Posters accepted : (as of Sept. 15th, 2006)
- Network Biology
- Complex Systems Biology
- Control and System Theory for Systems Biology
- Synthetic Biology
- Novel Computing Environments for systems biology
List by Category
Note: #Numbers in the list below are the IDs for your poster abstract submissions.
The POSTER ID is the id for your poster presentation.
* For authors > Poster information
- Network Biology
Reg#PosterIDTitleAuthors57 FN01 Evolutionary Conservation of Dynamic Protein-Protein Interaction Networks Chen-hsiung Chan, Sheng-An Lee, Cheng-Yan Kao 67 FN02 Correlation and Response of a Stochastic Gene Switch Yurie Okabe, Yuu Yagi, Masaki Sasai 118 FN03 Design principles in E. coli transcription network revealed by using a comprehensive library of fluorescent transcriptional reporters Alon Zaslaver, Anat Bren, Michal Ronen, shalev itzkovitz, Ilya Kikoin, Seagull Shavit, Wolfram Liebermeister, Mike Surette, uri alon 250 FN04 Network identification for the G1 to S transition in mammalian cells Milanesi Luciano, Chiaradonna Ferdinando, Alfieri Roberta, Gaglio Daniela, Vanoni Marco, Alberghina Lilia 316 FN05 Logic of transcriptional circuits underlying mammalian circadian clocks Maki Ukai-Tadenuma, Hiroki Ueda 392 FN06 Network conditions for instabilities in biochemical models Maya Mincheva 185 FN08 A stepwise structural equation modeling algorithm to predict genetic networks Grace Shwu-Rong Shieh, Ching-Yun Yu, Chung-Ming Chen, Juiling Huang, Woei-Fuh Wang 216 FN09 Pattern Recognition Method for Inferring of Genetic Networks Grace Shwu-Rong Shieh, Cheng-Long Chuang, Chung-Ming Chen 69 FN10 A Hybrid Simulation Framework for genome scale study of molecular dynamics in Escherichia Coli Samik Ghosh, Preetam Ghosh, Kalyan Basu, Sajal Das 139 FN11 Reconstruction of the human metabolic network and its relation with human disease Hongwu Ma, Anatoly Sorokin, Alex Selkov, Evgeni Selkov, Shakir Ali, Alexander Mazein, Saowalak Kalapanulak, Oleg Demin, Igor Goryanin 213 FN12 Finding perturbation-specific regulation pathways by integrating genetic regulatory and metabolic pathway Ho Jung NAM, Hyojin Kang, Sejun Lee, Doheon Lee 231 FN13 Highly correlated groups of multiple genes and/or metabolites in Arabidopsis thaliana detected by graph clustering (DPClus) Atsushi Fukushima, Md. Altaf-Ul-Amin, Ken Kurokawa, Shigehiko Kanaya, Masami Hirai, Kazuki Saito 274 FN14 Transcriptional regulation of the abiotic stress response in Arabidopsis Sue Rhee, Daniel MacLean 62 FN15 Phenotypic complexity during C. elegans early embryogenesis and systematic imterpretation of pleiotropy with protein interaction networks Lihua Zou, Brian Ross, Jun Liu, Hui Ge 209 FN16 Stochastic Model of a Biological Clock Hitesh Mistry 9 FN17 Methods for the Structural and Functional Analysis of Signaling Networks Steffen Klamt, Julio Saez-Rodriguez, Ernst Dieter Gilles 263 FN18 The Edinburgh Pathway Editor: a novel approach to creating and annotating complex biological networks Anatoly Sorokin, Alex Selkov, Shakir Ali, Stuart Moodie, Igor Goryanin 291 FN19 Algebraic method for the analysis of signaling crosstalk Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Kotaro Oka, Masaru Tomita 311 FN20 Maximum entropy approach to network reconstruction Gasper Tkacik, Elad Schneidman, William Bialek 383 FN21 Principles of microRNA regulation of a human cellular signaling network Qinghua Cui, Zhenbao Yu, Enrico Purisima, Edwin Wang 414 FN22 SignAlign: A Tool for Analysing Signaling Pathways Sridhar Hariharaputran, Thoralf Töpel 425 FN23 Network Systems Biology HepatoSys Ute Heisner 45 FN24 Setting the Framework for Large Scale System Biology: The Integration of Human Protein Interactome Matthias Futschik, Gautam Chaurasia, Erich