Advances in Systems Biology
暂无分享,去创建一个
Andrew B. Goryachev | J. M. Gephart | I. Goryanin | A. Goryachev | L. Opresko | Igor I. Goryanin | Michaela B. Mann
[1] Josep Clotet,et al. The stress-activated protein kinase Hog1 mediates S phase delay in response to osmostress. , 2009, Molecular biology of the cell.
[2] M. Ueda,et al. Stochastic signal processing and transduction in chemotactic response of eukaryotic cells. , 2007, Biophysical journal.
[3] J. Small,et al. The comings and goings of actin: coupling protrusion and retraction in cell motility. , 2005, Current opinion in cell biology.
[4] M. Klass,et al. Development of the reproductive system of Caenorhabditis elegans. , 1976, Developmental biology.
[5] W. Bialek,et al. Probing the Limits to Positional Information , 2007, Cell.
[6] J. Warringer,et al. The HOG Pathway Dictates the Short-Term Translational Response after Hyperosmotic Shock , 2010, Molecular biology of the cell.
[7] Zhi Wang,et al. Correction: In Search of the Biological Significance of Modular Structures in Protein Networks , 2007, PLoS Comput. Biol..
[8] Barbara M. Bakker,et al. Systems biology towards life in silico: mathematics of the control of living cells , 2009, Journal of mathematical biology.
[9] J. Thorner,et al. Stress resistance and signal fidelity independent of nuclear MAPK function , 2008, Proceedings of the National Academy of Sciences.
[10] Jun Dong,et al. Understanding network concepts in modules , 2007, BMC Systems Biology.
[11] Julien Gagneur,et al. Hierarchical Analysis of Dependency in Metabolic Networks , 2003, Bioinform..
[12] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[13] John J Tyson,et al. Functional motifs in biochemical reaction networks. , 2010, Annual review of physical chemistry.
[14] L. Hood,et al. Reverse Engineering of Biological Complexity , 2007 .
[15] Kazuo Tatebayashi,et al. Glycosylation defects activate filamentous growth Kss1 MAPK and inhibit osmoregulatory Hog1 MAPK , 2009, The EMBO journal.
[16] W. Rappel,et al. Receptor noise limitations on chemotactic sensing , 2008, Proceedings of the National Academy of Sciences.
[17] Léa Trichet,et al. VASP governs actin dynamics by modulating filament anchoring. , 2007, Biophysical journal.
[18] Jörg Stelling,et al. Towards a Virtual Biological Laboratory , 2001 .
[19] E. Hubbard,et al. Soma‐germline interactions that influence germline proliferation in Caenorhabditis elegans , 2010, Developmental dynamics : an official publication of the American Association of Anatomists.
[20] J. Albrecht,et al. Identification of gelsolin, a Ca2+-dependent regulatory protein of actin gel-sol transformation, and its intracellular distribution in a variety of cells and tissues , 1981, The Journal of cell biology.
[21] W. Bialek,et al. Physical limits to biochemical signaling. , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[22] K. Vahala. Handbook of stochastic methods for physics, chemistry and the natural sciences , 1986, IEEE Journal of Quantum Electronics.
[23] George Oster,et al. Force generation by actin polymerization II: the elastic ratchet and tethered filaments. , 2003, Biophysical journal.
[24] J. M. Oliver,et al. Thin-film theories for two-phase reactive flow models of active cell motion. , 2005, Mathematical medicine and biology : a journal of the IMA.
[25] Dana T Byrd,et al. Cellular analyses of the mitotic region in the Caenorhabditis elegans adult germ line. , 2006, Molecular biology of the cell.
[26] T. Stossel,et al. Control of cytoplasmic actin gel–sol transformation by gelsolin, a calcium-dependent regulatory protein , 1979, Nature.
[27] D. Lauffenburger,et al. Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data , 2009, Molecular systems biology.
