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ECCB 2008

 

ISMB 2008

 

 

 

Systems Biology & Networks Posters

C001

Co-evolution of transcriptional and post-translational cell-cycle regulation
Lars Juhl Jensen, Ulrik de, Søren Brunak, Peer Bork
 

C002

Scaffold Proteins Provide an Internal Clock to Protein Kinase Cascades
Jason Locasale
 

C003

An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits
Yves A Lussier, Li , Sam , Goh , Gerstein , Lussier
 

C004

Using Computational Intelligence and Evolutionary Computation as Tools to Build Faster Discriminative Networks for Biological Purposes
RENAN W. F. VITRAL
 

C005

Bayesian network search: relationship of search space structure to starting networks
Christoph Echtermeyer, V Anne Smith
 

C006

Inferring tissue-specific gene networks from spatiotemporal dynamics of gene expression in C. elegans
Hui Ge, Patrycja Missiuro, Kesheng Liu, Hui Ge
 

C007

Visualising and Analysing Properties of Integrated Biological Networks using ONDEX
Jan Taubert, Andre Skusa, Jochen Weile, Matthew Hindle, Jan Baumbach, Jacob Koehler
 

C008

Data Integration and Text Mining, for the analysis of Time-Series Gene expression data, from plant stress responses.
Matthew Morritt Hindle, Jan Taubert, Rainer Winnenburg, Marcela Baudo, Dimah Habash, Jacob Koehler
 

C009

Network motif identification in stochastic networks
Fengzhu Sun, Rui Jiang
 

C010

Predicting protein-protein interactions using network structure
Pao-Yang Chen, Gesine Reinert, Charlotte Deane
 

C011

Inferring topology from clustering coefficients in protein-protein interaction networks.
Caroline C. Friedel, Ralf Zimmer
 

C012

A flex view of metabolic network
Ko-Yun Lo, Andrew Dalby
 

C013

Learning global transcriptional dynamics from functional genomics data.
Richard Bonneau
 

C014

A predictive model of CRH-R1 Signalling Pathways
Yang Cheng, Dietrich Trümbach, Jan Deussing, Peter Weber, Cornelia Graf, Benno Pütz, Florian Holsboer, Wolfgang Wurst , Juliane Wunsch
 

C015

Receptome-Specific Phenotypes Distinguish Human Tissues
Julie Leonard, Errol Strain, Perry Haaland
 

C016

A Systems Biology Website for Pathway Modelling, Biomarker Analysis and Data Exchange for Live Cell Research in Apoptosis
Heinrich J Huber, Martin Plchut, Petronela Weisova, Heiko Duessmann, Manus Ward, Markus Rehm, Jochen Prehn
 

C017

Soil-plant system approach to modelling nitrogen uptake in Arabidopsis thaliana
Artem Lysenko, Anthony Miller, Goetz Richter, Charlie Hodgman, Jacob Koehler
 

C018

Understanding allosteric regulation through analysis of metabolic network structure.
Alex Gutteridge, Susumu Goto
 

C019

A Time Matching System Based on Time-course Microarray Gene Expression Profiles of Aerobic and Anaerobic Growth in Escherichia coli
Chi-Dung Yang, Hsi-Yuan Huang, Hsien-Da Huang, Ching-Ping Tseng
 

C020

Inferring dynamical protein networks from two-dimensional gel electrophoresis time series
Sara P. Garcia, Edward Krug, John Arthur, Eberhard Voit, Romesh Stanislaus, Jonas Almeida
 

C021

Modelling, Simulation, and Visualization Framework for Plant Growth & Development
Tully Yates, Charlie Hodgman, Andy Phillips, Jacob Koehler
 

C022

Life Works on AC Power
Andre Ptitsyn, Jeffrey Gimble
 

C023

Structural Representation of Signaling Pathway Based on Petri Net
Hiroshi Matsuno, Chen Li, Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano
 

C024

A likelihood ratio test
for revealing statistically significant differences
between metabolite profiles

