Poster Session 2

9/1 1:00 - 5:00, Arrillaga Alumni Center, McCaw Hall

Poster 2.001

PKR Regulates the Dynamics of Insulin Signaling: A Discrete Modelling Approach

Ming Wu, Xuerui Yang and Christina Chan

Michigan State University.

Poster 2.002

SignaLink: A signalling Pathway Resource in Three Metazoans for Cross-Talk Analysis

Tamas Korcsmaros, Illes J. Farkas, Mate Szalay, Petra Rovo, David Fazekas, Zoltan Spiro, Csaba Bode, Katalin Lenti, Tibor Vellai and Peter Csermely

Eotvos University. Semmelweis University. Hungarian Academy of Sciences. Morgan Stanley Hungary.

Poster 2.003

Model-based Deconvolution of Bacterial Cell Cycle Time-series Data Reveals Gene Expression Details at High Resolution

Dan Siegal-Gaskins1,2,3, Joshua N. Ash4 and Sean Crosson5,6

1.Mathematical Biosciences Institute. 2.Dept. of Plant Cellular and Molecular Biology, and 3.Plant Biotechnology Center, Ohio State University, Columbus, OH. 4.Dept. of Electrical and Computer Engineering, Ohio State University, Columbus, OH. 5.Dept. of Biochemistry and Molecular Biology and 6.The Committee on Microbiology, University of Chicago, Chicago, IL.

Poster 2.004

The Capacity for Multistability in Small Gene Regulatory Networks

Dan Siegal-Gaskins1,2,3, Erich Grotewold1,2,3 and Gregory D. Smith1,4

1.Mathematical Biosciences Institute, 2.Dept. of Plant Cellular and Molecular Biology, and 3.Plant Biotechnology Center, Ohio State University, Columbus, OH. 4.Dept. of Applied Science, The College of William and Mary, Williamsburg, VA.

Poster 2.005

Integrated Analysis of Fatty Acid Responsive Gene Regulatory Network in Saccharomyces cerevisiae

Alexander V. Ratushny1, Yakun Wan1, Stephen A Ramsey1, Theo A. Knijnenburg1, David J. Reiss1, Alistair G. Rust2 and John D. Aitchison1

1.Institute for Systems Biology, Seattle, WA, USA. 2.Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Poster 2.006

A Systems Biology Approach to Studying Development In Vivo

Wai Ee Max Fun and Thomas Lufkin

Genome Institute of Singapore.

Poster 2.007

Dynamic Model Building Using an Iterative Parametric Identification Procedure

Eva Balsa-Canto, Antonio A. Alonso and Julio R. Banga

(Bio)process Engineering Group. Spanish National Research Council (IIM-CSIC), Vigo-Spain.

Poster 2.008

Spontaneous Synchronization by Coupling Cell Cycle and Circadian Clocks

Qiong Yang1, Bernardo F. Pando1, Guogang Dong3, Susan S. Golden3 and Alexander van Oudenaarden1,2

1.Department of Physics, MIT, Cambridge MA 02139, USA. 2.Department of Biology, MIT, Cambridge MA 02139, USA. 3.Division of Biological Sciences, University of California-San Diego, La Jolla, USA.

Poster 2.009

Reverse-engineering “Hidden” Regulatory Circuits from High-Throughput Molecular Profiles

Zoltan Dezso and Andrej Bugrim

GeneGo, Inc. 500 Renaissance Dr. #106, Saint Joseph, Michigan 49085.

Poster 2.010

Stochastic Modelling in Biological Systems

Yang Luo and Lorenz Wernisch

MRC Biostatistics Unit Cambridge.

Poster 2.011

Stochastic Modelling of CaMKII Regulation

Melanie I. Stefan, David Marshall, Stuart J. Edelstein and Nicolas Le Novère

EMBL-European Bioinformatics Institute, Cambridge, UK.

Poster 2.012

Systematic Analysis of Gefitinib Sensitive/Resistant Lung Cancer Cell Lines

Yao Su and Hongxing Lei

Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China, 100029.

Poster 2.013

Uncovering Signaling Differences Between Normal and Transformed Hepatocytes Using Cell-Specific Logic-Based Models of Cell Signaling Circuits

Julio Saez-Rodriguez1,2,3, Leonidas Alexopoulos1,2,3,4, Jonathan Epperlein1,2, Regina Samaga5, Steffen Klamt5, Douglas A. Lauffenburger1,3 and Peter K. Sorger1,2,3

1.Center for Cell Decision Processes. 2.Harvard Medical School, Systems Biology Dept., Boston, MA. 3.M.I.T., Biological Engineering Dept., Cambridge, MA. 4.Current Address: Nat. Tech. University of Athens, Greece. 5.Max Planck Institute, Magdeburg, Germany.

