]  S. P. Fodor,et al.  Light-generated oligonucleotide arrays for rapid DNA sequence analysis. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[166]  Lotfi A. Zadeh,et al.  From Computing with Numbers to Computing with Words - from Manipulation of Measurements to Manipulation of Perceptions , 2005, Logic, Thought and Action.

[167]  Sunney Xie,et al.  Single‐Molecule Approach to Enzymology , 2001 .

[168]  J. S. Wicken Entropy and Information: Suggestions for Common Language , 1987, Philosophy of Science.

[169]  Ilya A. Balabin,et al.  Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. , 2004, Biophysical journal.

[170]  J. C. Clemens,et al.  Drosophila Dscam Is an Axon Guidance Receptor Exhibiting Extraordinary Molecular Diversity , 2000, Cell.

[171]  Howard Hunt Pattee,et al.  The Physical Basis of Coding and Reliability in Biological Evolution , 1967 .

[172]  Helge Kragh,et al.  Max Planck: the reluctant revolutionary , 2000 .

[173]  W. P. Russ,et al.  Evolutionary information for specifying a protein fold , 2005, Nature.

[174]  M. Nakasako,et al.  Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution , 2000, Nature.

[175]  R. Lumry,et al.  Mechanisms of Electron Transfer , 1966 .

[176]  J A Sullivan,et al.  Intracellular free calcium localization in neutrophils during phagocytosis. , 1985, Science.

[177]  Adilson E. Motter,et al.  Spontaneous Reaction Silencing in Metabolic Optimization , 2008, PLoS Comput. Biol..

[178]  Britt Anderson,et al.  A multielectrode study of the inferotemporal cortex in the monkey: effects of grouping on spike rates and synchrony , 2006, Neuroreport.

[179]  John D. Storey,et al.  Precision and functional specificity in mRNA decay , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[180]  Sungchul Ji,et al.  The electromechanochemical model of mitochondrial structure and function , 1972 .

[181]  Jennifer A Zallen,et al.  Patterned gene expression directs bipolar planar polarity in Drosophila. , 2004, Developmental cell.

[182]  Eliseo Fernández Signs and Instruments: The Convergence of Aristotelian and Kantian Intuitions in Biosemiotics , 2008, Biosemiotics.

[183]  H. Callen,et al.  Thermodynamics : an introduction to the physical theories of equilibrium thermostatics and irreversible thermodynamics. , 1966 .

[184]  D. Manolopoulos,et al.  Nonadiabatic Interactions in the Cl + H2 Reaction Probed by ClH2- and ClD2- Photoelectron Imaging , 2008, Science.

[185]  O. Hobert Gene Regulation by Transcription Factors and MicroRNAs , 2008, Science.

[186]  M. West-Eberhard,et al.  Evolution in the light of developmental and cell biology, and vice versa. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[187]  S. Johnston,et al.  Nondissociation of GAL4 and GAL80 in vivo after galactose induction. , 1992, Science.

[188]  J. K. Kundu,et al.  Nrf2-Keap1 Signaling as a Potential Target for Chemoprevention of Inflammation-Associated Carcinogenesis , 2010, Pharmaceutical Research.

[189]  Ernst Niebur,et al.  The Effects of Input Rate and Synchrony on a Coincidence Detector: Analytical Solution , 2003, Neural Computation.

[190]  D. Koshland Application of a Theory of Enzyme Specificity to Protein Synthesis. , 1958, Proceedings of the National Academy of Sciences of the United States of America.

[191]  C. Jung,et al.  Synchronicity: An Acausal Connecting Principle , 1960 .

[192]  S. Ji A general theory of chemical cytotoxicity based on a molecular model of the living cell, the Bhopalator , 2004, Archives of Toxicology.

[193]  Christian A. Rees,et al.  Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[194]  D. Corfield Conceptual mathematics: a first introduction to categories , 2002 .

[195]  J. Manautou,et al.  Emerging Role of Nrf2 in Protecting Against Hepatic and Gastrointestinal Disease , 2007, Toxicologic pathology.

[196]  C W McClare,et al.  Chemical machines, Maxwell's demon and living organisms. , 1971, Journal of theoretical biology.

[197]  D S Goodsell,et al.  Inside a living cell. , 1991, Trends in biochemical sciences.

[198]  M. Sano,et al.  Experimental demonstration of information-to-energy conversion and validation of the generalized Jarzynski equality , 2010 .

[199]  C. J. Roberts,et al.  Developing gene expression signatures of pathway deregulation in tumors , 2006, Molecular Cancer Therapeutics.

[200]  J. Kelso,et al.  The Complementary Nature , 2006 .

[201]  C. Allis,et al.  Linking the epigenetic ‘language’ of covalent histone modifications to cancer , 2004, British Journal of Cancer.