Wanker, Hanspeter Herzel 3 FN25 A System Biology approach to the immune system network reveals functional differences in health and Multiple Sclerosis Pablo Villoslada, Ricardo Palacios, Joaquin Goni, Nieves Velez, Jorge Sepulcre 123 FN26 Modeling the extracellular and cell-surface environment impacting Wnt signaling Anna Georgieva, Satish Tadepalli, Brian Stoll 178 FN27 Mathematical modelling of the role of HIF-1 in tumour growth Alexander Fletcher, Jonathan Chapman, Christopher Breward 28 FN28 Graph Theory and Networks in Biology Oliver Mason, Mark Verwoerd 119 FN29 TOWARDS A PROTEOME SCALE MAP OF THE HUMAN INTERACTOME NETWORK Jean-Francois Rual, et al. 190 FN30 LaPCA: A New Method for Inferring the Causal Relationship Between Genes from Temporal Exp. Profiles Yeoin Yoon, Kwang-Hyun Cho 194 FN31 Inference of transcript. regulatory networks from initial mRNA exp. profiles and DNA-binding motifs Hyoung-Seok Choi, Sang-Mok Choo, Jeong-Rae Kim, Kwang-Hyun Cho 327 FN32 Modeling and Sensitivity Analysis of circadian oscillatory network of Drosophila Yukino Ogawa, Kazuharu Arakawa, Fumihiko Miyoshi, Kazunari Kaizu, Masaru Tomita 342 FN33 An Evolutionary Systems Biology approach for analysing the dynamics of reductive genome evolution Amit Khachane, Jacek Puchalka, Kenneth Timmis, Vitor Martins dos Santos 146 FN34 Message-adjusted networks (MAN) in gastro-entero-pancreatic (GEP) endocrine system Faruk Aykan 381 FN35 REVERSE ENGINEERING BIOLOGICAL NETWORKS BY NONLINEAR REGRESSION Diogo Camacho, Pedro Mendes 93 FN36 Inferring Human Protein Interaction Network from Conservatively Hidden Family-Family Interactions Fan-Kai Lin, Chung-Yen Lin, Chao A. Hsiung 415 FN37 Hydrophobic, Hydrophilic and Charged amino acids' networks within protein Sudip Kundu, Md. Aftabuddin 198 FN38 Identification of mouse heart-specific subnetwork structures inferred from the expression profiles compendium using a new search algorithm Seong-Eui Hong, Seong-Hwan Rho, Do Han Kim 225 FN39 Structural transition in prokaryotic metabolic networks with growth temperature Kazuhiro Takemoto, Jose C. Nacher, Tatsuya Akuts 289 FN40 Toward Automatic Construction of an Evolutionary Network of Protein Families Fangfang Xia, Rick Stevens 298 FN41 Clustering of Gene Networks Using a Monte-Carlo Simulation Adolfo Torres, Jose Gonzalez, Haret Rosu 301 FN42 Comparison of metabolite production capability indices generated by network analysis methods Kyota Ishii , Seira Nakamura, Mineo Morohashi, Yoshiaki Ohashi, Shinichi Kikuchi, Masahiro Sugimoto, Masaru Tomita 393 FN43 Protein-protein interaction pathways reconstruction from domain-domain interactions Ka-Lok Ng, Hsiang-Chuan Liu, Chien-Hung Huang 13 FN44 INTEGRATED COMPUTATIONAL AND EXPERIMENTAL APPROACH TO IDENTIY THE TARGETS OF P63 ON GENOME SCALE Mukesh Bansal, Giusy Della Gatta, Laura De Rosa, Alberto Ambesi, Caterina Missero, Diego di Bernardo 111 FN45 Genes and functions that regulate redox status in a photosynthetic organism Rajeev Aurora, Rangesh Kunnavakkam, Abhay Singh, Maitrayee Bhattacharya-Pakrasi, Himadri Pakrasi 237 FN46 A systems biology approach to understand regulation of virulence factors in Staphylococcus aureus Erik Gustafsson, Stefan Karlsson, Jan Oscarsson, Peter Sogard, Patric Nilsson, Staffan Arvidson 315 FN47 Systems evolutionary biology: modular evolution of yeast protein interaction network Soichi Ogishima, Yasuhiro Suzuki, Takeshi Hase, So Nakagawa, Hiroshi Tanaka 333 FN48 Search for causative functional SNPs using in vitro virus method Hitomi Umeki, Shigeo Fujimori, Naohiro Yanagisawa, Takanori Washio, Etsuko Miyamoto-Sato, Masaru Tomita, Hiroshi Yanagawa 350 FN49 Toward a comprehensives analysis of human transcription factor networks using IVV Etsuko Miyamoto-Sato, Masamichi Ishizaka, Shigeo Fujimori, Rintaro Saito, Takanori Washio, Naoya Hirai, Kazuyo Masuoka, Tatsuhiro Yamashita, Tomohiro Oshikubo, Hiroshi Yanagawa 443 FN50 Inferring Protein Network by Multiple Domain Interactions Yong Wang, Xiang-Sun Zhang, Luonan Chen 444 FN51 Noise induced robust collective behaviors in a multicellular system Ruiqi Wang
