Poster Session 3
9/2 1:00 - 4:00, Arrillaga Alumni Center, McCaw Hall
Cell-Type Variation in Anticancer Drug Response Probed by Quantitative Microscopy
Jue Shi, Hsiao-chun Huang and Timothy J. Mitchison
Department of Physics, Hong Kong Baptist University. Department of Systems Biology, Harvard Medical School.
Development of Full-Thickness Human Skin Cultures to Investigate Dermal and Epidermal Photo-Ageing in a 3D Model
Jérémie Dedessus le Moutier
Cellular Biology Unit, University of Namur (FUNDP), Belgium.
In silico Approach to Identify the 3D Structure of Matrix Protein 1 of Influenza A (H5n1) Virus
Ashish Patel, Shashi Krishna Pandey, Sheetal Khatri and M K Verma
Sub-DIC Bioinformatics, National Institute of Technology Raipur.
Modular Control Analysis of Mouse Heart Energetics
Guillaume Calmettes, Veronique Deschodt-Arsac, Sylvain Miraux, Bernard Muller, Eric Thiaudiere and Philippe Diolez
Laboratoire de Resonance Magnetique des Systemes Biologiques (Bordeaux, France).
Investigation of Protein Interaction Network of Sphingolipid Metabolism in S. cerevisiae
Fatma Betul, Kavun Ozbayraktar and Kutlu O. Ulgen
Department of Chemical Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey.
Modular Control Analysis Demonstration of the Absence of Mitochondrial Effects During Levosimendan Inotropic Activation of Intact Hearts
Veronique Deschodt-Arsac, Guillaume Calmettes, Gérard Raffard, Philippe Massot, Jean Michel Franconi, Piero Pollesello and Philippe Diolez
UMR5536 CNRS/Univ Bordeaux 2.
Optimising Experiments for Parameter Identification
ETH, Zurich, Switzerland.
A Reduced Model of IKK Phosphorylation Dynamics
Johannes Witt1, Eva Schumann2, Sandra Barisic2, Dagmar Kulms2, Oliver Sawodny2 and Thomas Sauter1,3
1. ISYS & 2 IZI, University of Stuttgart, Germany. 3 Systems Biology Group, University of Luxembourg, Luxembourg.
Disease Associations and Postprandial Dynamics of Lipids Revealed by Metabolic Profiling and Biostatistical Analyses in Offspring of Type 2 Diabetic Patients
Michaela Vossen, Klaus Toedter, Ulrike Beisiegel and Ludger Scheja
UKE, Hamburg, Germany.
A Kinetic Simulation Modelling of a Negative Feedback Loop Pathway in the Ras-MAPK Pathway Based on Parameters Collected Experimentally
Shuhei Yasuda, Yuji Kamioka, Kazuhiro Aoki and Michiyuki Matsuda
Laboratory of Bioimaging and Cell Signaling, Division of Integrated Life Science, Graduate School of Biostudies, Kyoto university.
Hubba Plug-In for Cytoscape: Identify Hubs and Fragile Motifs from Complex Network
Chung-Yen Lin, Chia-Hao Chin, Hsin-Hung Wu, Shu-Hwa Chen, Chin-Wen Ho and Ming-Tat Ko
Insititute of Information Science, Academic Sinica, N401, IIS, #128, Academia Rd, Sec. 2, Nankang 115, Taipei, Taiwan.
Gene And Slide Specific Dye Bias COrrection (GASSCO)
Philip Lijnzaad and Thanasis Margaritis
Holstege Group, University Medical Centre Utrecht, The Netherlands.
Mathematical Modelling of Cell Signaling Networks: Cell Cycle Regulation of Schizosaccharomyces pombe
Anbumathi P, Sharad Bhartiya and KV Venkatesh
Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
Systems Approach Connects Distant Tissues and Functions: B Lymphocytes Affect Small Intestine Function and Body Fat Accumulation by Regulating GATA4 in the Intestinal Epithelium
Andrey Morgun1, Natalia Shulzhenko1, Oksana Gavrilova2 and Polly Matzinger1
1.Ghost lab, LCMI, NIAID, NIH. 2.NIDDK, NIH.
Alternative Inputs to Alpha-Factor
Hiromasa Tanaka and Tau-Mu Yi
University of California, Irvine (UCI), Department of Developmental and Cell Biology, Center for Complex Biological Systems.
Characterization of Heterogeneity in Phenotypic States of Corynebacterium glutamicum
Meghna Rajvanshi, Kalyan Gayen and KV Venkatesh
Department of Chemical Engineering, IIT Bombay, Powai, Mumbai 400076 India.