Poster 2.014

Gene Network of Helicobacter pylori-Infected Host Cell: Annexin A4-Involved Signaling and Regulation in Gastric Cancer

Li-Ling Lin, Yi-Te Chou, Hsuan-Cheng Huang, Chiung-Nien Chen and Hsueh-Fen Juan

Institute of Molecular and Cellular Biology, Department of Life Science, Department of Surgery, National Taiwan University. Institute of Biomedical Informatics & Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan.

Poster 2.015

Systems Biology Approach to Mastitis

Nicoline van Loenen, Don Kulasiri and Hans-Martin Seyfert

Lincoln University New Zealand, FBN Dummerstorf Germany.

Poster 2.016

Novel Features of the Rice Genome Revealed by Proteogenomic Analysis

Mohamed Helmy, Masaru Tomita and Yasushi Ishihama

Keio University, Institute for Advance Biosciences.

Poster 2.017

Just-In-Time Physiology: Self-Organisation of Amino Acid Regulation in Yeast

Kalesh Sasidharan, Douglas B. Murray, Rainer Machné and Masaru Tomita

Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.

Poster 2.018

Identification of Condition-Specific Functional Modules in the Signaling Network of Saccharomyces cerevisiae

Dongsan Kim, Man-Sun Kim, Jeong-Rae Kim and Kwang-Hyun Cho


Poster 2.019

A System-Level Investigation into the Feedback Regulatory Mechanisms of Ras-Raf-MEK-ERK Signal Transduction Pathway

Sung-Young Shin1, Tae-Hwan Kim1, Sang-Mok Choo2, Oliver Rath3, Frances Fee3, Brian McFerran3, Walter Kolch3,4 and Kwang-Hyun Cho1

1.Dept. Bio and Brain Eng., KAIST, Daejeon, Korea. 2.School of Elect. Eng., Univ. of Ulsan, Ulsan, Korea. 3.Beatson Institute Cancer Research, Cancer Research U.K. 4.Institute of Biomed. and Life Sci., Univ. of Glasgow, Glasgow, U.K.

Poster 2.020

Robust Extraction of Functional Signals from Gene Set Analysis Using a Generalized Threshold Free Scoring Function

Petri Toronen1, Pauli Ojala2, Pekka Marttinen3 and Liisa Holm1,4

1.Institute of Biotechnology. 3.Dept Mathematics and Statistics. 4.Dept Environmental and Biological Sciences, University of Helsinki, Finland. 2.Finnish Red Cross R&D, Helsinki, Finland.

Poster 2.021

Autogenous Control and Genome-Wide Adaptation in the Yeast Stress Response

Giovanna De Palo1, F. Eduati2, Mattia Zampieri1, Barbara Di Camillo2, Gianna Toffolo2 and Claudio Altafini1

1.Scuola Internazionale Superiore di Studi Avanzati - International School for Advanced Studies (SISSA-ISAS), Functional Analysis via Beirut 4, Trieste, Italy. 2.Department of Information Engineering, University of Padova via Gradenigo, 6/B, 35131 Padova, Italy.

Poster 2.022

Potency Prediction Pipeline: Automated Analysis of High-Throughput Screening Soft-Agar Assay Data

Marcos H. Woehrmann, Nadine Gassner, Walter Bray, Elisabeth X. Rocha, Scott Lokey and Josh Stuart

University of California, Santa Cruz.

Poster 2.023

Coarse-Grained Approach for Systems Biology: Causal Mapping (CMAP)

Gabriel E. Weinreb1, Timothy C. Elston2 and Ken Jacobson1

1.Department of Cell and Developmental Biology, CB #7090. 2.Department of Pharmacology, CB #7365; University of North Carolina at Chapel Hill Chapel Hill, NC, 27599.

Poster 2.024

On Multiple Regulatory Mechanisms in the Tryptophan Operon System in Escherichia coli: In Silico Study of Perturbation Dynamics

Lan K. Nguyen and Don Kulasiri

C-fACS (Centre for Advanced Computational Solutions), Lincoln University, New Zealand.

Poster 2.025

Position and Velocity Estimation of Cell Boundary

Jongrae Kim1 and Robert Insall2

1.Department of Aerospace Engineering, University of Glasgow, Glasgow, UK. 2.The Beatson Institute for Cancer Research, University of Glasgow, Glasgow, UK.

