Poster Session 1

8/31 1:00 - 4:00, Arrillaga Alumni Center, McCaw Hall

Poster 1.001

NF-κB Signaling and Dynamic Range in Response to TNFα and LPS

Savas Tay, Timothy Lee, Jacob Hughey, Anne Leyrat, Rafael Gomez-Sjoberg, Stephen R. Quake and Markus W. Covert

Department of Bioengineering, Stanford University.

Poster 1.002

Human microRNAs Co-Silence in Well-Separated Groups and Have Different Predicted Essentialities

Gabor Boross, Katalin Orosz and Illes J. Farkas

Hungarian Academy of Sciences, Eotvos University.

Poster 1.003

Towards Control Biomphalaria alexandrina Snails and the Free Living Larval Stages of Schistosoma mansoni Using the Microalga Spirulina platensis

Fathia Gawish

Environmental Research and Medical Malacology Dept. Theodor Bilharz Research Institute,Warrak El-Hadar, Imbaba, P.O. Box 30, Giza 12411, Egypt.

Poster 1.004

Nuclear Receptors Outside the Nucleus: the Emergence of Fast and Sensitive Response

Alexey N. Kolodkin, Martijn J. Moné, Frank J. Bruggeman and Hans V. Westerhoff

Molecular Cell Physiology, Netherlands Institute of Systems Biology, VU University Amsterdam, de Boelelaan 1085, NL-1081 HV Amsterdam, The Netherlands, EU.

Poster 1.005

High-Throughput Sequencing of the Zebrafish Antibody Repertoire

Joshua A. Weinstein, Ning Jiang, Richard A. White III, Daniel S. Fisher and Stephen R. Quake

Department of Bioengineering, Stanford University.

Poster 1.006

Reconstruction of Insulin Signaling Network

Pelin Ümit, Saliha D. Tekir, Kazim Yalcin Arga and Kutlu O. Ulgen

Department of Chemical Engineering, Boğaziçi University, 34342, Bebek, İstanbul, Turkey.

Poster 1.007

Calibration of Large-Scale Dynamic Models in Systems Biology

Jose A. Egea1, Wolfram Liebermeister2, Edda Klipp2 and Julio R. Banga1

1IIM-CSIC, Vigo, Spain. 2Humboldt University Berlin, Berlin, Germany.

Poster 1.008

A New Concept of Dynamic Network Motif in Time-Varying Molecular Regulatory Networks

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

KAIST.

Poster 1.009

Periodic Chemical Stimulation of Non-Excitable Cells Reveals Phase-Locked Calcium Responses

Andreja Jovic1, Bryan Howell1, Sue M. Wade2, Khamir Mehta3, Atsushi Miyawaki4, Richard Neubig2, Jennifer Linderman3 and Shuichi Takayama1,5

1.Department of Biomedical Engineering, University of Michigan- Ann Arbor. 2.Department of Pharmacology, University of Michigan- Ann Arbor. 3.Department of Chemical Engineering, University of Michigan- Ann Arbor. 4.Brain Science Institute, RIKEN.

Poster 1.010

Application of a Hill-Climbing Algorithm to Combine Information Across Different Microarray Studies

Amin Moghaddas Gholami1, Jörg Hoheisel1, Kurt Fellenberg2

1.German Cancer Research Center (DKFZ), Functional Genome Analysis, Heidelberg, Germany. 2.Technical University Munich, Centre for Integrated Protein Sciences Munich (CIPSM), Freising, Germany.

Poster 1.011

A Systems Biology Approach: Mathematical Modelling of Aquaporin-2 Regulation

Martina Froehlich1,2, Peter Deen3 and Edda Klipp1

1.Max Planck Institute for Molecular Genetics, Ihnestraße 73, D-14195 Berlin. 2.Humboldt-Universität zu Berlin, Theoretische Biophysik, Invalidenstrasse 42, D-10115 Berlin. 3.Department of Physiology, NCMLS, Radboud University Nijmegen, Netherlands.

Poster 1.012

PALM: A Parallel and Integrated Framework with the Substitution Model Estimation for Phylogenetic Inference

Shu-Hwa Chen, Sheng-Yao Su, Chen-Zen Lo, Teng-Jay Huang, Pao-Han Kuo and Chung-Yen Lin

Institute of Information Science, Academia Sinica, No. 128 Yan-Chiu-Yuan Rd., Sec. 2, Taipei 115, Taiwan.

Poster 1.013

Single Cell Analysis Reveals that HIV Viral Integration Position Alters the Mode of Stochastic HIV Gene Expression from Poisson to Infrequent Bursting

Jonathan E. Foley1, Ron Skupsky1, John Burnett2, Adam P. Arkin1 and David V. Schaffer1,2

1.Department of Bioengineering. 2.Department of Chemical Engineering, University of California at Berkeley.