- Complex Systems Biology
Reg#PosterIDTitleAuthors39 FX01 Phenomenological Modeling and Study for the Stability of A Microbial Community Masashi Tachikawa 318 FX02 Genome-wide Analysis of Cell Cycle Dependent Gene Expression Yoichi Minami, Takeya Kasukawa, Kenichiro Uno, Tamami Hirai, Hiroki Ueda 427 FX03 Plankton blooming Andrei Korobeinikov, Sergei Petrovskii 74 FX04 Model reduction for various levels of model development Gunnar Cedersund, Henning Schmidt, Mats Jirstrand 112 FX05 Regulation of E.coli respiration: gene network reconstruction and mathematical modeling Alexander Ratushny, Tamara Khlebodarova, Vitaly Likhoshvai 400 FX06 A multi-omics analysis of Escherichia coli metabolic network Martin Robert, Kenji Nakahigashi, Nobuyoshi Ishii, Tomoya Baba, Tomoyoshi Soga, Akio Kanai, Takashi Togashi, Takashi Hirasawa, Miki Naba, Kenta Hirai, Aminul Hoque, Kakazu Yuji, Kaori Sugawara, Saori Igarashi, Satoshi Harada, Takeshi Masuda, Naoyuki Sugiyama, Katsuyuki Yugi, Kazuharu Arakawa, Nayuta Iwata, Yoshihiro Toya, Yoichi Nakayama, Akiko Hagiya, Takaaki Nishioka, Kazuyuki Shimizu, Hirotada Mori, Masaru Tomita 7 FX07 Microtubule Dynamics Regulate Spindle Pole Oscillations and Posterior Displacement during Anaphase in the C.elegans Embryo Cleopatra Kozlowski, Martin Srayko, Henrik Bringmann, Anthony A. Hyman, Francois Nedelec 163 FX08 A Top-down Modelling Approach for Plant Systems Biology Adaoha Ihekwaba, Douglas Kell, Pedro Mendes 201 FX09 Analysis of mutation frequency in antibody affinity maturation: A hint at positively and negatively selected mutations Lei Zhang, Armin Weiser, Atijeh Valai, Michal Or-guil 364 FX10 In silico modelling of embryonic morphogenesis Philippe-Alexandre Pouille, Emmanuel Beaurepaire, Emmanuel Farge 90 FX11 Non-supervised phenotype learning and phenotype model reconstruction in the functional genomic screenings: Coordinated activity of early endosome motors Yannis Kalaidzidis, Jochen Rink, Marino Zerial 287 FX12 IL3-Induced JAK-STAT Signaling: A Complex Systems Biology Approach Radina Soebiyanto, Jayant Avva, Cheng-Kui Qu, Kevin Bunting, Kenneth Loparo, Mihajlo Mesarovic, Sree Sreenath 288 FX13 NFkB and PI3K/Akt Pathway in Prostate Cancer Jayant Avva, Michael Weis, Radina Soebiyanto, Kenneth Loparo, Sanjay Gupta, Sree Sreenath 324 FX14 Dynamic behavior of buffered calcium ions in stochastic and deterministic simulations Juergen Pahle, Sven Sahle, Ursula Kummer 10 FX16 The genetic code is nearly optimal for allowing arbitrary additional codes within protein-coding sequences Shalev Itzkovitz, Uri Alon 131 FX17 Graphical Causal Reasoning Tool for Systems Biology: CMAP Gabriel Weinreb, Ken Jacobson, Timothy Elston 391 FX18 Enzyme I of the PEP-dependent phosphotransferase system: mathematical modeling approach Tatyana Karelina, Oleg Demin 141 FX19 Systematic Determination of Biological Network Topology: Non-Integral Connectivity Method (NICM) Kumar Selvarajoo, Masa Tsuchiya 169 FX20 Bond graphs of network thermodynamics can express phenomenological equations in biological systems Yusuke Imai 179 FX21 Genome-Wide System Identification and Analysis Reveals Stable yet Flexible Network Dynamics in Yeast Mika Gustafsson, Michael Hornquist, Johan Bjorkgren, Jesper Tegner 293 FX22 Modeling Hsp70-Mediated Protein Folding Bin Hu, Matthias Mayer, Masaru Tomita 408 FX23 A Spectral Approach For A Priori Integration Of