Complete program as pdf
Proceedings as pdf
Abstract Band as pdf
Monday, September 28th
Morning Session
Afternoon Session
PC Dinner (by invitation only)
Tuesday, September 29th
Morning Session
Afternoon: Postersession
Afternoon: Sponsor presentations
Afternoon: Meetings of scientic oranizations
Conference dinner at the Moritzburg including admission to the exhibitions
Wednesday, September 30th
Morning Session
Afternoon Session
Thursday, October 1st: GCB Satellite Workshop
GCB Satellite Workshop: Data Analysis in Systems Biology
arranged by "Arbeitsausschusses Bioinformatik" and "Arbeitskreises Systembiologie" of Dechema
| Monday, September 28th | |
| Location: Auditorium Maximum (Audimax), Universitätsplatz 1 | |
| Chairs: S. Posch and J. Selbig (Morning session), S. Neumann and A. Torda (Afternoon session) |
|
| 08:00 | Registration opens |
| 09:00 | Opening (Prof. Dr. Wulf Diepenbrock, Rector of MLU) |
| 09:15 | S. Pääbo, MPI for Evolutionary Anthropology, Leipzig: A Neandertal Perspective on Human Origins (Invited talk) |
| 10:00 | R. Lorenz, C. Flamm and I. L. Hofacker: 2D Projections of RNA folding Landscapes |
| 10:30 | Coffee break (Löwengebäude) |
| 11:05 | T. Fober, M. Mernberger, R. Moritz and E. Hüllermeier: Graph-Kernels for the Comparative Analysis of Protein Active Sites |
| 11:35 | I. Wohlers, L. Petzold, F. S. Domingues and G. W. Klau: Aligning Protein Structures Using Distance Matrices and Combinatorial Optimization |
| 12:05 | T. Alexandrov: Self-taught learning for classification of mass spectrometry data: a case study of colorectal cancer |
| 12:35 | Lunch break (Mensa, Harz 42) |
| 14:00 | U. Schurr, Forschungszentrum Jülich: Phenotyping of Plants: Quantification of Structure and Function — Concepts and Infrastructure (Invited talk) |
| 14:45 | M. Haeussler, Y. Jaszczyszyn, L. Christiaen and J.-S. Joly: A cis-regulatory signature for chordate anterior neurectodermal genes (Short paper) |
| 15:05 | T. Fester, F. Schreiber and M. Strickert: CUDA-based multi-core implementation of MDS-based bioinformatics algorithms |
| 15:35 | Coffee break (Löwengebäude) |
| 16:15 | J. Perner, A. Altmann and T. Lengauer: Semi-Supervised Learning for Improving Prediction of HIV Drug Resistance |
| 16:45 | L. Royer, C. Plake and M. Schroeder: Identification of cancer and cell-cycle genes with protein interactions and literature mining |
| 17:15 | T. Ingalls, G. Martius, M. Marz and S. J. Prohaska: Converting DNA to Music: ComposAlign |
| 17:45 | Closing |
Tuesday, September 29th |
|
| Location: Auditorium Maximum (Audimax), Universitätsplatz 1 | |
| Chairs: B. Morgenstern and R. Backofen (Morning session), I. Grosse (Sponsor presentations), F. Schreiber (Public talk) |
|
| 08:00 | Registration opens |
| 08:30 | A. Graner, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben: Challenges of utilizing plant genetic resources (Invited talk) |
| 09:15 | H. Rohn, C. Klukas and F. Schreiber: Integration and Visualisation of Multimodal Biological Data |
| 09:45 | E. Gorrón, F. Rodríguez, D. Bernal, S. Restrepo and J. Tohme: A new method for the design of degenerate primers and its use to identify homologues of apomixis - associated genes in Brachiaria |
| 10:15 | Coffee break (Löwengebäude) |
| 10:55 | O. Stegle, K. Denby, D. Wild, S. McHattie, A. Meade, Z. Ghahramani and K. Borgwardt: Discovering temporal patterns of differential gene expression in microarray time series |
| 11:25 | J. Song, C.-C. Hong, Y. Zhang, L. Buttitta and B. Edgar: Comparative Generalized Logic Modeling Reveals Differential Gene Interactions during Cell Cycle Exit in Drosophila Wing Development |
