GCB 2011: German Conference on Bioinformatics 2011

GCB 2011 - German Conference on Bioinformatics 2011

Weihenstephan, September 7-9, 2011

All Tracks (sorted by track)

HTHT-02Ludwig Geistlinger
From Sets To Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems
HT-15Florian Rasche, Ales Svatos, Ravi Kumar Maddula, Christoph Böttcher and Sebastian Böcker
Fragmentation trees from mass spectra: a step towards metabolite identification
HT-18Sergio Grimbs, Anne Arnold, Aneta Koseska, Jürgen Kurths, Joachim Selbig and Zoran Nikoloski
Spatiotemporal dynamics of the Calvin cycle: Multistationarity and symmetry breaking instabilities
HT-21Caroline C. Friedel, Lars Dölken and Ralf Zimmer
High resolution profiling of RNA synthesis and decay
HT-22Jan Krumsiek, Karsten Suhre, Thomas Illig, Jerzy Adamski and Fabian J. Theis
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data
HT-28Christian Schudoma, Abdelhalim Larhlimi and Dirk Walther
The influence of the local sequence environment on RNA loop structures
HT-35Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will and Michael Beckstette
Structator: fast index-based search for RNA sequence-structure patterns
HT-46Sebastian Klie
Metabolomic and transcriptomic stress response of Escherichia coli
HT-58Jens Keilwagen, Jan Grau, Ivan A. Paponov, Stefan Posch, Marc Strickert and Ivo Grosse
De-Novo Discovery of Differentially Abundant DNA Binding Sites Including Their Positional Preference
HT-66Matthias Heinig, Enrico Petretto, Chris Wallace, Anja Bauerfeind, Stefan Blankenberg, Martin Vingron, Norbert Hubner and Stuart Cook
A conserved trans-acting regulatory locus underlies an inflammatory gene network and susceptibility to autoimmune type 1 diabetes
JTJT-10J. Patrick Pett, Daniel H. Mehnert, Jonas Ibn-Salem, Ole Eigenbrod, Raik Otto, Stephan Knorr, Stina-Stephanie M. Richter and Roland Krause
Identification of shared components of protein complexes
JT-20Huy Dinh, Ortrun Mittelsten Scheid and Arndt Von Haeseler
MethColor: a computational approach to uncover DNA methylation heterogeneity
JT-27Haroon Naeem, Ralf Zimmer and Robert Küffner
Rigorous assessment of gene set enrichment tests
JT-38Sabine Hug, Daniel Schmidl, Wei Bo Li, Matthias Greiter and Fabian J. Theis
Bayesian Model Selection for Zirconium Processing in the Human Body after Ingestion
JT-40Eva Vennmann, Nadine Schneider and Matthias Rarey
Discrimination of permanent and transient heterodimers: The real challenge in the classification of protein-protein interactions
JT-41Sebastian Dümcke, Martin Seizl, Nicole Pirkl, Steffanie Etzold, Dietmar Martin and Achim Tresch
One Hand Clapping: Detection of condition-specic Transcription Factor Interactions from genome-wide gene activity Data
JT-43Michael Schwarzfischer, Carsten Marr, Jan Krumsiek, Philipp S. Hoppe, Adam Filipczyk, Timm Schroeder and Fabian J. Theis
Automated cell quantication allows inference of protein half-life from single cell time-lapse microscopy
JT-48Matthias Böck, Constanze Schmitt and Stefan Kramer
A Study of Dynamic Time Warping for the Inference of Gene Regulatory Relationships
JT-49Florian Erhard and Ralf Zimmer
Detecting outlier peptides in quantitative High-Troughput mass spectrometry
JT-50Robert Pesch and Ralf Zimmer
To transfer or not to transfer - Complementing the eukaryotic protein-protein interactome