Poster 1.014

Application of Transcriptome and Proteome Analysis for Comparative Evaluation of Industrial E. coli Production Strains

Karoline Marisch1, Norbert Auer1, Gerhard Kastner1, Markus Luchner1, Ebrahim Razzazi-Fazeli2, Theresa Scharl1, Florian Strobl1, Gerald Striedner1 and Karl Bayer1

1.University of Natural Resources and Applied Life Sciences, Department of Biotechnology, 1190 Vienna, Austria. 2.University of Veterinary Medicine, VetOMICS Core Facility, 1210 Vienna, Austria.

Poster 1.015

Ligand Depletion In Vivo Modulates the Dynamic Range of Cooperative Signal Transduction

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

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton (Cambridge) CB10 1SD, UK.

Poster 1.016

Multi-Oscillatory Behaviour in Yeast Metabolsim

Douglas B. Murray, Rainer Machné, Tomoyoshi Soga, Kalesh Sasidharan, Cornelia Amariei, David Lloyd, Miguel Aon, Chieko Kimura, Kaori Igarashi and Masaru Tomita

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

Poster 1.017

Minimal Design Constraints for Noise Attenuation in Positive Feedback Systems

Liming Wang, Jack Xin and Qing Nie

University of California, Irvine.

Poster 1.018

Mitotic Exit: A Critical Analysis of a Mathematical Model

Paula Freire and Bela Novak

Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford.

Poster 1.019

Dynamic Behavior Determines the Design Strategy of Metabolic Regulation Networks

Ulf W. Liebal1,2, Jeong-Rae Kim1, Olaf Wolkenhauer2 and Kwang-Hyun Cho1

1.Dept. of Bio and Brain Engr., Korea Advanced Institute of Science and Technology, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea. 2.Institute of Computer Science, University of Rostock, Albert-Einstein Str. 21, 18051 Rostock, Germany.

Poster 1.020

Connecting Oxidative Stress Diseases to Metabolic Perturbation: A Probabilistic Boolean Model of Iron Homeostasis in Yeast

Fiona Achcar, Jean-Michel Camadro and Denis Mestivier

Institut Jacques Monod - UMR 7592 - CNRS - Univ Paris Diderot.

Poster 1.021

Reverse Engineering the Prion Interactome

Mattia Zampieri1,3, Giuseppe Legname2, Daniel Segrè3,4 and Claudio Altafini1

Scuola Internazionale Superiore di Studi Avanzati - International School for Advanced Studies (SISSA-ISAS), 1.Functional Analysis, and 2.Neurobiology Sector, via Beirut, 4.Trieste, Italy 3.Boston University - Bioinformatics Program, 24 Cummington St., Boston.

Poster 1.022

Tuning an Oscillatory Clock in Boolean Networks

Gabriele Scheler

Stanford University.

Poster 1.023

Gene Regulatory Network of Zebrafish Eye Development

Yuk Fai Leung1,2, Monica Hensley1, Sylvia Bonilla1, Liyun Zhang1, Yuqing Zhang1, Ping Ma3,4, Farida Emran2, Paul Grosu5, Brian A. Link6 and John E. Dowling2

1.Department of Biological Sciences, Purdue University, West Lafayette, IN. 2.Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA. 3.Department of Statistics, University of Illinois, Champaign, IL. 4.Institute for Genomic Biology, University of Illinois, Champaign, IL. 5.Bauer Center for Genomics Research, Harvard University, Cambridge, MA. 6.Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI.

Poster 1.024

Exploring the Genetic Complexity of microRNA-Mediated Regulation

Wan-Lin Su, Robert Kleinhanz and Eric E. Schadt

University of Washington; Rosetta Inpharmatics (a wholly-owned subsidiary of Merck).

Poster 1.025

Crosstalk of IL-6 and GM-CSF Signaling Pathways in HaCaT A5 Benign Tumor Keratinocytes

Sofia Depner, Andreas Sommer, Oliver Hauk, Alexander Schimming, Marco Nici, Mario Mommer, Johannes Schlöder and Margareta Mueller

German Cancer Research Center (Germany). IWR University Heidelberg (Germany).

Poster 1.026

Tools for Representation, Analysis, Simulation and Visualization of Metabolism

Christian Klukas, Eva Grafahrend-Belau, Stephan Weise, Dirk Koschützki, Björn H. Junker, Uwe Scholz and Falk Schreiber

IPK Gatersleben.

Poster 1.027

Investigations into the Time-Varying Gene Regulatory Network of Embryonic Stem Cell Developments

Sung-Hwan Cho, Junil Kim and Kwang-Hyun Cho

KAIST.

