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ICSB 2007 Welcome to the Eighth International Conference on Systems Biology
Long Beach, California October 1-6, 2007
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Abstract Submission Tutorials WorkshopsCommitteesPosters    Posters By Topic:
A. RTK Systems Biology
B. Morphogenesis
C. Synthetic Biology
D. Mathematical Frontiers
E. Technological Froniters
F. Regulatory Systems
G. Systems Bioinformatics: Tools
H. Systems Bioinformatics: Analysis
I. Systems Biomedicine
J. Multiscale Networks
   Posters By Author
   Submission Call (archive) LinksFAQ & InformationSponsors & HostsProceedings Journal Articles
Posters
rule(Alphabetical by presenting author)

a | b | c | d | e | f | g | h | i | j | k | l | m | n | o | p | q | r | s | t | u | v | w | x | y | z

Jiro Adachi (Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University)
Elucidating the Fitness Landscape of Protein Translation System

Sophia Ananiadou (School of Computer Science, The University of Manchester, UK)
SemText: A semantically enriched information retrieval system for biology

Dorit Arlt (Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ) Heidelberg, Germany)
From whole genome siRNA screens to systems biology: The glycosaminoglycan degradation pathway in cancer metastasis

Sriya Avadhani (Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, USA)
Systems Biology Study of Base Excision Repair Pathway to Improve Therapeutic Gain in Cancer Treatment

Roberto Ávila-Pozos (Área Académica de Matemáticas, Universidad Autónoma del Estado de Hidalgo)
Simulation of the Electrical Activity of the Pancreatic beta Cells Induced by Ingesting of Glucose During an Oral Glucose Tolerance Test

Tigran Bacarian (IGB, UC Ivine)
Integrating system for segmenting and tracking fluorescent objects on the image data of growing cell colonies

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Fayez A. Bakery (Department of Medical Malacology Theodor Bilharz Research Institute,Giza.Egypt)
Estimation of free amino acids and protein in bulinus truncatus snail infected with Schistosoma haematobium or Echinoparyphium recurvatum

Mukesh Bansal (Telethon Institute of Genetics and Medicin, Naples, Italy.)
Identification of transcriptional targets from dynamic gene expression profiles: An integrated computational and experimental approach applied to the transcription factor p63

Anastasia Barbina (Department of Clinical Diagnostics, Russian Research Institute for Cardiology, St-Petersburg, Russia.)
A systems analysis of metabolic syndrome in human and the role of gene polymorphisms AGTR1/A1166C, ACE/ID and FGA/T312A in its development

Satabdi Basu (Department of Bioinformatics, Purabi Das School of Information Technology, Bengal Engineering and Science University, Shibpur, Howrah-711 103,)
Bioinformatics analysis of protein domains involved in signal transducer activity in human and mouse

Eric Batchelor (Department of Systems Biology, Harvard Medical School, Boston)
Recurrent Initiation: A Mechanism for Triggering p53 Pulses in Response to DNA Damage

Chase L. Beisel (Division of Chemistry and Chemical Engineering, California Institute of Technology)
Ligand-regulated shRNA switches as programmable network components

Vincenzo Belcastro (Telethon Institute of Genetics and Medicine, Via P. Castellino, Naples, Italy)
An integrative reverse engineering algorithm to infer gene networks from multiple sources of data

Pedro Beltrao (European Molecular Biology Laboratory)
Predicting the binding specificity of peptide binding domains using structural information and the FoldX algorithm

Frank T. Bergmann (Department of Bioengineering, University of Washington, Seattle)
CAD/CAM Software for Synthetic Biology

Aarash Bordbar (Bioengineering Department, University of California, San Diego, La Jolla, CA, USA)
Extending the predictive potential of metabolic genome-scale reconstructions by accounting for the transcriptional and translational network

Elhanan Borenstein (Department of Biological Sciences, Stanford University, Stanford and Santa Fe Institute, Santa Fe)
Large-Scale Reconstruction and Analysis of Growth Environments

Jildau Bouwman (Molecular Cell Physiology, Institute for Molecular Cell Biology (IMC), Vrije Universiteit, Amsterdam, NL)
Regulation of the glycerol pathway during osmotic stress

David K. Breslow (Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute of Quantitative Biomedical Research, University of California, San Francisco)
A High-Throughput Flow Cytometry-Based Approach to High-Resolution Genetic Interaction Measurements

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Yizhi Cai (Virginia Bioinformatics Institute)
GenoCAD.org: A web site to design and verify synthetic genetic constructs derived from standard biological parts

Laurence Calzone (Institut Curie)
BiNoM: A Cytoscape plugin for using and analyzing biological networks

Manuel Cánovas (Dept. Biochemistry and Mol. Biol. B, University of Murcia)
In silico model of the mitochondrial role in the cardiac cell pathology

Ivan Chang (Department of Biomedical Engineering, University of California, Irvine)
A new systems biology model of mitochondrial bioenergetics: Application to mitochondrial pathologies

Peter S. Chang (Department of Chemical Engineering, University of California, Santa Barbara)
Phase Dependent Gating of the Vasoactive Intestinal Polypeptide Signaling Pathway in the Suprachiasmatic Nucleus

Rima Chaudhuri (Center for Pharmaceutical Biotechnology and Dept. of Bioengineering/Bioinformatics Program, University of Illinois at Chicago)
Classification and structural analysis of coronavirus papain-like proteases based on the active site residues of SARS-CoV-PLpro

Arvind K. Chavali (Department of Biomedical Engineering, University of Virginia)
Intra- and inter-cellular network analyses for characterizing pathogen-host interactions

Gal Chechik (Google Research)
Tuned protein variability in yeast metabolism

Chu-Shiang Chen (Center for General Education, National Tsing Hua University, Hsinchu, Taiwan)
Systems Traditional Chinese Medicine

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Po-Wei Chen (Lab. of Systems biology, National Tsing-Hua University)
Robust and Circuit Design of Biochemical Networks under Stochastic Intrinsic Fluctuations and Extrinsic Noises

Jingchun Chen (Institute for Systems Biology, Seattle, Washington)
Integrated Data Mining for Identification of Biomarker Candidates

William K.C. Cheung (Department of Chemistry, The University of Hong Kong)
Signaling Network of MIF Knockdown in Inhibiting Tumor Growth and Metastasis in Gastric and Colorectal Cancers

Vijay S. Chickarmane (Division of Biology, California Institute of Technology, Pasadena, USA)
How does the hematopoietic erythroid-myeloid switch live up to its commitment?