Poster 2.026

SBGN-ED: A VANTED Add-on for Systems Biology Graphical Notation

Tobias Czauderna, Christian Klukas and Falk Schreiber

IPK Gatersleben.

Poster 2.027

Role of Buffering Capacity in Proton Translocation in Bacteria

Morgiane Richard1,2, Susan Black2,, Samantha Miller2, Celso Grebogi1, Ian Booth2 and Alessandro de Moura 1

1.Insitute for Complex System and Mathematical Biology, King's College, AB24 3UE. 2 Institute of Medical Sciences, Foresterhill, AB252ZD, University of Aberdeen, Aberdeen, UK.

Poster 2.028

A Novel Scoring Approach for Co-purification Data Reveals Fundamental Differences in Protein Interaction Data

Xueping Yu, Joseph Ivanic, Anders Wallqvist and Jaques Reifman

Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Ft. Detrick, MD 21702, USA.

Poster 2.029

Algorithm for Modular Clustering of PPI Network

Nassim Sohaee and Chrictian V. Forst

University of Texas, South Western Medical Center.

Poster 2.030

Stochastic Modelling and Simulation of Cell Polarization During Mating in Budding Yeast

Michael Lawson, Brian Drawert, Tau-Mu Yi, Linda Petzold and Mustafa Khammash

University of California, Santa Barbara - Biomolecular Science and Engineering.

Poster 2.031

Modulation of Transcriptional Burst Dynamics by Genomic Integration of the HIV Promoter

Ron Skupsky, John Burnett, Jonathan Foley, David V. Schaffer and Adam P. Arkin

University of California, Berkeley.

Poster 2.032

Phenotype Switching in Response to a Cancer Drug: TRAIL-Induced Death and Transient Resistance

Deborah Flusberg, Sabrina L. Spencer and Peter K. Sorger

Department of Systems Biology, Harvard Medical School, and Center for Cell Decision Processes, MIT.

Poster 2.033

PCIT: An R package for Applying Partial Correlation and Information Theory Approaches to Gene Co-Expression Networks

Nathan S. Watson-Haigh, Haja N. Kadarmideen and Antonio Reverter

CSIRO Livestock Industries.

Poster 2.034

Construction of Arabidopsis Specialized Gene Sets for Modular-Scale Interpretation of Microarray Data Sets

Hyejoon Joo and Donghee Lee

Dept. Biological Sciences, Ewha Womans University, Seoul, Korea.

Poster 2.035

Systemic Effect of EWS/FLI-1 Chimeric Oncogene on Tumoral Phenotypes in Ewing Sarcoma

Gautier Stoll, Didier Surdez, Karine Laud-Duval, Franck Tirode, Emmanuel Barillot, Olivier Delattre and Andrei Zinovyev

Institut Curie, INSERM U900, INSERM U830, Mines ParisTech.

Poster 2.036

A New HIV Treatment Paradigm: Switching Drugs Before Failure

Max von Kleist, Stephan Menz and Wilhelm Huisinga

Hamilton Institute, National University of Ireland, Maynooth.

Poster 2.037

Hypoxia Induced HIF-1 Response: Identifying a Mechanism for its Exponential Behavior

Christian Tiemann, Peter Hilbers and Natal van Riel

Eindhoven University of Technology, The Netherlands, BioModeling & BioInformatics group.

Poster 2.038

Comprehensive Rate Control Analysis of the Eukaryotic Translation Pathway

Helena M. Firczuk, Shichina Kannambath, Xi Wang, Helen Bryant, Hans V. Westerhoff, Pedro Mendes and John E. G. McCarthy

University of Manchester, UK.

Poster 2.039

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot and Andrei Zinovyev

Institut Curie, Mines ParisTech, Inserm U900, Université de la Méditerranée, Karolinska Institute.

Poster 2.040

Modelling Down's Syndrome Pathology in the Human Cellular Interaction Network by Using a Monte Carlo Strategy

Elisabeth Maschke-Dutz1, Christoph Wierling1, Mireia Vilardell2, Axel Rasche1, Luis A. Pérez-Jurado3 and Ralf Herwig1

1.Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 73, 14195 Berlin, Germany. 2CIBER Epidemiology and Public Health (CIBERESP). 3.Genetics Unit, Department of Experimental and Health Sciences, Pompeu Fabra University Barcelona, Spain.

Poster 2.041

Nonlinear Effects of Copy Number Variation on Gene Expression

Yuriy Mileyko1, Richard I. Joh 2, Russell D. Monds3 and Joshua S. Weitz1,2

1.School of Biology, Georgia Institute of Technology. 2.School of Physics, Georgia Institute of Technology. 3Dept. of Chemical and Systems Biology, Stanford University.