Tuning the Transcriptome: Metabolic Feedback on Nucleosomes
Cornelia Amariei, Douglas B. Murray, Rainer Machné and Masaru Tomita
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
Identification of Gene Regulatory Networks with Time Delays
Jeong-Rae Kim1, Sang-Mok Choo2 and Kwang-Hyun Cho1
1.Dept. of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea. 2.School of Electrical Engineering, University of Ulsan, Ulsan, 680-749, Republic of Korea.
HepINT: Introducing GAG-Protein Interactions to Systems Biology
Alessandro Ori, Mark C Wilkinson and David G Fernig
School of Biological Sciences and Centre for Glycobiology, University of Liverpool, Liverpool, United Kingdom.
A Snapshot of a Protein in One Experiment - β-Catenin and its Functions
Katrin Luckert1, Oliver Pötz1, Frank Götschel2, Peter K. Sorger3, Andreas Hecht2 and Thomas O. Joos1
1.NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany. 2.University of Freiburg, Freiburg, Germany. 3.Harvard Medical School, Boston, MA, USA.
A Mechanistic Analysis of Frequency Demultiplication
Christian I Hong1, Antonio M Pregueiro1, Jennifer J Loros1,2 and Jay C. Dunlap1
Department of 1.Genetics and 2.Biochemistry, Dartmouth Medical School, Hanover, NH, USA.
Traveling Wave Formation in Vertebrate Segmentation
Koichiro Uriu, Yoshihiro Morishita and Yoh Iwasa
Department of Biology, Faculty of Sciences, Kyushu University.
The Bi-Phasic Regulatory Role of Hub Transcription Factors in the Gene Regulatory Network of HepG2 Cells
Junil Kim, Minsoo Choi and Kwang-Hyun Cho
Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea.
An Improved Gene Network of C. elegans Predicts Genetic Interaction Partners of Human Disease-Related Genes
Insuk Lee1, Andrew Fraser2, Edward Marcotte3 and Ben Lehner4
1.Department of Biotechnology, College of Life science and Biotechnology, Yonsei University, 134 Shinchon-dong, Seodaemun-ku, Seoul 120-749, South Korea. 2.Banting and Best department of Medical Research University of Toronto, Canada. 3.Center for Systems and Synthetic Biology, University of Texas at Austin, TX, USA. 4.EMBL-CRG Systems Biology Research Unit and ICREA, Centre for Genomic Regulation, UPF, Barcelona 08003, Spain.
Meta-Analysis of Pancreatic Cancer Microarray Dataset Using DAVID Algorithm
1.Department of Internal Medicine, Yonsei University College of Medicine. 2.Department of Biotechnology, College of Life science and Biotechnology, Yonsei University.
A System-Level Investigation into the Functional Role of RKIP in the ERK and NF-κB Signaling Networks
Jonghoon Lee, Sung-Young Shin and Kwang-Hyun Cho
Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST).
The Role of Hypoxia Inducible Factor-1 in Cellular Oxygen Homeostasis: Insights From a Rate-Equation Model
Bernhard Schmierer, Christopher J. Schofield and Béla Novák
Oxford Centre for Integrative Systems Biology (OCISB), University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
Comparative Modelling of the Photosynthetic Water Splitting: Impact of Simplifications
Palacky University, Faculty of Science, Laboratory of Biophysics, Olomouc, Czech Republic.
Statistical Inference for the CheZ Phosphatase Localisation in the Cytoplasm of Escherichia Coli
Yoon-Dong Yu and Andrew Dalby
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, Oxfordshire, OX1 3TG, UK.
Impairment of the Effector - Regulatory T Cell Cross-Regulation Generates the Relapsing Dynamics in Autoimmune Diseases
Pablo Villoslada, Nieves Vélez de Mendizábal, Jorge Carneiro, Jean Bragard, Joaquín Goñi, Ivan Martinez-Forero, Sara Martinez-Pasamar, Jorge Sepulcre and Javier Torrealdea
Institut Biomedical Rsearch August Pi Sunyer, Barcelona, Spain. University of Navarra, Spain. Gulbenkian Institute, Portugal.
Evidence that ERK is Processively Phosphorylated in Mammalian Cells
Kazuhiro Aoki, Masashi Yamada, Katsuyuki Kunida and Michiyuki Matsuda
Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University.
Topological Network Alignment Uncovers Biological Function and Phylogeny
Oleksii Kuchaiev, Tijana Milenkovic, Vesna Memisevic, Wayne Hayes and Natasa Przulj
University of California, Irvine.