Yu-Wei Chiu (Institute of Biomedical Informatics, National Yang-Ming University)
Prediction of Functional Associated Proteins Using Topological Similarity in Protein-Protein Interaction Network

Hojung Cho (Department of Biomedical engineering, The Johns Hopkins University)
Monitoring the propagation of quorum sensing gene responses in highly dense colonies

Ching-Shan Chou (Department of Mathematics, UCI)
Modeling Robustness Tradeoffs in Cell Polarization Induced by Spatial Gradients: Steady-State Analysis

Han-Yu Chuang (Bioinformatics Program, Univ. of California, San Diego)
Network-based classification of breast cancer metastasis

Victor Chubukov (Joint Graduate Group in Bioengineering, Universirt of California, Berkeley/Univesirt of California, San Francisco)
Dynamics and design principles of a basic regulatory module controlling metabolic pathways

Cynthia H. Collins (Department of Microbiology and Infectious Diseases, University of Calgary)
Construction and transcriptional analysis of a tunable polymicrobial community

Sean R. Collins (Department of Cellular and Molecular Pharmacology and The California Institute for Quantitative Biomedical Research, San Francisco, U.S.A.)
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map

Alejandro Colman-Lerner (Instituto de Fisiología, Biología Molecular y Neurociencias, CONICET; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina and Molecular Sciences Institute, Berkeley, California, USA)
Single-cell imaging of membrane recruitment of signaling scaffold: fractional receptor occupancy is sensed quantitatively seconds after addition of ligand

Behnam Compani-Tabrizi (1) Institute for Genomics and Bioinformatics, 2) School of Information and Computer Sciences, University of California, Irvine)
Sigmoid: A Scalable System for Pathway Bioinformatics and Systems Biology

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Mike Cooling (Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand)
Modeling NFAT cycling sensitivity in the cardiac myocyte

Robert Sidney Cox III (Division of Biology, California Institute of Technology)
Programming gene expression with combinatorial promoters

Robert Sidney Cox III (Division of Biology, California Institute of Technology)
A synthetic three-color reporter framework for monitoring genetic regulation and noise

Edmund J. Crampin (Bioengineering Institute, University of Auckland, New Zealand)
CellML: Cellml.org, Tools and Community

Kam D. Dahlquist (Department of Biology, Loyola Marymount University)
Mathematical Modeling of the Transcriptional Network Controlling the Environmental Stress Response in Saccharomyces cerevisiae

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Neil Dalchau (Department of Plant Sciences, University of Cambridge, UK)
Mathematical models of circadian Ca2+ oscillations

Maria Davidich ( Institute for Theoretical Physics, University Bremen, Bremen, Germany )
Robustness of the fission yeast cell cycle network

Adel Dayarian (Department of Physics and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ)
Geometry, Functionality and Robustness: Exploring the Parameter Space of the Segment Polarity Network

Pedro de Atauri (Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain)
Energy metabolism of human muscle and training

Domitilla Del Vecchio (Electrical Engineering and Computer Science, Univ. of Michigan)
Modules and Retroactivity: Theoretical Framework, Analysis, and Design

Duygu Dikicioglu (Department of Chemical Engineering, Bogazici University, Istanbul, Turkey)
Dynamic response of Saccharomyces cerevisiae to transient perturbations in ammonia concentration and integration of metabolome and transcriptome data

Marko Djordjevic (Mathematical Biosciences Institute, The Ohio State University)
Quantitative modeling of transcription initiation by bacterial RNA polymerase

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Kim-Anh Do (Department of Biostatistics, U. T. M. D. Anderson Cancer Center, Houston)
Bayesian Mixture Models for Phage Display Experiments: Translation from Mice to Humans

Samuel Drulhe (Helix, Institut National de Recherche en Informatique et en Automatique, Grenoble, France)
Identification Procedure for Piecewise Affine Models of Genetic Regulatory Networks

Xiuxia Du (Fundamental Science Division, Pacific Northwest National Laboratory)
A Strategy to Analyze Temporal Bottom-up Proteomics Data

Daniel Edsgard (Center for Biological Sequence Analysis, Technical University of Denmark)
Linking Phenome, Genome and Toxicological Space

Avigdor Eldar (Division of Biology and Department of Applied Physics, California Institute of Technology, Pasadena, Ca)
Noise-dependent developmental plasticity and the evolution of novel morphologies in B. subtilis

Fred Elisma (Ottawa Institute of System Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa)
Interaction Graph Validator a New Type of Relation Database for Protein-Protein Interaction Mapping by Mass Spectrometry-Based

Hunter L Elliott (Department of Cell Biology, Scripps Research Institute, La Jolla)
Pathway reconstruction via analysis of constitutive fluctuations in molecular activities

Thanura R Elvitigala (Department of Electrical and Systems Engineering, Washington University, St.Louis, MO 63130)
Computational Analysis of the Redox Stress Response in Organisms

Frank Emmert-Streib (Department of Biostatistics, Department of Genome Sciences, University of Washington, Seattle)
Annotating Genes with Unknown Function by a Systems Approach

Abraham (Avi) Ericsson (Cell and molecular biology, Göteborgs University, Göteborg, Sweden)
Modeling PDC1 and PDC5 expression as a function of thiamine availability in yeast S. cerevisiae

Dirk Fey (Industrial Control Centre, University of Strathclyde, Glasgow, Scotland, UK)
Parameter estimation in regulatory networks of biochemical reactions

Charless C. Fowlkes (Department of Electrical Engineering and Computer Science, University of California, Berkeley)
Building a Quantitative Spatio-temporal Atlas of Gene Expression in the Drosophila Blastoderm

Akira Funahashi (Department of Biosciences and Informatics, Keio University)
CellDesigner 4.0beta: A Modeling Tool for Biochemical Networks

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Kate E. Galloway (Department of Chemical Engineering, California Institute of Technology)
RNA-based control systems and their application to a model MAPK pathway

Shouguo Gao (Max McGee National Research Center for Juvenile Diabetes & Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee)
Discovery of Phenotype Related Modules by Incorporating Expression Data to Protein Interaction Networks

Juntao Gao (Stowers Institute for Medical Research, Kansas City 64110, MO)
Modular Organization and Dynamics of the Budding Yeast Polarity Protein Network

Geert Geeven (Department of Mathematics, VU University, Amsterdam, the Netherlands)
Transcriptional regulatory networks in neuronal regeneration

C.-M. Ghim (Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory)
Structural and Functional Characterization of Combined Regulatory Network Motifs

Samik Ghosh (Deprtment of Computer Sc. & Engineering, The University of Arlington)
Connecting the dots: An integrated database for studying cellular dynamics

Erwin P. Gianchandani (Department of Biomedical Engineering, University of Virginia, Charlottesville)
Integrated, Dynamic Flux Balance Analysis of a Representative Module in Saccharomyces cerevisiae

Erwin P. Gianchandani (Department of Biomedical Engineering, University of Virginia, Charlottesville)
Analysis of Large-Scale Signaling Networks in Therapeutics

Martin Golebiewski (EML Research, Heidelberg, Germany)
Biochemical Data Integration: Standardization of Parameter Units and Normalization of Chemical Compound Names in SABIO-RK

Yunchen Gong (Banting & Best Department of Medical Research, University of Toronto)
Network reachability does not guarantee dynamic perturbation due to multiple positive feedbacks

Yunchen Gong (Banting & Best Department of Medical Research (BBDMR), Donnelly Center for Cellular & Biomolecular Research (CCBR), University of Toronto)
Global robustness and identifiability of random, scale-free and small-world networks