Gene Network Knowledge Into Microarray Classification. Franck Rapaport, Andrei Zinovyev, Emmanuel Barillot, Jean-Philippe Vert 411 FX24 Rule-Based Modeling of Biochemical Networks Based on Protein Interactions: Theory, Software, and Applications James Faeder, Michael Blinov, Jin Yang, Byron Goldstein, William Hlavacek 418 FX25 Factoring glucokinase sequestration in silico affects glycolytic network kinetics Satya Arjunan, Kumar Selvarajoo 54 FX26 Single-cell analysis and modeling reveal that HIV & Herpes use feedback circuits tocontrol lifecycle Leor Weinberger, Thomas Shenk 64 FX27 Chaotic thermoregulation in the spadix of skunk cabbage, Symplocarpus foetidus Takanori Ito, Hiroshi Osada, Kikukatsu Ito 103 FX28 Adjoint based parameter identification algorithm for protein networks with application to Planar Cell Polarity Robin Raffard, Claire Tomlin, Keith Amonlirdviman, Jeffrey Axelrod 183 FX29 Selection of Optimal Growth State by Stochastic Noise Chikara Furusawa, Kunihiko Kaneko 230 FX30 "Systems Energetics" -a new approach for cellular systems dynamics- Noriko Hiroi, Akira Funahashi, Hiroaki Suzuki, Takatoki Yamamoto, Douglas Murray 314 FX31 Characterization of proteins from the matrix of sclerites from the alcyonarian, Lobophytum crassum. M. Azizur Rahman, Yeishin Isa, Tsuyoshi Uehara 180 FX32 An Attempt at Using the Approaches in Systems Biology to Explore Traditional Chinese Medicine Chu Chen, Sheng-Ying Pao, Song Lin, Katherine Chen 241 FX33 The benefit of combining systems biology and experiments for understanding complex biological system Magnus Fagerlind, Erik Gustafsson, Elie Jarnmark, Maria Svensson, Peter Sogard 363 FX34 Quantitative Biology of Embryo-Maternal Communication and Implantation Stefan Bauersachs, Claudia Klein, Frank Berendt, Thomas Frohlich, Helmut Blum, Georg J. Arnold, Ulrich Mansmann, Eckhard Wolf
- Control and System Theory for Systems Biology
Reg#PosterIDTitleAuthors25 FT01 A finite model for the random behavior in the lactose regulation system of Escherichia coli Agung Julius, Adam Halasz, Vijay Kumar, George Pappas 70 FT02 In vivo reaction modeling by DRRK Noriko Hiroi, Akira Funahashi, Hiroaki Kitano 122 FT03 Modeling, simulation & stability analysis of p53-mdm2 oscillations Arun Krishnan, Masaru Tomita 191 FT04 Parameter Perturbation Analysis of Bacterial Chemotaxis Tae-Hwan Kim, Sung Hoon Jung, Kwang-Hyun Cho 50 FT05 Experimental design for parameter estimation in models combining signal transduction and metabolic pathways: Control and System Theory for Systems Biology of nitrogen uptake in yeast Natal Van Riel 68 FT06 Proportion preservation in a growing tissue Akihiko Nakajima, Kunihiko Kaneko 31 FT07 Experiment design for optimal excitation of gene regulatory networks Torbjörn Nordling, Elling Jacobsen 203 FT08 Evolutionary Design Principles of Bacterial Chemotaxis Markus Kollmann, Linda Lovdok, Kilian Bartholome, Jens Timmer, Victor Sourjik 262 FT09 Ensemble modelling reveals a novel logic of TOR signalling in yeast Lars Kuepfer, Matthias Peter, Uwe Sauer, Joerg Stelling 313 FT10 Systems Biology of Bone Remodeling in Osteoporosis Kalyan Mynampati, Wen Wan Ling, Peter Lee 378 FT11 From bursts to molecular memory: finding the fundamental units of biochemical fluctuations Juan Pedraza, Johan Paulsson 38 FT12 Tackling the uncertainty of tumour dynamics Abhik Mukherjee, Durjoy Majumder, Suryasarathi Barat 142 FT14 Robust identification of biochemical networks from noisy measurements Jongrae Kim, Declan Bates, Ian Postlethwaite, Pat Heslop-Harrison, Kwang-Hyun Cho 368 FT15 Cellogica: A tool to analyze and Control and System Theory for Systems Biology the dynamics of cis-regulatory systems Satya Arjunan, Zhen Xuan Yeo, Masaru Tomita, Masa Tsuchiya 