Emergent Collective Attractors in Lipopolysaccharide Stimulated Macrophages
Vincent Piras, Masaru Tomita, Kumar Selvarajoo and Masa Tsuchiya
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
Knowledge-Based Identification of Gene Modules Involved in Crosstalk Among Nine Environmental Stresses
Hyejoon Joo and Donghee Lee
Dept. Biological Sciences, Ewha Womans University, Seoul, Korea.
In Silico Screening of Protein-Protein Interactions with All-To-All Rigid Docking and Clustering: An Application to Pathway Analysis
Yuri Matsuzaki, Yusuke Matsuzaki, Masahito Ohue, Toshiyuki Sato and Yutaka Akiyama
Graduate School of Information Science and Engineering, Tokyo Institute of Technology.
Coordinated Energy-Conservation Programs are Conserved on the Metabolic and Transcript Level During Escherichia coli Stress Responses
Szymon Jozefczuk, Gareth Catchpole, Jedrzej Szymanski, Alvaro Cuadros-Inostroza, Dirk Steinhauser and Lothar Willmitzer
Max Planck Institute of Molecular Plant Physiology.
Spatial and Temporal Information Coding by the NF-κB System
Louise Ashall, Caroline Horton, David Nelson, Pawel Paszek, Claire Harper, Kate Sillitoe, Sheila Ryan, David Spiller, John Unitt, Dave Broomhead, Douglas Kell, David Rand, Violaine See and Michael White
University of Liverpool, University of Manchester, University of Warwick, Astra Zeneca.
Parameter Conditions for Multistability in Biochemical Reaction Networks: Interval Based Search
Irene Otero-Muras, Julio R. Banga and Antonio A. Alonso
Process Engineering Group, IIM-CSIC, Spanish Council for Scientific Research. Eduardo Cabello 6, 36208 Vigo, Spain.
Retrovirus HTLV-1 Gene Circuit is a Potential Tunable Oscillator for Eukaryotes
Alberto Corradin1, Barbara Di Camillo1, Donna D'Agostino2, Vincenzo Ciminale2, Gianna Toffolo1 and Claudio Cobelli1
1.Department of Information engineering, University of Padua, Italy. 2.Department of Oncology and Surgical Sciences, University of Padua, Italy.
Systems Analysis of Bounded Signaling Modules Generates Novel Insight Into Eight Major Diseases
Kelly Benedict, Feilim Mac Gabhann*, Robert Amanfu*, Arvind Chavali*, Erwin Gianchandani*, Lydia Glaw*, Matthew Oberhardt*, Jason Yang*, Bryan Thorne*, Jason A. Papin, Shayn Peirce, Jeffrey Saucerman and Thomas Skalak
Department of Biomedical Engineering, University of Virginia, Charlottesville, VA.
Stochastic Control Analysis for Biological Reaction Systems
Kyung Hyuk Kim and Herbert M. Sauro
University of Washington, Department of Bioengineering.
Single Cell Analysis of Differential p53 Dynamics in Response to DNA Damage
Eric Batchelor and Galit Lahav
Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
An Integrative Approach To Modelling in Systems Biology
Frank T. Bergmann1,2
1.Department of Bioengineering, University of Washington. 2.Keck Graduate Institute.
Buffering - Dose Related Gene Regulation in Drosophila melanogaster
Yu Zhang, John Malone and Brian Oliver
Laboratory of Cellular and Developmental Biology / National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Single Cell Proliferation Measurements Using Cell Cycle Responsive Reporters
Ryan Peacock, Kathryn Sullivan, Michael Santos and Clifford Wang
Cain: Stochastic Simulations for Chemical Kinetics
California Institute of Technology, Center for Advanced Computing Research.
Sensitivity Analysis of a Kinetic Model of Interactions Among Ca2+, Calmodulin, and CaMKII
Tamara L. Kinzer-Ursem, Shirley L. Pepke, Stefan Mihalas and Mary B. Kennedy
Division of Biology and the Center for Advanced Computing Research, California Institute of Biology.
Extended Treatment of Yeast Cells with Alpha-Factor: Describing the Relationship between Morphology, ROS, and Aging
Steven Chang and Tau-Mu Yi
University of California, Irvine.
Event-Driven Particle-Based Monte Carlo Simulation: Theory and Applications in Systems Biology
Yoshihisa Kubota and M. Neal Waxham
Department of Neurobiology and Anatomy University of Texas Medical School at Houston.
