GCB 2010
Call for Papers
Invited Speakers
Submission
Registration
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Accomodation
Social Event
Organisers
Program
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and Sponsors
Conference
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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
| 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 | |
| P1 | Schumann et al. | Synchronisation of clocks Comparing mechanisms in biological and technical distributed systems |
| P2 | Gernert et al. | SignalNet Looking at signaling networks from quantitative proteome data |
| P3 | Ante et al. | Filtering networks with gene expression data - How much tissue-specificity is retained by including the network neighborhood? |
| P4 | Hollunder et al. | DASS-GUI – a new data mining framework |
| P5 | Dröge et al. | Evolution of Neuroglobin |
| P6 | Schmidt-Heck et al. | Ensemble Learning of Gene Regulatory Networks in E. coli under recombinant protein production conditions |
| P7 | Rücker et al. | A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network |
| P8 | Philippi et al. | Different road blocks on the route to apoptosis modelled for fibroblasts, epithelial cells and cytomegalovirus |
| P9 | Stelzer et al. | Construction of an integrated biochemical reaction database |
| P10 | Chang et al. | The BRENDA Enzyme Information System in 2010 Advancement in the Database Content and Online Tools |
| P11 | Söhngen et al. | BRENDA text-mining enzyme-related disease information from the scientific literature |
| P12 | Sperschneider et al. | DotKnot heuristic pseudoknot prediction using the probability dot plot |
| P13 | Rex et al. | Automated creation of simulation-ready Metabolic Models |
| P14 | Rother et al. | ModeRNA A new tool for RNA 3D structure prediction |
| P15 | Engel et al. | Functional and phylogenetic evaluation of codon usage bias |
| P16 | Quester et al. | EnzymeDetector integrated enzyme function prediction tool |
| P17 | Lang et al. | GapFiller – a tool for the identification of missing enzymes in biochemical pathways |
| P18 | Joseph et al. | Protein structural comparison using a structural alphabet |
| P19 | Nöhen et al. | Building a Petri net from a metabolic subnetwork of Arabidopsis thaliana |
| P20 | Childs et al. | mRNA structural effects on translation initiation and efficiency in bacteria |
| P21 | Leha et al. | Correlating Survival Times with Gene Expression Data in Interim Analyses |
| P22 | Sun et al. | The Complexity of Gene Expression Dynamics Revealed by Permutation Entropy |
| P23 | Aschoff et al. | Defining Control and Function of Alternative Splicing During Tumorigenesis |
| P24 | Byl | Development of a tool for identifying tumoras sociated autoantibodies |
| P25 | Schmitz et al. | The role of microRNAs in malignant melanoma progression |
| P26 | Heinke et al. | Energy based Prediction and Comparison of Protein Structure |
| P27 | Xiang et al. | New computational pipeline to analyze reverse phase protein array data from adult rats exposed to cigarette smoke |
| P28 | Mosisch et al. | Molecular side-chain optimisation of glucose-6-phosphate dehydrogenase for industrial use |
| P29 | Eichborn et al. | PROMISCUOUS A resource to explore drug-target relationships |
| P30 | Woelke et al. | Defining the interaction strength between immune receptors and their ligands used in agent-based modeling |
| P31 | Lustrek et al. | Epitope Prediction Based on Peptide Array Data102 |
| P32 | Peter et al. | Evolutionary Fate of Minor-type Spliceosomal Introns among Insecta |
| P33 | Glaab et al. | EnrichNet network-based gene set enrichment analysis |
| P34 | Bartsch et al. | GeneReporter – Sequenced based literature mining and annotation |
| P35 | Hummel et al. | The Golm Metabolome Database featuring decision-tree-supported substructure prediction of metabolites from GC-MS profiles |