[28] M. Roizen,et al. Hallmarks of Cancer: The Next Generation , 2012 .
[29] W. Bialek,et al. Information flow and optimization in transcriptional regulation , 2007, Proceedings of the National Academy of Sciences.
[30] Kazuyuki Aihara,et al. An optimal number of molecules for signal amplification and discrimination in a chemical cascade. , 2006, Biophysical journal.
[31] H. Saito,et al. Dynamic control of yeast MAP kinase network by induced association and dissociation between the Ste50 scaffold and the Opy2 membrane anchor. , 2010, Molecular cell.
[32] F. Tostevin,et al. Effect of feedback on the fidelity of information transmission of time-varying signals. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.
[33] Masahiro Ueda,et al. Noise generation, amplification and propagation in chemotactic signaling systems of living cells , 2008, Biosyst..
[34] Johan Paulsson,et al. Summing up the noise , 2004 .
[35] Tim Schedl,et al. Multi-pathway control of the proliferation versus meiotic development decision in the Caenorhabditis elegans germline. , 2004, Developmental biology.
[36] T. Beyer,et al. Multiscale modeling of cell mechanics and tissue organization , 2009, IEEE Engineering in Medicine and Biology Magazine.
[37] Julio Saez-Rodriguez,et al. Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules , 2008, ECCB.
[38] R. Quirion,et al. Molecular basis of programmed cell death involved in neurodegeneration , 2005, Trends in Neurosciences.
[39] Josep Clotet,et al. Control of Cell Cycle Progression by the Stress-Activated Hog1 MAPK , 2005, Cell cycle.
[40] James Monypenny,et al. Ezrin is a downstream effector of trafficking PKC–integrin complexes involved in the control of cell motility , 2001, The EMBO journal.
[41] K. Rottner,et al. Regulation of actin dynamics by WASP and WAVE family proteins. , 2004, Trends in cell biology.
[42] Klemens Rottner,et al. The lamellipodium: where motility begins. , 2002, Trends in cell biology.
[43] P. Vallotton,et al. Shifting views on the leading role of the lamellipodium in cell migration: speckle tracking revisited , 2009, Journal of Cell Science.
[44] Jonathan A. Cooper,et al. Dynamics of capping protein and actin assembly in vitro: uncapping barbed ends by polyphosphoinositides , 1996, The Journal of cell biology.
[45] W. Rappel,et al. Receptor noise and directional sensing in eukaryotic chemotaxis. , 2008, Physical review letters.
[46] Tilo Beyer,et al. Modeling emergent tissue organization involving high-speed migrating cells in a flow equilibrium. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.
[47] S. Hohmann,et al. Combination of Two Activating Mutations in One HOG1 Gene Forms Hyperactive Enzymes That Induce Growth Arrest , 2003, Molecular and Cellular Biology.
[48] D. Lauffenburger. Cell signaling pathways as control modules: complexity for simplicity? , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[49] Frank Allgöwer,et al. An Approach for Dividing Models of Biological Reaction Networks into Functional Units , 2003, Simul..
[50] E. Klipp,et al. Signal integration in budding yeast. , 2010, Biochemical Society transactions.
[51] J. Stelling,et al. Genome‐scale metabolic networks , 2009, Wiley interdisciplinary reviews. Systems biology and medicine.
[52] A. Gartner,et al. Germline survival and apoptosis. , 2008, WormBook : the online review of C. elegans biology.
[53] Y. Iwasa,et al. Prey Distribution as a Factor Determining the Choice of Optimal Foraging Strategy , 1981, The American Naturalist.
[54] W. Richards,et al. Perception as Bayesian Inference , 2008 .
[55] A. K. Corsi. A biochemist's guide to Caenorhabditis elegans. , 2006, Analytical biochemistry.
[56] N. Saito,et al. Unphosphorylated MARCKS is involved in neurite initiation induced by insulin‐like growth factor‐I in SH‐SY5Y cells , 2006, Journal of cellular physiology.