Stochasticity in Mitochondrial DNA Point Mutations and its Relevance to Caenorhabditis elegans Aging
Suresh Kumar Poovathingal1, Jan Gruber2, Barry Halliwell2 and Rudiyanto Gunawan1
1.Department of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Blk E5 #02-09 Singapore 117576. 2.Department of Biochemistry, Neurobiology and Ageing Program, Centre for Life Science (CeLS), 28 Medical Drive Singapore 117456.
A Pseudo-Global Method for Detecting Parameter Correlations in Dynamic Models of Biological Systems
Maria Rodriguez-Fernandez1, Theresa M. Yuraszeck2, Francis J. Doyle III2,3 and Julio R. Banga1
1.Process Engineering Group, IIM-CSIC, Spanish Council for Scientific Research. Vigo, Spain, 36208. 2.Dept of Chemical Engineering, Univ of California, Santa Barbara, Santa Barbara CA 93106-5080. 3.Institute for Collaborative Biotechnologies, Univ of California, Santa Barbara, Santa Barbara, CA 93106.
A Genome-Wide siRNA Screen for Modifiers of the Circadian Clock in Human Cells
Eric E. Zhang*, Andrew C. Liu*, Tsuyoshi Hirota*, Loren J. Miraglia, Genevieve Welch, Pagkapol Y. Pongsawakul, Xianzhong Liu, Ann Atwood, Jeff Janes, Jon W. Huss III, Andrew I. Su, John B. Hogenesch and Steve A. Kay
GNF & University of California, San Diego.
A Systems Biology Approach To Influenza Virus Infection
Yukiko Matsuoka, Jason E. Shoemaker, Natalia Polouliakh, Yukiko Muramoto, Ken Fujii, Samik Ghosh, Richard Nock, Frank Nielsen, Yoshihiro Kawaoka and Hiroaki Kitano
The Systems Biology Institute. JST ERATO Kawaoka Infection Induced Host Response Network Project. Sony Computer Science Laboratories, Inc. University of Tokyo, Universite Antilles-Guyane. Ecole Polytechnique.
Geometries of Robustness in Circadian Clocks
Ariane Ibig and Jörg Stelling
ETH Zurich, BSSE, Computational Systems Biology Group.
A Physiological Systems Approach to Modelling and Resetting of Mammalian Thermoregulation Under Heat Stress
Osman S. Shaik, Bryan G. Helwig, Lisa R. Leon and Francis J. Doyle III
Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California. Thermal and Mountain Medicine Division, United States Army Research Institute of Environmental Medicine, Natick, Massachusetts, USA.
Robustness Analysis of Chemotaxis Models in R. sphaeroides
Abdullah Hamadeh1,3, Mark A. J. Roberts1,2,3, Elias August1,3, Nassia Inglessis1, Philip K. Maini3,4, Patrick E. McSharry3,5, Judith P. Armitage2,3 and Antonis Papachristodoulou1,3
1.Control Group, Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK. 2.Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK. 3.Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK. 4.Centre for Mathematical Biology, Mathematical Institute, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK. 5.Mathematical Institute, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK.
Scaffold Proteins Can Directly Control Switch-Like Decisions of Cell Fate
Mohan K. Malleshaiah1, Vahid Shahrezaei2, Peter S. Swain3 and Stephen W. Michnick1
1.Département de Biochimie, Université de Montréal, Montréal, Québec, Canada. 2.Department of Mathematics, Imperial College London, London, UK. 3.Centre for Systems Biology at Edinburgh, University of Edinburgh, Scotland, UK.
Dynamic Pathway Modelling of Negative Feedback Regulation Restraining TGFβ Signalling in Hepatocytes
Peter Nickel, Stefan Legewie, Thomas Maiwald, Seong-Hwan Rho, Stephanie Müller, Sebastian Bohl, Thomas Frahm, Lorenza D'Alessandro, Kunxin Luo, Hanspeter Herzel, Jens Timmer and Ursula Klingmüller
Division Systems Biology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg.
Cis-Interactions Between Notch and Delta Generate Mutually Exclusive Signaling States
David Sprinzak1, Amit Lakhanpal1, Lauren LeBon1, Leah Santat1, Michelle E. Fontes1, Jordi Garcia-Ojalvo2 and Michael B. Elowitz1
1.Howard Hughes Medical Institute and Departments of Biology and Applied physics, California Institute of Technology. MC114-96 1200 E. California Blvd, Pasadena CA 91125. 2.Department de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Colom 11, E-08222 Terrassa, Spain.