Poster 1.028

The Dynamical Regulatory Role of Synthetic Lethal Paralogous Gene Pairs

Min-Gyoung Shin, Dongsan Kim and Kwang-Hyun Cho

KAIST.

Poster 1.029

The Association between Genetic Variants of Stromal Cell-Derived Factor-1 and CXCR4 and Hepatocellular Carcinoma

Hsiu-Ting Tsaia, Yi-Chen Chenb, Tzy-Yen Chenc, Po-Hui Wangd, Long-Yau Lind and Shun-Fa Yange

1.School of Nursing, Chung Shan Medical University, Taichung, Taiwan. 2.School of Nutrition, Chung Shan Medical University, Taichung, Taiwan. 3.Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan. 4.School of Medicine, Chung Shan Medical University, Taichung, Taiwan. 5.Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.

Poster 1.030

Cell Growth and Size Homeostasis in Proliferating Animal Cells

Amit Tzur, Ran Kafri, Valerie S. LeBleu, Galit Lahav and Marc W. Kirschner

Harvard Medical School, Dept. of Systems Biology.

Poster 1.031

Modelling Extra- and Intracellular Aspects of the FcεRI Signaling Cascade

Michael I. Monine, Ambarish Nag, Ryan Gutenkunst, S. Gnanakaran and Byron Goldstein

Theoretical Biology and Biophysics Group, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM.

Poster 1.032

Combined Proteomic-RNAi Screen for Host Factors Involved in Human Hepatitis Delta Virus Replication

Dan Cao, Dirk Haussecker, Yong Huang and Mark A. Kay

Departments of Pediatrics and Genetics, Stanford University.

Poster 1.033

Learning the Structure of Protein-Protein Interaction Networks

Oleksii Kuchaiev and Natasa Przulj

University of California, Irvine.

Poster 1.034

Growth Factor Signaling Systems Identify Critical Genes for Survival Prediction in Lung Adenocarcinoma

Mai Yamauchi, Rui Yamaguchi, Masao Nagasaki, Teppei Shimamura, Seiya Imoto, Ayumu Saito, Kazuko Ueno, Yousuke Hatanaka, Ryo Yoshida, Tomoyuki Higuchi, Takashi Kohno, Jun Yokota, Satoru Miyano and Noriko Gotoh

Division of Systems Biomedical Technology, Institute of Medical Science, University of Tokyo., Human Genome Center, Institute of Medical Science, University of Tokyo., Institute of Statistical Mathematics., Biology Division, National Cancer Center Research Institute.

Poster 1.035

Analysis of the Early Phase of Insulin Signalling in Adipocytes: An Integrated Experimental-Mathematical Modelling Approach

Cecilia Brännmark, Gunnar Cedersund, Peter Strålfors

Linköping University.

Poster 1.037

Data-Driven Inverse Analysis of a Negative Feedback Mechanism in Pituitary Gland Cells

James Lu, Clemens Zarzer, Philipp Kuegler, Martin Puchinger, Aamir Shahzad, Gottfried Koehler, Christoph Flamm and Rainer Machné

Austrian Academy of Sciences (RICAM), University of Vienna (MFPL, TBI).

Poster 1.038

Chemical Genomics and Live Cell Microscopy to Study NF-κB Oscillations

Catherine Heyward1, Yogendra Patel2, David Spiller1, Douglas Kell2 and Michael White1

1.University of Liverpool. 2.University of Manchester.

Poster 1.039

Non-genetic Heterogeneity Originating at Cell Division

Dann Huh and Johan Paulsson

Harvard Medical School, Department of Systems Biology.

Poster 1.040

A Molecular Mechanism for STAT/Socs Oscillations

Nuria Domedel-Puig1, Evgenii Volkov2, Pablo Villoslada3 and Jordi Garcia-Ojalvo1

1.Department of Physics and Nuclear Engineering, Universitat Politecnica de Catalunya, Terrassa, Spain. 2.Department of Theoretical Physics, Lebedev Physical Institute, Moscow, Russia. 3.Department of Neurosciences, IDIBAPS Hospital Clinic, Barcelona, Spain.

Poster 1.041

Identification of Novel Cellular Roles of Pex11, a Regulator of Peroxisome Proliferation, by Combining Genetic and Protein Interactome with Transcriptome Analysis in Yeast

Mojca Mattiazzi, Janez Kokosar, Matej Somrak and Uros Petrovic

Jozef Stefan Institute, Department of Molecular and Biomedical Sciences, Ljubljana, Slovenia.

Poster 1.042

Polarization Response of G-protein Systems to Dynamic Spatial Gradients

Travis I Moore, Ching-Shan Chou, Hiromasa Tanaka, Noo Li Jeon, Qing Nie and Tau-Mu Yi

University of California, Irvine.