JT-54Lukas Windhager, Jonas Zierer and Ralf Zimmer
Module Extraction from Ensembles of Networks
JT-56Martin Preusse, Andreas Kowarsch, Carsten Marr and Fabian J. Theis
miTALOS: Analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs
JT-59Andre Dau and Johannes Krugel
tt-analyze and tt-generate: Tools to Analyze and Generate Sequences with Trained Statistical Properties
JT-64Alena Mysickova and Martin Vingron
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity
JT-65Thomas Hoffmann and Iris Antes
Modeling the variable regions of T-Cell Receptors
JT-68Manuel Andreas Glaser and Iris Antes
Docking Peptides into MHC Class II Complexes
PTPT-4Tim Schäfer, Patrick May and Ina Koch
Extension of protein topologies by ligand interactions: computation and visualization
PT-14Achim Brunner, Eva Keidel, Josef Kellermann and Friedrich Lottspeich
ICPLQuant - a directed proteomics tool for isotope labelling proteomics
PT-17Tobias Petri, Evi Berchtold, Ralf Zimmer and Caroline C. Friedel
Detection and correction of probe-level measurement artefacts on microarrays
PT-25Ivan Kondofersky
Estimating hidden components in kinetic systems using functional data analysis
PT-33Rainer Von Den Berken and Markus Gumbel
OODB4Genomics: An object-oriented database approach for biomedical data in clinical bioinformatics
PT-36Hendrik Schäfer and Ina Koch
A pipeline to explore alternative splicing events
PT-45Ferdinand Stückler, Jan Krumsiek, Gabriele Kastenmüller, Susanne Krug, Manuela Rist, Thomas Skurk, Karsten Suhre, Hans Hauner, Hannelore Daniel and Fabian J. Theis
Analysis of metabolic profiles using model-driven metabolite ratios
PT-51Björn Schwalb, Mai Sun, Daniel Schulz, Nicole Pirkl, Laurent Lariviere, Kerstin Maier, Achim Tresch and Patrick Cramer
Comparative Dynamic Transcriptome Analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation
PT-67Alexander Leow
IntronBase: A new resource for mining gene structure of orthologous genes from nine metazoa.
PT-73Baiba Vilne, Monika Kröger, Rouzanna Istvanffy, Christina Eckl, Franziska Bock, Matthias Schiemann, Christian Peschel, Volker Stümpflen, Hans-Werner Mewes and Robert A.J. Oostendorp
Regulatory networks of hematopoietic stem cells and their micro-environment
PT-74Manuela Hische, Abdelhalim Larhlimi, Franziska Schwarz, Antje Fischer-Rosinsky, Thomas Bobbert, Anke Assmann, Gareth Catchpole, Andreas Pfeiffer, Lothar Willmitzer, Joachim Selbig and Joachim Spranger
A distinct metabolic signature predicts development of fasting plasma glucose
PT-75Tina Meyer, Natascha Hill, Ralph Tiedemann and Stefanie Hartmann
Computational Analysis of Mobile Elements in Intron-Sequences of Invertebrates
PT-77Nadine Albrecht, Hans-Werner Mewes and Thorsten Schmidt
Regulatory action of lincRNAs on alternative transcript events
PT-78Martin Kötzing, Christoph Kaleta, Martin Bartl and Stefan Schuster
Dynamic Optimization of Nitrogen Assimilation in Chlamydomonas reinhardtii
PT-79Palani Kannan Kandavel, Markus Goeker and Hans-Peter Klenk
Inferring functional genome classifications from their annotated proteins
PT-80Andreas Ströhlein, Hon Q. Tran, Antje Krause and Paul M. Selzer
Bacterial Pathogens and their Pan-Proteome - From Next-Generation Sequencing to Target Identification
PT-81Christine Gläßer, Georg Haberer and Klaus F. X. Mayer
Retrograde Signaling in Plants: its nature and contributing pathways