| P36 | Kleessen et al. | Towards transcriptomic markers for drought tolerance in Barley |
| P37 | Ulas et al. | Genome-scale reconstruction of the metabolic network in Sulfolobus solfataricus |
| P38 | Alawi et al. | ChIP-munk an integrated software-system for the interactive analysis of ChIP-seq data |
| P39 | Kaever et al. | MarVis-Filter Interactive ranking, filtering, adduct detection, isotope correction, and molecular formula calculation in LC/MS data analysis112 |
| P40 | Poos et al. | Using ChIP-seq to identify EWS-FLI1 target genes in Ewing Sarcomas |
| P41 | Winkler et al. | ProteinReactor A novel algorithm for designing chimeric proteins |
| P42 | Grützmann et al. | The alternative messages of fungal genomes |
| P43 | Bekel et al. | MetaSAMS – Sequence Analysis and Management System for Metagenomics Datasets |
| P44 | Klein et al. | PRODORIC – a platform for the elucidation of gene regulatory networks in prokaryotes - from data to models |
| P45 | Eggeling et al. | De-novo motif discovery using parsimonious Markov models |
| P46 | Mangin et al. | Turning Dr. Jekyll into Mr. Hyde - A Genome-Scale Model To Analyse C. albicans and Host Interactions During Host Infection |
| P47 | Scheer et al. | BRENDA Map of Biochemical Reactions and Metabolic Pathways |
| P48 | Schudoma et al. | RNA 3D structure is partially determined by the local sequence context |
| P49 | Rother et al. | Lightweight techniques for developing bioinformatics software |
| P50 | Lohdi et al. | Visualizing protein coverage from multiple LC-MS/MS datasets for biotherapeutical drug characterization |
| P51 | Stutz et al. | MassCUDA High-throughput mass spectrometry analysis using Graphics Processing Units |
| P52 | Lenz et al. | Comparative analysis of miRNAs and their targets across four plant species |
| P53 | Wehner et al. | Promotor Associated RNAs in Metazoas |
| P54 | Riemer et al. | metano – A Toolkit for Metabolic Network Analysis and Optimization |
| P55 | Margraf et al. | A Pseudometric Scoring Function for Protein Structure Alignments |
| P56 | Lechner et al. | BacProt - Automated Bacterial Protein Annotation |
| P57 | Gonnella et al. | Readjoiner a space efficient string-graph based sequence assembler |
| P58 | Dötsch et al. | Whole genome pooled sequencing of clinical Pseudomonas aeruginosa genomes reveals resistance-associated mutations |
| P59 | Schweizer et al. | Structural influence of sequence variations upon inhibitor binding in the hepatitis C virus serine protease |
| P60 | Jurinovic et al. | Validation of graph inferring algorithms with emphasis on graph topology |
| P61 | Ovezmyradov et al. | Gene Ontology Annotation of Hearing |
| P62 | Ast et al. | iCHIP - integration Center for High-throughPut experiments |
| P63 | Eckstein et al. | ONTOSYNC – Synchronising biological databases and ontologies for system spanning queries |
| P64 | Bonin et al. | Identification of co-expression networks by comparison of a multitude of different functional states of genome activity |
| P65 | Wolf et al. | Global Biclustering of high throughput data |
| P66 | Geyer et al. | Bridging the Gap Linking Molecular Simulations and Systemic Descriptions of Metabolic Systems |
| P67 | Matthies et al. | Nucleic Acid Sequence Design, Newtonian Dynamics and Mean Fields |
| P68 | Schenk et al. | Protein design in probabilistic fields |
| P69 | Hoffmann et al. | Molecular dynamics simulations of DNA interactions with the SRA domain of UHRF1 |
| P70 | Herzog et al. | Benchmarking shotgun lipidomics software |
| P71 | Stein et al. | SYCAMORE - A web-based integrating systems biology's workbench |
| P72 | Choudhury et al. | Protein transmembrane regions: prediction and statistical analysis |
| P73 | Deyneko et al. | HUMAN-CHIMPANZEE PROPERTY-DEPENDANT CONSERVATION |
| 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 | ||