Poster 2.042

Inhibition of EGFR: Optimizing Therapeutic Antibodies using Cell-level Modelling

Ben-Fillippo Krippendorff1,2, Diego Oyarzún1 and Wilhelm Huisinga1

1.Hamilton Institute, National University of Ireland, Maynooth. 2.International Max-Planck Research School CBCS, Berlin/ Germany.

Poster 2.043

Oxford Centre for Integrative Systems Biology and Systems Biology Doctoral Training Centre

Nick Jones

Oxford Centre for Integrative Systems Biology.

Poster 2.044

Probing a Hopf Bifurcation in a Cell-Autonomous Circadian Oscillator

Thomas d'Eysmond, Charna Dibner, Ueli Schibler and Felix Naef

Ecole Polytechnique Federale de Lausanne (EPFL). University of Geneva.

Poster 2.045

Using Labeled Hybrid Petri Nets for Efficient Markovian Analysis of Genetic Circuit Models

Curtis K. Madsen and Chris J. Myers

University of Utah.

Poster 2.046

Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model

Samuel Bandara1, Johannes Schlöder2, Roland Eils3, Hans Georg Bock2 and Tobias Meyer1

1.Department of Chemical and Systems Biology, Stanford University. 2.Interdisciplinary Center for Scientific Computing, University of Heidelberg. 3.German Cancer Research Center, Heidelberg, and Instititute of Pharmacy and Molecular Biotechnology / BIOQUANT, University of Heidelberg.

Poster 2.047

An Integrative Approach to Modelling Biological Networks

Vesna Memisevic, Tijana Milenkovic, Oleksii Kuchaiev and Natasa Przulj

University of California, Irvine.

Poster 2.048

Discovering Transcriptional Modules Involved in A. thaliana Growth and Development

Steven Maere, Eric Bonnet and Yves Van de Peer

Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052 Gent, Belgium; Department of Molecular Genetics, Ghent University, 9052 Gent, Belgium.

Poster 2.049

Tagged Transposon Mutagenesis as a Tool for Building Barcoded Mutant Collections

Julia Oh1, Eula Fung2, Corey Nislow3, Ron Davis1,2, Adam P. Arkin4,5 and Adam Deutschbauer 4,5

1.Department of Genetics, Stanford University, Stanford, CA. 2.Department of Biochemistry, Stanford University, Stanford, CA. 3.Department of Medical Genetics & Microbiology, University of Toronto, ON, Canada. 4.Lawrence Berkeley National Laboratory, Berkeley, CA. 5.VIMSS (Virtual Institute of Microbial Stress and Survival), Berkeley, CA.

Poster 2.050

Development of Systems Biology Tools to Indentify Causal SNPs for Complex Traits

Stephen J. Goodswen, Nathan S. Watson-Haigh, Haja N. Kadarmideen and Cedric Gondro

CSIRO Livestock Industries and University of New England.

Poster 2.051

Genome-Wide Classification of deepCAGE Promoters According to their Surrounding H3K9 Acetylation Signal

Anton Kratz1,2, Erik Arner2, Rintaro Saito1, Atsutaka Kubosaki2, Jun Kawai2, Harukazu Suzuki2, Piero Carninci2, Takahiro Arakawa2, Masaru Tomita1, Yoshihide Hayashizaki2 and Carsten O. Daub2

1.Keio University, Graduate School of Media and Governance, 5322 Endo, Fujisawa-shi, Kanagawa 252-8520, Japan. 2.RIKEN Omics Sciences Center (OSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

Poster 2.052

Discovery of Tri-Split tRNA

Kosuke Fujishima, Junichi Sugahara, Kaoru Kikuta, Asako Sato, Masaru Tomita and Akio Kanai

Institute for Advanced Biosciences, Keio University, Tsuruoka Yamagata 997-0017 Japan.

Poster 2.053

Systems Biology of Neonatal and Adult Ventricular Cells: Significance of Na+-Ca2+ Exchange

Hitomi I. Sano, Yasuhiro Naito and Masaru Tomita

Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan.

Poster 2.054

Modelling Complex Systems Implicated in Cancer and Diabetes

Joshua Havumaki, Ty Thomson, Isha Antani and Gordon Webster

Plectix BioSystems 20 Holland St Ste 400, Somerville, MA 02144-2749.

Poster 2.055

A Distribution-Based Sensitivity Analysis Metric for Highly-Variable Biochemical Systems

Henry P Mirsky1, Stephanie R Taylor2, Jörg Stelling3 and Francis J. Doyle III1,4

1.Program in Biomolecular Science and Engineering, UC Santa Barbara. 2.Department of Computer Science, Colby College. 3.Department of Biosystems Science and Engineering, ETH Zurich. 4.Department of Chemical Engineering, UC Santa Barbara.