[57] P. Dayan,et al. Optimizing chemotaxis by measuring unbound–bound transitions , 2010 .
[58] N. Munakata. [Genetics of Caenorhabditis elegans]. , 1989, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.
[59] Tetsuya J. Kobayashi,et al. Dynamics of intracellular information decoding , 2011, Physical biology.
[60] Eduardo D. Sontag,et al. Adaptation and regulation with signal detection implies internal model , 2003, Syst. Control. Lett..
[61] Eduardo D. Sontag,et al. Monotone and near-monotone biochemical networks , 2007, Systems and Synthetic Biology.
[62] A. Barabasi,et al. Power Laws in Biological Networks , 2004, q-bio/0401010.
[63] Thomas Duke,et al. Simulation of cell motility that reproduces the force–velocity relationship , 2010, Proceedings of the National Academy of Sciences.
[64] Gasper Tkacik,et al. Optimizing information flow in small genetic networks. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.
[65] Yanchi Liu,et al. Community detection in graphs through correlation , 2014, KDD.
[66] Ricard V Solé,et al. When metabolism meets topology: Reconciling metabolite and reaction networks , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.
[67] T. Stradal,et al. Protein complexes regulating Arp2/3-mediated actin assembly. , 2006, Current opinion in cell biology.
[68] H. Nagumo,et al. Rho-associated kinase phosphorylates MARCKS in human neuronal cells. , 2001, Biochemical and biophysical research communications.
[69] Helen L. Yin,et al. Gelsolin, a Multifunctional Actin Regulatory Protein* , 1999, The Journal of Biological Chemistry.
[70] Jörg Stelling,et al. Computational design of synthetic gene circuits with composable parts , 2008, Bioinform..
[71] Rajesh P. N. Rao,et al. Bayesian brain : probabilistic approaches to neural coding , 2006 .
[72] Ned S Wingreen,et al. Information processing and signal integration in bacterial quorum sensing , 2009, Molecular systems biology.
[73] J. Stark,et al. Network motifs: structure does not determine function , 2006, BMC Genomics.
[74] T. Svitkina,et al. Orientational order of the lamellipodial actin network as demonstrated in living motile cells. , 2003, Molecular biology of the cell.
[75] Lena Gustafsson,et al. Distinct Intracellular Localization of Gpd1p and Gpd2p, the Two Yeast Isoforms of NAD+-dependent Glycerol-3-phosphate Dehydrogenase, Explains Their Different Contributions to Redox-driven Glycerol Production* , 2004, Journal of Biological Chemistry.
[76] Steffen Klamt,et al. Hypergraphs and Cellular Networks , 2009, PLoS Comput. Biol..
[77] J. Doyle,et al. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[78] K. Kaibuchi,et al. Phosphorylation of Moesin by Rho-associated Kinase (Rho-kinase) Plays a Crucial Role in the Formation of Microvilli-like Structures* , 1998, The Journal of Biological Chemistry.
[79] Edda Klipp,et al. A Quantitative Study of the Hog1 MAPK Response to Fluctuating Osmotic Stress in Saccharomyces cerevisiae , 2010, PloS one.
[80] Guenter P. Resch,et al. Electron tomography reveals unbranched networks of actin filaments in lamellipodia , 2010, Nature Cell Biology.
[81] E D Sontag,et al. Some new directions in control theory inspired by systems biology. , 2004, Systems biology.
[82] Thierry Emonet,et al. Understanding Modularity in Molecular Networks Requires Dynamics , 2009, Science Signaling.
[83] Hal L. Smith. Monotone Dynamical Systems: A Quick Tour , 2011 .
[84] E. Hubbard,et al. Introduction to the germ line. , 2005, WormBook : the online review of C. elegans biology.
[85] Tetsuya J Kobayashi,et al. Implementation of dynamic Bayesian decision making by intracellular kinetics. , 2010, Physical review letters.