Jeff Gore (Department of Physics, Massachusetts Institute of Technology, MA, USA)
Cooperation in Yeast Sucrose Metabolism

I Goryanin (School of Informatics, university of Edinburgh)
The Edinburgh human metabolic network reconstruction

Rudiyanto Gunawan (Department of Chemical and Biomolecular Engineering, National University of Singapore)
In Silico Robustness Analysis of Cellular Systems: A Molecular Perturbation Approach

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Stephen J. Hagen (Physics Department, University of Florida)
Noise in the Quorum Sensing Genetic Network of Vibrio fischeri

Adam Halasz (GRASP Lab, University of Pennsylvania)
Quantitative Model of Stringent Response in E.coli Explains Spontaneous Persister Generation

Sangjo Han (1 Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea)
Cellular machine-based Bayesian factor analysis: Exploring drug’s mode-of-action in a cell

Adam R. Hardy (Physiomics plc, Oxford, UK)
Modelling DNA Damage-Induced Apoptosis

Eric L. Haseltine (Division of Chemistry & Chemical Engineering, California Institute of Technology)
Implications of Rewiring Bacterial Quorum Sensing

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Ute Heisner (HepatoSys, Institute for Physics, University of Freiburg)
The Competence Network HepatoSys

Noriko Hiroi (EMBL-European Bioinformatics Institute (EBI), UK)
Dynamic modes in biological systems: Why should a biologist care?

Noriko Hiroi (EMBL-EBI)
Comparison of insulin signaling pathways among 4 species and 3 tissues of mouse

Joshua W.K. Ho (School of Information Technologies, University of Sydney)
Modeling the Evolution of Gene Regulatory Networks

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Stefan Hoehme (Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany)
Mathematical modeling of liver regeneration after intoxication with CCl4

Kevin G. Hoff (Department of Chemistry and Chemical Engineering, California Institute of Technology)
Genetic circuits for monitoring dynamic changes in post-translational modifications

Seong-Eui Hong (Department of Life Science, Gwangju Institute of Science and Technology (GIST) Gwangju, Korea)
Revealing a heart-specific gene network by a new algorithm of spectral graph clustering using a compendium of microarray expression data

Brian S. Hooker (Pacific Northwest National Laboratory)
A Protocol for the Identification of Membrane Protein Interaction Networks

Russell Howes (IDeA Labs, Computer Science Department, Brigham Young University)
Reconstruction of Biological Networks through Gene Silencing and Overexpression

Chun-Wei Hsu (Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan)
Characterization of microRNA-Regulated Protein-Protein Interaction Network

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Michael Hucka (Beckman Institute BNMC, California Institute of Technology, Pasadena, CA, USA)
LibSBML 3.0: An API library for SBML

Pablo A. Iglesias (Department of Electrical & Computer Engineering, Johns Hopkins University)
Information-theoretic Analysis of Signal Transduction Pathways

Marcin Imielinski (MD/PhD Program, University of Pennsylvania School of Medicine)
Uncovering complex essential reaction sets in E. coli metabolism through pathway fragment analysis

Francesco Iorio (Telethon Institute of Genetics and Medicine (TIGEM) - Naples, Italy)
Identification and visualisation of drug mode of action from molecular signatures using an unsupervised classification approach

Nobuyoshi Ishii (Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan)
Multi-omics data reveals the response of Escherichia coli to perturbations

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Hitomi Itoh (Institute for Advanced Biosciences, Keio University)
Dynamics of induced spontaneous electrical activity of cardiomyocytes connected by gap junctions

M. Sriram Iyengar (School of Health Information Sciences, University of Texas Health Science Center at Houston)
A Layered Cell Model for Morphoproteomics

M. Sriram Iyengar (School of Health Information Sciences, University of Texas Health Science Center at Houston )
Imprecise and Qualitative Probability in Systems Biology

Alexandra Jauhiainen (Mathematical Sciences, Chalmers University of Technology , Gothenburg, Sweden)
Stress-Induced Post-Transcriptional Regulation in Yeast

Priya Jayaswal (Bioinformatics Group, Purabi Das school of Information Technology, Bengal Engineering and Science University, Shibpur, B.Garden, Howrah-711 103, West Bengal, India)
Comparative analysis of usage of protein domains and their architectures involved in transcription regulatory activity

Fang Jin (Mathematics Department, University of California, Irvine)
Invasive Behaviors of Growing Solid Tumors

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Mats Jirstrand (Systems Biology and Bioinformatics, Fraunhofer-Chalmers Research Centre, Gothenburg, Sweden)
Parameter Estimation in Biochemical Reaction Networks—Observer Based Prediction Error Minimization

Hsueh-Fen Juan (Departments of Life Science, National Taiwan University)
MicroRNAs-involved regulatory network of ATRA- and Am80-induced human leukemia cell line HL-60 differentiation

Anak Agung Julius (Dept. Electrical & Systems Eng, University of Pennsylvania)
Genetic network identification using convex programming

Agnieszka S. Juncker (Center for Biological Sequence Analysis, BioCentrum-DTU, Lyngby, Denmark)
Dynamics of splicing during the yeast cell cycle

Quincey A. Justman (Graduate Group in Biophysics, University of California, San Francisco)
Glycogen Synthase Kinase-3beta Exploits Intracellular Noise to Regulate Xenopus Oocyte Maturation

Ozan Kahramanogullari (Department of Computing, Imperial College, London, UK)
A Process Model of Rho GTP-binding Proteins

Kazunari Kaizu (Department of Science and Technology, Keio University, Kanagawa, Japan)
Revealing genetic interactions conferring robustness of the cell cycle in yeast by 2 dimensional genetic tug-of-war method

Torbjörn J. Karfunkel (Department of Computing Science, Chalmers University of Technology, Gothenburg, Sweden)
HGT and innovation of Genome Systems Complexity: Where do the selective pressures originate from?

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Yiannis Kaznessis (Department of Chemical Engineering and Materials Science, University of Minnesota)
Mathematics for biological engineering: Model-driven design of a synthetic bio-logical AND gate

Sarah M. Keating (STRI, University of Hertfordshire, Hertfordshire, UK)
SBML Level 2 Version 3

Douglas B. Kell (MCISB, University of Manchester)
Proximate Parameter Tuning: A novel strategy for system identification

Abha Khandelwal (Dept. of Biology, Washington University in St. Louis)
Systems approach divulges redox regulation of Arabidopsis transcriptome

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Takashi Kido (Stanford University)
Quality Assessment of Microarray Data and Optimal Filtering Criteria

Shinichi Kikuchi (Institute for Advanced Biosciences, Keio University)
Algebraic Method for the Analysis of Signaling Crosstalk

Taeyong Kim (Department of Life Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea)
A system level approach to decipher the differences between physiological and pathological cardiac hypertrophy in the aspect of the signaling efficiency

Sohyoung Kim (Laboratory of Molecular Pharmacology, National Cancer Insitute, National Institute of Health, Bethesda, MD, USA)
Fine tuning of p53-Mdm2-MdmX network by MdmX during DNA damage response