Poster 2.056

Consequences of Heterogeneous IL7 Responsiveness in Shaping the Naïve T Cell Repertoire

Megan J Palmer, Vinay S Mahajan, Jianzhu Chen, Darrell J Irvine and Douglas A. Lauffenburger

Massachusetts Institute of Technology.

Poster 2.057

CFinder: From Gene Interactions to the Network of Overlapping Complexes and Novel Functional Modules

Daniel Abel, Balazs Adamcsek, Imre Derenyi, Illes J. Farkas, Gergely Palla, Peter Pollner and Tamas Vicsek

Hungarian Academy of Sciences and Eotvos University, Budapest, Hungary.

Poster 2.058

An Asymmetric Gene Regulatory Network in the Zebrafish Embryonic Segmentation Clock

Christian Schroter1, Saul Ares2, Luis G. Morelli1 and Andrew C. Oates1

1.Max Planck Institute of Molecular Cell Biology and Genetics, Dresden. 2.Max Planck Institute for the Physics of Complex Systems, Dresden.

Poster 2.059

Metabolic Network Analysis Algorithms in Pathway Tools

Peter Karp and Markus Krummenacker

SRI International.

Poster 2.060

CryptoNet: Integrated Functional Gene Network of Human Pathogenic Fungus, Cryptococcus neoformans

Hanhae Kim

Yonsei University.

Poster 2.061

Dyes for Live Cell Imaging: Detecting Endogenous Cdc42 Activation

Chia-Wen Hsu1, Alexei Toutchkine2, Dmitriy Gremiachinskiy2 and Klaus Hahn1,2

1.Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill, Chapel Hill, USA. 2.Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, USA.

Poster 2.063

Spatio-Temporal Correlations can Drastically Change the Response of a MAPK Pathway

Koichi Takahashi1, Sorin Tanase-Nicola2 and Pieter Rein ten Wolde3

1.RIKEN, Japan. 2University of Michigan, USA. 3.AMOLF, the Netherland.

Poster 2.064

Robustness and Entrainment of the Drosophila Circadian Clock

Marc Hafner1,2,3, Heinz Koeppl1, Laura Symul1,4, Rodolphe Sepulchre4 and Andreas Wagner2,3,5,6

1.Ecole Polytechnique Fédérale de Lausanne, Switzerland. 2.University of Zurich, Switzerland. 3.Swiss Institute of Bioinformatics, Switzerland. 4.University of Liège, Belgium. 5.The Santa Fe Institute. 6.University of New Mexico, Department of Biology.

Poster 2.065

Kinetic Modelling of Storage Metabolism in Plants

Kai Schallau and Björn H. Junker

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK).

Poster 2.066

Experimental Analysis of Non-Linear Responses in Gene Expression Dynamics Due to Small Changes in Regulatory Motif Copy Number

Anu C. Villapakkam, Richard I. Joh, Joshua S. Weitz and Russell D. Monds

Bio-X Program, Department of Chemical and Systems Biology, Stanford University School of Medicine.

Poster 2.067

Evolution Rate as a Function of Protein Folding Robustness

Alexander Lobkovsky Meitiv and Eugene V. Koonin and Yuri I. Wolf

National Institutes of Health.

Poster 2.068

Information Transfer in Biological Network Motifs

Thanneer Malai Perumal1 and Rudiyanto Gunawan1,2

1.Department of Chemical and Biomolecular Engineering, 2.Bioinformatics Programme, National University of Singapore, Singapore 117576.

Poster 2.069

Synergistic and Antagonistic Host-Target Relationships Mediated by Intronic microRNAs

Dominik Lutter1, Carsten Marr1, Jan Krumsiek1, Elmar W. Lang2, Fabian J. Theis1

1.Institute of Bioinformatics and Systems Biology, CMB, Helmholtz Zentrum München, Germany. 2.CIML Group, Institute of Biophysics, University of Regensburg, 93040 Regensburg, Germany.

Poster 2.070

Analysis and Modelling of Hedgehog/GLI Signaling and Regulatory Networks in Cancer

Hendrik Hache1, Fritz Aberger2, Markus Eberl2, Annemarie Frischauf2, Alexandra Kaser2, Ulricke Korf3, Wilfried Nietfeld1, Hans Lehrach1 and Christoph Wierling1

1.Max Planck Institute for Molecular Genetics, Department Vertebrate Genomics, Ihnestr. 63-73, D-14195 Berlin, Germany. 2.Department of Molecular Biology, Division of Genomics, University of Salzburg, Heilbrunnerstr. 34, A-5020 Salzburg, Austria. 3.Department of Molecular Genome Analysis, German Cancer Research Center, Im neuenheimer Feld 580, D-69120 Heidelberg, Germany.

