Overview

Monday, September 20th
Morning Session
Afternoon Session

Tuesday, September 21st
Morning Session
Afternoon Poster session (Haus der Wissenschaft, 5th floor) and Sponsor presentations ("Haus der Wissenschaft", assembly hall 3rd floor)
Evening Social Event and Conference dinner

Wednesday, September 22nd
Morning Session
Afternoon Session

Program

GCB 2010

Program

Talks will be held in the main lecture hall "Haus der Wissenschaft", assembly hall 3rd floor unless otherwise noted.
Monday, September 20th
08:00 Registration opens
09:00 Welcome - Dean of the Dept. of Life Sciences Dieter Jahn
09:05 Opening
Chair: Dietmar Schomburg
09:15 Keynote: Stefan Schuster Road games in metabolism - A biotechnological perspective
10:00 Florian Blöchl, Mara L. Hartsperger, Volker Stümpflen & Fabian J. Theis Uncovering the structure of heterogeneus biological data: fuzzy graph partitioning in the k-partite setting
10:25 Coffee break
Chair: Andrew Torda
10:55 Karsten Hiller, Christian M Metallo, Joanne K Kelleher & Gregory Stephanopoulos Stable-isotope assisted and non-targeted analysis of cellular metabolism: Generating global fingerprints of enzyme activity
11:20 Jan Budczies, Carsten Denkert, Berit M Müller, Scarlet F Brockmöller, Manfred Dietel, Jules L Griffin, Matej Oresic & Oliver Fiehn. METAtarget – extracting key enzymes of metabolic regulation from high-throughput metabolomics data using KEGG REACTION information
11:45 Katrin Bohl, Luis Filipe de Figueiredo, Oliver Hädicke, Steffen Klamt, Christian Kost, Stefan Schuster & Christoph Kaleta CASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks
12:10 Lunch Break
Chair: Jens Stoye
13:30 Keynote: Greg Stephanopoulos After a decade of systems biology, time for a record card
14:15 Steffen Klamt, Robert Flassig & Kai Sundmacher Inferring the causality structure of cellular networks using a novel variant of transitive reduction
14:40 Peter Husemann & Jens Stoye Repeat-aware Comparative Genome Assembly
15:05 Arli A. Parikesit, Peter Stadler & Sonja J. Prohaska Quantitative Comparison of Genomic-Wide Protein Domain   Distributions
15:30 Coffee break
Chair: Greg Stephanopoulos
16:00 Konrad Grützmann, Karol Szafranski, Martin Pohl, Matthias Platzer & Stefan Schuster The alternative messages of fungal genomes
16:25 Franziska Metge, Jan-Martin Josten, Federico Apelt, Maik Müller, Christoph Hartmann, Tobias von Falkenhausen, Paula Korkuc, Jana Manin & Roland Krause Context-dependent annotation of protein domains
16:50 Enrico Glaab, Jonathan M. Garibaldi & Natalio Krasnogor. Learning pathway-based decision rules to classify microarray cancer samples Learning pathway-based decision rules to classify microarray cancer samples






Tuesday, September 21st



Chair: Stefan Schuster
09:00 Keynote: Thomas Lengauer HIV Bioinformatics: Analyzing viral evolution for the benefit of AIDS patients
09:45 Juliane Klein, Korbinian Schneeberger, Stephan Ossowski, Detlef Weigel & Daniel Huson LOCAS - A Low Coverage  Assembly Tool for Resequencing Projects
10:10 Florian Battke, Stephan Körner, Steffen Hüttner & Kay Nieselt Efficient sequence clustering for RNA-seq data without a reference genome
10:35 Coffee break
Chair: Ina Koch
11:00 Andreas Gogol-Döring & Wei Chen Finding Optimal Sets of Enriched Regions in ChIP-Seq Data
11:25 Thomas Fober, Marco Mernberger & Eyke Hüllermeier Efficient Similarity Retrieval for Protein Structures based on Histogram Comparison
11:50 Antonio del Sol The New View of protein allostery:  The role of protein structure and dynamics in signaling
12:15-16:00 Buffet / Poster Session (Haus der Wissenschaft, 5. OG) / Sponsor Presentations (Haus der Wissenschaft, Aula, chaired by Dr. Maurice Scheer and Alexander Riemer)
13:00 GI Gremium (Biozentrum, BZ046)
14:00 DECHEMA Gremium (closed session,
Biozentrum BZ046)