[86] Eduardo Sontag,et al. Untangling the wires: A strategy to trace functional interactions in signaling and gene networks , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[87] K. Fujimoto,et al. Noisy signal amplification in ultrasensitive signal transduction. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[88] Filipe Tostevin,et al. Mutual information in time-varying biochemical systems. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.
[89] Markus J. Tamás,et al. The glycerol channel Fps1p mediates the uptake of arsenite and antimonite in Saccharomyces cerevisiae , 2001, Molecular microbiology.
[90] F. Tostevin,et al. Mutual information between input and output trajectories of biochemical networks. , 2009, Physical review letters.
[91] J. Levine,et al. Intrinsic fluctuations, robustness, and tunability in signaling cycles. , 2006, Biophysical journal.
[92] Konrad Paul Kording,et al. Review TRENDS in Cognitive Sciences Vol.10 No.7 July 2006 Special Issue: Probabilistic models of cognition Bayesian decision theory in sensorimotor control , 2022 .
[93] Peter Dayan,et al. Bayes-Optimal Chemotaxis , 2011, Neural Computation.
[94] J. Small,et al. Unravelling the structure of the lamellipodium , 2008, Journal of microscopy.
[95] 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.
[96] B. Vanhaesebroeck,et al. The p110delta isoform of PI 3-kinase negatively controls RhoA and PTEN. , 2007, The EMBO journal.
[97] Eduardo D. Sontag,et al. Algorithmic and complexity results for decompositions of biological networks into monotone subsystems , 2007, Biosyst..
[98] Carl T. Bergstrom,et al. The fitness value of information , 2005, Oikos.
[99] J. McCaskill,et al. Monte Carlo approach to tissue-cell populations. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[100] J. Joanny,et al. Deformations in actin comets from rocketing beads. , 2006, Biophysical journal.
[101] T. Svitkina. N-WASP Generates a Buzz at Membranes on the Move , 2007, Cell.
[102] C S Peskin,et al. Cellular motions and thermal fluctuations: the Brownian ratchet. , 1993, Biophysical journal.
[103] A. Ridley,et al. Cell migration in development and disease. , 2002, Developmental cell.
[104] Manfred Radmacher,et al. Direct measurement of the lamellipodial protrusive force in a migrating cell , 2006, The Journal of cell biology.
[105] G. Danuser,et al. Two Distinct Actin Networks Drive the Protrusion of Migrating Cells , 2004, Science.
[106] H. Kitano. Systems Biology: A Brief Overview , 2002, Science.
[107] J. Kimble,et al. Germline proliferation and its control. , 2005, WormBook : the online review of C. elegans biology.
[108] K. Fukami,et al. MARCKS regulates lamellipodia formation induced by IGF‐I via association with PIP2 and β‐actin at membrane microdomains , 2009, Journal of cellular physiology.
[109] J. Small,et al. Actin filament organization in the fish keratocyte lamellipodium , 1995, The Journal of cell biology.
[110] D. Sherrington. Stochastic Processes in Physics and Chemistry , 1983 .
[111] Y. Iwasa,et al. Optimal placement of multiple morphogen sources. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.
[112] Edmund J. Crampin,et al. Minimum Information About a Simulation Experiment (MIASE) , 2011, PLoS Comput. Biol..
[113] Cristiana Sebu,et al. Modular decomposition of metabolic systems via null-space analysis. , 2007, Journal of theoretical biology.
[114] H. Othmer,et al. A model for individual and collective cell movement in Dictyostelium discoideum. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[115] Anna H. Klemm,et al. CapZ-lipid membrane interactions: a computer analysis , 2006, Theoretical Biology and Medical Modelling.
[116] V. Reinke,et al. Extrinsic and intrinsic control of germ cell proliferation in Caenorhabditis elegans , 2011, Molecular reproduction and development.
[117] U. Alon. Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.