Poster 2.071

Oscillations in the Expression of a Self-Repressed Gene Induced by a Slow Transcriptional Dynamics

Pierre-Emmanuel Morant1, Jingkui Wang1, Quentin Thommen1, François Lemaire2, Constant Vandermoere1, Benjamin Parent3,4 and Marc Lefranc 1,4

1.PhLAM, Université Lille 1, France. 2.LIFL, Université Lille 1, France. 3.UGSF, Université Lille 1, France. 4IRI, Université Lille 1, France.

Poster 2.072

Elucidating Mechanisms of Early Insulin Signalling in Primary Adipocytes and Hepatocytes: A Joint Systems Biology Effort

Rikard Johansson, C. Kreutz, C. Johansson, M. M. Bartolomé Rodríguez, P. Strålfors, J. Timmer and G. Cedersund

University of Freiburg / University of Linköping.

Poster 2.073

A Unified Bayesian Method for Multiple Genome Comparison of Time-Course Data

Wei Huang, Xiaoyi Cao, Guixian Lin and Sheng Zhong

Key Laboratory for Applied Statistics of Ministry of Education, Northeast Normal University, Changchun, China; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign; Department of Statistics, University of Illinois at Urbana-Champaign; Department of Bioengineering, University of Illinois at Urbana-Champaign.

Poster 2.074

Timing Robustness in the Budding and Fission Yeast Cell Cycles

David L. Dill and Karan Mangla

Stanford University.

Poster 2.075

Design Principles of the Scl-Gata2-Fli1 Regulatory Module in Hematopoietic Differentiation Network

Jatin Narula and Oleg Igoshin

Department of Bioengineering, Rice University, Houston TX.

Poster 2.076

Genome-Level Respiratory Plasticity as Revealed by Insertion Sequence-Mediated Adaptive Evolution in Shewanella oneidensis MR-1

Carmen Cordova, Marcus Schicklberger, Yang Yu and Alfred M Spormann

Departments of Chemical Engineering, of Civil and Environmental Engineering, of Geological and Environmental Sciences, of Biological Sciences, Stanford University.

Poster 2.077

Systems Biology Approaches for Identifying Cultured Dupuytren's Disease Samples for Analysis

Samrina Rehman, Magnus Rattray, Royston Goodacre, Ardeshir Bayat, Gerold Baier, Hans V. Westerhoff and Philip J Day

Doctoral Training Centre, Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester UK.

Poster 2.078

A Bistable Switch Regulates the Cytoplasmic Polyadenylation

Naveed Aslam and Harel Z. Shouval

Department of Neurobiology and Anatomy The University of Texas, Medical School at Houston.

Poster 2.079

Molecular Machines and Networks Contributions to Understanding Cellular Functions

Roberto Sacco, Tilmann Buerckstuemmer, Uwe Rix, Oliver Hantschel, Jacques Colinge, Keiryn L. Bennett and Giulio Superti-Furga

CeMM, Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

Poster 2.080

Modeling Framework for Scaling up Genetic Processes to Predict Tomato Fruit Yield and Quality in Different Growing Conditions

Pieter De Visser, Julienne Fanwoua, Paul Struik, Leo Marcelis, Ep Heuvelink, Gerco Angenent and Xinyou Yin

Wageningen University and Research centre, P.O. Box 16, 6700 AA Wageningen, NL.

Poster 2.081

Small RNAs Establish Delays and Temporal Thresholds in Gene Expression

Ilka M. Axmann, Stefan Legewie, Dennis Dienst, Annegret Wilde and Hanspeter Herzel

Charité - Universitätsmedizin Berlin, Institute for Theoretical Biology, D-10115 Berlin, Germany.

Poster 2.082

Designing Maximally Informative Experiments for the Selection of Pathway Models

Alberto Giovanni Busetto1,3, Sotiris Dimopoulos1,2,3, Mikael A. Sunnaker1,2,3, Alain Hauser1,2, Cheng Soon Ong1, Jörg Stelling1,2,3 and Joachim M. Buhmann1,3

1.Department of Computer Science, ETH Zurich. 2.Department of Biosystems Science and Engineering, ETH Zurich. 3.Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich and University of Zurich.