15:00 GBM Gremium
Chair: Werner Mewes
16:00 Dietmar Schomburg Enzyme Functional Data and the Metabolic Modelling Platform
16:25 Katrin Stierand, Matthias Hilbig & Matthias Rarey The art of drawing molecular complexes
17:30 Social Event
20:00 Conference Dinner






Wednesday, September 22nd



Chair: Thomas Lengauer
09:00 Keynote: Edda Klipp Cellular stress response and regulation of metabolism
09:45 Gundolf Schenk & Andrew E. Torda Sequence optimization in probabilistic fields
10:10 Andreas Gruber, Stephan Bernhart, You Zhou & Ivo Hofacker RNALfoldz: efficient prediction of thermodynamically stable, local secondary structures
10:35 Coffee break
Chair: Erich Bornberg-Bauer
11:00 Sergiy Bogomolov, Martin Mann, Björn Voss, Andreas Podelski & Rolf Backofen Shape-based barrier estimation for RNAs
11:25 Jan Grau, Daniel Arend, Ivo Grosse, Artemis Hatzigeorgiou, Jens Keilwagen, Manolis Maragkakis, Claus Weinholdt & Stefan Posch Predicting miRNA targets utilizing an extended profile HMM
11:50 Florian Büttner, Daniel Ellwanger, Hans-Werner Mewes & Volker Stümpflen Large scale analysis reveals novel insights in the characteristics of miRNA targeting
12:15 Lunch Break
Chair: Dietmar Schomburg
13:15 Keynote: Werner Mewes The data deluge: can simple models explain complex biological systems?
14:00 Syed Asad Rahman, Janet M. Thornton EC-­BLAST-­Looking beyond sequence similarity
14:30 Poster Award
ca. 15:00 End of the Conference