| 11:55 | A. Chokkathukalam, M. Poolman, C. Ferrazzi and D. Fell: Expression profiles of metabolic models to predict compartmentation of enzymes in multi-compartmental systems |
| 12:25 | Introduction to GCB 2010 |
| 12:30 | Lunch break (Mensa, Harz 42) |
| 14:00–17:00 | Poster Session/Sponsor Presentations (Löwengebäude) |
| 14:00 | GI Gremium (Musikzimmer, Burse zur Tulpe) |
| 15:00 | GBM Gremium (Musikzimmer, Burse zur Tulpe) |
| 17:00 | Break |
| 17:30 | T. van Hintum, Centre for Genetic Resources, Wageningen: The role of bioinformatics in a global attempt to fight hunger (Invited talk, open to the public) |
| 19:00 | Social event (Moritzburg) |
Wednesday, September 30th |
|
| Location: Auditorium Maximum (Audimax), Universitätsplatz 1 | |
| Chairs: I. Koch and P. F. Stadler (Morning session), I. Grosse (Afternoon session) |
|
| 08:00 | Registration opens |
| 08:30 | D. Fell, Oxford Brookes University: Building and Analyzing Genome-Scale Models of Metabolism (Invited talk) |
| 09:15 | Z. Ouyang and M. Song: Comparative Identification of Differential Interactions from Trajectories of Dynamic Biological Networks |
| 09:45 | M. Arita: Traceable Analysis of Multiple-Stage Mass Spectra through Precursor-Product Annotations (Short paper) |
| 10:05 | Coffee break (Löwengebäude) |
| 10:45 | C. Kaleta, L. F. de Figueiredo, J. Behre and S. Schuster: EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks |
| 11:15 | M. Kronfeld, A. Dräger, M. Aschoff and A. Zell: On the Benefits of Multimodal Optimization for Metabolic Network Modeling |
| 11:45 | A. K. Dehof, A. Rurainski, H.-P. Lenhof and A. Hildebrandt: Automated Bond Order Assignment as an Optimization Problem |
| 12:15 | Lunch break (Mensa, Harz 42) |
| 13:45 | J. Lehmann, C. Eisenhardt, P. F. Stadler and V. Krauss: Novel intron positions in Drosophila are mostly caused by intron sliding and tandem duplications (Short paper) |
| 14:05 | M. Pohl, D. Holste, R. Bortfeldt, K. Grützmann and S. Schuster: Mutually exclusive spliced exons show non-adjacent and grouped patterns (Short paper) |
| 14:25 | P. Menzel, J. Gorodkin and P. F. Stadler: Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search |
| 14:55 | E. Birney, European Bioinformatics Institute: Ensembl and ENCODE: Understanding our genome and its variation (Invited talk) |
| 15:40 | Closing and Poster award |
| 16:00 | End of conference |
Thursday, October 1st: GCB Satellite Workshop |
|
| Location: Seminar Room 5.09, Institute of Computer Science, von-Seckendorff-Platz 1 |
|
| 09:00 | Introduction |
| 09:05 | M. Vingron, Berlin: Transcription factor affinity prediction: methods, statistics, and delineation of tissue specific binding sites |
| 09:40 | S. Bergmann, Lausanne: A Modular Approach for Integrative Analysis of Large-scale Gene-expression and Drug-Response Data |
| 10:15 | S. Klamt, Magdeburg: Causal modeling of cellular signaling networks: Concepts, algorithms and applications |
| 10:50 | Break |
| 11:35 | T. Höfer, Heidelberg: Two waves of T-bet: Mammalian gene networks and mathematical models |
| 12:10 | Ralf Takors, Stuttgart: Systems Biology - Aiming at Autonomous Models for Pro- and Eukaryotic Cells |
| 12:45 | A. Schuppert, Leverkusen: From -omics to clinics — the key challenge for systems biology |
| 13:20 | Lunch break |
| 14:30 | Discussion |
| 15:30 | Brief separate meetings of the DECHEMA working groups on bioinformatics and systems and sythetic biology (Rooms 1.02 and 1.03) |
| 16:30 | Closing |
| 1 | S. Schäuble, I. Heiland, O. Voytsekh, M. Mittag and S. Schuster: Modelling changes in amino acid metabolism during day-night cycles |
| 2 | I. Heiland, T. Hinze, O. Voytsekh, M. Mittag and S. Schuster: Temperature regulation of circadian rhythms |