Kyung Hyuk Kim (Department of Bioengineering, University of Washington, Seattle)
Stochastic Biochemical Control Theory

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Tae Kyung Kim (Host-Microbe Systems Theme, Institute for Genomic Biology, )
Heterogeneity of Vaginal Bacterial Communities within Individuals: Impact of Anatomical Site and Sampling Method on Microbial Detection

Jeong-Rae Kim (Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea)
Dynamic Motifs of Cellular Networks: Coupled Feedback Loops

Tae Yong Kim (Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology)
Deciphering the functional robustness of Escherichia coli using the metabolite essentiality

Hyun Uk Kim (Department of Chemical and Biomolecular Engineering (BK21 Program), Metabolic and Biomolecular Engineering National Research Laboratory, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea)
Application of genome-scale stoichiometric model of Vibrio vulnificus CMCP6 for in silico drug targeting

Junil Kim (Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea)
In Silico TCDD Toxicity Evaluation System

Tae Yong Kim (Center for Systems and Synthetic Biotechnology, Institute for the BioCentury; Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center; Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST)
Identification of the in silico targets using the metabolite availability

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Hiroaki Kitano (Okinawa Institute of Science and Technology, Okinawa, Japan, The Systems Biology Institute, Tokyo, Japan)
"Payao": Web 2.0 community tagging system for biological networks

Rune Kleppe (Department of Biomedicine, University of Bergen, Norway)
Compartment modeling of nitric-oxide mediated activation of the cAMP-dependent protein kinase in platelets

Edda Klipp (Computational Systems Biology, Max Planck Institute for Molecular Genetics, Berlin )
AUTOMATIC INTEGRATION OF KINETIC DATA FOR METABOLIC NETWORK MODELING

Johannes F. Knabe (Adaptive Systems Research Group, University of Hertfordshire, UK)
In Silico Evolution of Biological Clocks with Genetic Regulatory Networks

Dagmar Koehn (graduate school dIEM oSiRiS, University of Rostock, Germany)
The Pi Markup Language - Toward Pi-Model Exchange

Fedor A. Kolpakov (Institute of Systems Biology, Novosibirsk, Russia; Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia)
Formal description and visual modeling of complex biological systems using BioUML workbench and BioUML Network Edition

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Yuriy V. Kondrakhin (Institute of Systems Biology, Novosibirsk, Russia; Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia)
Meta-analysis of breast cancer microarray data: Reliable identification of up- and down-regulated genes

Pawel Krupinski (Institute for Genomics and Bioinformatics: Bren School of information and Computer Sciences, University of California, Irvine, CA 92607, USA)
Finite Element Modeling of mechanical properties of plant cells in Arabidopsis thaliana

Andrzej Kudlicki (Dept. of Biochemistry, UT Southestern Medical Center, Dallas)
High Resolution Timing with Model Based Deconvolution of Timecourse Microarray Data with Maximum Entropy Prior

Anne Kuemmel (Institute of Molecular Systems Biology, ETH Zurich, Zurich)
Elucidating compartmentalized flux direction patterns in yeast

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Camille Laibe (Computational Neurobiology, European Bioinformatics Institute, Cambridge, UK)
MIRIAM Resources: Robust Cross-References in Systems Biology

Sotiria Lampoudi (Dept of Computer Science, University of California, Santa Barbara)
How does reactant size affect the propensity functions of the SSA?

Arthur D. Lander (University of California, Irvine)
Feedback control of size, cellular composition, and regeneration speed in neural epithelia: experimental and computational analysis

Roberto Larcher (The Microsoft Research, University of Trento Centre for Computational Systems Biology)
BetaWB—A language for modular representation of biological SYSTEMS

Reinhard Laubenbacher (Virginia Bioinformatics Institute/Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061)
The effect of negative feedback loops on the dynamics of Boolean networks

Mario Lauria (TIGEM - Napoli, Italy)
Simultaneous gene network and mode of action inference with mNIr

Nicolas Le Novere (EBI, EMBL)
Semantic annotation of kinetic models in Systems Biology

Paola Lecca (The Microsoft Research - University of Trento Centre for Computational and Systems Biology (Italy))
A new method for inferring rate coefficients from experimental time-consecutive measurements of reactant concentrations

Chih Lee (Institute of Statistical Science, Academia Sinica)
Inferring Genetic Networks via Nonlinear Models and Optimization Alogrithms

Bonghee Lee (Institute for Systems Medicine, Gachon University Gil Medical Center, Incheon, Korea)
Systemic analysis of genome-wide transcriptional changes associated with olig2-induced differentiation of human neural stem cells

Erel Levine (Center for Theoretical Biological Physics, University of California, San Diego)
Small Regulatory RNAs May Sharpen Spatial Expression Patterns

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Cheng-Wei Li (Lab. of Systems biology, National Tsing Hua University)
Spatio-Temporal Dynamic Model in Drosophila Early Development via Protein Data and Microarray Data

Chen Li (European Bioinformatics Institute, Hinxton, CB10 1SD, UK)
BioModels Database, a curated and annotated resource of published quantitative kinetic models

Lu Li (Computational Neurobiology, European Bioinformatics Institute, Cambridge, UK)
Computational Modelling of Dopamine and Glutamate Signal Integration and ERK-mediated neuroadaptation

Nicole yee-key Li (Department of Communication Science and Disorders, University of Pittsburgh)
A Patient-Specific in silico Model of Inflammation and Healing Tested in Acute Vocal Fold Injury

Shuwang Li (Math Department, University of California, Irvine)
Surface phase separation and morphological transition of a multicomponent vesicle

Willem P. A. Ligtenberg (Department of BioMedical Engineering, Eindhoven University of Technology, Eindhoven)
ReConn: Explore past the edges of pathways

Gabriele Lillacci (Department of Mechanical Engineering, University of California, Santa Barbara)
Dynamic modeling of DNA damage and repair processes

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Chen-Ching Lin (Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan)
An Essential Core of Protein-Protein Interaction Network in Escherichia coli

Haoping Liu (1Department of Biological Chemistry,University of California, Irvine, CA 92697)
Tec1 Reduces Pheromone Responsive Transcription Output by Differential Ste12 Complex Formation

Corinne N. Locke (Department of Molecular Physiology & Biological Physics, University of Virginia)
Systems analysis of intracellular signaling networks in cancer: from tissue microarrays to clinical outcomes

Alexaner Loewer (Department of Systems Biology, Harvard Medial School, Boston)
Dynamics of the p53 signaling pathway in the absence of external stimuli

James Lu (Johann Radon Institute for Computational and Applied Mathematics, Linz, Austria)
SBML ODE Solver Library: Extensions for Inverse Analysis

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Rainer Machne (Institute for Theoretical Chemistry, University of Vienna, Austria)
The evolution of the bifurcation phenotype: Phylogenetic and dynamical analysis of fungal GATA networks

Cameron MacKay (Safety and Environmental Assurance Centre, Unilever, UK)
An in silico approach to aid in assessing the risk of chemical-induced skin sensitization