List of Posters

P1Schumann et al. Synchronisation of clocks Comparing mechanisms in biological and technical distributed systems
P2Gernert et al. SignalNet Looking at signaling networks from quantitative proteome data
P3Ante et al.Filtering networks with gene expression data - How much tissue-specificity is retained by including the network neighborhood?
P4Hollunder et al.DASS-GUI – a new data mining framework
P5Dröge et al.Evolution of Neuroglobin
P6Schmidt-Heck et al.Ensemble Learning of Gene Regulatory Networks in E. coli under recombinant protein production conditions
P7Rücker et al.A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network
P8Philippi et al.Different road blocks on the route to apoptosis modelled for fibroblasts, epithelial cells and cytomegalovirus
P9Stelzer et al.Construction of an integrated biochemical reaction database
P10Chang et al.The BRENDA Enzyme Information System in 2010 Advancement in the Database Content and Online Tools
P11Söhngen et al.BRENDA text-mining enzyme-related disease information from the scientific literature
P12Sperschneider et al.DotKnot heuristic pseudoknot prediction using the probability dot plot
P13Rex et al.Automated creation of simulation-ready Metabolic Models
P14Rother et al.ModeRNA A new tool for RNA 3D structure prediction
P15Engel et al.Functional and phylogenetic evaluation of codon usage bias
P16Quester et al.EnzymeDetector integrated enzyme function prediction tool
P17Lang et al.GapFiller – a tool for the identification of missing enzymes in biochemical pathways
P18Joseph et al.Protein structural comparison using a structural alphabet
P19Nöhen et al.Building a Petri net from a metabolic subnetwork of Arabidopsis thaliana
P20Childs et al.mRNA structural effects on translation initiation and efficiency in bacteria
P21Leha et al.Correlating Survival Times with Gene Expression Data in Interim Analyses
P22Sun et al.The Complexity of Gene Expression Dynamics Revealed by Permutation Entropy
P23Aschoff et al.Defining Control and Function of Alternative Splicing During Tumorigenesis
P24BylDevelopment of a tool for identifying tumoras sociated autoantibodies
P25Schmitz et al.The role of microRNAs in malignant melanoma progression
P26Heinke et al.Energy based Prediction and Comparison of Protein Structure
P27Xiang et al.New computational pipeline to analyze reverse phase protein array data from adult rats exposed to cigarette smoke
P28Mosisch et al.Molecular side-chain optimisation of glucose-6-phosphate dehydrogenase for industrial use
P29Eichborn et al.PROMISCUOUS A resource to explore drug-target relationships
P30Woelke et al.Defining the interaction strength between immune receptors and their ligands used in agent-based modeling
P31Lustrek et al.Epitope Prediction Based on Peptide Array Data102
P32Peter et al.Evolutionary Fate of Minor-type Spliceosomal Introns among Insecta
P33Glaab et al.EnrichNet network-based gene set enrichment analysis
P34Bartsch et al.GeneReporter – Sequenced based literature mining and annotation
P35Hummel et al.The Golm Metabolome Database featuring decision-tree-supported substructure prediction of metabolites from GC-MS profiles
P36Kleessen et al.Towards transcriptomic markers for drought tolerance in Barley
P37Ulas et al.Genome-scale reconstruction of the metabolic network in Sulfolobus solfataricus
P38Alawi et al.ChIP-munk an integrated software-system for the interactive analysis of ChIP-seq data
P39Kaever et al.MarVis-Filter Interactive ranking, filtering, adduct detection, isotope correction, and molecular formula calculation in LC/MS data analysis112
P40Poos et al.Using ChIP-seq to identify EWS-FLI1 target genes in Ewing Sarcomas
P41Winkler et al.ProteinReactor A novel algorithm for designing chimeric proteins
P42Grützmann et al.The alternative messages of fungal genomes
P43Bekel et al.MetaSAMS – Sequence Analysis and Management System for Metagenomics Datasets
P44Klein et al.PRODORIC – a platform for the elucidation of gene regulatory networks in prokaryotes - from data to models
P45Eggeling et al.De-novo motif discovery using parsimonious Markov models
P46Mangin et al.Turning Dr. Jekyll into Mr. Hyde - A Genome-Scale Model To Analyse C. albicans and Host Interactions During Host Infection
P47Scheer et al.BRENDA Map of Biochemical Reactions and Metabolic Pathways
P48Schudoma et al.RNA 3D structure is partially determined by the local sequence context
P49Rother et al.Lightweight techniques for developing bioinformatics software
P50Lohdi et al.Visualizing protein coverage from multiple LC-MS/MS datasets for biotherapeutical drug characterization
P51Stutz et al.MassCUDA High-throughput mass spectrometry analysis using Graphics Processing Units
P52Lenz et al.Comparative analysis of miRNAs and their targets across four plant species
P53Wehner et al.Promotor Associated RNAs in Metazoas
P54Riemer et al.metano – A Toolkit for Metabolic Network Analysis and Optimization
P55Margraf et al.A Pseudometric Scoring Function for Protein Structure Alignments
P56Lechner et al.BacProt - Automated Bacterial Protein Annotation
P57Gonnella et al.Readjoiner a space efficient string-graph based sequence assembler
P58Dötsch et al.Whole genome pooled sequencing of clinical Pseudomonas aeruginosa genomes reveals resistance-associated mutations
P59Schweizer et al.Structural influence of sequence variations upon inhibitor binding in the hepatitis C virus serine protease
P60Jurinovic et al.Validation of graph inferring algorithms with emphasis on graph topology
P61Ovezmyradov et al.Gene Ontology Annotation of Hearing
P62Ast et al.iCHIP - integration Center for High-throughPut experiments
P63Eckstein et al.ONTOSYNC – Synchronising biological databases and ontologies for system spanning queries
P64Bonin et al.Identification of co-expression networks by comparison of a multitude of different functional states of genome activity
P65Wolf et al.Global Biclustering of high throughput data
P66Geyer et al.Bridging the Gap Linking Molecular Simulations and Systemic Descriptions of Metabolic Systems
P67Matthies et al.Nucleic Acid Sequence Design, Newtonian Dynamics and Mean Fields
P68Schenk et al.Protein design in probabilistic fields
P69Hoffmann et al.Molecular dynamics simulations of DNA interactions with the SRA domain of UHRF1
P70Herzog et al.Benchmarking shotgun lipidomics software
P71Stein et al.SYCAMORE - A web-based integrating systems biology's workbench
P72Choudhury et al.Protein transmembrane regions: prediction and statistical analysis
P73Deyneko et al.HUMAN-CHIMPANZEE PROPERTY-DEPENDANT CONSERVATION

Tuesday, 21st of September 2010
 
Chairs: Dr. Maurice Scheer & Alexander Riemer
13:00 Convey Computer Corporation / HMK Computer Technologies, Ernst Mutke: Hybrid Core Computing for High-Throughput Bioinformatics
13:30 CLC bio, Patrick Dekker: CLC Genomics Workbench dominating Next Generation Sequencing data analysis on all platforms - sequencers and computers
14:00 Biobase GmbH, Frank Schacherer: Understanding genomic variations in NGS data
14:30 GeneXplain GmbH, Alexander Kel: GeneXplain - from networks to drugs
15:00 Genomatix Software GmbH, Thomas Werner (University of Michigan, Genomatix): High-Troughput sequence analysis: from technology to functional genomics