Claudia Choi, Beatrice Benkert, Richard Münch, Dieter Jahn, Frank Klawonn
 

C025

The role of multi-protein complexes in synthetic lethality
Nolwenn Le Meur, ROBERT GENTLEMAN
 

C026

Cerebral: a Cytoscape plugin for constraint based-layout of biomolecular interaction networks using function and localization annotation.
Aaron Barsky, Jennifer Gardy, Robert Hancock, Tamara Munzner
 

C027

GPCR signaling architecture of mammalian immune cells
Natalia Polouliakh
 

C028

LifeExplorer : a visualization tool for molecular and synthetic biology
Damien Larivière, Eric Fourmentin
 

C029

Motif decomposition of the pY proteome reveals a new N-terminal binding motif for SHIP2
Martin Lee Miller, Stefan Hanke, Matthias Mann, Anders Hinsby, Carsten Friis, Søren Brunak, Nikolaj Blom
 

C030

PATIKAweb v2.0: An improved Web service for querying, visualizing and analyzing a pathway database
Ozgun Babur, Ahmet Cetintas, Recep Colak, Emek Demir, Ugur Dogrusoz, E.Zeynep Erson
 

C031

Peptide separation prediction: A new kernel-based approach for computational proteomics
Nico Pfeifer
 

C032

Finding genes involved in plants response to drought
Maital Ashkenazi
 

C033

Statistical interpretation of the interplay between noise and chaos
Kamil Erguler, Michael Stumpf
 

C034

Complexes Interfaces of Human Hub Proteins: insights into SNPs and Variants association.
Luis Pera Fernandes, Franca Fraternali
 

C035

A resolution sweep approach to query-driven biclustering in microarray data
Thomas F.E. Dhollander, Qizheng Sheng, Karen Lemmens, Bart De Moor, Kathleen Marchal, Yves Moreau
 

C036

MicroRNA-mediated Feedback and Feedforward Loops are Recurrent Network Motifs in Mammals
John Tsang, Jun Zhu, Alexander van Oudenaarden
 

C037

A Priori Integration of Gene Network Knowledge Into Microarray Analysis
Franck Rapaport, Andrei Zinovyev, Emmanuel Barillot, Jean-Philippe Vert
 

C038

Web-based applications for building, managing and analyzing cellular network models
Dong-Yup Lee, Rajib Saha, Wonjun Park, I.A. Karimi
 

C039

Free-Scale and Multi-Layer Phylogenetic Profiling Approach to Generate Functional Linkage Map of RNAs and Proteins
Nozomu Yachie, Hiroyuki Nakamura, Junichi Sugahara, Rintaro Saito, Masaru Tomita
 

C040

A kinetic core model of the glucose-stimulated insulin secretion network of pancreatic β-cells
John M Hancock, Nan Jiang, Roger Cox, John Hancock
 

C041

Construction and simulation of local sparse networks identifies putative therapeutic intervention points.
Harri T Kiiveri, David Mitchell, Bill Wilson
 

C042

Gene Network Interconnectedness and the Generalized Topological Overlap Measure
Andy M Yip, Steve Horvath
 

C043

Pig mitochondrial EST analysis reveal novel expression patterns and hundreds of polymorphisms
Karsten Scheibye-Knudsen, Merete Fredholm, Susanna Cirera, Jan Gorodkin, Mike Gilchrist
 

C044

Signal integration in the transcriptional regulatory networks of E. coli and S. cerevisiae
Illes J Farkas, Ivet Bahar, Qasim K. Beg, Chuang Wu, Chakra Chennubhotla
 

C045

Learning gene regulatory networks in Arabidopsis thaliana
Chris J Needham, James Bradford, Andrew Bulpitt, Phil Gilmartin, Iain Manfield, David Westhead
 

C046

Flux minimization analysis: gene downregulation indicates hierarchical control of metabolic fluxes
Rogier JP van Berlo, Marcel Reinders, Walter van Gulik, Dick de Ridder, Rogier van Berlo
 

