Advances in Systems Biology (Advances in Experimental Medicine and Biology Book 736)

Part Of The Aemb Series -- This Volume Covers The Proceedings Of The 11th International Conference On Systems Biology -- The Conference Is Designed To Bring Together A Broad Spectrum Of Professionals Involved In Disciplines Such As Biology Medicine, Mathematics, Computer Science, Engineering, Physics And Chemistry. The International Society For Systems Biology (issb) Is A Society Aimed At Advancing World-wide Systems Biology Research By Providing A Forum For Scientific Discussions And Various Academic Services. The Issb Helps Coordinate Researchers To Form Alliances For Meeting The Unique Needs Of Multidisciplinary And International Systems Biology Research. The Annual International Conference On Systems Biology (icsb) Serves As The Main Meeting For The Society And Is One Of The Largest Academic And Commercial Gatherings Under The Broad Heading Of Systems Biology.--publisher's Website. Part I Multiscale Biological Networks: Identification, Modeling And Analysis. Modular Analysis Of Biological Networks / Hans-michael Kaltenbach And Jörg Stelling ; Modeling Signaling Networks Using High-throughput Phospho-proteomics / Camille Terfve And Julio Saez-rodriguez ; An Integrated Bayesian Framework For Identifying Phosphorylation Networks In Stimulated Cells / Tapesh Santra, Boris Kholodenko, And Walter Kolch ; Signaling Cascades: Consequences Of Varying Substrate And Phosphatase Levels / Elisenda Feliu, Michael Knudsen, And Carsten Wiuf ; Heterogeneous Biological Network Visualization System: Case Study In Context Of Medical Image Data / Erno Lindfors, Jussi Mattila, Peddinti V. Gopalacharyulu, Antti Pesonen, Jyrki Lötjönen, And Matej Orešič ; Evolution Of The Cognitive Proteome: From Static To Dynamic Network Models / J.^ Douglas Armstrong And Oksana Sorokina ; Molecular Systems Biology Of Sic1 In Yeast Cell Cycle Regulation Through Multiscale Modeling / Matteo Barberis ; Proteome-wide Screens In Saccharomyces Cerevisiae Using The Yeast Gfp Collection / Yolanda T. Chong, Michael J. Cox, And Brenda Andrews ; Unraveling The Complex Regulatory Relationships Between Metabolism And Signal Transduction In Cancer / Michelle L. Wynn, Sofia D. Merajver, And Santiago Schnell. --^ Part Ii: Cellular Decision Making: Adaptation, Differentiation And Death. The Cell As A Thermostat: How Much Does It Know? / Dennis Bray ; Stem Cell Differentiation As A Renewal-reward Process: Predictions And Validation In The Colonic Crypt / Kiran Gireesan Vanaja, Andrew P. Feinberg, And Andre Levchenko ; A Dynamic Physical Model Of Cell Migration, Differentiation And Apoptosis In Caenorhabditis Elegans / Antje Beyer, Ralf Eberhard, Nir Piterman, Michael O. Hengartner, Alex Hajnal, And Jasmin Fisher ; A Modular Model Of The Apoptosis Machinery / E.o. Kutumova, I.n. Kiselev, R.n. Sharipov, I.n. Lavrik, And Fedor A. Kolpakov ; An Ensemble Approach For Inferring Semi-quantitative Regulatory Dynamics For The Differentiation Of Mouse Embryonic Stem Cells Using Prior Knowledge / Dominik Lutter, Philipp Bruns, And Fabian J.