Poster Session 3

9/2 1:00 - 4:00, Arrillaga Alumni Center, McCaw Hall

Poster 3.001

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.

Poster 3.002

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.

Poster 3.003

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.

Poster 3.004

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).

Poster 3.005

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.

Poster 3.006

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.

Poster 3.007

Optimising Experiments for Parameter Identification

Elias August

ETH, Zurich, Switzerland.

Poster 3.008

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.

Poster 3.009

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.

Poster 3.010

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.

Poster 3.011

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.

Poster 3.012

Gene And Slide Specific Dye Bias COrrection (GASSCO)

Philip Lijnzaad and Thanasis Margaritis

Holstege Group, University Medical Centre Utrecht, The Netherlands.

Poster 3.013

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.

Poster 3.014

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.

Poster 3.015

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.

Poster 3.016

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.

Poster 3.017

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.

Poster 3.018

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.

Poster 3.019

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.

Poster 3.020

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.

Poster 3.021

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.

Poster 3.022

Traveling Wave Formation in Vertebrate Segmentation

Koichiro Uriu, Yoshihiro Morishita and Yoh Iwasa

Department of Biology, Faculty of Sciences, Kyushu University.

Poster 3.023

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.

Poster 3.024

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.

Poster 3.025

Meta-Analysis of Pancreatic Cancer Microarray Dataset Using DAVID Algorithm

Taeyun Oh

1.Department of Internal Medicine, Yonsei University College of Medicine. 2.Department of Biotechnology, College of Life science and Biotechnology, Yonsei University.

Poster 3.026

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).

Poster 3.027

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.

Poster 3.028

Comparative Modelling of the Photosynthetic Water Splitting: Impact of Simplifications

Jiri Jablonsky

Palacky University, Faculty of Science, Laboratory of Biophysics, Olomouc, Czech Republic.

Poster 3.029

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.

Poster 3.030

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.

Poster 3.031

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.

Poster 3.032

Topological Network Alignment Uncovers Biological Function and Phylogeny

Oleksii Kuchaiev, Tijana Milenkovic, Vesna Memisevic, Wayne Hayes and Natasa Przulj

University of California, Irvine.

Poster 3.033

Emergent Collective Attractors in Lipopolysaccharide Stimulated Macrophages

Vincent Piras, Masaru Tomita, Kumar Selvarajoo and Masa Tsuchiya

Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.

Poster 3.034

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.

Poster 3.035

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.

Poster 3.036

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.

Poster 3.037

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.

Poster 3.038

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.

Poster 3.039

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.

Poster 3.040

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.

Poster 3.041

Stochastic Control Analysis for Biological Reaction Systems

Kyung Hyuk Kim and Herbert M. Sauro

University of Washington, Department of Bioengineering.

Poster 3.042

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.

Poster 3.043

An Integrative Approach To Modelling in Systems Biology

Frank T. Bergmann1,2

1.Department of Bioengineering, University of Washington. 2.Keck Graduate Institute.

Poster 3.044

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.

Poster 3.045

Single Cell Proliferation Measurements Using Cell Cycle Responsive Reporters

Ryan Peacock, Kathryn Sullivan, Michael Santos and Clifford Wang

Stanford University.

Poster 3.046

Cain: Stochastic Simulations for Chemical Kinetics

Sean Mauch

California Institute of Technology, Center for Advanced Computing Research.

Poster 3.047

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.

Poster 3.048

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.

Poster 3.049

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.

Poster 3.050

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.

Poster 3.051

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.

Poster 3.052

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.

Poster 3.053

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.

Poster 3.054

Geometries of Robustness in Circadian Clocks

Ariane Ibig and Jörg Stelling

ETH Zurich, BSSE, Computational Systems Biology Group.

Poster 3.055

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.

Poster 3.056

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.

Poster 3.057

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.

Poster 3.058

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.

Poster 3.059

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.

Poster 3.060

A Model for Micro-Dosimetry in Virtual Liver Tissues

John Wambaugh and Imran Shah

Environment Protection Agency.

Poster 3.061

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.

Poster 3.062

Nonlinear EM for Parameter Estimation of Biological Networks

Hao Xiong

Department of Epidemiology & Biostatistics, UCSF.

Poster 3.063

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.

Poster 3.064

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.

Poster 3.065

Gene Regulation in Metabolic Pathways – Principles from Optimization Theory

Victor Chubukov and Hao Li

University of California, San Francisco.

Poster 3.066

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.

Poster 3.067

Novel Methodologies for Characterizing Gene Co-Expression

Kshitij Khare, Bala Rajaratnam and Julia Salzman

Stanford University.

Poster 3.068

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.

Poster 3.069

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.

Poster 3.070

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.

Poster 3.071

Spatiotemporal Structure for Proliferation in Discrete Chemical Reaction System

Atsunari Katsuki

Nihon University.

Poster 3.072

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.

Poster 3.073

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.

Poster 3.074

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.

Poster 3.075

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.

Poster 3.076

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.

Poster 3.077

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.

Poster 3.078

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.

Poster 3.079

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.

Poster 3.080

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.

Poster 3.081

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.

Poster 3.082

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.

Poster 3.083

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.

Poster 3.084

Boolean Analysis of Mutations in Human Cancers

Debashis Sahoo and Joseph Lipsick

Department of Pathology, Stanford University, CA, 94305, USA.

Poster 3.085

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.

Poster 3.086

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.

Poster 3.087

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.

Poster 3.088

Core Stemness Mechanisms Revealed Through Homology

Martina Koeva, Camilla Forsberg and Josh Stuart

Department of Biomolecular Engineering, University of California, Santa Cruz.

Poster 3.089

Fluctuating the Other Way - Noise from Degradation

Anna Andersson and Johan Paulsson

Systems Biology Harvard University.

Poster 3.090

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.

Poster 3.091

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.

Poster 3.092

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.

Poster 3.093

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.

Poster 3.094

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.

Poster 3.095

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.

Poster 3.096

Determination of Cell Fate During Phage Lambda Infection

Francois St-Pierre and Drew Endy

Department of Bioengineering, Stanford University.

Poster 3.097

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.

Poster 3.098

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.

Poster 3.099

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.

Poster 3.101

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.

Poster 3.102

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).

Poster 3.103

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.

Poster 3.104

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.

Poster 3.105

Lethality and Isolation in the Ueast Transcriptional Network

Sara E. Dempster

Massachusetts Institute of Technology.

Poster 3.106

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.

Poster 3.107

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.

Poster 3.108

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.

Poster 3.109

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.

Poster 3.110

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.

Poster 3.111

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.

Poster 3.112

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.