C047

Construction and Analysis of Protein-Protein Interaction Network of Aspergillus fumigatus
Alper Soyler, Tolga Can, Zumrut B. Ogel
 

C048

A Comprehensive Map of Protein Interactions Regulating RB Activity
Laurence Calzone, Andrei Zinovyev, François Radvanyi, Emmanuel Barillot, Amelie Gelay
 

C049

Estimating Nested Effect Models from Secondary Intervention Effects in Microarray Data
Holger Froehlich, Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beissbarth
 

C050

Analysis of gene expression data on metabolic networks
Anna-Lena Kranz, Marcus Oswald, Thorsten Bonato, Hanna Seitz, Gerhard Reinelt, Heiko Runz, Johannes Zschocke, Roland Eils, Rainer König
 

C051

Analysis of gene regulation in Duchenne Muscular Dystrophy by Petri net modelling
Ina Koch, Stefanie Grunwald, Astrid Speer, Jörg Ackermann
 

C052

Modularisation of biochemical networks by clustering of Petri net t-invariants
Ina Koch, Eva Grafahrend-Belau, Falk Schreiber
 

C053

A new, adaptive binning algorithm for NMR metabolomics
Tim De Meyer, Davy Sinnaeve, Sofie Bekaert, Elena Tsiporkova, José Martins
 

C054

SIPDAR: A Service prototype for Integration of biological Pathway Database, retrieval And pathway Reconstruction on the Web
Taesung Jung, Wan-Sup Cho
 

C055

Integrating an Ensemble of Distributed Biochemical Network Models
Shiva Ayyadurai
 

C056

Automated image analysis for high throughput cell-based microscopy assays using R and Bioconductor
Oleg Sklyar, Wolfgang Huber
 

C057

GraphCrunch: A Tool for Large Network Analysis
Tijana Milenkovic, Natasa Przulj, Jason Lai
 

C058

E-Cell 3D: 3-dimensional visulization of cellular simulation results
Kazuharu Arakawa, Nozomu Yachie, Masaru Tomita
 

C059

Informatics strategies for phenotype characterization using lipid pathways
Laxman Rao Yetukuri, Mikko Katajamaa, Tuulikki Seppänen-Laakso, matej Ore?ič, Gema Medina-Gomez, Antonio Vidal Puig
 

C060

DYNAMIC NETWORK TOPOLOGY CHANGES AS RESULT OF CELLULAR STRESS
Gopalacharyulu V Peddinti, Vidya Velagapudi, Erno Lindfors, Eran Halperin, Matej Oresic
 

C061

Genomewide analysis of Dynamical genetic network of Escherichia coli
Yung-Hao Wong, Hsien-Da Huang, Ching-Ping Tseng
 

C062

Hysteresis analysis for the dynamic model of the nitrogen assimilation system in E. coli
Koichi Masaki, Hiroyuki Kurata
 

C063

Discovery of Auto-Regulatory Feed-Back Loops involving Micro-RNAS and Transcription Factors
Veronique Lisi, François Major
 

C064

Duplicate genes with different network roles contribute to genetic robustness differently
Bing Liu, Xingpeng Jiang, Bing Liu, Jiefeng Jiang, Tianzi Jiang, Huizhi Zhao, Jing Zhang, Wenhai Chen
 

C065

The human orthologs of the E.coli indispensable genes in the metabolic network are more stable
Bing Liu, Huizhi Zhao, Bing Liu, Tianzi Jiang, Xingpeng Jiang, Jing Zhang, Wenhai Chen
 

C066

Module network ensembles for reverse engineering transcription regulatory networks
Tom Michoel, Anagha Joshi, Steven Maere, Eric Bonnet, Yves Van de Peer
 

C067

IDENTIFICATION OF NEW AP-2 REGULATED GENES: A BIOLOGICAL AND BIOINFORMATIC APPROACH
Francesca Orso, Davide Corà, Elisa Penna, Daniela Cimino, Michele De Bortoli, Daniela Taverna, Michele Caselle
 

C068

Exploring human SH2 mediated interactomes
Lars Kiemer, Michele Tinti, Gianni Cesareni, Martin Miller, Soren Brunak
 