| 3 | V. Zayats, A. Samad and R. Ettrich: Structure and functions of TRPA1 |
| 4 | S.-A. Sansone and P. Rocca-Serra: Standards and infrastructure for managing experimental metadata |
| 5 | F. Kreusch, A. Gaarz, S. Debey-Pascher and A. Staratschek-Jox: Definition of Quality Control check points critical to obtain optimal results in Microarray Data Analysis |
| 6 | T. Geyer, F. Lauck and V. Helms: The Pools-and-Proteins Approach: Dynamic Networks from Single-Molecule-Reactions |
| 7 | F. Lauck, V. Helms and T. Geyer: Graph Measures Reveal Fine Structure of Complexes Forming in Multiparticle Simulations |
| 8 | A. Hattesohl, S. Noeske, R. Bals, C. Vogelmeier and R. Koczulla: Distinguishing the exhaled breath condensates of two patient groups with an electronic nose |
| 9 | N. Kleinbölting, G. Huep, Y. Li and B. Weisshaar: Mapping of GABI-Kat Flanking Sequence Tags from A. thaliana to the TAIR9 Annotation Data Set |
| 10 | H. Mehlhorn and I. Grosse: Systematic evaluation of centroid algorithms for de-novo motif detection |
| 11 | F. Battke, S. Symons and K. Nieselt: Mayday and RLink |
| 12 | M. Beckstette, R. Homann, R. Giegerich and S. Kurtz: Acceleration of hidden Markov model based database searches with PSSM family models |
| 13 | D. Holtgraewe, T. R. Soerensen, P. Dirksen, P. Viehoever, C. Lange, H. Himmelbauer, B. Schulz and B. Weisshaar: A reliable pipeline for in silico identification of sequence polymorphisms by combining 454 and Sanger reads of sugar beet |
| 14 | F. Meyer, S. Will and M. Beckstette: An implementation of index-based bidirectional pattern search with an application to RNA structural motifs |
| 15 | C. Bannert and D. Schomburg: An automatic method to create function-specific sequence patterns for enzymes |
| 16 | K. Luck, S. Fournane, S. Charbonnier, M. Masson, B. Kieffer and G. Travé: Predicting PDZ domain - motif interaction specificities from large-scale experimental data: a comparative study |
| 17 | D. Bindreither, S. Wegenkittl, F. Auer and P. Lackner: Expert knowledge enhanced structure based profile HMMs for protein sequence families |
| 18 | M. Stelzer and D. Schomburg: Construction of an integrated biochemical reaction database |
| 19 | K. Wolff, M. Vendruscolo and M. Porto: Improving protein structure prediction using sequence-derived structure profiles |
| 20 | A. Grote, M. Scheer, A. Chang, I. Schomburg, C. Söhngen, M. Stelzer, M. Rother, J. Thiele, C. Munaretto and D. Schomburg: New features for the BRENDA enzyme information system |
| 21 | S. Mitra, M. Schubach and D. Huson: Next-Generation sequencing and Metagenomics |
| 22 | F. Teichert, J. Minning, U. Bastolla and M. Porto: High Quality Protein Sequence Alignment by combining Structural Profile Prediction and Profile Alignment using SABERTOOTH |
| 23 | T. Margraf and A. E. Torda: Better Guide Trees from Non-Metric Structural Similarity/Distance Measures |
| 24 | J. A. Ghanem, M. Guéroult, B. Heddi, M. Baaden and B. Hartmann: New insights on non-specific protein-DNA interactions: the DNase I model |
| 25 | D. Groth, S. Müller and J. Selbig: The Bioscanners project at sourceforge |
| 26 | M. Hiller, S. Findeiß, S. Lein, M. Marz, C. Nickel, D. Rose, C. Schulz, R. Backofen, S. J. Prohaska, G. Reuter and P. F. Stadler: Conserved introns reveal novel transcripts in eukaryotic genomes |
| 27 | M. Mernberger, F. Finkernagel, E. Huellermeier and G. Klebe: SEGA — A Semi-Global Approach to Graph Alignment |
| 28 | C. Jardin and H. Sticht: Dual-Specificity Phosphatases Specifically Recognise their STAT Partner |
| 29 | B.-S. Kim, J.-H. Yoon, H.-D. Joo and B.-S. Change: Development of Software System for Serological Analysis to Control Porcine Respiratory Disease Complex on a Herd level |