[202]  Hong Qian,et al.  Phosphorylation energy hypothesis: open chemical systems and their biological functions. , 2007, Annual review of physical chemistry.

[203]  M. Gelfand,et al.  Riboswitches: the oldest mechanism for the regulation of gene expression? , 2004, Trends in genetics : TIG.

[204]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[205]  Ann M Stock,et al.  Two-component signal transduction. , 2000, Annual review of biochemistry.

[206]  D. Laskin,et al.  Potential role of activated macrophages in acetaminophen hepatotoxicity. II. Mechanism of macrophage accumulation and activation. , 1986, Toxicology and applied pharmacology.

[207]  J. Feibleman An introduction to Peirce's philosophy : interpreted as a system , 1948 .

[208]  Gheorghe Paun,et al.  Membrane Computing , 2002, Natural Computing Series.

[209]  J. Winderickx,et al.  From feast to famine; adaptation to nutrient availability in yeast , 2003 .

[210]  E. Greenberg,et al.  Signalling: Listening in on bacteria: acyl-homoserine lactone signalling , 2002, Nature Reviews Molecular Cell Biology.

[211]  Daniel McNeill Fuzzy Logic: The Revolutionary Computer Technology That Is Changing Our World , 1993 .

[212]  Patrick Aloy,et al.  Ten thousand interactions for the molecular biologist , 2004, Nature Biotechnology.

[213]  Shing-Tung Yau Mathematics: Its content, methods, and meaning , 2014 .

[214]  Dan S. Tawfik,et al.  A propagating ERKII switch forms zones of elevated dendritic activation correlated with plasticity. , 2007, HFSP journal.

[215]  Pierluigi Frisco,et al.  Towards a Hierarchy of Conformons-P Systems , 2002, WMC-CdeA.

[216]  Robert H. Wilkinson,et al.  A Method of Generating Functions of Several Variables Using Analog Diode Logic , 1963, IEEE Trans. Electron. Comput..

[217]  Hiroyuki Noji,et al.  High-Speed Atomic Force Microscopy Reveals Rotary Catalysis of Rotorless F1-ATPase , 2011, Science.

[218]  Charles Seife Decoding the Universe: How the New Science of Information Is Explaining Everything in the Cosmos, from Our Brains to Black Holes , 2007 .

[219]  T. Gelder,et al.  It's about time: an overview of the dynamical approach to cognition , 1996 .

[220]  R R Breaker,et al.  Structural diversity of self-cleaving ribozymes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[221]  J. Kelso,et al.  Coordination Dynamics: Issues and Trends , 2004, Understanding Complex Systems.

[222]  Joshua D. Rabinowitz,et al.  Quorum Sensing Controls Biofilm Formation in Vibrio cholerae through Modulation of Cyclic Di-GMP Levels and Repression of vpsT , 2004, Journal of bacteriology.

[223]  G. R. Welch,et al.  On the "cytosociology" of enzyme action in vivo: a novel thermodynamic correlate of biological evolution. , 1981, Journal of theoretical biology.

[224]  Waldo E. Haisley,et al.  The Cosmic Code: Quantum Physics as the Language of Nature by Heinz R. Pagels (review) , 2017 .

[225]  M. Gorospe,et al.  Global analysis of stress-regulated mRNA turnover by using cDNA arrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[226]  Robert J.P. Williams,et al.  Electron Transfer and Energy Conservation , 1969 .

[227]  Robert Zwanzig,et al.  Rate processes with dynamical disorder , 1990 .

[228]  J. Murray How the Leopard Gets Its Spots. , 1988 .

[229]  R. Breaker,et al.  Riboswitches as versatile gene control elements. , 2005, Current opinion in structural biology.

[230]  J. Kelso,et al.  Coordination dynamics of learning and transfer: collective and component levels. , 1997, Journal of experimental psychology. Human perception and performance.

[231]  Christian A. Rees,et al.  Molecular portraits of human breast tumours , 2000, Nature.

[232]  Y. Surh,et al.  Cancer chemoprevention with dietary phytochemicals , 2003, Nature Reviews Cancer.

[233]  C. Will,et al.  Spliceosome structure and function. , 2011, Cold Spring Harbor perspectives in biology.

[234]  Li Rong Gene expression microarray data mining system , 2009 .

[235]  P. Wolynes,et al.  Spin glasses and the statistical mechanics of protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[236]  Rainer Goebel,et al.  Genetic Contribution to Variation in Cognitive Function: An fMRI Study in Twins , 2009, Science.

[237]  J. Schwartz,et al.  Theory of Self-Reproducing Automata , 1967 .

[238]  M. Burczynski,et al.  Clinical pharmacogenomics and transcriptional profiling in early phase oncology clinical trials. , 2005, Current molecular medicine.