C069

Identification of overlapping biclusters using probabilistic relational models, applied to simulated gene expression data.
Tim Van den Bulcke, Hui Zhao, Kristof Engelen, Bart De Moor, Kathleen Marchal
 

C070

CPAT: Cellular Pathway Analysis Tool
Abhishek Pratap, Prateek Singh, Arnold Emerson
 

C071

Detecting functional and evolutionary relationships by aligning protein interaction networks
Michal Kolár, Michael Lässig, Johannes Berg
 

C072

A prototype platform for flexible comparison analyses of interactions and pathways
Hiroshi Fukagawa, Wataru Iwasaki, Toshihisa Takagi
 

C073

Cell System Markup Language CSML 3.0 Enhanced with System Dynamics Ontology and Its Application to Cell Illustrator 3.5
Satoru Miyano Miyano, Euna Jeong, Atsushi Doi, Kazuko Ueno, Emi Ikeda, Kaname Kojima, Ayumu Saito, Masao Nagasaki
 

C074

DYNAMIC PATTERNS SEARCH AND BAYESIAN INFERENCE OF TRANSCRIPTIONAL NETWORKS
Barbara Di Camillo, Gianna Toffolo, Claudio Cobelli
 

C075

Characterization of Networks Using Probabilistic Sequences of Subgraphs
Koenraad Van Leemput, Bart Naudts, Kris Laukens, Alain Verschoren, Piet van Remortel
 

C076

PRISM: A Web Server for Prediction and Visualization of Protein-Protein Interactions
Nurcan Tuncbag, Emre Guney, Mehmet Cengiz Ulubas, Ozlem Keskin, Attila Gursoy
 

C077

Logical Modelling of the Budding Yeast Cell Cycle Network
Adrien Fauré, Claudine Chaouiya, Andrea Ciliberto, Denis Thieffry
 

C078

Unveiling combinatorial transcriptional regulation using microarray and motif compendia
Karen Lemmens, Tijl De Bie, Thomas Dhollander, Kristof Engelen, Bart De Moor, Kathleen Marchal
 

C079

Dynamics on ?signed motifs? in a Yeast Gene Network
Alberto de la Fuente, Enrico Pieroni, Fabio Maggio, Giorgio Fotia, Gianmaria Mancosu
 

C080

Modeling and visualization of cell/tissue type relationships
Larisa Kiseleva, Paul Horton
 

C081

Inference and structural analysis of a Yeast Gene Network
Gianmaria Mancosu, Giorgio Fotia, Enrico Pieroni, Fabio Maggio, Alberto de la Fuente
 

C082

Construction of biological pathways on the basis of literature available on MEDLINE by using natural language processing technology
Tatsuya Kushida, Yoshiyuki Kobayashi, Takao Asanuma, Yo Shidahara, Jun?ichi Tsujii, Toshihisa Takagi
 

C083

Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)
Chi-Ying F. Huang, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung , Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen, Gen-Cher Lee, D. T., Yow-Ling Shiue, Chang-Wei Yeh, Chao-Hui Chang, Cheng-Yan Kao , Chi-Ying F.
 

C084

Mutually exclusive binding in protein interaction networks
Konstantinos Mitsopoulos, Marketa Zvelebil
 

C085

Integration of an Arabidopsis thaliana TAP/MS protein identification dataset into a cell cycle protein-protein interaction network.
Kim Henderickx, Erwin Witters, Dominique Eeckhout, Hilde Stals, Jelle Van Leene, Filip Lemière, Koenraad Van Leemput, Alain Verschoren, Geert De Jaeger , Kris Laukens
 

C086

MetabolomeExplorer: Inferring Metabolic Networks From High Resolution Mass Spectrometry Data
Richard A Scheltema, Frans Stellaard, Ritsert Jansen, Michael Barrett, Rainer Breitling
 

C087

Gene Regulatory Network Analysis using Frequent Pattern Mining and Naïve Bayesian from Gene Expression Data
Heon Gyu Lee, Keun Ho Ryu
 