Poster 1.043

In Silico Feasibility of Novel Biodegradation Pathways

Stacey D. Finley, Linda J. Broadbelt and Vassily Hatzimanikatis

Northwestern University.

Poster 1.044

Construction and Control of Biosynthetic Pathways

Joshua K. Michener1 and Christina D. Smolke2

1.Bioengineering Option, California Institute of Technology. 2.Bioengineering Department, Stanford University.

Poster 1.045

Impact on A1C of Tissue Specific Restorations in Insulin Sensitivity

Michael J Reed

Entelos, Inc., Foster City, CA USA.

Poster 1.046

GetBonNie - A Web Based Tool for Building, Analyzing, and Sharing Rule-Based Models

Bin Hu1,2, G. Matthew Fricke3, James R. Faeder4, Richard G. Posner5 and William S. Hlavacek1,2,6

1.Department of Biology and Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM 87131. 2.Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545. 3.Department of Computer Science, University of New Mexico, Albuquerque, NM 87131. 4.Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260. 5.Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004. 6.Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

Poster 1.047

Systems-Level Cancer Gene Identification from Protein Interaction Network Topology Applied to Melanogenesis-Related Functional Genomics datL

Tijana Milenkovic, Vesna Memisevic, Oleksii Kuchaiev, Anand K. Ganesan and Natasa Przulj

University of California, Irvine.

Poster 1.048

Kinetic Models of Interactions Among Ca2+, Calmodulin, and CaMKII; Molecular Components of Learning and Memory

Shirley L. Pepke, Tamara L. Kinzer-Ursem, Stefan Mihalas and Mary B. Kennedy

Division of Biology and the Center for Advanced Computing Research, California Institute of Technology.

Poster 1.049

E-Cell IDE: An Integrated Modelling and Simulation Environment for Systems-Biology

Takeshi Sakurada1, Moriyoshi Koizumi1,2, Sachio Nohara3, Chihiro Okada3, Yuri Matsuzaki4 and Masaru Tomita1

1.Institute for Advanced Biosciences, Keio University. 2.Japan Science and Technology Agency (JST). 3.Mitsubishi Space Software Co., Ltd. 4.Tokyo Institute of Technology.

Poster 1.050

Analyzing the Breakpoint Regions of Genomic Rearrangement Events at Nucleotide Level by Sequence Alignment

Te-Chin Chu1,2, Tsunglin Liu3, D.T. Lee1,4,5, Greg C. Lee2 and Arthur Chun-Chieh Shih1,4

1.Institute of Information Science. 3.Biodiversity Research Center, and 4.Research Center for Information Technology Innova-tion, Academia Sinica, Taipei, Taiwan. 2.Department of Computer Science and Information Engineering, National Taiwan Normal University, Taipei, Taiwan. 5.Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan.

Poster 1.051

Discovery of Functional Linkages Between S. cerevisiae Genes by Phylogenetic Profiling with Eighty Fully Sequenced Fungal Genomes

Junha Shin and Insuk Lee

Department of Biotechnology, College of Life science and Biotechnology, Yonsei University, 134 Shinchon-dong, Seodaemun-ku, Seoul 120-749, South Korea.

Poster 1.052

SensSB - A software Toolbox for Sensitivity Analysis in Systems Biology Models

Maria Rodriguez-Fernandez and Julio R. Banga

Process Engineering Group, IIM-CSIC, Spanish Council for Scientific Research. Vigo, Spain, 36208.

Poster 1.053

Robustness to Parameter Variations in System Biology Models: Efficient Sampling of Complex Viable Volumes

Elias Zamora-Sillero1,2,3, Marc Hafner1,3,4, Andreas Wagner1,3,5,6 and Jörg Stelling2,3

1.Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. 2.Institute of Computational Science ETH Zurich, 8092 Zurich, Switzerland. 3.The Swiss Institute of Bioinformatics. 4.School of Computer and Communications Science, Ecole Polytecnique Federale de Lausanne, 1015, Lausanne, Switzerland. 5.The Santa Fe Institute. 6.University of New Mexico, Department of Biology.

Poster 1.054

Fabrication of an E. coli Proteome Chip and its Application on Surveying Infant to Adult Human Immune Response to Commensal Microorganisms

Chien-Sheng Chen, Aik Choon Tan, Kwang Sik Kim and Heng Zhu

Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan. Division of Medical Oncology, Department of Medicine, School of Medicine University of Colorado Denver, Aurora CO. Department of Pharmacology and Molecular Sciences & High Throughput Biology Center, Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD.