A Model for Micro-Dosimetry in Virtual Liver Tissues
John Wambaugh and Imran Shah
Environment Protection Agency.
Network Analysis of Dengue Virus - Human Protein-Protein Interaction Network
Prasad Siddavatam1, Rushika Perera1, Douglas LaCount2, Richard J. Kuhn1 and Michael Gribskov1
1.Department of Biological Sciences, 2.Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA.
Nonlinear EM for Parameter Estimation of Biological Networks
Department of Epidemiology & Biostatistics, UCSF.
Characterization of Diseasomal Proteins from Liver Disease- and Liver Cancer-Related Disease Networks
Yoon Kyeong Lee1, Hyun-Il Shin1, Ja Eul Ku1, Byul Na Park1, Yu Ri Hwang1, Mun Young Kang1, Gi Young Park1, Myeong Ho Yeo2, Tae Ho Kang2, Jae Soo Yoo2 and Hak Yong Kim1
1.Department of Biochemistry, 2.Department of Information and Communication, Chungbuk National University, Cheongju, 361-763, Republic of Korea.
Metabolic Analysis of Lactate Production in Escherichia coli Introduced Heterologous L-lactate Dehydrogenase Genes
Ayaka Hiroe1,2, Natsumi Saito1, Nobuyoshi Ishii1, Kenji Nakahigashi1,2, Hirotada Mori1,3 and Masaru Tomita1,2
1.Inst. Adv. Biosci., Keio Univ. 2.Syst. Biol. Prog. Grad. Sch. Media and Governance, Keio Univ. 3.Bio, Nara Inst. Sci. Tech.
Gene Regulation in Metabolic Pathways – Principles from Optimization Theory
Victor Chubukov and Hao Li
University of California, San Francisco.
In Silico Modelling and Metabolome Analysis of Preserved Red Blood Cells Towards Improvement of Blood Storage
Taiko Nishino1,2, Ayako Yachie-Kinoshita1,3, Akiyoshi Hirayama1, Tomoyoshi Soga1,4, Makoto Suematsu1,3 and Masaru Tomita1,2,4
1.Institute for Advanced Biosciences, Keio University. 2.System Biology Program, Graduate School of Media and Governance, Keio University. 3.Biochemistry and Integrative Medical Biology, School of Medicine, Keio University. 4.Faculty of Environment and Information Studies, Keio University.
Novel Methodologies for Characterizing Gene Co-Expression
Kshitij Khare, Bala Rajaratnam and Julia Salzman
Enhanced High-Throughput Widefield Microscope for Time-Lapse Experiments
Lars Lehmann1,2, Jonas Mossler1,2 and Peter Fischer2
1.Heidelberg University, Viroquant / Bioquant, Heidelberg, Germany. 2.Heidelberg University, Institute for Computer Engineering, Heidelberg, Germany.
Bacterial Alginate Biosynthesis: New Genes Identified by High-Throughput Screening
Mali Maerk1, Trond Ellingsen2, Helga Ertesvaag1, Oeyvind Jakobsen2, Geir Klinkenberg2, Haavard Sletta2, Anne Toendervik2, Svein Valla1
1.Norwegian University of Science and Technology, Department of Biotechnology, Trondheim, Norway. 2.SINTEF Materials and Chemistry, Trondheim, Norway.
Crosstalk Dynamics Netween the ErbB and ER Pathways During Acquisition of Anti-Cancer Therapy Resistance: Experimental and Modelling Approach
Samik Ghosh1, Yukiko Matsuoka1, Ken Suzuki1, Hiroko Hata2, Michiko Murohashi2, Takeshi Nagashima3, Yoko Kuroki3, Masaaki Oyama2, Noriko Gotoh2, Kazuhiro Ikeda4, Satoshi Inoue4 and Hiroaki Kitano1
1.The Systems Biology Institute, Tokyo, Japan. 2.Institute of Medical Sciences, University of Tokyo, Tokyo, Japan. 3.Computational Systems Biology Research Group, RIKEN Advanced Science Institute, Kanagawa, Japan. 4.Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan.
Spatiotemporal Structure for Proliferation in Discrete Chemical Reaction System
Wnt/β-Catenin Pathway: Systems Level Analysis of Mammalian Cells
Chin Wee Tan1,3, Bruce Gardiner2, Maree Faux3, Meredith Layton3, Antony Burgess3 and David Smith2
1.Department of Civil and Environmental Engineering, Melbourne School of Engineering, University of Melbourne, Parkville, VIC, Australia. 2.Faculty of Engineering, Computing and Mathematics, The University of Western Australia, WA, Australia. 3.Melbourne Tumor Biology Branch, Ludwig Institute for Cancer Research, Melbourne, VIC, Australia.
