BookIgor I. Goryanin, Andrew B. Goryachev, editors.
Contents:
Part 1. 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 and Jyrki Lötjönen, et al.
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 2. 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 and Alex Hajnal, et al.
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 3. 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: From Multi-flagella Propulsion to Logarithmic Sensing / Tine Curk, Franziska Matthäus, Yifat Brill-Karniely and Jure Dobnikar
Self-Feedback in Actin Polymerization / Anders E. Carlsson
Part 4. 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 and Pietro Liò, et al.
Formal Methods for Checking the Consistency of Biological Models / 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
Leveraging Modeling Approaches: Reaction Networks and Rules / Michael L. Blinov and Ion I. Moraru
Part 5. 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 and José Sánchez, et al.
Early Patient Stratification and Predictive Biomarkers in Drug Discovery and Development / Daphna Laifenfeld, David A. Drubin, Natalie L. Catlett, Jennifer S. Park and Aaron A. Van Hooser, et al.
Biomedical Atlases: Systematics, Informatics and Analysis / Richard A. Baldock and Albert Burger.
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