Poster 1.055

Comprehensive Expressional Analyses of Antisense Transcripts in Colon Cancer Tissues Using Artificial Probes to Detect Potential Regulatory Antisense RNAs

Rintaro Saito1,8,*, Keisuke Kohno2,*, Yuki Okada1,3, Yuko Osada1, Koji Numata4, Kazufumi Watanabe6, Hajime Nakaoka7, Naoyuki Yamamoto7, Akio Kanai1,3,8, Hiroshi Yasue9, Soichiro Murata2, Kuniya Abe4,5, Masaru Tomita1,3,8, Nobuhiro Ohkohchi2 and Hidenori Kiyosawa4,5

1.Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan. 2.Department of Surgery, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575, Japan. 3.Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-8520, Japan. 4.Technology and Development Team for Mammalian Cellular Dynamics, BioResource Center (BRC), RIKEN Tsukuba Institute, Ibaraki 305-0074, Japan. 5.Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-0006, Japan. 6.Custom Biotechnology Service Group, Hokkaido System Science Co. Ltd, 2-1 Shinkawa Nishi 2-1, Kita-ku, Sapporo 001-0932, Japan. 7.C's Lab Co. Ltd. Maruito Sapporo Bldg., 7F, Kita 2 Nishi 1, Kita-ku, Sapporo 060-0002, Japan. 8.Faculty of Environment and Information Studies, Keio University, Fujisawa, 252-8520, Japan. 9.National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.

Poster 1.056

Linear Control Analysis of the Autocatalytic Glycolytic System

Fiona Chandra, Genti Buzi and John Doyle

California Institute of Technology.

Poster 1.057

The German HepatoSys Network

Johannes Bausch and Jens Timmer

University Freiburg.

Poster 1.058

Smoldyn: A Simulator for Cellular Systems Biology

Steven S. Andrews and Karen Lipkow

the Molecular Sciences Institute and University of Cambridge.

Poster 1.059

Novel Tool for Identification and Comparison of Gene-Gene Association Networks

Jeff Skinner1, Sudhir Varma1, Anatoli Yambartsev2, Yuri Kotliarov3, Tram Huyen1 and Andrey Morgun4

1.Bioinformatics and Computational Biosciences Branch (BCBB), National Institute of Allergy and Infectious Diseases (NIAID). 2.Instituto de Matematica e Estatistica (IME), Universidade de Sao Paulo (USP). 3.Neuro-Oncology Branch (NOB), National Cancer Institute (NCI). 4.Laboratory of Cellular and Molecular Immunology (LCMI), NIAID.

Poster 1.060

BioModels Database, a Curated and Annotated Resource of Quantitative, Kinetic Models

Chen Li, Lukas Endler, Vijayalakshmi Chelliah, Nicolas Rodriguez and Nicolas Le Novère

Computational Neurobiology Group, EMBL-EBI, Cambridge, United Kingdom.

Poster 1.061

Phenotypic Analysis of the Osmoadaptation in Saccharomyces Cerevisiae

Jignesh Parmar, Sharad Bhartiya and KV Venkatesh

Department of Chemical Engineering, IIT Bombay, Powai, Mumbai 400076 India.

Poster 1.062

Prediction of Stem Cell Fates through Molecular Concept Modelling

Sun-Gou Ji and Insuk Lee

Yonsei University.

Poster 1.063

An Efficient Engineering Platform for Genetic Switches in Escherichia coli

Norihito Muranaka and Yohei Yokobayashi

Department of Biomedical Engineering, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616.

Poster 1.064

Predicting Local Interactions and Global Entrainment for Synchrony in Coral Mass Spawning

Bharath Ananthasubramaniam, Roger M. Nisbet, Daniel E. Morse and Francis J. Doyle III

Institute of Collaborative Biotechnologies, Ecology, Evolution and Developmental Biology, Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106.

Poster 1.065

Biocharts: A Visual Formalism for Complex Biological Systems

Hillel Kugler, Antti Larjo and David Harel

Microsoft Research Cambridge.

Poster 1.066

Simulated Annealing Improves Consistency of Metabolic Networks

Mathias Ganter and Jörg Stelling

Department of Biosystems Science and Engineering and Swiss Institute of Bioinformatics, ETH Zürich, Basel, Switzerland.

Poster 1.067

The TNF Receptor Signalling Network: Modular Modelling and Cell-Type Specific Analysis

Steffen Waldherr, Malgorzata Doszczak, Monica Schliemann, Jens Schreiner, Peter Scheurich and Frank Allgöwer

Universität Stuttgart, Center for Systems Biology.

Poster 1.068

System Biology Assessment of Molecular and Physiological Dynamics in the Social Amoeba Dictyostelium discoideum Exposed to the Heavy Metal Mercury

Francesco Dondero1, Gareth Bloomfield2, Francesco Marsano1, Lara Boatti1, Oliver Jones3, Julian Griffin3, Robert Kay2, Al Ivens4 and Aldo Viarengo1

1.Department of Environmental and Life Sciences (DISAV), University of Piemonte Orientale “Avogadro”, Alessandria, Italy. 2.MRC Laboratory of Molecular Biology, Cambridge, UK. 3.Department of Biochemisty, Cambridge University, Cambridge, UK. 4.Wellcome Trust Sanger Institute, Hinxton, UK.