Community Platform for Pathway Model Building
Yukiko Matsuoka1,2, Samik Ghosh, Norihiko Kikuchi3, Rene Sære4, Brian Kemper4, N. Okazaki4, S. Ananiadou5,6,, J. Tsujii4,5,6 and Hiroaki Kitano1,7
1.The Systems Biology Institute, Tokyo, Japan. 2.JST ERATO Kawaoka Infection Induced Host Response Network Project, Tokyo, Japan. 3.Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan. 4.Department of Computer Science, University of Tokyo. 5.School of Computer Science, University of Manchester. 6.National Centre for Text Mining (NaCTeM). 7.Okinawa Institute of Science and Technology, Okinawa, Japan.
Understanding Combinatorial Interactions of Transcription Factors and DNA Sequences by Biophysical Modeling: Application to ChIPSeq Data of Embryonic Stem Cells
Xin He, Chieh-Chun Chen, Feng Hong, Saurabh Sinha and Sheng Zhong
University of Illinois, Urbana-Champaign.
A Mathematical Model Describing the Pathophysiology of the 3R and 4R Tau Isoforms and its Implications for Understanding Alzheimer's Disease
Theresa M. Yuraszeck1, Pierre Neveu2,5, Maria Rodriguez-Fernandez3, Anne Robinson4, Kenneth S. Kosik5,6 and Francis J. Doyle III1,7
1.Dept of Chemical Engineering, Univ of California, Santa Barbara, Santa Barbara CA 93106-5080. 2.Kavli Institute for Theoretical Physics, Univ of California, Santa Barbara, Santa Barbara, CA 93106. 3.Process Engineering Group, IIM-CSIC, Spanish Council for Scientific Research. Vigo, Spain, 36208. 4.Dept of Chemical Engineering, Univ of Delaware, Newark, DE 19716. 5.Dept of Molecular, Cellular, and Developmental Biology, Univ of California, Santa Barbara, Santa Barbara, CA 93106-9610. 6.Neuroscience Research Institute, Univ of California, Santa Barbara, Santa Barbara, CA 93106-5060. 7.Institute for Collaborative Biotechnologies, Univ of California, Santa Barbara, Santa Barbara, CA 93106.
Analysis of a Model of sigB Activation Following Glucose Starvation
Ulf W. Liebal1, Thomas Millat1, Olaf Wolkenhauer1, Praveen Kumar Sappa2, Leif Steil2 and Uwe Völker2
1.Institute of Computer Science, University of Rostock, Albert-Einstein-Str. 21, 18051 Rostock, Germany. 2.Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt University of Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17487 Greifswald, Germany.
Functional Properties of Signaling Networks in Enteroviral Myocarditis
Farshid S. Garmaroudi1,2, David Marchant1,2, Ali Bashashati5, Mitra Esfandiarei1,2, Raymond T. Ng1,4, Kevin Murphy3,4, Honglin Luo1,2 and Bruce M. McManus1,2
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, Providence Heart + Lung Institute at St. Paul's Hospital 1.Departments of Pathology and Laboratory Medicine, 2.Statistics, and 3.Computer Science. 4.Terry Fox Laboratory-British Columbia Cancer Agency. 5.University of British Columbia, Vancouver, British Columbia, Canada, V6Z 1Y6.
Dissecting Differentially Expressed Genes in Complex Microarray Studies by Venn Diagrams
Peter Juvan1, Viola Tamasi2, Urs A. Meyer2, Damjana Rozman1
1.Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia. 2.Genome Scale Biology, Biozentrum, University of Basel, Basel, Switzerland.
A Quantitative, Predictive Model for the Regulation of RelE-RelB Toxin-Antitoxins Under Stress
Dagmar Iber, Martin Overgaard and Kenn Gerdes
ETH Zurich, University of Southern Denmark, University of Newcastle.
Generalized Quantitative Measures - How Integrals Over Dynamic Signals can Unravel Characteristic Properties of Signal Transduction Pathways
Thomas Millat, Simone Frey and Olaf Wolkenhauer
Institute of Computer Science, University of Rostock, Albert-Einstein-Str. 21, 18051 Rostock, Germany.
Cell-To-Cell Variability in the Height of the Threshold for Apoptosis
Sabrina L. Spencer, Deborah Flusberg, John G. Albeck and Peter K. Sorger
Department of Systems Biology, Harvard Medical School.