^ Theis ; Cell Death And Life In Cancer: Mathematical Modeling Of Cell Fate Decisions / Andrei Zinovyev, Simon Fourquet, Laurent Tournier, Laurence Calzone, And Emmanuel Barillot ; Theoretical Aspects Of Cellular Decision-making And Information-processing / Tetsuya J. Kobayashi And Atsushi Kamimura ; Zooming In On Yeast Osmoadaptation / Clemens Kühn And Edda Klipp. --^ Part Iii: Spatial And Temporal Dymensions Of Intracellular Dynamics. Receptor Dynamics In Signaling / Verena Becker, Jens Timmer, And Ursula Klingmüller ; A Systems-biology Approach To Yeast Actin Cables / Tyler Drake, Eddy Yusuf, And Dimitrios Vavylonis ; Modeling Morphodynamic Phenotypes And Dynamic Regimes Of Cell Motion / Mihaela Enculescu And Martin Falcke ; Time-structure Of The Yeast Metabolism In Vivo / Kalesh Sasidharan, Masaru Tomita, Miguel Aon, David Lloyd, And Douglas B. Murray ; Coarse Graining Escherichia Coli Chemotaxis: Frommulti-flagella Propulsion To Logarithmic Sensing / Tine Curk, Franziska Matthäus, Yifat Brill-karniely, And Jure Dobnikar ; Self-feedback In Actin Polymerization / Anders E. Carlsson. --^ Part Iv: Computational Tools, Algorithms And Theoretical Methods For Systems Biology. Global Optimization In Systems Biology: Stochastic Methods And Their Applications / Eva Balsa-canto, J.r. Banga, J.a. Egea, A. Fernandez-villaverde, And G.m. De Hijas-liste ; Mathematical Modeling Of The Human Energy Metabolism Based On The Selfish Brain Theory / Matthias Chung And Britta Göbel ; Identification Of Sensitive Enzymes In The Photosynthetic Carbon Metabolism / Renato Umeton, Giovanni Stracquadanio, Alessio Papini, Jole Costanza, Pietro Liò, And Giuseppe Nicosia ; Formal Methods For Checking The Consistency Of Biologicalmodels / Allan Clark, Vashti Galpin, Stephen Gilmore, Maria Luisa Guerriero, And Jane Hillston ; Global Parameter Identification Of Stochastic Reaction Networks From Single Trajectories / Christian L. Müller, Rajesh Ramaswamy, And Ivo F. Sbalzarini ; A Systems Biology View Of Adaptation In Sensory Mechanisms / Pablo A.^ Iglesias ; Leveragingmodeling Approaches: Reaction Networks And Rules / Michael L. Blinov And Ion I. Moraru. --^ Part V: Applications Of Systems Biology In Medicine, Biotechnology And Pharmaceutical Industry ; Why And How To Expand The Role Of Systems Biology In Pharmaceutical Research And Development / Robert D. Phair ; Multiscale Mechanistic Modeling In Pharmaceutical Research And Development / Lars Kuepfer, Jörg Lippert, And Thomas Eissing ; Re-analysis Of Bipolar Disorder And Schizophrenia Gene Expression Complements The Kraepelinian Dichotomy / Kui Qian, Antonio Di Lieto, Jukka Corander, Petri Auvinen, And Dario Greco ; Bringing Together Models From Bottom-up And Top-down Approaches: An Application For Growth Of Escherichia Coli On Different Carbohydrates / Andeas Kremling ; A Differential Equation Model To Investigate The Dynamics Of The Bovine Estrous Cycle / H.m.t. Boer, C. Stötzel, S. Röblitz, And H. Woelders ; Reducing Systems Biology To Practice In Pharmaceutical Company Research; Selected Case Studies/ N. Benson, L. Cucurull-sanchez, O. Demin, S. Smirnov, And P.^ Van Der Graaf ; System-scale Network Modeling Of Cancer Using Epoc / Tobias Abenius, Rebecka Jörnsten, Teresia Kling, Linnéa Schmidt, José Sánchez, And Sven Nelander ; Early Patient Stratification And Predictive Biomarkers In Drug Discovery And Development / Daphna Laifenfeld, David A. Drubin, Natalie L. Catlett, Jennifer S. Park, Aaron A. Van Hooser, Brian P. Frushour, David De Graaf, David A. Fryburg, And Renée Deehan ; Biomedical Atlases: Systematics, Informatics And Analysis / Richard A. Baldock And Albert Burger. Igor I. Goryanin, Andrew B. Goryachev, Editors. The Present Collection Of Articles Has Emerged From The Contributions Provided By The Speakers Of Icsb 2010 As Well As By Other Leaders Of Systems Biology Who Could Not Attend The Meeting--pref. Includes Bibliographic References And Index. Front Matter....Pages i-xxii Front Matter....Pages 1-1 Modular Analysis of Biological Networks....Pages 3-17 Modeling Signaling Networks Using High-throughput Phospho-proteomics....Pages 19-57 An Integrated Bayesian Framework for