C088

Functional coupling of human gene coexpression and protein interaction networks
Carlos Prieto, Javier De Las Rivas
 

C089

Identification of Key Processes underlying Cancer Phenotypes using Biologic Pathway Analysis
Sol Efroni
 

C090

Gene Expression Patterning in Tissues - A Stochastic Approach to Test Validity of Putative Multi-Cell Gene Interaction Networks
Tim Hohm, Eckart Zitzler
 

C091

Extended Fractional Averagine Modeling and Improved Peak Identification in Mass Spectrometry Data
Bernhard Y. Renard, Marc Kirchner, Judith A. J. Steen, Hanno Steen, Fred A. Hamprecht
 

C092

EZplot, a Graph Based Tool for the Annotation and Representation of Data.
Cameron Ross MacPherson, Sebastian Schmeier, Vladimir Bajic
 

C093

BioPhenics : Therapeutic Target Identification via high-throughput cellular phenotyping
Patrick Poullet, Fanny Coffin, Isabel Brito, Philippe La Rosa, Philippe Hupé, Aurianne Lescure, Elaine Del-Nery, Philippe Benaroch, Franck Perez , Jacques Camonis, Alexandre Hamburger, Emmanuel Barillot
 

C094

Inferring biological networks with output kernel trees
Pierre Geurts, Nizar Touleimat, Marie Dutreix, Florence d'Alche-Buc
 

C095

ClueGene - Recommending pathway genes using a compendium of clustering solutions
Marcos H Woehrmann, David Ng, Josh Stuart
 

C096

Comparing Organisms Based on Metabolic Capabilities
Sebastian Oehm, Alexander Goesmann
 

C097

S. cerevisiae Mitochondria: Validating Predictions from Microarray Integration
Curtis Huttenhower, David Hess, Amy Caudy, Olga Troyanskaya
 

C098

Coordinated Meso-Dynamics: A method for visualizing molecular pathway models in a stochastic, spatial and particle-based manner
Antonio Carlos Mora-Ortiz, Ian Donaldson, Antonio Mora-Ortiz
 

C099

GOAna: Assessing upstream events in gene expression microarray experiments using Gene Ontology
Daniela Eggle, Thomas Zander, Benedikt Brors, Julia Driesen, Svenja Debey-Pascher, Roland Eils, Joachim L. Schultze
 

C100

From Computational Linguistics to Systems Biology
Daniel A Jacobson, Junaid Gamieldien, Darren Otgaar
 

C101

Improving Estimation of In Vitro HIV-1 Virus Fitness by Linear Regression Methods
Jingming Ma
 

C102

Temporal and modular organization in the D. melanogaster transcriptional program
Ana Paula Leite, Aviv Regev
 

C103

MeltDB: A Framework for Metabolomic Experiment Analysis and Integration
Heiko Neuweger, Jens Stoye, Alexander Goesmann, Karsten Niehaus, Tony Watt
 

C104

Mathematical Modeling of the Transcriptional Network Controlling the Environmental Stress Response in Saccharomyces cerevisiae
Kam D Dahlquist, Nathan Wanner, Erika Camacho
 

C105

Linking Chemical and Genomic Information: Chemoinformatics Classification of Enzyme Function
Diogo A.R.S. Latino, João Aires-de-Sousa
 

C106

eXpanda: an integrated platform for network analysis and visualization
Hiroyuki Nakamura, Yoshiteru Negishi, Haruna Imamura, Nozomu Yachie, Rintaro Saito, Masaru Tomita
 

C107

The representation of metabolic reaction systems using object bipartite graphs and associated matrices
James Joseph Connolly
 

C108

Extraction of Groups of Related Metabolic Reactions from Microarray Experiment Data
Adam Podhorski, Elizabeth Guruceaga, Victoriano Segura, Jose Luis Sevilla, Iera Loinaz, Angel Rubio
 

C109

A within-species comparison of metabolic networks
Miranda Daniёlle Stobbe, A.H. van Kampen, P.D. Moerland
 