An Integrated Mathematical Model for Studying Toxicokinetic and Toxicodynamic Processes following Exposures of Human Hepatocytes to Arsenic Compounds
Spyridon Stamatelos, Christopher Brinkerhoff, Sastry Isukapalli and Panos Georgopoulos
Environmental and Occupational Health Sciences Institute. A joint Institute of UMDNJ RW Johnson Medical School and Rutgers, The State University of New Jersey. 170 Frelinghuysen Road, Piscataway, NJ 08854.
An Adaptive Algorithm for Simulation of Stochastic Reaction-Diffusion Processes
Andreas Hellander, Lars Ferm and Per Lötstedt
Division of Scientific Computing, Department of Information Technology, Uppsala University.
Boolean Analysis of Mutations in Human Cancers
Debashis Sahoo and Joseph Lipsick
Department of Pathology, Stanford University, CA, 94305, USA.
The Metabolic Shift of Clostridium acetobutylicum - The Role of pH-Dependent Enzyme Activities
Thomas Millat, Sylvia Haus, Olaf Wolkenhauer, Ralf-Jörg Fischer, Holger Janssen and Hubert Bahl
University of Rostock, 18051 Rostock, Germany.
The Geometry of Microarray Data Reveals Best Survival Hormone Receptor Positive Subtype in Breast Cancer
Monica Nicolau1, Janine T Erler2 and Gunnar Carlsson1
1.Department of Mathematics, Stanford Mathematics. 2.Cell & Molecular Biology Section, Institute for Cancer Research, London.
Modeling of Detailed Insulin Receptor Kinetics Affects Downstream Signaling Sensitivity in Adipocytes
Camilla Luni, Eric C. Kwei and Francis J. Doyle III
University of California, Santa Barbara.
Core Stemness Mechanisms Revealed Through Homology
Martina Koeva, Camilla Forsberg and Josh Stuart
Department of Biomolecular Engineering, University of California, Santa Cruz.
Fluctuating the Other Way - Noise from Degradation
Anna Andersson and Johan Paulsson
Systems Biology Harvard University.
Systems Biology Analysis of the cis-Regulatory Control of the Novel Expression of Drosophila Even-Skipped Stripes 2 and 3
Ah-Ram Kim, John Ionides and John Reinitz
Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY.
Decoupling of Receptor and Downstream Signals in Akt Pathway by its Low-Pass Filter Characteristics
Kazuhiro Fujita, Yu Toyoshima, Shinsuke Uda, Yu-ichi Ozaki, Hiroyuki Kubota and Shinya Kuroda
Department of Computational Biology, Graduate School of Frontier Sciences and Department of Biophysics and Biochemistry, Graduate School of Science, CREST, Japan Science and Technology Agency, University of Tokyo.
Nutritional Effectors of Chronological Aging in Yeast: Insights from Methionine Metabolism
Allegra Petti, Christopher Crutchfield, Joshua Rabinowitz and David Botstein
Lewis-Sigler Institute, Princeton University.
Parameter Estimation from Microscopy Experiments
James C. Schaff, Dan Vascilescu, Boris M. Slepchenko and Ann E. Cowan
Center for Cell Analysis and Modeling, University of Connecticut health Center, Farmington, CT 06032.
Modularity and Dynamics of a Cell Polarity Protein Network
Juntao Gao1, Roger Guimera2, Xiaoxue Fan1, Stephanie Wai1, Mei Xue1, Luis Amaral2 and Rong Li1
1.Stowers Institute for Medical Research, Kansas, MO 64110. 2.Department of Chemical and Biological Engineering and Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208.
Comparison of the Effects of Two Different Drugs for Cardiac Hypertrophic Signaling Pathways in HL-1 Cell
Hye-Min Hong, Eulsik Oh, Eun Joo Song and Young Sook Yoo
Korea Institute of Science and Technology.
Determination of Cell Fate During Phage Lambda Infection
Francois St-Pierre and Drew Endy
Department of Bioengineering, Stanford University.
Cancer as a Collection of Competing Clones
Calum MacAulay, Martial Guillaud, Stephen Lam and Wan Lam
BC Cancer Agency / BC Cancer Research Centre, Vancouver BC.
In Silico Model of the AcMNPV/Sf-9 System for Viral Protein Expression and RLP Assembly: a Bottom-Up System Biology Approach
António Roldão1,2, Manuel J. T. Carrondo1,2,4, Paula M. Alves1,2 and Rui Oliveira3
1.ITQB-UNL, Apartado 127, P2781-901, Oeiras, Portugal. 2.IBET, Apartado 12, P2781-901, Oeiras, Portugal. 3.REQUIMTE, FCT/UNL, 2829-516, Caparica, Portugal. 4.FCT/UNL, 2825, Monte de Caparica, Portugal.