[239]  Hans Christian,et al.  Information: The New Language of Science , 2003 .

[240]  John Lyons,et al.  Language and linguistics , 1974, Language Teaching: Abstracts.

[241]  Bor-Sen Chen,et al.  Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets , 2008, BMC Systems Biology.

[242]  L. MacMillan-Crow,et al.  Reactive nitrogen species in acetaminophen-induced mitochondrial damage and toxicity in mouse hepatocytes. , 2010, Chemical research in toxicology.

[243]  Andrew S. Tanenbaum,et al.  Structured Computer Organization , 1976 .

[244]  Steven Horst,et al.  Symbols and Computation A Critique of the Computational Theory of Mind , 1999, Minds and Machines.

[245]  S. Ji A model of oxidative phosphorylation that accommodates the chemical intermediate, chemiosmotic, localized proton and conformational hypotheses. , 1976, Journal of theoretical biology.

[246]  R. Oerter The Theory of Almost Everything: The Standard Model, the Unsung Triumph of Modern Physics , 2005 .

[247]  A. M. Turing,et al.  The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

[248]  Clive R. Bagshaw,et al.  Blinking fluorophores: what do they tell us about protein dynamics? , 2006, Biochemical Society transactions.

[249]  J. Wheeler Information, physics, quantum: the search for links , 1999 .

[250]  Masataka Kinjo,et al.  A quantum dot-based ratiometric pH sensor. , 2010, Chemical communications.

[251]  M. Burgin THE ESSENCE OF INFORMATION: PARADOXES, CONTRADICTIONS, AND SOLUTIONS , 2002 .

[252]  H Frauenfelder,et al.  The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[253]  R. Breaker,et al.  Deoxyribozymes: new activities and new applications , 2002, Cellular and Molecular Life Sciences CMLS.

[254]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[255]  Yixue Li,et al.  Regulation of Cellular Metabolism by Protein Lysine Acetylation , 2010, Science.

[256]  Gerald E. Flueckiger The Law of Requisite Variety , 1995 .

[257]  R. Tolman,et al.  The Principles of Statistical Mechanics. By R. C. Tolman. Pp. xix, 661. 40s. 1938. International series of monographs on physics. (Oxford) , 1939, The Mathematical Gazette.

[258]  A. A. Frost,et al.  Kinetics and mechanism : a study of homogeneous chemical reactions , 1961 .

[259]  I. McGilvray,et al.  Atoms, metaphors, and paradoxes , 1993 .

[260]  Yoash Shapira,et al.  Seeking the foundations of cognition in bacteria: From Schrödinger's negative entropy to latent information , 2006 .

[261]  B. Alberts The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists , 1998, Cell.

[262]  H. Pattee How Does a Molecule Become a Message , 2012 .

[263]  Andrei Paun,et al.  Computing by Communication in Networks of Membranes , 2002, Int. J. Found. Comput. Sci..

[264]  Roman Bauer,et al.  Perceptual grouping correlates with short synchronization in monkey prestriate cortex , 2002, Neuroreport.

[265]  Wolf Singer,et al.  Features of neuronal synchrony in mouse visual cortex. , 2003, Journal of neurophysiology.

[266]  R. Marchase,et al.  The posttranslational modification of phosphoglucomutase is regulated by galactose induction and glucose repression in Saccharomyces cerevisiae , 1995, Journal of bacteriology.

[267]  F. T. Wall Chemical thermodynamics : a course of study , 1965 .

[268]  S. Armstrong,et al.  Microarrays to identify new therapeutic strategies for cancer. , 2007, Advances in cancer research.

[269]  Alexander Gorban,et al.  ELASTIC PRINCIPAL MANIFOLDS AND THEIR PRACTICAL APPLICATIONS , 2004 .

[270]  S. Ji,et al.  Reversible and irreversible inhibition of hepatic mitochondrial respiration by acetaminophen and its toxic metabolite, N-acetyl-p-benzoquinoneimine (NAPQI). , 1989, Biochemical pharmacology.

[271]  J Umerez,et al.  Howard Pattee's theoretical biology--a radical epistemological stance to approach life, evolution and complexity. , 2001, Bio Systems.

[272]  D. Kaiser Growing Explanations: Historical Perspectives on Recent Science , 2006 .

[273]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[274]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[275]  Peter Atkins,et al.  Four Laws That Drive the Universe , 2007 .

[276]  Michio Kaku,et al.  Beyond Einstein: The Cosmic Quest for the Theory of the Universe , 1987 .

[277]  R. Guimarães The Organic Codes: an introduction to semantic biology , 2003 .

[278]  Geoffrey B. West,et al.  Life's Universal Scaling Laws , 2004 .