PT-82Susann Vorberg, Christian Buning and Ina Koch
Sodium Dependent Glucose Transporter (SGLT) 1 / 2 - Elucidating Inhibitor SAR and Selectivity using Homology Modelling and 3D QSAR Studies
PT-83Hendrik B. Tiedemann, Elida Schneltzer, Bastian Hoesel, Johannes Beckers, Gerhard K. H. Przemeck and Martin Hrabé De Angelis
From Dynamic Expression Patterns to Boundary Formation in the Presomitic Mesoderm
PT-84Christoph J. Thieme, Lydia Gramzow and Günter Theißen
SplamiR - Predicting a new class of plant microRNAs
PT-85Daniel Ellwanger, Florian Büttner, Hans-Werner Mewes and Volker Stümpflen
The sufficient minimal set of miRNA seed types
PT-86Kai Christian Bader and Harald Meier
Interactive primer- and probe-design with CaSSiS
PT-87Regina Augustin, Stefan F. Lichtenthaler, Kristina Endres, Sven Reinhardt, Peer-Hendrik Kuhn, Michael Greeff, Daniela Vogt-Weisenhorn, Jens Hansen, Wolfgang Wurst and Dietrich Trümbach
Bioinformatics approach: Regulation of Alzheimer's disease-related genes by modules of TFBSs and microRNAs
PT-88Christoph Kaleta, Luis Filipe De Figueiredo, Sarah Werner, Reinhard Guthke, Michael Ristow and Stefan Schuster
In Silico Evidence for Gluconeogenesis From Fatty Acids in Humans
PT-89Florian Heinke, Anne Tuukkanen and Dirk Labudde
Analysis of membrane protein stability in nephrogenic diabetes insipidus by multiple energy profile alignment approach, MEPAL
PT-90Günter Jäger, Florian Battke and Kay Nieselt
TIALA - Visual Time Series Alignment Analysis
PT-91Thomas Ulas and Dietmar Schomburg
Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic Archaeon Sulfolobus solfataricus
PT-92Susanne Quester and Dietmar Schomburg
Enzyme Detector - integrated genomic enzyme function prediction
PT-93Simon Domke, Suparna Mitra, Nico Weber, Stephan Schuster, Thomas Rattei and Daniel Huson
MEGAN-DB - The MEtaGenome ANalyzer DataBase
PT-94Thomas Bonfert, Gergely Csaba, Ralf Zimmer and Caroline C. Friedel
Maximizing the number of aligned reads from RNA-Seq data
PT-95Holger Maier, Christoph Lengger, Ralph Steinkamp, Anja Berger, Helmut Fuchs, Valérie Gailus-Durner and Martin Hrabé De Angelis
MausDB: the phenotype- and mouse management system of the German Mouse Clinic
PT-96 Daniela Keller and Joerg Schultz
Language dynamics revealed by morpheme networks
PT-97Michaela Matthes, Julia Schechter, Martin Preusse, Sebastian Götz, Bernd Lentes, Daniela Mayer, Fabian J. Theis, Wolfgang Wurst, Nilima Prakash and Dietrich Trümbach
IDGenes: A reference database for dynamic modelling of genetic interactions in the developing mouse brain
PT-98Joachim Nöthen, Jörg Ackermann, Enrico Schleiff and Ina Koch
Reduction techniques for validation of metabolic networks in Arabidopsis thaliana
PT-99Christian Ried, Jan Kirrbach and Dieter Langosch
Mapping the human single-span membrane proteome for self-interacting transmembrane domains
PT-100Philipp Gormanns, Stefan Reckow, Joseph C. Poczatek, Chris W. Turck and Claude Lechene
Semi-automated image segmentation of Multi Isotope Imaging Mass Spectrometry data in the ImageJ plugin "OpenMIMS"
PT-101Rocio Rebollido-Rios and Daniel Hoffmann
The role of calcium ions for the stability of Sonic Hedgehog protein
PT-102Stefan Dietrich, Natascha Hill, Christoph Bleidorn and Stefanie Hartmann
Survey & evolutionary analysis of snoRNAs in annelid introns.