Yusuke T. Maeda (Department of Physics, the University of Tokyo)
Self-organized coordination between morphological dynamics and cell movement in single Dictyostelium discoideum cells

Steven Maere (Department of Plant Systems Biology, VIB, Ghent (Belgium))
Combinatorial Analysis of Perturbational Gene Expression Compendia

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Tetsuya Maeshiro (School of Library and Information Science)
Description model of gene regulatory networks for simulation and analysis

Nick I. Markevich (Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, USA )
Quantitative analysis of EGF-induced signaling responses in hepatocytes from control and ethanol-fed rats

Ivan Martinez (Department of Physics and Applied Mathematics University of Navarra, Neuroimmunology Lab Center for Applied Medical Research (CIMA))
A systems biology approach to regulation of apoptosis by type I interferons

Michael J. Mason (Department of Statistics, University of California, Los Angeles)
An Extension of Weighted Gene Coexpression Analysis to Include Signed Interactions

Yukiko Matsuoka (Systems Biology Institute, Tokyo, Japan)
Systems Biology Graphical Notation

Yuri Matsuzaki (Institute for Advanced Biosciences, Keio University, Fujisawa, Japan)
Effects of Tsr–CheBp and CheA–CheYp affinity in bacterial chemotaxis

Erin M. Mattern (Department of Physics and Astronomy, University of California, Irvine)
Radical Pair-Based Magnetoreception

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Mary F. McGuire (University of Texas School of Health Information Sciences, Houston)
Signaling Pathways in Multiple Organ Failure

Pontus Melke (Department of Theoretical Physics, Lund University, Lund, Sweden)
A single-cell based modeling approach to bacterial colony growth

Jerome Mettetal (Department of Physics, Massachusetts Institute of Technology)
Probing Osmo-adaptation Kinetics in Saccharomyces cerevisiae with Periodic Stimuli

Joshua K. Michener (Program in Bioengineering, California Institute of Technology)
Synthetic Regulatory Circuits for Dynamic Control of Metabolism

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Luis Mier-y-Teran R (Physics dept., Northwestern University)
Development of a Time-Delay Model of Protein Translation Starting from First Principles

Antonio F. Miguel (Department of Physics, University of Evora, Portugal)
Constructal View of Formation of Dissimilar Patterns inside Similar Living Systems

Tijana Milenkovic (Department of Computer Science, University of California, Irvine)
GraphCrunch: A Tool for Large Network Analyses

Tijana Milenkovic (Department of Computer Science, University of California, Irvine)
Geometricity of Residue Interaction Graphs

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Jonathan Miller (Human Genome Sequencing Center, Baylor College of Medicine, Houston)
Genomic Imprint of the Interactome: Universality of Genome Evolution

David J Miller (Department of Physics, Drexel University)
A Systems Approach for the Prediction of Wild Type MAPK Pathway Response to Targeted Drugs

Vladimir Mironov (VIB Department of Plant Systems Biology, Ghent University., Technologiepark 927, Ghent, Belgium )
Ontology driven data integration for enabling systems biology

Henry P. Mirsky (Program in Biomolecular Science and Engineering, University of California, Santa Barbara)
A Model of the Uncoupled Mammalian Circadian Clock

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Alexander Y. Mitrophanov (Howard Hughes Medical Institute, Department of Molecular Microbiology, Washington University School of Medicine)
Dynamical properties of connector-mediated pathways in two-component signal transduction

Eric D. Mjolsness (University of California, Irvine CA 92607, USA)
1D modeling of auxin distribution in plant roots

Dominik Mojzita (Cell and molecular biology, Göteborgs University, Göteborg, Sweden)
Thiamine uptake in yeast Saccharomyces cerevisiae—A modelling aproach

Michael Monine (Theoretical Biology and Biophysics, Center for Nonlinear Studies, LANL, Los Alamos, NM)
Simulation of systems marked by combinatorial complexity

Stuart L. Moodie (University of Edinburgh)
The Edinburgh Pathway Editor—a graphical editor for biological pathways

Travis I Moore (Department of Developmental and Cell Biology, University of California, Irvine)
Dynamic Polarized Response of Yeast to Microfluidically Generated Alpha-Factor Gradients

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Ion I. Moraru (Center for Cell Analysis and Modeling, University of Connecticut Health Center)
Modeling Complex Networks: Integrating Rules (BioNetGen) and Data Mining (BioPAX Ontology) into the Virtual Cell Framework

Pablo Moreno (Bioinformatics and Mathematics of Genome Laboratory, Centre for Mathematical Modeling, University of Chile, Chile)
Gene regulation of metabolic pathways: A continuous model for Escherichia coli carbon sources uptake

Hirotada Mori (Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101 Japan)
Towards modeling and simulation of Glycolysis and TCA cycle

Masaki S. Morioka (Dept. of Computational Biology, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan)
Temporal gene expression analysis of hypoxia in human muscle cell

Hisao Moriya (Cancer Institute)
In vivo robustness analysis of cell division cycle related genes in the fission yeast S. pombe

Fangping Mu (Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA)
Transcription factor binding sites discovery by structural and molecular interaction field features

Shankar Mukherji (Division of Health Sciences and Technology, Massachusetts Institute of Technology and Harvard University)
Evolvability of proteins in a signaling cascade: The importance of network topology

Brian E. Munsky (Center for Control, Dynamical Systems, and Computation; University of California, Santa Barbara)
Sensitivity Analysis and Parameter Identification of Stochastic Gene Regulatory Networks Using Finite State Projection Techniques

Ettore Murabito (Doctoral Training Centre in Systems Biology, Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, 131 Princess Street, M1 7DN, Manchester, United Kingdom; School of Chemical Engineering and Analytical Science, The University of Manchester, PO Box 88, Sackville Street, M60 1QD, Manchester, United Kingdom)
Selecting among the multiple alternate optimal solutions of the Flux Balance Analysis of yeast metabolism: Use of the adaptational potential of the organism

Kevin F. Murphy (Department of Biomedical Engineering, Center for Biodynamics and Center for Advanced Biotechnology, Boston University)
Combinatorial promoter design for engineering noisy gene expression

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Nagarajan (Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA)
Progression Analysis of Disease

Tarek S. Najdi (Institute for Genomics and Bioinformatics, University of California, Irvine)
Enzyme-mechanism models and simulations of central metabolism pathways and amino acid biosynthesis in Escherichia coli

Tadashi Nakano (Department of Computer Science, University of California, Irvine)
Intercellular Ca2+ Wave Propagation through Patterned HeLa Cx43 Cells

Honda Naoki (Graduate School of Information Science, Nara Institute of Science and Technology, Japan.)
Spontaneous signal generation induced by reaction noise for gradient sensing in chemotaxis

Ali Navid (Chemistry, Materials and Life Sciences Directorate, Lawrence Livermore National Laboratory)
System-level analysis of metabolism in Yersinia pseudotuberculosis and the biovars of Yersinia pestis using a genome-scale mathematical model