C110

Clustering biochemical networks using experimental data
Kyongryun Lee, Michael Lawrence, Julie Dickerson
 

C111

Electrical Circuit Analysis of Expression Quantitative Trait Loci
Silpa Suthram, Andreas Beyer, Trey Ideker
 

C112

SBML Level 2 Version 3
Michael Hucka, Andrew Finney, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère
 

C113

Mathematica Platforms for Systems Biology Modeling: MathSBML and xCellerator
Bruce E Shapiro, Michael Hucka, James Lu, Eric Mjolsness
 

C114

Gene Network-based Analysis for Microarray Time Course data in Multiple Biological Conditions
Zhi Wei, Hongzhe Li
 

C115

Mining Homologous Genomic Segments (HGS) using related prokaryotic fully sequenced genomes
Eduardo Righi Capanema
 

C116

A hybrid computational-experimental approach for mapping the global yeast genetic interaction network
Chad L Myers, Michael Costanzo, Anastasija Baryshnikova, Huiming Ding, Olga Troyanskaya, Charles Boone
 

C117

Quantitative Modeling of the Asymmetric Cell Division Cycle in Caulobacter crescentus
Paul Brazhnik, Shenghua Li, John Tyson
 

C118

Beyond Epistasis Analysis: Combinatorial Perturbation Analysis by Dynamic Modeling
Sven Nelander, Peter Gennemark, Solmaz Shahalizadeh, Chris Sander
 

C119

Paxtools: A software library for accessing and analyzing biological pathway information
Emek Demir, Ken Ichiro Fukuda, Toshihisa Takagi, Chris Sander
 

C120

Deciphering breast cancer metastasis using protein networks
Han-Yu Chuang, Eunjung Lee, Doheon Lee, Trey Ideker
 

C121

Integrating Evidence of Essential Genes from Metabolic and Protein Network Analysis
Noppadon Khiripet
 

C122

Mining expression-dependent modules in the human interaction network
Elisabeth Georgii, Sabine Dietmann, Koji Tsuda
 

C123

MEGU: Pathway mapping web-service based on KEGG and SVG
Nobuaki Kono, Kazuharu Arakawa, Masaru Tomita
 

C124

BioPAX - A Community Standard for Pathway Data Sharing
BioPAX Workgroup
 

C125

Detection of functional modules in graphs depend on a linearisation of the biochemical network
Noriko Hiroi, Torbjörn Nordling, Akira Funahashi, Hiroaki Kitano
 

C126

Semantic annotation of kinetic models in Systems Biology
Nicolas Le Novere, Camille Laibe, Melanie Courtot, Christian Knuepfer, Michael Hucka
 

C127

Reconstruction of Mammalian Cell Cycle Regulatory Network from Microarray Data using Stochastic Logical Networks
Bartek Wilczynski, Bartek Wilczyński, Jerzy Tiuryn
 

C128

An integrative scoring scheme for protein identification in tandem mass spectrometry experiments
Smriti R Ramakrishnan, Christine Vogel, John T. Prince, Zhihua Li, Edward M. Marcotte, Daniel P. Miranker
 

C129

Non-Genetic Individuality in the Host-Phage Interaction
Sivan Pearl, Chana Gabay, Nathalie Balaban, Amos Oppenheim-~--
 

C130

Edinburgh Pathway Editor - a visualization tool for biological pathways
Richard R Adams
 

C131

ANNOTATION BASED DISCOVERY OF TEMPORAL PATTERNS IN GENE EXPRESSION STUDIES
Barbara Di Camillo, Gianna Toffolo, Claudio Cobelli
 

C132

Systematic Discovery of In Vivo Phosphorylation Networks
Rune Linding, Lars Juhl Jensen, Gerry Ostheimer, Rob Russell, Peer Bork, Mike Yaffe, Tony Pawson
 

C133

Novel In Silico Methods to Study and Anticipate Drug-drug Interactions
C. Anthony Hunt, Tai Lam
 

 

 

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