PT-103Marius Byl, Thomas Bukur, Jelle Scholtalbers, Ludmila Schemarow, Martin Löwer, John Castle and Ugur Sahin
TEA - TRON Expression Atlas: A Web-based Tool for Visualizing and Interpreting Next Generation Sequencing Expression Data
PT-104Alexander Schmitz, Jörg Ackermann, Claudia Döring, Martin-Leo Hansmann and Ina Koch
Image analysis of cancerous cells
PT-105Mohammad Aminisharifabad, Verena Wolf and David Spieler
Efficient Steady State Solution of Stochastic Systems Chemical Reactions
PT-106Katrin Illner
Bayesian blind source separation of microarray data using graph-delayed correlation
PT-107Moritz Aschoff, Agnes Hotz-Wagenblatt, Karl-Heinz Glatting, Matthias Fischer, Roland Eils and Rainer König
Computational Analysis of Alternative Splicing in Cancer using RNA-Seq
PT-108Nils Hoffmann, Mathias Wilhelm, Kai Stadermann and Jens Stoye
Maui and Maltcms - A Graphical User Interface and Application Framework for High-Throughput Metabolomics
PT-109Malte Mader, Ronald Simon, Sascha Steinbiss and Stefan Kurtz
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context
PT-110Tim Kacprowski, Nadezhda T. Doncheva, David Buezas and Mario Albrecht
Disease gene prioritization by combining network information and functional knowledge
PT-111Harald Marx, Thomas Rattei, Simone Lemeer and Bernhard Kuster
MScDB: A mass spectrometry centric protein sequence database
PT-112Alexander Cecil, Santosh Nilla, Benjamin Schaefer, Christoph Sotriffer and Thomas Dandekar
DrugPoint - a retrieval software and databank to connect proteins, drugs and targets.
PT-113Timo Lühr, Maurice Scheer, Melanie Busch, Michael Rother, Ida Schomburg and Dietmar Schomburg
BRIME: A tool for visualization of metabolic models
PT-114René Rex and Dietmar Schomburg
Xeledon: Efficient enumeration of all steady state cycles in metabolic networks
PT-115Maurice Scheer, Antje Chang, Ida Schomburg, Andreas Grote, Michael Rother, Cornelia Munaretto, Carola Söhngen, Sandra Placzek and Dietmar Schomburg
The BRENDA enzyme information resource in 2011
PT-116Martin Macguill, Tobias Petri and Ralf Zimmer
On Risk Stratification Strategies in Intensive Care Medicine
PT-117Sergii Novotarskyi, Iurii Sushko, Robert Körner and Igor Tetko
Using docking-derived protein-ligand atom pair descriptors to increase performance of QSAR models for human CYP450 inhibition
PT-118Iurii Sushko, Sergii Novotarskyi, Robert Körner and Igor Tetko
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of physicochemical and biological activities of small molecules
PT-119Bernhard Renard, Martin Löwer, Jos De Graaf, Mustafa Diken, Özlem Türeci, Cedrik Britten, Sebastian Kreiter, Michael Koslowski, John Castle and Ugur Sahin
Framework for confidence-based somatic mutation detection
PT-120Mahmut Kara and Martin Zacharias
Comparison of the fine structure and dynamics of damaged and intact DNA
PT-121Franziska Zickmann and Bernhard Renard
Influence of Target and Decoy Database Size on Peptide Identification Confidence
PT-122Philipp Koch, Bryan Downie, Andreas Petzold, Niels Jahn, Marco Groth, Stefan Taudien, Kathrin Reichwald and Matthias Platzer
KILAPE: A novel pipeline for the assembly of complex genomes from next-generation sequencing data.