Gregor Neuert (Department of Physics, Massachusetts Institute of Technology, Cambridge)
An All-or-None Response in Osmolyte-Dependent Gene Expression in Saccharomyces cerevisiae

Sergey Nikolaev (Institute for Cytology and Genetics, Novosibirsk, Russia)
Modeling of the Shoot Apical Meristem Structure Regulation Based on CLV1, CLV2, CLV3 and WUS Interactions

Zoran Nikoloski (University of Potsdam, Institute for Biochemistry and Biology, Potsdam, Brandenburg, Germany)
Systematic framework for metabolic networks with constrained biological information: Analysis and applications

Masaki Nishikawa (Institute of Industrial Science (IIS), University of Tokyo)
Novel in vitro system for primary culture of hepatocytes toward the study of circadian rhythms of the liver

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Yurie Okabe (Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan)
Effects of the DNA state fluctuation on single-cell dynamics of self-regulating gene

Roberto Olivares (Center for Microbial Biotechnology, BioCentrum-DTU, Building 223, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark. )
Comparing protein and mRNA expression level on a genome scale: posttranscriptional regulation in yeast Saccharomyces cerevisiae

Brett G. Olivier (Department of Biochemistry, University of Stellenbosch, Stellenbosch)
Investigating cellular regulation with PySCeS/Kraken

Shuichi Onami (RIKEN GSC)
Quantitative and computational phenotype analysis of early C. elegans RNAi embryos

David W. Orendorff (University of California, Irvine)
High-accuracy R-leaping: Implementing and exploring a potentially exact method for accelerated stochastic simulation

Lars-Göran Ottosson (Department of Cell and Molecular Biology, Göteborg University, Göteborg)
Robustness analysis of HOG pathway related genes in budding yeast

Sri R. Paladugu (Keck Graduate Institute of Applied Life Sciences, Claremont)
Predicting synthetic genetic interactions in yeast through machine-learning analysis of protein interaction data

Saurabh Paliwal (Department of Biomedical Engineering, The Johns Hopkins University)
A mechanism for regulation of bistability in gene expression

Myung-June Park (Department of Chemical Engineering, Ajou Universiy, Suwon, Korea)
Mathematical modeling for hybrid gonadotrope biosynthetic response to gonadotropin-releasing hormone

Myung-June Park (Department of Chemical Engineering, Ajou Universiy, Suwon, Korea)
Mathematical modeling for hybrid gonadotrope biosynthetic response to gonadotropin-releasing hormone

John Parkinson (Hospital for Sick Children, Toronto)
The Conservation and Evolutionary Modularity of Metabolism

Kate Patterson (Department of Mathematics, Montana State University, Bozeman)
When activators repress and repressors activate: A qualitative analysis of the Shea-Ackers model

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Anusua Paul (Bioinformatics group, PDSIT, Bengal Engineering and Science University, Shibpur, Howrah,West Bengal,India)
Comparative analysis of amino acid usage of the Connexin super family in human and mouse

Michael D. Pedersen (LFCS, School of Informatics, University of Edinburgh)
LBS—A Language of Biological Systems

Paul Perco (Department of Nephrology, KH Elisabethinen Linz; Department of Nephrology, Medical University of Vienna; emergentec biodevelopment GmbH, Vienna)
A systems biology approach for identifying deregulated molecular pathways in proximal tubular epithelial cells characterizing progressive proteinuric nephropathies

C. Gustavo Pesce (Molecular Sciences Institute, Berkeley, California)
A single-cell-based genetic screen identifies gene mutations that alter novel axes of quantitative system behavior in the pheromone pathway of Saccharomyces cerevisiae

Vladislav A. Petyuk (Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA)
A Novel Approach for Multiplex Imaging of Protein Abundances in Tissues and Organs: Initial Application to the Mouse Brain

Revonda Pokrzywa (Virginia Bioinformatics Institute, Virginia Tech, Blacksburg)
In Silico Determination of Stress-Activated Metabolic Networks in Medicago truncatula

Natalia Polouliakh (Fundamental Research Lab., Sony CSL, Tokyo, Japan)
GPCR signaling architecture in mammalian immune cells

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Anca Radulescu (Department of Applied Mathematics, University of Colorado at Boulder)
A systems approach to schizophrenia

Ofer Rahat (Biochemistry Department, Weizmann Inst. of Science, Rehovot, Israel )
Network Motifs Profile of Proteins Contact Map: A Novel Pattern Recognition Tool for Fold Prediction

Arjun Raj (MIT)
Noise in Gene Expression: Behavior and Consequences

Karthik Raman (Indian Institute of Science, Bangalore)
Impact of drug action in TB: A study using protein–protein influence networks and flux balance analysis

Ranjit Randhawa (Department Of Computer Science, Virginia Tech, Blacksburg)
Aggregation in Macromolecular Regulatory Network Models

Marija Rasajski (Department of Computer Science, University of California, Irvine)
Fitting a Geometric Graph to a Protein-Protein Interaction Network

Alexander V. Ratushny (Institute for Systems Biology, Seattle, WA)
Modeling the dynamic behavior of an oleate-responsive gene regulatory network in Saccharomyces cerevisiae

Shubhra S. Ray (Center for Soft Computing Research, Indian Statistical Institute, Kolkata, India)
Predicting Gene Function in Yeast through Adaptive Weighting of Multi-Source Information

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Ingmar H. Riedel-Kruse (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Division of Biology, California Institute of Technology, Pasadena, CA )
Coupling vs. noise: The rise and fall of synchrony in the segmentation clock

John M. Robinson (Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham)
The Brownian flip-flop, a 5\Deg-level design for high-fidelity, high-speed biochemical signal transduction

Nicolas Rodriguez (Computational Neurobiology group, EMBL-European Bioinformatics Institute)
SBMLeditor toward SBML Level 3 and modularisation

Johann M. Rohwer (Dept. of Biochemistry, Stellenbosch University, South Africa)
Plant-Scale Kinetic and Structural Modeling of Sucrose Accumulation in Sugarcane

Maga Rowicka (University of Texas Southwestern Medical Center)
Transcriptional Program of the Cell Cycle: High Resolution Timing

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Özgür Sahin (Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg)
Modeling of ErbB receptor regulated G1/S transition using combinatorial RNAi

Sven Sahle (Department for Modeling of biological Processes, University of Heidelberg, Germany)
COPASI—A complex pathway simulator

Patrik Sahlin (Department of Theoretical Physics, Lund University)
A pattern generating model inspired by plant phyllotaxis: Analysis of requirements and capabilities

M. Selman Sakar (Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia)
Microfabricated Structures Powered by Flagellated Bacteria

Armindo Salvador (Center for Neuroscience and Cell Biology – University of Coimbra, Coimbra, Portugal)
Gene expression profiles in Saccharomyces cerevisiae strongly reflect energetic costs of gene products

Lukasz Salwinski (UCLA-DOE Institute for Genomics and Proteomics, Los Angeles)
Tapping the Web for interaction data: MiTap & MiSink extensions to Firefox and Cytoscape

Silvia Santos (EMBL, Cell Biology and Biophysics, Heidelberg, Germany)
MAPK network properties determining cell fate decision in PC-12 cells

