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Program & Speakers

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Posters: Fronts in Systems Biology

Posters accepted : (as of Sept. 15th, 2006)

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#
    PosterID
    Title
    Authors
    57  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
    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
    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#
    PosterID
    Title
    Authors
    39  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
    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#
    PosterID
    Title
    Authors
    25  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
    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#
    PosterID
    Title
    Authors
    174  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#
    PosterID
    Title
    Authors
    266  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 pattern
    Peter 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

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