| 30 | P. Dirauf and H. Sticht: Molecular Dynamics of Viral Glycoproteins |
| 31 | T. Bekel, C. Ander, M. Zakrzewski, J. Stoye and A. Goesmann: MetaSAMS — Sequence Analysis and Management System for Metagenomics Datasets |
| 32 | S. Quester and D. Schomburg: EnzymeDetector: a comparison of genome annotations from common databases and an up-to-date BLAST-Search to help the user find the right annotation |
| 33 | M. Lang and D. Schomburg: GapFiller — a tool for the identification of missing enzymes in biochemical pathways |
| 34 | S. Quester, M. Scheer, M. Rother and D. Schomburg: BRAVEMAP: a tool for displaying a metabolic network and its different aspects |
| 35 | T. Luehr and D. Schomburg: MetaboliteExplorer: A GUI based program for the managment of metabolome data, their visualization and database assisted storage of metabolite libraries |
| 36 | J. Schneider, E. Trost, A. Tauch and A. Goesmann: Reconstructing metabolic networks in silico using CARMEN |
| 37 | M. Zakrzewski, A. Schlüter, F. Tille, W. Gerlach, J. Stoye and A. Goesmann: Computational tools for the integration and analyses of metagenome data |
| 38 | D. Langenberger, S. Hoffmann, C. Bermudez-Santana and P. F. Stadler: Classification and identification of non-coding RNAs using High Throughput Sequencing Data |
| 39 | K. Klotzbücher, Y. Kobayashi, N. Shervashidze, K. Borgwardt and D. Weigel: A flowering-time gene network model for association analysis in Arabidopsis thaliana |
| 40 | P. Gellert, S. Uchida and T. Braun: Systematically Screening for Tissue-Specific Alternative Splicing: heart as an example |
| 41 | M. Bruckskotten, M. Looso, A. Konzer, F. Cemic and T. Braun: A Gene Ontology based analysis of high-throughput data via a multivariate approach |
| 42 | A. R. Gruber, S. Findeiß, S. Washietl, I. L. Hofacker and P. F. Stadler: RNAz 2.0: improved noncoding RNA detection |
| 43 | M. Fasold, P. F. Stadler, S. Preibisch and H. Binder: The 'GGG'-bias of Microarray Data — Analysis and Correction |
| 44 | M. Fasold and H. Binder: The 3'-bias of expression values and RNA degradation — quality control and correction in microarray analysis |
| 45 | T. Ulas and D. Schomburg: Reconstruction, modeling and analysis of Sulfolobus solfataricus metabolism |
| 46 | C. Bodenstein, B. Knoke, M. Marhl, M. Perc and S. Schuster: Calcium Oscillations and Jensen's Inequality |
| 47 | H. Wirth, H. Binder, M. von Bergen and A. Oberbach: Combining the "OMICS": Integrative analysis of proteomics and targeted metabolomics data improves the resolution of classification markers of obesity |
| 48 | L. Kapsokalivas, A. Albrecht and K. Steinhofel: Uphill Unfolding of Native Protein Conformations |
| 49 | P. Schwientek: RepFish: A program for guided repeat-finishing of genome-scale shotgun sequencing projects |
| 50 | H. Brinck, F. Domurath and V. Tischler: Modelling of ADP-induced Platelet Activation |
| 51 | S. Grosser, C. Schroeder, C. Bleidorn, D. Groth, R. Tiedemann, J. Selbig and S. Hartmann: Harnessing the phylogenetic signal in mobile elements to understand the evolution of fin-footed marine mammals |
| 52 | V. Shelest, E. Fazius, D. Albrecht and E. Shelest: Two novel tools for promoter analysis |
| 53 | M. Gerlich and S. Neumann: Workflow-based Integration of Metabolite Identification |
| 54 | N. Bernhardt, S. Grosser, F. Hollandt, K. Kruse and H. Seichter: Evolution across Scales: enhancing evolutionary thinking and knowledge in the biosciences |
| 55 | H. Gundlach, G. Haberer, M. Spannagl and K. F. X. Mayer: Transposons Shape the Architecture of Plant Genomes |
| 56 | T. Bonfert, R. Rupp and D. Huson: Phylogenetic networks from multilabeled trees |