Herbert M. Sauro (University of Washington, Seattle)
In Silico Evolution of Reaction Networks

James C. Schaff (Center for Cell Analysis and Modeling, University of Connecticut Health Center)
VCell: An Open Framework for Computational Cell Biology

Gabriele Scheler (Department of Computer Science, Stanford University)
Network Topology and Pattern Storage: Applications to Hippocampal CA3 Synaptic Connectivity

Jan Schellenberger (Department of Bioinformatics, University of California, San Diego)
Exploring the Concentration Space of Genome Scale Metabolic Networks

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Torgom Ye. Seferyan (Department of Biophysics, Yerevan State University, Yerevan, Armenia)
Influence of Post Electro-Induced Free Radicals on Chemiluminescence of Liposomes

Jun Seita (Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine)
Network Analysis between Hematopoietic Stem Cells and Multipotent Progenitor Cells

Kandarp Shah (Department of Developmental and Cell Biology, University of California, Irvine)
Docking and scaffolding contribute differently to regulation of two overlapping yeast MAPK pathways

Bruce E. Shapiro (Biological Network Modeling Center, Caltech, Pasadena, CA USA)
Platforms for Modeling in Systems Biology: Recent Developments in MathSBML and Cellerator

Ruslan N. Sharipov (Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; Institute of Systems Biology, Novosibirsk, Russia; Design Technological Institute of Digital Techniques SB RAS, Novosibirsk, Russia)
Integrated approach for modeling physiological, biomechanical, and molecular-genetic aspects of human cardiovascular system in health and essential hypertension

Brendan Sheehan (Systems Research Group, School of Computer Science and Informatics, University College Dublin, Ireland)
CellTransformer: A Tool to Generate Reaction Networks through Graph Transformation

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Xiling Shen (Department of Electrical Engineering, Stanford University)
Hybrid modeling and robustness analysis on Caulobacter cell cycle regulation

Patrick W. Sheppard (Department of Mechanical Engineering, University of California, Santa Barbara)
A Computational Model of Apoptosis and Inflammation Signaling in Microglia

Dongkwan Shin (Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea)
Modulation of NF-kappaB Oscillatory Patterns Mediated by beta-TrCP

Sung-Young Shin (Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea)
System-Level Investigations into the Functional role of RKIP in the Ras-Raf-MEK-ERK Signal Transduction Pathway

Tetsuya Shiraishi (Sony Computer Science Laboratories, Inc.)
Bistable molecular switches in human protein-protein interactions

Jason E. Shoemaker (Department of Chemical Engineering, University of California, Santa Barbara)
Measurement Identification and Robustness Analysis of the Fathead Minnow Steroidogenesis Model

Dan Siegal-Gaskins (Department of Physics, University of Chicago)
Control and Inheritance of Division Time in Caulobacter crescentus

Ariosto Silva (Centro Medico Boldrini, Campinas, Brazil)
A 3D Computer Model to Map Modifications in Cellular Metabolism into Different Tumor Phenotypes

Evangelos Simeonidis (Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, 131 Princess Street, M1 7DN, Manchester, UK; School of Chemical Engineering and Analytical Science, The University of Manchester, PO Box 88, Sackville Street, M60 1QD, Manchester, UK)
Bridging the Gap between Constraint-based and Kinetic Modelling

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Ana CQ Simoes (Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, Brazil)
Active Modules and Relevance Networks during the cell cycle in HeLa cells

You Q. Song (Department of Biochemistry, University of Hong Kong, Pokfulam, Hong Kong)
In silico mapping of a Charcot-Marie-Tooth Disease gene in a Pedigree of Hong Kong Chinese

Anatoly Sorokin (Computational Systems Biology Group, The University of Edinburgh, Edinburgh)
Visual framework for bio-medical knowledge organization

Irena Spasic (Manchester Centre for Integrative Systems Biology, The University of Manchester, UK)
Systematic screening of yeast kinetic parameters for metabolic models using a text mining toolbox

Pradeep K. Sreenivasaiah (Department of Life Science, Gwangju Institute of Science and Technology (GIST) Gwangju, Korea)
CIDMS: Cardiac Integrated Database Management System for Cardiac Systems Biology

Shyam Srinivasan (Department of Computer Science, University of California, Irvine)
Developmental mechanisms underlying sharp yet robust border formation in the forebrain

Marvin N. Steijaert (Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands)
A Biochemical Reaction Network with Multiple Functionalities

Camille Stephan-Otto Attolini (Group of Bioinformatics, Department of Computer Science, University of Leipzig, Germany)
SomoS: A Multi-scale Model for Somite Formation

Sarah R. Stockwell (Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA)
Building Networks From the Ground Up: Robustness and Predictability of Regulatory Modules

Gautier Stoll (Service bioinformatique, Institut Curie, Paris, France)
Model-based approach for analysis of transcriptome perturbation reveals Ewing oncogene interaction network

Holger Sültmann (German Cancer Research Center, Division of Molecular Genome Analysis, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany)
Integrated analysis of prostate cancer progression

Silpa Suthram (Bioinformatics Program, University of California, San Diego)
eQED: An Electrical Circuit Analysis of Expression Quantitative Trait Loci

Neil Swainston (Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester M1 7ND, UK)
Development of an extensible system for the capture and storage of experimental enzyme kinetics data

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Koichi Takahashi (The Molecular Sciences Institute)
Towards computational systems biology

Makio Tamura (Biology, Atmosphere, Chemistry, and Earth Division, Lawrence Livermore National Laboratory)
Comparative Genome Content Analysis with Respect to Basic Microbial Phenotypes by Class Association Rule Mining

Kai Tan (Department of Bioengineering, University of California, San Diego)
A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in DNA damage response

Hiromasa Tanaka (Department of Developmental and Cell Biology, University of California, Irvine, Center for Complex Biological Systems, University of California, Irvine)
Role of Regulation of the RGS protein Sst2p on Polarization and Mating in Yeast

Bogdan Tanasa (The Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, CA 92037)
Systems biology analyses of molecular networks in human tissues and misfolding diseases

Paul L.F. Tang (Department of Biochemistry, University of Hong Kong)
Genetic Modifier(s) of Embryonic Lethality in Type IIA Procollagen Deficient Mice

Ines Thiele (Bioengineering Department, University of California, San Diego)
Genome-Scale reconstruction of the transcriptional and translational machinery in Escherichia coli: A knowledge-database and its mathematical formulation

Jason D. Thompson (Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada)
The Use of Forced Oscillations to Study Biochemical Interactions

Jens Timmer (Institute of Physics, University of Freiburg, Freiburg, Germany)
Identifiability analysis for systematic parameter reduction and module identification in large signaling networks

Tsz-Leung To (Department of Chemical Engineering, Massachusetts Institute of Technology)
Quantitative characterization of synthetic gene regulatory network libraries

Jared E. Toettcher (Department of Biological Engineering, Massachusetts Institute of Technology)
Investigating the Systems Properties of the Mammalian DNA-Damage Response