20 FT16 Analyzing Robustness in Biophysical Networks: Application to Apoptosis Jason Shoemaker, Francis Doyle 84 FT17 Experimental design and model selection for signal transduction pathways Thomas Maiwald, Clemens Kreutz, Sebastian Bohl, Marcel Schilling, Andrea Pfeifer, Ursula Klingmuller, Jens Timmer 365 FT18 A MDE Perspective on Coding of Systems Biology: Proof of concept using transformations to BioAmbients and analysis Debora Rosa, Magali Roux-Rouquie, Marie-Noelle Terrasse, Corrado Priami 399 FT19 Biological Regulations as Finite Markov Process Reiko Tanaka, Hidenori Kimura, Hiroyuki Okano 6 FT20 Genome size estimates and karyotypes for three important freshwater molluscs, the Lymnaea natalensis and the schistosomiasis vector snails (Biomphalaria alexandrina and Bulinus truncatus) Fayez A. Bakry, Ahmed T. Sharaf El-Din 80 FT21 TSim, a Platform for Simulation of Multi-cellular Systems Ariosto Silva, Jose Yunes 37 FT22 Dynamics of HIV infection studied with Conformon-P systems David Corne, Pierluigi Frisco 47 FT23 A Systematic Modeling Framework for Biochemical and Biological Systems Henning Schmidt, Mats Jirstrand, Gunnar Cedersund 53 FT24 Parameter Estimation Using Alternative Cost Functions Henning Schmidt, Gunnar Cedersund, Mats Jirstrand 86 FT26 Moment closure approximations for studying stochasticity in biological systems Abhyudai Singh, Joao Hespanha 32 FT27 Unraveling Feedback Structures in Gene Regulatory Networks with Application to the Manmmalian Circadian Clock Camilla Trane, Elling Jacobsen
- Synthetic Biology
Reg#PosterIDTitleAuthors174 FS01 Testing Biological Ergodicity of Toggle Switch: Reconstruction of Single-cell-level Behavior from Population-Level Measurement Hirokazu Tozaki, Tetsuya Kobayashi, Hiroyuki Okano, Ryo Yamamoto, Kazuyuki Aihara, Hidenori Kimura 303 FS02 Stopping Mammalian Circadian Clock by Critical Light Pulse: Death of individual oscillators or desynchronization of oscillators? Tetsuya Kobayashi, Hideki Ukai, Hiroki Ueda 83 FS03 Construction and Performance Characteristics of a Self-Generating In Vitro Metabolic Reaction Nancy Kelley-Loughnane, Mauricio Rodriguez, Marlin Linger, Latha Narayanan, John Frazier 345 FS05 Programmable Bacterial Catalysts Miguel Godinho, Jacek Puchalka, Amit Khachane, Kenneth Timmis, Vitor Martins dos Santos 376 FS06 Regulatory Dynamics of Synthetic Gene Networks with Positive Feedback Yusuke Maeda, Masaki Sano 439 FS07 De novo construction of gene regulation network in small vesicle Daisuke Kiga, Masahiro Takinoue, Koh-ichiroh Shohda, Akira Suyama 78 FS08 In silico genome-scale analysis of the hyperthermophilic bacterium, Thermotoga neapolitana Jin Sik Kim, jae Jong Kim, Ki Jung Park, Sang Yup Lee 151 FS09 Engineering Synthetic Trans-Splicing Ribozyme Systems Austin Che 221 FS10 Population analysis of liposomes with protein synthesis and a cascading genetic network Takeshi Sunami, Kanetomo Sato, Keitaro Ishikawa, Tetsuya Yomo
- Novel Computing Environments for systems biology
Reg#PosterIDTitleAuthors266 FI01 SBML Level 2 Version 2 Andrew Finney, Michael Hucka, Nicolas Le Novere 240 FI02 The SBML Layout Extension and Beyond Ralph Gauges, Sven Sahle, Ursula Rost, Katja Wegner 156 FI03 The Systems Biology Ontology Melanie Courtot, Michael Hucka, Nicolas Le Novere 153 FI04 MIRIAM Database and Webservices Camille Laibe, Melanie Courtot, Marco Donizelli, Chen Li, Nicolas Le Novere 157 FI05 BioModels Database, A Curated Resource of Annotated Published Models Chen Li, Marco Donizelli, Lu Li, Harish Dharuri, Arnaud Henry, Michael Hucka, Nicolas Le Novere 317 FI06 Recent Updates to libSBML, MathSBML, SBMLToolbox, and the SBML.org Online Validator Benjamin Bornstein, Sarah Keating, Bruce Shapiro, Joanna Murakami, Michael Hucka 