Poster 2.083

Global Map of Kinase Function Revealed by Genetic Networks

Sara Sharifpoor, Dewald van Dyk, Helena Friesen, Alison Ralph, Kathy Lam, Chad Myers, Balazs Papp, Charles Boone and Brenda Andrews

University of Toronto, University of Minnesota and Hungarian Academy of Sciences.

Poster 2.084

Identification of Core Predictions – Uniquely Identified Properties of Over-Parametrised Models

Gunnar Cedersund

Department of Clinical and Experimental Medicine, Diabetes Research Centre, Linköping University, Sweden; FRIAS, Freiburg, Germany.

Poster 2.085

Transcripts of Functionally Related Genes in Individual S. cerevisiae Cells are Uncorrelated Due to Stochastic Fluctuations

Saumil J. Gandhi, Daniel Zenklusen and Robert H. Singer

Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY.

Poster 2.086

What Happens When Two Biological Systems Merge? The Generation and Investigation of Yeast Interspecific Hybrids

Jennifer Bellon1, Anthony R Borneman1, Christopher Ford2 and Paul J Chambers1

1.Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064 Australia. 2.School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB 1, Glen Osmond, Adelaide, SA, 5064.

Poster 2.087

Systems Approach for Identifying Transcriptional and Metabolic Changes in Shewanella oneidensis MR-1 During Growth-Phase Transitions

Qasim K. Beg1,*, Mattia Zampieri2,5,*, Niels Klitgord2, Sara Baldwin2, Timothy Gardner1,4 and Daniel Segrè1,2,3

1.Department of Biomedical Engineering, 2.Bioinformatics Program, 3.Department of Biology, Boston University, Boston, MA. 4.Amyris Biotechnologies, Emeryville, CA. 5.International School for Advanced Studies, Trieste, Italy.

Poster 2.088

MOA Analysis of Bioactive Compounds Using Budding Yeast Saccharomyces cerevisiae

Cheuk Hei Ho, Leslie Magtanong, Sarah Barker, Anastasija Baryshnikova, Michael Costanzo, Minoru Yoshida and Charles Boone

Department of Molecular Genetics, University of Toronto.

Poster 2.090

FooFunc: A browser for Quantitative M. musculus, H. sapiens and S. cerevisiae Gene Function Annotations and Underlying Evidence

John E. Beaver1, Weidong Tian1, Francis D. Gibbons1, Murat Tasan1, Joseph Mellor1, Gabriel F. Berriz1, Timothy R. Hughes3 and Frederick P. Roth1,2

1.Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School. 2.Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute. 3.Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto.

Poster 2.091

Structured Reduction of Dynamic Biochemical Models: A case Study Using Models of Yeast Glycolytic Oscillations

Gunnar Cedersund1 and George C. Verghese2

1.Department of Clinical and Experimental Medicine, Division of Cell Biology, Linköping University. 2.Research Laboratory of Electronics, Massachusetts Institute of Technology.

Poster 2.092

Improving Parameter Identifiability in Dynamical Models Using the Multi-Experiment Fitting MATLAB Toolbox PottersWheel

Thomas Maiwald1, Stefan Hengl2, Andreas Raue2, Peter K. Sorger1 and Jens Timmer2

1.Harvard Medical School, Department of Systems Biology, Boston, MA, USA. 2.University of Freiburg, Institute of Physics, Freiburg, Germany.

Poster 2.093

Integrated Analysis of the Molecular Pathology of Human Diseases Reveals Their Global Inter-Relationships

Silpa Suthram and Atul J. Butte

Stanford University.

Poster 2.095

Robustness and Fragility in the High Osmolarity Glycerol (HOG) Pathway in S. cerevisiae

Marcus Krantz, Doryaneh Ahmadpour, Lars-Göran Ottosson, Jonas Warringer, Christian Waltermann, Bodil Nordlander, Edda Klipp, Anders Blomberg, Stefan Hohmann and Hiroaki Kitano

Universtity of Gothenburg. Humboldt-University of Berlin. The Systems Biology Institute in Tokyo.

Poster 2.096

Modeling Prediction of Environmental Changes by Microorganisms

Amir Mitchell, Orna Dahan and Yitzhak Pilpel

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

Poster 2.097

Computational Modeling of the Regulation of the Inflammatory Signaling Pathway in Microglia

Patrick Sheppard1, Xiaoyun Sun2, John Emery2, Mustafa Khammash1 and Rona Giffard2

1.Dept. of Mechanical Engineering, University of California, Santa Barbara. 2.Dept. of Anesthesia, Stanford University School of Medicine.