[118] J. White,et al. On the control of germ cell development in Caenorhabditis elegans. , 1981, Developmental biology.
[119] Eduardo Sontag,et al. Modular cell biology: retroactivity and insulation , 2008, Molecular systems biology.
[120] T. Pollard. The cytoskeleton, cellular motility and the reductionist agenda , 2003, Nature.
[121] S. Shen-Orr,et al. Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.
[122] W. Bialek,et al. Optimizing information flow in small genetic networks. II. Feed-forward interactions. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.
[123] C Reder,et al. Metabolic control theory: a structural approach. , 1988, Journal of theoretical biology.
[124] Alex Mogilner,et al. Multiscale Two-Dimensional Modeling of a Motile Simple-Shaped Cell , 2005, Multiscale Model. Simul..
[125] G. Wagner,et al. The road to modularity , 2007, Nature Reviews Genetics.
[126] Bruce A. Francis,et al. The internal model principle of control theory , 1976, Autom..
[127] A. van Oudenaarden,et al. Quantitative time-lapse fluorescence microscopy in single cells. , 2009, Annual review of cell and developmental biology.
[128] Onn Brandman,et al. Feedback Loops Shape Cellular Signals in Space and Time , 2008, Science.
[129] J. Thevelein,et al. Induction of neutral trehalase Nth1 by heat and osmotic stress is controlled by STRE elements and Msn2/Msn4 transcription factors: variations of PKA effect during stress and growth , 2000, Molecular microbiology.
[130] Hans G Othmer,et al. Multi-scale models of cell and tissue dynamics , 2009, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
[131] Jacques Droulez,et al. The Probabilistic Cell: Implementation of a Probabilistic Inference by the Biochemical Mechanisms of Phototransduction , 2010, Acta biotheoretica.
[132] F. Bruggeman,et al. Control, responses and modularity of cellular regulatory networks: a control analysis perspective. , 2008, IET systems biology.
[133] E. Palsson,et al. A three-dimensional model of cell movement in multicellular systems , 2001, Future Gener. Comput. Syst..
[134] Julie A. Theriot,et al. Loading history determines the velocity of actin-network growth , 2005, Nature Cell Biology.
[135] Kyongbum Lee,et al. BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm374 Systems biology Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection , 2022 .
[136] Bud Mishra,et al. Quantitative analysis of germline mitosis in adult C. elegans. , 2006, Developmental biology.
[137] J. Stelling,et al. Combinatorial Complexity of Pathway Analysis in Metabolic Networks , 2004, Molecular Biology Reports.
[138] N. Gov,et al. Exciting cytoskeleton-membrane waves. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.
[139] J. Sulston,et al. Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. , 1977, Developmental biology.
[140] B. Kholodenko,et al. Modular response analysis of cellular regulatory networks. , 2002, Journal of theoretical biology.
[141] J. Thorner,et al. Analysis of Mitogen-Activated Protein Kinase Signaling Specificity in Response to Hyperosmotic Stress: Use of an Analog-Sensitive HOG1 Allele , 2006, Eukaryotic Cell.
[142] P. Dayan,et al. A Bayesian model predicts the response of axons to molecular gradients , 2009, Proceedings of the National Academy of Sciences.
[143] M. Sheetz,et al. Continuous membrane-cytoskeleton adhesion requires continuous accommodation to lipid and cytoskeleton dynamics. , 2006, Annual review of biophysics and biomolecular structure.
[144] P. Swain,et al. Noisy information processing through transcriptional regulation , 2007, Proceedings of the National Academy of Sciences.
[145] Natasa Przulj,et al. Biological network comparison using graphlet degree distribution , 2007, Bioinform..
[146] C. Sardet,et al. Growth factors induce phosphorylation of the Na+/H+ antiporter, glycoprotein of 110 kD. , 1990, Science.
[147] P. Bongrand,et al. How cells tiptoe on adhesive surfaces before sticking. , 2008, Biophysical journal.