162 FI07 SBMLeditor: An editor for models in the Systems Biology Markup Language Nicolas Rodriguez, Nicolas Le Novere, Marco Donizelli 96 FI08 CellDesigner3.1: A Process Diagram Editor for Gene-regulatory and Biochemical Networks Akira Funahashi, Akiya Jouraku, Yukiko Matsuoka, Norihiro Kikuchi, Hiroaki Kitano 26 FI09 Integrating Tools for Computational Systems Biology: PySCeS and JWS Online Brett Olivier, Johann Rohwer, Jacky Snoep, Jan-Hendrik Hofmeyr 165 FI10 Taverna workflows for systems biology Peter Li, Andy Brass, John Pinney, Tom Oinn, Douglas Kell, Carole Goble 351 FI11 COPASI - a COmplex PAthway SImulator Sven Sahle, Stefan Hoops, Ralph Gauges, Jürgen Pahle, Pedro Mendes, Ursula Kummer 172 FI12 Systems Biology Software Support in Mathematica: Recent Developments in Cellerator Bruce Shapiro, Alexey Vorobyov, Joanna Murakami, Eric Mjolsness 419 FI13 SIBioNet: SBML application for system identification of biochemical reaction networks Atsushi Shinkai, Junichiro Yoshimoto, Kenji Doya 294 FI14 DynaBioS.Cell: A New General Simulator for Cell Physiological Models to Facilitate Simulation of Experimental Protocols Takao Shimayoshi, Akira Amano, Tetsuya Matsuda 193 FI15 CADLIVE: Computer-Aided Design of Living Systems Kentarou Inoue, Hiroyuki Kurata 423 FI16 Comprehensive Study of Numerical Solvers in Complex Oscillatory Biochemical Systems Modeling May Wang, Chang F Quo 184 FI17 A Tool for Analysis in "Dynamical Change Behavior over Motifs" Jittisak Senachak, Tomoyuki Yamamoto, Kokichi Futatsugi 14 FI18 Fly-DPI: Database of Protein Interactomes for D. melanogaster in the approach of Systems Biology Chung-Yen Lin, Chi-Shiang Cho, Chia-Ling Chen, Fan-Kai Lin, Chieh-Hua Lin, Pao-Yang Chen, Shu-Hwa Chen, Chen-Zen Lo, Chao A. Hsiung 36 FI19 Database driven approach for automatic construction of dynamic cell-wide metabolic pathway models Kazuharu Arakawa, Yukino Ogawa, Masaru Tomita 166 FI20 Visualization of CellML Models Sarala Dissanayake, Matt Halstead, Poul Nielsen 206 FI21 A GRAPHICAL NOTATION TO DESCRIBE THE LOGICAL INTERACTIONS OF BIOLOGICAL PATHWAYS Stuart Moodie, Anatoly Sorokin, Igor Goryanin, Peter Ghazal 66 FI22 Googling credible interactions from protein-protein interaction networks Kinya Okada, Masanori Arita, Kiyoshi Asai 332 FI23 An integrative database for biochemical reaction kinetics: SABIO-RK Renate Kania, Ulrike Wittig, Martin Golebiewski, Andreas Weidemann, Olga Krebs, Saqib Mir, Isabel Rojas 281 FI24 Integration of gene expression data with bio-molecular interaction networks using Reporter Features algorithm Ana Paula Oliveira, Kiran Patil, Jens Nielsen 336 FI25 Using variable selection method to infer gene regulatory networks from time series microarray data Dougu Nam, Cheol-Goo Hur, Jihyun F. Kim 229 FI26 Towards a signal transduction network of yeast Kutlu O. Ulgen, K. Yalcin Arga, Z. Ilsen Onsan, Betul Kirdar, Jens Nielsen 257 FI27 Computer-based screening of functional conformers of proteins Hector Montiel, Gabriel Del Rio 280 FI28 An Infrastructure to Construct Genome-Scale Metabolic Models Automatically Xnghua Shi, Rick Stevens 384 FI29 TRNDy: A Bioinformatics Tool for Investigating the Topological Dynamics of Differentially Expressed Genes in Transcriptional Regulatory Networks Duangdao Wichadakul, Ram Samudrala 398 FI30 Protein Network Construction of Candida albicans from Saccharomyces cerevisiae's protein-protein interactions Chieh-Hua Lin, Chung-Yen Lin, Fan-Kai Lin 402 FI31 Interactive visualization of complex and structured biological networks Sebastian Mirschel, Martin Ginkel, Julio Saez-Rodriguez, Ernst Dieter Gilles 33 FI32 KinetikonHT, a database of kinetic parameters, created using high throughput techniques. Axel Kowald, Sebastian Schmeier, Marvin