Poster 2.098

Idefics: In Silico Platform for the Study of Epithelial Preneoplastic Processes

Martial Guillaud and Calum MacAulay

Cancer Imaging, BC Cancer Research Centre, Vancouver, BC, Canada.

Poster 2.099

A Direct Comparative Approach to Dissect Antigen Presentation in the Liver

Mohammad R. Ebrahimkhani and I. Nicholas Crispe

Seattle Biomedical Research Institute, Seattle, WA, USA.

Poster 2.100

Systems Biology Approach for Irreversible Differentiation in a Stem Cell System: Chaos Hypothesis

Chikara Furusawa and Kunihiko Kaneko

Graduate School of Information Science and Technology, Osaka University.

Poster 2.101

High-Priority Drug Targets Against Leishmania major from Novel Systems Analysis

Arvind K. Chavali and Jason A. Papin

Dept. of Biomedical Engineering, University of Virginia, Charlottesville, VA.

Poster 2.102

Highly Corregulated Biochemical Network of Chlamydomonas reihnhardtii Responsive System to Reduced Levels of Nitrogen

Do Yup Lee, Dinesh Kumar Barupal and Oliver Fiehn

UC Davis Genome Center, Davis, CA 95616.

Poster 2.103

Improvement of Genomic Researches in Wheat Breeding

Ural Khalmanov

Leading specialist, Republican Center for Cotton Seed.

Poster 2.104

The Helmholtz Alliance on Systems Biology

Roland Eils1, Ulrike Conrad2 and Jan Eufinger3

German Cancer Research Center (DKFZ) Heidelberg and BioQuant, University of Heidelberg, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.

Poster 2.105

A Cellular Context Memory in Peripheral Sensory Neurons Acts as XOR Switch

Tim Hucho, Vanessa Suckow, Olayinka Dina, Xiaojie Chen, Julia Kuhn, Jan Schmoranzer, Matthias Karst, Michael Bernateck, Jon D. Levine and Hans-Hilger Ropers

Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.

Poster 2.106

Cell Alignment Along Micro-Vessels as Order Principle to Restore Tissue Architecture During Liver Regeneration: from Experiment to Virtual Tissues and Back

Stefan Hoehme1, Marc Brulport2, Alexander Bauer2, Essam Bedawy2, Wiebke Schormann2, Matthias Hermes2, Verena Puppe2, Rolf Gebhardt5, Sebastian Zellmer5, Michael Schwarz4, Ernesto Bockamp6, Tobias Timmel7, Jan G. Hengstler2 and Dirk Drasdo1,3

1.Interdisciplinary Centre for Bioinformatics (IZBI), University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany. 2.Leibniz Research Centre for Working Environment and Human Factors (IfADo); University of Dortmund, Ardeystraße 67, D-44139 Dortmund, Germany. 3.Institut National de Recherche en Informatique et en Automatique (INRIA), Unit Rocquencourt B.P.105, 78153, Le Chesnay Cedex, France. 4.Institute of Exp. and Clinical Pharmacology and Toxicology, Dept. of Toxicology, University of Tübingen, Wilhelmstr. 56, 72074 Tübingen, Germany. 5.Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany. 6.Clinical School of the Johannes Gutenberg-University Mainz Institute for Toxicology Obere Zahlbacher Str. 67, 55131 Mainz, Germany. 7.Biofluidmechanics Laboratory, Charité - Universitätsmedizin Berlin, Berlin, Germany.

Poster 2.107

Host Genetic Requirements for Viral Infection: A Systems Virology Approach

Elsa W. Birch1, Nate Maynard2 and Markus W. Covert2

1.Department of Chemical Engineering, 2.Department of Bioengineering, Stanford University.

Poster 2.108

A Noisy Paracrine Signal Determines the Cellular NF-κB Response to LPS

Timothy Lee and Markus W. Covert

Department of Bioengineering, Stanford University.

Poster 2.109

The Transcription Unit Architecture of the Escherichia coli K-12 MG1655 Genome and its Application for Genome-scale Reconstruction of Transcriptional Regulatory Network

Byung-Kwan Cho, Karsten Zengler, Yu Qiu, Young Seoub Park, Eric M Knight, Christian Barrett, Harish Nagarajan and Bernhard Ø. Palsson

Systems Biology Research Group. Department of Bioengineering, 9500 Gilman Drive, University of California San Diego, La Jolla.

Poster 2.110

Toward a Whole-Cell Model of Mycoplasma genitalium

Jayodita Sanghvi1*, Jonathan R. Karr2* and Markus W. Covert1

1.Department of Bioengineering, 2.Biophysics Program, Stanford University.