A Computational Model of Plant Life Cycle: Chromatin Modification at FLOWERING LOCUS C and Regulation of Resource Allocation Contribute to Control Annual and Perennial Trait
Akiko Satake1,2, Masaki Kobayashi3, Kentaro Shimizu3 and Hiroshi Kudoh4
1.Hokkaido University, Japan. 2.PRESTO, Japan Science and Technology Agency. 3.University of Zurich, Switzerland. 4.Kyoto University, Japan.
A Systems Level Analysis of the Effects of Actin Gene Dosage Implicates a Large Portion of the Yeast Genome in Actin Related and/or Actin Dependent Functions
Brian Haarer, Susan Viggiano and David C. Amberg
SUNY Upstate Medical University.
Recent Developments in SBML and SBML Infrastructure
Michael Hucka, Sarah Keating, Akiya Jouraku and the SBML Editors
California Institute of Technology (USA) and Keio University (Japan).
Tissue Specificity of DNA Copy Number in Healthy Mice
Teresia Kling*1, Debora S. Marks*2, Sven Nelander°1 and Chris Sander°4
1.Wallenberg Laboratory and Sahlgrenska-CMR, Department of Clinical and Molecular Medicine, University of Gothenburg, SE 413 45 Göteborg, Sweden. 2.Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. 3.Computational Biology Center, Memorial Sloan Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA.
Deciphering the Regulation of Cell-Type Specific Gene Expression in Arabidopsis Roots During Salt Stress
Chong Han Ng and José R. Dinneny
Temasek Lifescience Laboratory, Singapore.
Lethality and Isolation in the Ueast Transcriptional Network
Sara E. Dempster
Massachusetts Institute of Technology.
Dynamics Proteomics of Individual Cancer Cells in Response to Drugs
Naama Geva-Zatorsky, Ariel A. Cohen, Eran Eden, Erez Dekel, Milana Frenkel-Morgenstern, Irina Issaeva, Tamar Danon, Lydia Cohen, Natalie Perzov, Ron Milo, Alex Sigal and Uri Alon
Department of Molecular Cell Biology, Weizmann Institute of Science.
Modelling of Peripheral Pain Switches (MoPS)
Ralf Baron1, Monika Heiner2, Friedrich Herberg3, Wolfgang Marwan4, Peter Reeh5, Harald Seitz6, Tim Hucho6 and Christof Stein 7
1.Christian-Albrechts-Universität Kiel. 2.Brandenburgische Technische Universität Cottbus. 3.Universität Kassel. 4.Otto-von-Guericke-Universität Magdeburg. 5.Universität Erlangen-Nürnberg. 6.Max-Planck-Institut für molekulare Genetik, Berlin. 7.Charité Universitätsmedizin Berlin.
Structural Sources of Robustness in Biochemical Reaction Networks
Guy Shinar1 and Martin Feinberg2
1.Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel. 2.William G. Lowrie Department of Chemical & Biomolecular Engineering and Department of Mathematics, Ohio State University, 125 Koffolt Laboratories, 140 W. 19th Avenue, Columbus, OH 43210.
NetworkAnalyzer: Web Application for Visualization of High-Throughput Systems-Level Data
Jonathan R. Karr1, Harendra Guturu2, Ed Chen3 and Markus W. Covert3
1.Biophysics Program, 2.Department of Electrical Engineering, 3.Department of Bioengineering, Stanford University.
Quantitative targeted proteomics for the analysis of cellular networks
Paola Picotti1, B. Bodenmiller1, H. Lam2, D. Campbell2, E. Deutsch2 and R. Aebersold1,2
1.Institute of Molecular Systems Biology, ETH Zuerich, 8093 Zuerich, Switzerland. 2.Institute for Systems Biology, Seattle, WA, 98103.
Dose-Dependent NF-κB Signaling Dynamics and Gene Expression in Response to TNFα
Jacob Hughey, Savas Tay, Timothy Lee, Markus W. Covert and Stephen R. Quake
Department of Bioengineering, Stanford University.
Expanding the E. coli Regulatory Network within EcoCyc
Peter Karp, Ingrid Keseler, Alexander Shearer, Mario Latendrese and Julio Collado-Vides
SRI International. Universidad Nacional Autonoma de Mexico.