Schulz, Wolfram Liebermeister, Simon Borger, Edda Klipp 75 FI33 PottersWheel: User-friendly high-performance parameter estimation & model selection Matlab framework Thomas Maiwald, Clemens Kreutz, Jens Timmer 92 FI34 Systems Biology Analysis of Endocytosis and Signalling in mammalian cells Marino Zerial, Jochen Rink, Claudio Collinet, Charles Bradshaw, Bianca Habermann, Yannis Kalaidzidis, Perla Del Conte-Zerial, Lutz Brusch, Andreas Deutsch 94 FI35 Thermodynamical model of DNA hybridization on short oligonucleotide microarray Naoaki Ono , Shingo Suzuki, Chikara Furusawa, Akiko Kashiwagi, Tetsuya Yomo 116 FI36 Predicting Deleterious SNPs with Site-Specific Evolutionary Models Anna Chernova, Benjamin Blackburne, Richard Goldstein 134 FI37 Evaluating the functional coherence of protein groups via protein-semantic network Bin Zheng, Xinghua Lu 220 FI38 From In Silico QTLs to System Biology: An Example of using in silico mapping to identify genetic contribution to variation of Bono Mass Density in inbred strains Paul L. F. Tang, Matthew S. Y. Chan, Pak C. Sham, You-qiang Song 286 FI39 Numerical Simulation and Molecular Systems Biology Koichi Takahashi 334 FI40 Parameter estimation for stiff equations of biosystems using radial basis function networks Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Masaru Tomita 346 FI41 BioUML - open source extensible workbench for systems biology Fedor Kolpakov, Mikhail Puzanov, Alexander Koshukov 40 FI42 A Universal Rate Equation for Computational Systems Biology Johann Rohwer, Arno Hanekom, Jan-Hendrik Hofmeyr 109 FI43 MetaFluxNet2: an integrated environment for modeling and simulation of genome-scale metabolic network model Hongseok Yun, Choamun Yun, Hyun Uk Kim, Sang Yup Lee 215 FI44 System-level identification of transcriptional circuits underlying Drosophila circadian clocks using Drosophila Tiling Arrays Rikuhiro Yamada, Maki Tadenuma, Ken-ichiro Uno, Takeya Kasukawa, Akira Matsumoto, Hiroki Ueda 268 FI45 Identifying Genes with Significant Interaction Effects in Toxicological Time-Course Microarray Data Yan Ma, E. Harner 46 FI46 Development of Computational methods for analysis of Metabolite screening data Talwar Priti, Lengauer Thomas, Wittmann Christoph, Velagapudhi Vidya, Heinzle Elmar 51 FI47 Top-down Approach for Deciphering Characteristics of Metabolic Reactions from Experimental Data Jung-Wook Bang, Tim Ebbels, Florencio Pazos 76 FI48 A generic mass spectrometry-based platform for enzyme kinetic data acquisition and analysis Richard Baran, Takamasa Ishikawa, Saito Natsumi, Kakazu Yuji, Tomoyoshi Soga, Takaaki Nishioka, Martin Robert, Masaru Tomita 114 FI49 Role of the bgl operon of Escherichia coli in stationary phase Ranjna Madan 147 FI50 The Manchester Centre for Integrative Systems Biology Douglas Kell, David Broomhead, Simon Gaskell, John McCarthy, Steve Oliver, Norman Paton, Hans Westerhoff 275 FI51 A kinetic approach to the analysis of non-steady state isotope tracer data Vitaly Selivanov, Silvia Marin, Antonio Ramos-Montoya, Josep Sentelles, Paul Lee, Marta Cascante 422 FI52 Interpret Lipid Metabolomic Pathway Data Using Visualization Geoffrey Wang, Jin-Young Hong, Alfred Merrill, May Wang 12 FI53 Reverse Engineering for Embryonic Gene Regulatory Network in Zebrafish via Evolutionary Optimization with Data Collocation Wen-Hung Hunag, Chiou-Hwa Yuh, Feng-Sheng Wang 170 FI54 Genome annotation and metabolic network construction of Aspergillus oryzae Wanwipa Vongsangnak, Peter Bjarke Olsen, Steen Krogsgaard, Jens Nielsen 432 FI55 Characterization of regulatory modules associated with stem cell differentiation by latent variable models Je-Gun Joung, Dongho Shin, Rho Hyun Seong, Byoung-Tak Zhang 91 FI56 Virtual Microscopy - Modular