[148] B. Alder,et al. Studies in Molecular Dynamics. I. General Method , 1959 .
[149] N. Wingreen,et al. Accuracy of direct gradient sensing by single cells , 2008, Proceedings of the National Academy of Sciences.
[150] S. Tsukita,et al. A new 82-kD barbed end-capping protein (radixin) localized in the cell- to-cell adherens junction: purification and characterization , 1989, The Journal of cell biology.
[151] A. Coulson,et al. Genomics in C. elegans: so many genes, such a little worm. , 2005, Genome research.
[152] P. Timpson,et al. Distinction at the leading edge of the cell. , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.
[153] Katherine C. Chen,et al. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. , 2003, Current opinion in cell biology.
[154] Misty R. Riddle,et al. Caenorhabditis elegans as a model for stem cell biology , 2010, Developmental dynamics : an official publication of the American Association of Anatomists.
[155] Leslie M Loew,et al. Cooperativity between cell contractility and adhesion. , 2004, Physical review letters.
[156] Gernot Schaller,et al. Multicellular tumor spheroid in an off-lattice Voronoi-Delaunay cell model. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.
[157] Jörg Schultz,et al. Protein Interaction Networks—More Than Mere Modules , 2008, PLoS Comput. Biol..
[158] K. Guan,et al. Three genes of the MAP kinase cascade, mek-2, mpk-1/sur-1 and let-60 ras, are required for meiotic cell cycle progression in Caenorhabditis elegans. , 1995, Development.
[159] S. Cameron,et al. Cell lineage and cell death: Caenorhabditis elegans and cancer research , 2011, Nature Reviews Cancer.
[160] Thomas M. Cover,et al. Elements of Information Theory , 2005 .
[161] M. Bennett,et al. Microfluidic devices for measuring gene network dynamics in single cells , 2009, Nature Reviews Genetics.
[162] Ola Olsson,et al. Bayes' theorem and its applications in animal behaviour , 2006 .
[163] J. Ferrell,et al. Interlinked Fast and Slow Positive Feedback Loops Drive Reliable Cell Decisions , 2005, Science.
[164] I. Nemenman,et al. Optimal Signal Processing in Small Stochastic Biochemical Networks , 2006, PloS one.
[165] G. Vinnicombe,et al. Fundamental limits on the suppression of molecular fluctuations , 2010, Nature.
[166] S. Kuroda,et al. Phosphorylation of ERM proteins at filopodia induced by Cdc42 , 2000, Genes to cells : devoted to molecular & cellular mechanisms.
[167] C. Wolgemuth,et al. Lamellipodial contractions during crawling and spreading. , 2005, Biophysical journal.
[168] C. Downes,et al. Subcellular localization of phosphatidylinositol 4,5-bisphosphate using the pleckstrin homology domain of phospholipase C delta1. , 2002, The Biochemical journal.
[169] Julian Weichsel,et al. Two competing orientation patterns explain experimentally observed anomalies in growing actin networks , 2010, Proceedings of the National Academy of Sciences.
[170] J. Hopfield,et al. From molecular to modular cell biology , 1999, Nature.
[171] Gary G. Borisy,et al. Analysis of the Actin–Myosin II System in Fish Epidermal Keratocytes: Mechanism of Cell Body Translocation , 1997, The Journal of cell biology.
[172] E. Kipreos,et al. Developmental cell biology: C. elegans cell cycles: invariance and stem cell divisions , 2005, Nature Reviews Molecular Cell Biology.
[173] H. Horvitz,et al. Genetic control of programmed cell death in the Caenorhabditis elegans hermaphrodite germline. , 1999, Development.
[174] A. Gavin,et al. SnapShot: Protein-Protein Interaction Networks , 2011, Cell.
[175] N. Gov,et al. Membrane waves driven by actin and Myosin. , 2007, Physical review letters.