Poster 1.069

Stability of Metabolic Correlations Under Changing Environmental Conditions in Escherichia coli - A Systems Approach

Jedrzej Szymanski, Szymon Jozefczuk, Zoran Nikoloski, Joachim Selbig, Victoria Nikiforova, Gareth Catchpole and Lothar Willmitzer

Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.

Poster 1.070

Changing States: Using a Constraint Based Approach to Investigate Microbial Interactions

Brett G. Olivier1, Steven M. Kelk2, Leen Stougie2,3, Wilfred F.M. Röling1, Ruchir Khandelwal 1, Hans V. Westerhoff1 and Frank J. Bruggeman1,2

1.Molecular Cell Physiology, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands. 2.Life Sciences, Centrum voor Wiskunde en Informatica (CWI), Science Park 123, NL-1098 XG Amsterdam, The Netherlands 3.Econometrics, VU University Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands.

Poster 1.071

Switch-Like Behavior on Cell Membrane Arising from Dimerization of ErbB Receptor Family

Takashi Nakakuki1 and Mariko Hatakeyama2

1.Department of Mechanical Systems Engineering, Faculty of Engineering, Kogakuin University. 2.Cellular Systems Modeling Team, Computational Systems Biology Research Group, RIKEN ASI.

Poster 1.072

Modelling of the Circadian Clock of Unicellular Green Alga Ostreococcus tauri

Quentin Thommen1,2, Pierre-Emmanuel Morant1,2, Florence Corellou3, Constant Vandermoere1,2, François-Yves Bouget3 and Marc Lefranc1,2

1.PhLAM, Université Lille 1, France. 2.IRI, Université Lille 1, France. 3.Observatoire océanologique de Banyuls/mer, UMR CNRS 7628, Université Pierre et Marie Curie, France.

Poster 1.073

FORSYS-Partner: Systems Biology of Cyanobacterial Biofuel Production

Ralf Steuer1, Karl Ziegler2, Dan Kramer2, Wolfgang Lockau1, Yvonne Zilliges1, Henning Knoop1, Jan-Christoph Kehr1, Wolfgang R. Hess3, Annegret Wilde4, Thomas Boerner1

1.Humboldt-Universitaet zu Berlin. 2.Cyano Biofuels GmbH. 3.Albert-Ludwigs-Universitaet Freiburg (FRISYS). 4.Justus-Liebig-Universitaet Giessen.

Poster 1.074

The Identification of Rich2 in an siRNA Screen for Regulators of Synapse Formation and Maturation

Milos Galic, Samuel Bandara and Tobias Meyer

Chemical and Systems Biology, School of Medicine, Stanford University.

Poster 1.075

A Dependency Graph Analysis in the Context of Disease Classification

Andreas Bernthaler, Raul Fechete, Martin Wiesinger, Paul Perco, Konrad Mönks, Rudolf Freund and Bernd Mayer

Vienna University of Technology, Institute of Computer Languages, Theory and Logics Group, Favoritenstrasse 9-11, A - 1040 Vienna, Austria.

Poster 1.076

Discovering Basic Network Motifs that Underlie Gastrin Induced Gene Expression

Torunn Bruland, Endre Anderssen, Kristine Misund, Vidar Beisvåg, Arne K Sandvik, Liv Thommesen and Astrid Lægreid

Dept. of Cancer Research and Molecular Medicine, The NTNU Microarray FUGE PLatform, Norwegian University of Science and Technology, and Dept. of Food Science and Medical Technology, Sør-Trøndelag College, Trondheim Norway.

Poster 1.077

4D Quality Assurance for Enhanced High-Throughput Microscopy

Jonas Mossler1,3, Lars Lehmann1,2, Peter Fischer2 and Roland Eils1,3

1.Heidelberg University, Viroquant / Bioquant, Heidelberg, Germany. 2.Heidelberg University, Institute for Computer Engineering, Heidelberg, Germany. 3.Intelligent Bioinformatics Systems Division, German Cancer Research Center.

Poster 1.078

Partial Correlation Signaling Networks in Virus-Infected Cardiomyocytes

Farshid S. Garmaroudi1,2, David Marchant1,2, Ali Bashashati5, Abbas Khalili3, Brian W. Wong1,2, 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 1.079

Information Processing at the Erythropoietin Receptor Level

Verena Becker1, Marcel Schilling1, Julie Bachmann1, Ute Baumann1, Andreas Raue2, Thomas Maiwald3, Jens Timmer2, Ursula Klingmüller1

1.German Cancer Research Center, Heidelberg. 2.University of Freiburg, Germany. 3.Department of Systems Biology, Harvard Medical School, Boston.