modeling of Experimental Protocols and Instrumentation James Schaff, Anuradha Lakshminarayana, Ion Moraru, Leslie Loew 98 FI57 High-throughput image analysis for the classification of subcellular localization patterns of fluorescently labelled proteins Fabian Kamper, Olaf Selchow, Dimitrios Kalamatianos, Harald Wajant, Klaus Pfizenmaier, Eric Bullinger 244 FI58 Applied genome-scale modelling of Aspergillus niger Mikael Andersen, Michael L. Nielsen, Jens Nielsen 261 FI59 Quality control and improved quantitative Western blotting with the GelInspector Thomas Maiwald, Marcel Schilling, Sebastian Bohl, Clemens Kreutz, Ursula Klingmuller, Jens Timmer 362 FI60 Integration of biological pathways Yu-Tai Wang, Yeing-Wen Deng, Cheng-Min Wei, Ueng-Cheng Yang 409 FI61 Bayesian system identification of biochemical signaling pathways Junichiro Yoshimoto, Atsushi Shinkai, Kenji Doya 252 FI62 Integrative Bioinformatics Analysis that Deconvolutes the Changes of Transcriptional Regulatory Programs during Carcinogenesis Atsushi Niida, Shuich Tsutsumi, Andrew Smith, Michael Q. Zhang, Hiroyuki Aburatani, Tetsu Akiyama 259 FI63 Genomic signatures for drug-induced apoptosis in cancer cell lines: a combined experimental and stat Laurent Gautier, Christopher Taylor, Harold Brooks, Philip Iversen, Charles Spencer, Xiang Yang, Greg Tukcer-Kellogg 246 FI64 Optimization of cDNA microarrays using criteria that do not rely on external standards Torunn Bruland, Endre Anderssen, Berit Doseth Eitrem, Hallgeir Bergum, Vidar Beisvag, Astrid Laegreid 359 FI65 Identification and design of inter- and intra-molecular atomic network by using the genomic sequences and the structural information Yohei Koyama, Tetsuya Kobayashi, Shuji Tomoda, Hiroki Ueda 17 FI66 Composition and Aggregation for Biological Pathway Modeling Ranjit Randhawa, Cliff Shaffer, John Tyson 309 FI67 An Acceleration of a Biochemical Simulator on Programmable Hardware Yow Iwaoka, Yasunori Osana, Masato Yoshimi, Tosinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano 276 FI68 FiD - a tool for prediction of molecular fragments from tandem mass spectrometry data Markus Heinonen, Ari Rantanen, Taneli Mielikainen, Esa Pitkanen, Juho Rousu 323 FI69 Comparative 'Omics' Analysis of Escherichia coli B and K-12 Sung Ho Yoon, Haeyoung Jeong, Cheol-Goo Hur, Tae Kwang Oh, Jihyun F. Kim 440 FI70 Systems Biology Graphical Notation (SBGN) Project Hiroaki Kitano, Michael Hucka, Nicolas Le Novere, Akira Funahashi 390 FI71 Predicting antigenic drift in human influenza A virus H3 hemagglutinin Yu-Chieh Liao, Chin-Yu Ko, Min-Shi Lee, Chao A. Hsiung 117 FI72 WebCell: a web-based integrated environment for managing and analyzing cellular network models Choamun Yun, Dong-Yup Lee, Ayoun Cho, Sunwon Park, Sang Yup Lee 431 FI73 Linear and Conformational Epitopes Prediction from Member of Protein Families Tun-Wen Pai, Wei-Jun Zhung, Chih-Hong Liu, Wen-Shyong Tzou 420 FI74 Identification of heterogeneous named entities in biology texts and resolution of anaphora Julien Lorec, Gerard Ramstein, Yannick Jacques 205 FI75 BioCAD: Web service based Integrated System for Inferring Genetic Regulatory Circuits Sangwoo Kim, Kiryong Ha, Doheon Lee 99 FI76 Integrating microarray data analysis and protein-protein
interaction database to construct dynamic biological networks
which represent the characteristics of gene expression patternPeter Kuan-Yeu Pan, Chen-Hsiung Chan, Sheng-An Lee, Cheng-Yan Kau, I-Ming Chu 441 FI77 A View to the Evolution of Biological Pathways using PANTHER. Huaiyu Mi, Nan Guo, Anish Kejariwal, Paul Thomas 386 FI78 SBW - a modular framework for Systems Biology Frank Bergmann, Herbert Sauro 445 FI79 Gene function prediction using one-class technique Xian-Ming Zhao