| 57 | C. Kuhl and S. Neumann: Automatic annotation of metabolomic ESI-LC/MS Data with CAMERA |
| 58 | M. Martis, H. Gundlach, K. F. X. Mayer, S. Taudien, H. Simkova, P. Suchankova, J. Dolezel, N. Stein, U. Scholz, B. Steuernagel, A. Graner, T. Wicker, A. Petzold, M. Felder and M. Platzer: Unraveling the Barley Genome from Short Sequence Reads |
| 59 | S. Kleessen, D. M. Riaño-Pachón, P. Durek, J. Neigenfind, W. Engelsberger, D. Walther, J. Selbig, W. Schulze and B. Kersten: Protein phosphorylation patterns affected by nuclear DNA polymorphisms in a genome-wide scale in Arabidopsis |
| 60 | S. Wolf and S. Neumann: MetFrag — Match Predicted Fragments with Mass Spectra |
| 61 | S. Boldt, K. Knops, R. Kriehuber and O. Wolkenhauer: A Data Analysis Workflow for the Identification of Expression Signatures Functioning as Molecular Biodosimeters |
| 62 | R. Wagner, P. Durek and B. Kersten: GABI GAIN: Data Integration in Genomics-based Plant Breeding |
| 63 | A. Herbig and K. Nieselt: Characterisation of non-coding RNAs and RNA-RNA interactions in S. coelicolor |
| 64 | B. Schau, T. Hinze, T. Lenser, I. Heiland and S. Schuster: Control System-Based Reverse Engineering of Circadian Oscillators |
| 65 | M. Cserzo, G. Turu, P. Varnai and L. Hunyady: Assemblies of Uncommon DNA Patterns at the Transcription Start Sites of Genes in Human and Mouse Genomes |
| 66 | D. Boronczyk, Y. Pöschl, I. Grosse and S. Neumann: Exploiting the Characteristics of Metabolomics Data |
| 67 | S. Kalyoncu, O. Keskin and A. Gursoy: Interaction prediction and classification of PDZ domains |
| 68 | K. Faber, K.-H. Glatting, A. Risch and A. Hotz-Wagenblatt: A pipeline to identify SNPs causing variation in the splicing pattern |
| 69 | J. Behre, R. Samaga, S. Klamt and S. Schuster: Structural Modelling of Signal Transduction in Hepatocytes exemplified by the Insulin Network |
| 70 | T. Schmutzer, U. Scholz, N. Stein, C.-C. Schön, G. Haseneyer, E. Bauer, K. F. X. Mayer and M. Seidel: Exploring the Genomic Diversity in Rye Using a SNP Detection Pipeline |
| 71 | A. Hartmann, T. Czauderna and F. Schreiber: Automated data acquisition and image processing for high-throughput phenotyping of barley |
| 72 | R. Basekow, J. Neigenfind, A. Nagel, C. Gebhardt and B. Kersten: ConquestExplorer — a genomic and phenotypic Data Repository and Processing Tool towards Omics Data |
| 73 | M. Pohl, D. Holste, K. Grützmann, R. Bortfeldt and S. Schuster: Mutually exclusive spliced exons show non-adjacent and grouped patterns |
| 74 | K. Grützmann, M. Pohl, K. Szafranski and S. Schuster: Towards a workflow of cross-species analysis of alternative splicing — A case study of the fungal domain |
| 75 | M. Lange, M. Weißbach, M. Klapperstück, S. Flemming and U. Scholz: The LAILAPS Search Engine: A Text Index Infrastructure for Relevance Ranking over Life Science Database Entries |
| 76 | D. Misiak, S. Posch, N. Stöhr, S. Hüttelmaier and B. Möller: Automatic Detection of Fluorescence Labeled Neurites in Microscope Images |
| 77 | R. Marin and J. Vanicek: MicroRNA target prediction improved by RNA secondary structure calculations |
| 78 | A. K. Dehof, L. Marsalek, I. Georgiev, D. Stoeckel, S. Nickels, H.-P. Lenhof, P. Slusallek and A. Hildebrandt: Interactive real time ray tracing in Molecular Visualization |
| 79 | J. Engelhardt, P. F. Stadler and K. Reiche: SoupViewer — efficient analysis of large cluster trees |
| 80 | L. Kaderali, E. Dazert, B. Knapp, N. A. Kiani, M. Frese, U. Zeuge, R. Bartenschlager: Reverse Engineering of Signaling Pathways from RNAi Data |
| 81 | N. Hoffmann, M. Wilhelm and J. Stoye: Maltcms — an Application Framework for Processing of Metabolomics-Data |