Poster 1.080

ConsensusPathDB – Towards a More Complete Picture of Cell Biology

Atanas Kamburov, Christoph Wierling, Hans Lehrach and Ralf Herwig

Max Planck Institute for Molecular Genetics.

Poster 1.081

Combinatorial Stress Response Models in Pathogenic Fungi

Piers Ingram

Imperial College London.

Poster 1.082

Computational Modeling of Taste Papillae Patterning during Development

Scott Christley1, Piper Hollenbeck2,4, Ching-Shan Chou1, Arthur Lander3,4, Anne Calof2,3,4 and Qing Nie1,4

Departments of 1.Mathematics, 2.Anatomy & Neurobiology, 3.Developmental & Cell Biology, and 4.Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA.

Poster 1.083

A Synthetic Genetic Edge Detection Program

Jeffrey J. Tabor, Howard Salis, Zachary B. Simpson, Aaron A. Chevalier, Anselm Levskaya, Edward Marcotte, Christopher A. Voigt and Andrew D. Ellington

University of California San Francisco.

Poster 1.084

Deterministic and Stochastic Modeling of DNA Replication in Budding Yeast

Thomas Spiesser, Christian Diener, Matteo Barberis and Edda Klipp

Humboldt-Universität zu Berlin.

Poster 1.085

Multi-Level Hierarchical Modelling of Glucose Homeostasis

Elin Nyman1,2, Cecilia Johansson1, Anita Öst1, Jan Brugård2, Fredrik Nyström1, Peter Strålfors1 and Gunnar Cedersund2

1.Department of Clinical and Experimental Medicine, Diabetes Research Centre, Linköping University, Sweden. 2.MathCore Engineering AB, Linköping, Sweden.

Poster 1.086

Systems Biology: A New Approach to Industrial Yeast Strain Development

Paul J Chambers, Simon A Schmidt, Anthony R Borneman, Cristian Varela, Jeremy Hack, Meagan Mercurio, Daniel Cozzolino, Maurizio Ugliano and Chris D Curtin

Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia.

Poster 1.087

Forward Engineering of Synthetic Bio-Logical AND Gates

Poonam Srivastava, Kavita Iyer Ramalingam, Jonathan Tomshine, John Barrett and Yiannis Kaznessis

Department of Chemical Engineering and Material Sciences, University of Minnesota.

Poster 1.088

The Genome-Wide Expression Switching on Differentiation of Naïve CD4 Positive T Cell

Midori Hashimoto, Vincent Piras, Masaru Tomita, Kumar Selvarajoo and Masa Tsuchiya

Institute for Advanced Biosciences, Keio University.

Poster 1.089

Independent Kinetic Competition Between Mitotic Slippage and Death Activation Governs Live-or-Die Decisions in Response to Kinesin-5 Inhibitors

Hsiao-Chun Huang, Timothy J. Mitchison and Jue Shi

Department of Systems Biology, Harvard Medical School.

Poster 1.090

Cardiac Integrated Database Management System-Pathway Database (CIDMS-PD): An Innovative Systems Biology Knowledgebase for Cellular Pathways in Heart

Pradeep Sreenivasaiah, Siva Arunachalam and Do Han Kim

Department of Life Science, Systems Biology Research Center, Gwangju Institute of Science and Technology, 1 Oryong-dong, Buk-gu, Gwangju 500-712, Republic of Korea.

Poster 1.091

ProtozoaDB: Towards a Knowledgebase Approach for a Systems Biology Database

Alberto M. R. Dávila1, Rodrigo Jardim1, Milene P. Guimarães1,2, Daniel Loureiro1,2, Sérgio M. S. Cruz2, Pablo N. Mendes3, Glauber Wagner4,5, Diogo A. Tschoeke1, Rafael R. Cuadrat1, Kary A. Ocaña1, M. Ruiz-Olazar1,2, Floriano P. Silva Jr1, Christian M. Probst1, Edmundo C. Grisard4, Maria C. Cavalcanti6, Maria L. Campos2 and Marta Mattoso2

1.FIOCRUZ. 2.UFRJ. 3.Wright State University University. 4.UFSC. 5.UNOESC. 6.IME.

Poster 1.092

Genome Sequencing and Comparative Genomics of Industrial Saccharomyces cerevisiae Strains

Anthony Borneman1, Jason Affourtit2, Isak Pretorius1, Michael Egholm2 and Paul J Chambers1

1.The Australian Wine Research Institute, Adelaide, SA 5064, Australia. 2.454 Life Sciences, A Roche Company, Branford, CT 06405, USA.