Identifying Phosphorylation Networks in Stimulated Cells....Pages 59-80 Signaling Cascades: Consequences of Varying Substrate and Phosphatase Levels....Pages 81-94 Heterogeneous Biological Network Visualization System: Case Study in Context of Medical Image Data....Pages 95-118 Evolution of the Cognitive Proteome: From Static to Dynamic Network Models....Pages 119-134 Molecular Systems Biology of Sic1 in Yeast Cell Cycle Regulation Through Multiscale Modeling....Pages 135-167 Proteome-Wide Screens in Saccharomyces cerevisiae Using the Yeast GFP Collection....Pages 169-178 Unraveling the Complex Regulatory Relationships Between Metabolism and Signal Transduction in Cancer....Pages 179-189 Front Matter....Pages 191-191 The Cell as a Thermostat: How Much does it Know?....Pages 193-198 Stem Cell Differentiation as a Renewal-Reward Process: Predictions and Validation in the Colonic Crypt....Pages 199-209 A Dynamic Physical Model of Cell Migration, Differentiation and Apoptosis in Caenorhabditis elegans ....Pages 211-233 A Modular Model of the Apoptosis Machinery....Pages 235-245 An Ensemble Approach for Inferring Semi-quantitative Regulatory Dynamics for the Differentiation of Mouse Embryonic Stem Cells Using Prior Knowledge....Pages 247-260 Cell Death and Life in Cancer: Mathematical Modeling of Cell Fate Decisions....Pages 261-274 Theoretical Aspects of Cellular Decision-Making and Information-Processing....Pages 275-291 Zooming in on Yeast Osmoadaptation....Pages 293-310 Front Matter....Pages 311-311 Receptor Dynamics in Signaling....Pages 313-323 A Systems-Biology Approach to Yeast Actin Cables....Pages 325-335 Modeling Morphodynamic Phenotypes and Dynamic Regimes of Cell Motion....Pages 337-358 Front Matter....Pages 311-311 Time-Structure of the Yeast Metabolism In vivo....Pages 359-379 Coarse Graining Escherichia coli Chemotaxis: From Multi-flagella Propulsion to Logarithmic Sensing....Pages 381-396 Self-Feedback in Actin Polymerization....Pages 397-406 Front Matter....Pages 407-407 Global Optimization in Systems Biology: Stochastic Methods and Their Applications....Pages 409-424 Mathematical Modeling of the Human Energy Metabolism Based on the Selfish Brain Theory....Pages 425-440 Identification of Sensitive Enzymes in the Photosynthetic Carbon Metabolism....Pages 441-459 Formal Methods for Checking the Consistency of Biological Models....Pages 461-475 Global Parameter Identification of Stochastic Reaction Networks from Single Trajectories....Pages 477-498 A Systems Biology View of Adaptation in Sensory Mechanisms....Pages 499-516 Leveraging Modeling Approaches: Reaction Networks and Rules....Pages 517-530 Front Matter....Pages 531-531 Why and How to Expand the Role of Systems Biology in Pharmaceutical Research and Development....Pages 533-542 Multiscale Mechanistic Modeling in Pharmaceutical Research and Development....Pages 543-561 Re-analysis of Bipolar Disorder and Schizophrenia Gene Expression Complements the Kraepelinian Dichotomy....Pages 563-577 Bringing Together Models from Bottom-Up and Top-Down Approaches: An Application for Growth of Escherichia coli on Different Carbohydrates....Pages 579-595 A Differential Equation Model to Investigate the Dynamics of the Bovine Estrous Cycle....Pages 597-605 Reducing Systems Biology to Practice in Pharmaceutical Company Research; Selected Case Studies....Pages 607-615 System-Scale Network Modeling of Cancer Using EPoC....Pages 617-643 Early Patient Stratification and Predictive Biomarkers in Drug Discovery and Development....Pages 645-653 Biomedical Atlases: Systematics, Informatics and Analysis....Pages 655-677 Back Matter....Pages 679-682