PT-123Martin S. Lindner and Bernhard Y. Renard
Risks for Specificity and Sensitivity in Metagenomic Classification Experiments
PT-124Vipul Patel, Geo Velikkakam James, Ales Pecinka and Korbinian Schneeberger
Genotyping-by-sequencing of thousands of individuals
PT-125Piotr Wojtek Dabrowski, Michael Goltz and Andreas Nitsche
An alignment editing tool for the design of nucleotide sequence-based assays
PT-126Anton Thomma, Stefanie Widder and Thomas Rattei
Age Classification of Genomic DNA from Metagenomes
PT-127Xavier Lucas, Björn Andreas Grüning, Christian Senger and Stefan Günther
Compound Library Preparation in Galaxy: Application to HT Docking
PT-128Tihamer Geyer
Using Dynamic Graphs to Quantitatively Visualize Agglomeration in Spatial Simulations
PT-129Thomas Weinmaier, Dmitrij Turaev, Yuliang Jin, Hernan Makse and Thomas Rattei
Protein interaction networks - now and then
PT-130Dmitrij Turaev, Michael Sommer and Thomas Rattei
Evaluation And Comparison Of Different Taxonomic Classification Approaches Of Metagenomic Sequences
PT-131Jörg Bartel, Melanie Kahle, Jörn Leonhardt, Susanne Neschen and Volker Stümpflen
A systems-biological perspective of non-alcoholic fatty liver disease in mice
PT-132Dirk Willrodt, Bernhard Haubold and Stefan Kurtz
Memory efficient calculation of phylogenetic distances for whole genome sequences
PT-133Dmitry Ivankov, Stefano Bonissoni, Pavel Pevzner and Dmitrij Frishman
Analysis of cleaved N-terminal sequences coming from MS/MS proteomics for E.coli and S.cerevisiae
PT-134Stephan Flemming, Björn Andreas Grüning, Thomas Häupl and Stefan Günther
A framework for analysis of DNA methylation data
PT-135Jan Budczies, Frederick Klauschen, Wolfgang D Schmitt and Carsten Denkert
CutoffFinder - Cutoff optimization for diagnostic variables and correlation with clinical outcome and survival data
PT-136Stefan Brandmaier, Ullrika Sahlin, Tomas Öberg and Igor Tetko
Stepwise D-Optimal design based on latent variables
PT-137Haroon Naeem, Ralf Zimmer and Robert Küffner
Rigorous assessment of gene set enrichment tests
PT-138Stefan Altmann, Ralf Zimmer and Robert Küffner
Network Inference in Eukaryotes
PT-140Pegah Tavakkolkhah, Ralf Zimmer and Robert Küffner
Time-sensitive inference of gene regulatory networks
PT-141Arli A. Parikesit, Peter F. Stadler and Sonja J. Prohaska
Evolution of domain co-occurrences: some striking results
PT-142Ahmed Abdelaziz, Iurii Sushko, Wolfram Teetz, Robert Körner, Sergii Novotarskyi and Igor Tetko
QSAR modeling for In vitro assays: linking ToxCast database to the integrated modeling framework OCHEM
PT-143Stefka Tyanova, Jürgen Cox, Dmitrij Frishman and Matthias Mann
Effect of Phosphorylation on Ionization Efficiency during Mass-spectrometry Experiments
PT-144Ulrike Haase, Marc Bonin, Stephan Flemming, Frank Buttgereit, Till Sörensen and Thomas Häupl
A clinical database for networking in multicenter studies
PT-145Till Sörensen, Ursula Schulte-Wrede, Andreas Grützkau and Thomas Häupl
Automated and Standardized Clustering of Flow Cytometry Data
PT-146Konrad Grützmann, Sebastian Böcker and Stefan Schuster
Combinatorics of aliphatic amino acids
RTRT-19Martin Macguill, Tobias Petri and Ralf Zimmer
On Risk Stratification Strategies in Intensive Care Medicine
RT-31Jiabin Huang and Björn Voß
RNAHeliCes - Folding space analysis based on position aware structure abstraction
RT-34Ralf Eggeling, Jens Keilwagen and Ivo Grosse
Recognition of splice sites and transcription factor binding sites using generalized maximum entropy models
RT-44Orland Gonzalez, Georg Malterer, Ralf Zimmer and Jürgen Haas
Guilt by Association in Human RNAi Screens
RT-47Mathias Möhl, Christina Schmiedl and Shay Zakov
Sparsification in Algebraic Dynamic Programming
RT-55Anna Katharina Dehof, Hans-Peter Lenhof and Andreas Hildebrandt
Predicting Protein NMR Chemical Shifts in the Presence of Ligands and Ions using Force Field-based Features
RT-61Marco Mernberger and Eyke Huellermeier
Prediction of Protein Localization for Specialized Compartments using Time Series Kernels
RT-62Andreas S. Richter and Rolf Backofen
Accessibility and conservation in bacterial small RNA-mRNA interactions and implications for genome-wide target predictions