Tony Y. Tsai (Department of Biomathematics, University of California, Los Angeles)
Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator

Ka-Po Tse (Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan)
MCP-1 Promoter Polymorphism at -2518 is Associated with Metastasis of Nasopharyngeal Carcinoma after Treatment

Lam C. Tsoi (Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina)
Identification of genes with common differential expression pattern across different metastatic microarray data

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Yoshihiro Usuda (Life Science Institute, Ajinomoto Co., Inc.)
Dynamic modeling of central metabolism and regulatory network of Escherichia coli for amino acid production simulation

Ravishankar R. Vallabhajosyula (Keck Graduate Institute of Applied Life Sciences)
Objective criteria for defining hubs in protein interaction networks

Karen van Eunen (Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, NL)
Changes in fermentative capacity during nitrogen starvation in baker’s yeast are initially regulated by multi-site modulation

Natal van Riel (Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands)
Qualitative analysis of nonlinear biochemical networks

Alejandra C. Ventura (Deparment of Internal Medicine and Comprehensive Cancer Center, University of Michigan)
A different model for signaling cascades

Pablo Villoslada (University of Navarra, Spain)
Therapeutic target identification and validation using gene expression networks for autoimmune diseases

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LaChelle Waller (Department of Genetics Bioinformatics and Computational Biology, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University)
Transcriptional profiling of potential regulatory factors modulating defense mechanisms in soybean under P. sojae infection

Christian Waltermann (Computational Systems Biology Group, Max Planck Institute for Molecular Genetics, Berlin, Germany)
Mathematical modeling of the cAMP/PKA pathway in S. cerevisiae

Kai Wang (Department of Biomedical Informatics, Columbia University, New York, NY, USA)
Signalome-Transfactome Networks in Human B Cells

Liming Wang (Department of Mathematics, Rutgers University, New Brunswick)
On the number of steady states in a multisite phosphorylation-dephosphorylation cycle

Wenxue Wang (Department of Mathematics and Statistics, Texas Tech University)
Identification and Modeling of Co-Rhythmic Genes from Micro-array Time Series Data

Barry L. Wanner (1Purdue University, Biological Sciences, West Lafayette, IN 47907 USA)
EcoliHub Information Resource for Experimentation and Modeling

Karen H. Watanabe (Department of Environmental & Biomolecular Systems, Oregon Health & Science University)
A Computational Model of Male Fathead Minnow Reproductive System Regulation: Linking changes in gene expression with reproductive effects

Katja Wegner (Biological and Neural Computation Group , Science & Technology Research Institute , University of Hertfordshire, Hatfield)
NetBuilder—A tool for the modeling and simulation of genetic regulatory networks

Michael C. Weis (Department of Electrical Engineering and Computer Science, Case Western Reserve University)
Complex Systems Biology of Prostate Cancer

Thomas Whisenant (Developmental and Cell Biology Department, UCI)
Computationally Searching the Genome for Novel JNK Substrates

Lucia Wille (Merrimack Pharmaceuticals Inc., Cambridge, MA 02139, USA)
Understanding IGF signaling dynamics through computational modeling

Cranos Williams (North Carolina State University)
Optimal Control Formulation of Constrained Least-Squares Estimation for Biochemical Pathway Estimation

Chao-Jen Wong (Computational Science Research Center, San Diego State University)
Global Gene Expression Profiling in Neonatal Rat Myocardium in Response to the Anti-diabetic Drug Rosiglitazone

Xuebing Wu (MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, China)
Global inference of human phenotype-genotype associations by integrating interactome, phenome and diseasome

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Joao B. Xavier (FAS Center for Systems Biology, Harvard University, Cambridge)
Scale-dependent social interactions drive morphogenesis and evolution in microbial biofilms

Dan Xi (Office of Cancer Complementary and Alternative Medicine, National Cancer Institute, NIH)
Toward Systems Biology Approaches to Cancer Complementary and Alternative Medicine Research

Hao Xiong (Department of computer Science, Texas A&M University)
Genetic Networks Show Strong Differential Dynamical Properties

Momiao Xiong (Human Genetics Center, University of Texas School of Public Health )
Evolution of the Structure of Metabolic Networks

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Tadashi Yamada (Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University)
Analysis of the relationship between noise in gene expression and regulatory structure in amino acid biosynthesis pathways

An Yan (Department of Botany and Plant Sciences and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside)
Models for oscillation of Rho GTPase Signaling

Bin Yan (NIDCD, NIH)
Systems biology-defined NF-kappaB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer

Laurence Yang (Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada)
Fitness Profiles Identify Enzyme Capacities

Tau-Mu Yi (Department of Developmental and Cell Biology, UCI)
Building a Toolbox for Quantitative Image Analysis of Yeast Cells for Systems Biology Using CellProfiler

Zhizhong Yin (Department of Biomedical Engineering, Johns Hopkins University)
Combining Microfluidics and Microarray for Complex Cell Signaling Study

Guy Yosiphon (Department of Computer Science, Center for Complex Biological Systems, University of California, Irvine)
Dynamical Grammar Modeling of Cellular Proliferative Dynamics in the Olfactory Epithelium

Richard Yu (Molecular Sciences Insitute, Berkeley, CA)
Rapid feedback minimizes loss of information during signal transduction

Katsuyuki Yugi (Department of Biosciences and Informatics, Keio University, JAPAN)
Towards construction of genetic relaxation oscillators

Hongseok Yun (Department of Chemical and Biomolecular Engineering, KAIST)
EcoProDB: The protein knowledge base for Escherichia coli

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Tingting Zhang (Roche Palo Alto LLC)
The IRAK Regulatory Module in IL-1 Signaling

Zhihua Zhang (Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor)
Topological Importance of Transcriptional Regulatory Network Revealed by Genetic Perturbation in Yeast

Jie Zhang (BioCentrum-DTU, Technical University of Denmark)
Glucose regulation and Snf1 protein kinase in Saccharomyces cerevisiae

Li Zhang (Computer Science Department,Donald Bren School of Information and Computer Sciences,University of California,Irvine,California,U.S.A.)
Dynamic Pathway Modeling of DNA Damage Response System and Parameter Estimation

Yanan Zheng (Entelos, Inc., Foster City, CA)
Use of biosimulation to identify novel strategies for inducing type 1 diabetes remission in the NOD mouse

Xuefeng Zhou (Department of Computer Science, Washington University, Saint Louis, USA)
Regulatory Circuits of MicroRNAs and Transcription Factors in Plant

Kai Zhuang (Department of Chemical Engineering, University of Toronto)
Race to Domination: A community competition study of Escherichia coli, Geobacter sulfurreducens, and Rhodoferax ferrireducens

Zhike Zi (Computational Systems Biology, Max Planck Institute for Molecular Genetics)
Constraint-based Modeling and Kinetic Analysis of the Smad Dependent TGF-beta Signaling Pathway

Guy E. Zinman (Department of Computational Biology, Carnegie Mellon University, Pittsburgh, USA)
Degradome project: Insights into intracellular protein degradation

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