| 82 | M. Kircher, U. Stenzel and J. Kelso: IBIS — Improved base calling for the Illumina Genome Analyzer |
| 83 | J. Mazur, D. Ritter, G. Reinelt and L. Kaderali: Reverse Engineering of Gene Regulatory Networks with a Nonlinear ODE-Model Embedded into a Bayesian Framework |
| 84 | C. Bielow, S. Aiche, S. Andreotti, A. Bertsch, C. Gröpl, R. Hussong, N. Pfeifer, M. Sturm, A. Zerck, A. Hildebrandt, K. Reinert and O. Kohlbacher: OpenMS — An Open Source Framework for Mass Spectrometry Data |
| 85 | J. Brücker, P. F. Stadler and H. Binder: Adequate Usage of Affymetrix' background probes on Exon and Gene 1.0 ST arrays |
| 86 | A. Thormann, K. Rudolph and I. Koch: TInA (T-Invariant Analysis) A Tool Box for Exploring Pathways in Biochemical Systems at Steady State |
| 87 | M. Schaefer and M. A. Andrade-Navarro: Evidence for a functional role of CAG/glutamine repeats |
| 88 | K. Lotz, F. Schreiber and R. Wünschiers: Nutrilyzer — a Tool for Deciphering Atomic Compositon of Differentially Expressed Orthologous Proteins |
| 89 | A. Donath, F. Externbrink, F. Jühling, M. Bernd, M. Middendorf and P. F. Stadler: Improved Automatic Annotation of Metazoan Mitochondrial Genomes |
| 90 | C. Göbel, K. Feussner, A. Kaever, P. Meinicke, I. Feussner, M. Landesfeind and B. Morgenstern: Identifying metabolic markers of Verticillium longisporum infection by means of one-dimensional self-organizing maps |
| 91 | H.-M. Lee, K.-J. Dietz and R. Hofestaedt: Prediction of reversibly oxidized proteins in human tissue and organelle |
| 92 | B. Sommer, T. Dingersen, S. Schneider, S. Rubert and C. Gamroth: CELLmicrocosmos 2.2: Advancements in Modeling of three-dimensional PDB Membranes |
| 93 | C. Schudoma, P. May and D. Walther: Modeling RNA loops based on sequence homology and geometric constraints |
| 94 | L. Childs, Z. Nikoloski, P. May and D. Walther: Identification and classification of ncRNA molecules using graph properties |
| 95 | J. Neigenfind, J. Huege, J. Kopka, O. Ebenhoeh, M. Hagemann, J. Selbig and B. Kersten: Inference of Synechocystis sp. strain PCC 6803's carbon metabolism using elementary modes |
| 96 | K. Strassburg, P. Durek, J. Kopka and D. Walther: Application of Granger causality testing to the detection of cause-effect relationships between metabolites and transcripts in yeast adapting to temperature stress |
| 97 | S. Steinbiss, G. Gremme, C. Schaerfer, M. Mader and S. Kurtz: The AnnotationSketch genome annotation drawing library |
| 98 | F. Wessely, C. Kaleta and S. Schuster: Flux Coupling Analysis meets Gene Expression Analysis |
| 99 | S. Andorf, J. Selbig, T. Altmann, H. Witucka-Wall and D. Repsilber: A systems biological approach to heterosis: Analysis of molecular network structures in Arabidopsis thaliana |
| 100 | N. Melzer, D. Wittenburg and D. Repsilber: A simulation approach to analyse genotype-phenotype-mapping via the metabolome level |
| 101 | A. Thormann, A. Rasche, R. Herwig: Composition and Characterization of a Type 2 Diabetes Mellitus Topological Model |
| 102 | L. Zhu, P. F. Stadler and A. Mosig: fragrep3: Combining fragmented sequence homology with secondary constraints for annotating non-coding RNA |
| 103 | M. Naseem, N. Philippi and T. Dandekar: Dynamic simulation; exploring a fit between immunity and hormones in plants |
| 104 | H. Froehlich and T. Beissbarth: Deterministic Effects Propagation Networks for Reconstructing Protein Signalling Networks from Multiple Interventions |
| 105 | E. Pairo, S. Marco and A. Perera: Transcription Factor Binding Site Detection Using Nucleotide Covariance |
| 106 | G. Petznick, S. Strunk, S. Tscherneck, P. Hammer, R. Amberg and P. Beyerlein: Analysis of A Cell Cycle Model Using the Wildau Interaction Knowledgebase WINTER |