Poster 1.093

Stochastic Gene Expression Bursts in Feed Forward Loops

Mark Kittisopikul and Gurol M Suel

Green Center for Systems Biology, Department of Pharmacology, UT Southwestern, Dallas, TX 75390.

Poster 1.095

Latest from the Data Integration Frontier: Using Pathway Data to Build and Annotate Systems Biology Models

Oliver Ruebenacker, Ion I. Moraru and Michael Blinov

University of Connecticut Health Center.

Poster 1.096

Under-Representation of Combinatorial Transcriptional Regulation in Yeast

Ho-Joon Lee

Deptartment of Systems Biology, Harvard Medical School.

Poster 1.097

Gene Expression Commons: Web Platform for Definitive Microarray Profiling

Jun Seita1, Debashis Sahoo2,3, David L. Dill2,3 and Irving L. Weissman1

1.Institute for Stem Cell Biology and Regenerative Medicine, 2.Department of Computer Science, and 3.Department of Electrical Engineering, Stanford University.

Poster 1.098

Systemic Analysis of Stress response and Proteasome Inhibition

Hee-Jung Kim, Hye Joon Joo, Kyu-Baek Hwang, Donghee Lee and Kong-Joo Lee

College of Pharmacey, Division of Life & Pharmaceutical Sciences, Ewha Womans University, School of Computing, Soongsil University, Seoul, Korea.

Poster 1.099

Insights from Methionine Metabolism into the Modular Organization of Yeast Cell Biology

Allegra Petti, Christopher Crutchfield, Joshua Rabinowitz and David Botstein

Lewis-Sigler Institute, Princeton University.

Poster 1.100

Deterministic Heterogeneity Patterns of Virus Infection, Lipid Composition and Endocytosis in Human Cell populations

Berend Snijder, Raphael Sacher, Pauli Rämö, Eva-Maria Damm, Prisca Liberali and Lucas Pelkmans

Institute of Molecular Systems Biology, ETH Zurich.

Poster 1.101

The Effect of pH on the Metabolic Shift in AB Fermentation in Clostridium acetobutylicum

Sylvia Haus1, Sara Jabbari2, Thomas Millat1, Olaf Wolkenhauer1 and John R. King2

1.University of Rostock, Germany. 2.University of Nottingham, UK.

Poster 1.103

On the Equivalence of the Equilibrium Correlation and Non-Equilibrium Response in Stochastic Chemical Kinetics

Ching-Cher Sanders Yan and Chao-Ping Hsu

Institute of Chemistry, Academia Sinica.

Poster 1.104

Competition and Saturation in microRNA Gene Regulation

Aly Khan, Doron Betel, Martin Miller, Chris Sander, Christina Leslie and Debora Marks

Memorial Sloan-Kettering Cancer Center.

Poster 1.105

Robust Tissue Patterning Via Dynamic Protrusion-Mediated Lateral Inhibition

Michael Cohen, Marios Georgiou, Mark Miodownik and Buzz Baum.

University College London.

Poster 1.106

Predicting and Controlling the Reactivity of Immune Cell Populations Against Cancer

Eran Eden*,Kfir Oved*, Martin Akerman, Roy Noy, Ron Wolchinsky, Orit Izhaki, Ester Schallmach, Adva Kubi, Naama Zabari, Jacob Schachter, Uri Alon, Yael Mandel-Gutfreund, Michal J Besser and Yoram Reiter

Weizmann Institute of Science.

Poster 1.107

Scalable Methods for Modeling Complex Cell Signaling Systems

Ty Thomson, Josh Havumaki, Isha Antani and Gordon Webster

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

Poster 1.108

The Proteomes and Transcriptomes of Adaptively Evolved Escherichia coli Strains are Consistent with Computed Optimal Growth States from Genome-Scale Models

Nathan E. Lewis1, Kim K. Hixson3, Tom Conrad2, Pep Charusanti1, Ashoka D. Polpitiya3, Richard D. Smith3 and Bernhard Ø. Palsson1

1.Department of Bioengineering, University of California, San Diego. 2.Department of Biochemistry, University of California, San Diego. 3.Pacific Northwest National Laboratory.

Poster 1.110

A Bioinformatics Pipeline for Metagenome-Wide Metabolic Network Modeling and its Application to an Acid Mine Drainage Microbial Community

Yu Chen, Tom Douce, Marc E. Singer and Xiaoxia Nina Lin

University of Michigan, Ann Arbor.

Poster 1.111

Genetic-metabolic networks in physiological admixed populations

Mogens Fenger1, Allan Linneberg2, Thomas Werge3 and Torben Jorgensen4

1.University of Copenhagen and Capital Hospitals of Denmark. 2.Research Center for Prevention and Health, Glostrup, Denmark. 3.Physchiatric Research Centre, Roskilde, Denmark. 4.Research Center for Prevention and Health, Glostrup, Denmark.