| 107 | M. Siebauer, K. Reiche, S. Will, P. F. Stadler and R. Backofen: Efficient ncRNA gene finding: Scanning whole genomes using a fast variant of the Sankoff algorithm |
| 108 | J. Grau, C. Weinholdt, D. Arend and S. Posch: Conditional profile hidden Markov models for microRNA target prediction |
| 109 | J. Grau, M. Porsch, I. Lemnian, J. Keilwagen, I. Grosse and S. Posch: Predicting nucleosome positioning from DNA sequence |
| 110 | C. Lippert, O. Stegle, S. Jegelka, Y. Altun and K. M. Borgwardt: Predicting related traits from SNP markers by multi-task learning |
| 111 | J. Keilwagen, J. Grau, S. Posch, M. Strickert and I. Grosse: GenDisMix: combining generative and discriminative learning approaches for the recognition of sequence motifs |
| 112 | R. Amberg, A. Auner, P. Hammer, G. Petznick and P. Beyerlein: Agnostic RNA-seq Transcriptome Analysis for Quantification of Gene and Transcript Expression |
| 113 | A. Tillich, S. Pallartz, R. Amberg, P. Hammer, G. Petznick and P. Beyerlein: HMM based Identification of Polyglutamin-Islands |
| 114 | Y. Pöschl, C. Delker, M. Quint and I. Grosse: Using micro arrays to detect natural variation in hormone induced expression changes |
| 115 | J. Keilwagen, J. Baumbach, T. Kohl and I. Grosse: MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations |
| 116 | J. Keilwagen, J. Grau, S. Posch and I. Grosse: How to assess de-novo motif discovery approaches? |
| 117 | C. Bermudez-Santana, C. S.-O. Attolini, T. Kirsten, S. J. Prohaska, S. Steigele, J. Engelhardt and P. F. Stadler: tRNA Cluster |
| 118 | U. Stenzel: Rapid and Accurate Semi-Global Alignment of Diverged Sequencing Reads |
| 119 | J. Keilwagen, J. Grau, S. Posch and I. Grosse: Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis |
| 120 | M. Gleditzsch, S. Posch and I. Grosse: Combining Phylogenetic Footprinting with Realistic Motif Models |
| 121 | S. Diehl, H. Blankenburg, F. Ramírez, I. Wörz, T. Lengauer, R. Bartenschlager and M. Albrecht: Functional Characterization of Hepatitis C Virus Host Factors identified by RNA Interference |
| 122 | S. Roessner: Crows Nest, a synteny driven plant comparative genome framework component |
| 123 | R. Herzog, D. Schwudke, M. Schroeder and A. Shevchenko: LipidX: a truly platform independent lipid analysis suite |
| 124 | F. Krull, M.-H. Chae and E.-W. Knapp: Scoring geometries of protein-protein complexes |
| 125 | K.-M. Meiß, W. Eisenberg and S. Fiedler: Modelling of Biotechnological Processes |
| 126 | M. Matthies, S. Bienert and A. E. Torda: RNA Sequence Design, Newtonian Dynamics and Mean Fields |
| 127 | S. Möller, H. N. Krabbenhöft, A.-K. Grimm, B. Bauer and S. Ibrahim: Expression QTL Infrastructure |
| 128 | K. Kolczyk, S. Mirschel, M. Rempel and E. D. Gilles: Modular Modeling with ProMoT in Systems Biology |
| 14:00 | BIOBASE GmbH, P. Stegmaier: ExPlain tool: from TF binding sites in promoters to key nodes in signal transduction networks |
| 14:20 | Genomatix Software GmbH, K. Grote: Downstream analysis workflow of a ChIP-Seq study on the Genomatix Genome Analyzer |
| 14:40 | Illumina, Inc., D. Evers: Cancer Tumour/Normal Pair Analysis with the Illumina Genome Analyzer |
| 15:00 | Break |
| 15:10 | ClusterVision BV, A. Ziebart: ClusterVisionOS — Cluster Management Made Really Easy |
| 15:30 | MEGWARE Computer GmbH, J. Heydemüller: HPC Supercomputer aus Sachsen |
| 15:50 | Break |
| 16:00 | transtec AG, O. Tennert: transtec — 30 Years' Experience in HPC |
| 16:10 | NVIDIA Corp., T. Lanfear: High-Performance Computing with NVIDIA Tesla GPUs |
| 16:35 | Microsoft Deutschland GmbH: High Performance Computing with Microsoft Windows HPC Server 2008 |