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Programme BioRange Project Meeting

This has been a closed meeting only accessible for people working in a NBIC Partner organisation. Goal of this meeting was to bring together the researchers related to the NBIC programmes, to exchange information between projects, open discussion and to get to know each other.

All participants were asked to sign a non-disclosure agreement. Because of IP regulations the files of the presentations will not be available online.

Programme, March 29

   
Opening by Prof. dr. Antoine van Kampen (Chair Day 1)  
   
Parallel session 1, Theme: Sequencing  
Victor de Jager (NBIC)  
Biodiversity, functional analysis and dynamics of a complex microbial consortium containing mainly Lactic Acid Bacteria.  
Christian Gilissen (Human Genetics, UMC St. Radboud Nijmegen)  
Mutation prioritization for next-generation sequencing  
Bas Dutilh, (CMBI, UMC St. Radboud Nijmegen)  
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly  
Yanju Zhang (Leiden University)  
Comparison and Integration of Target Prediction Algorithms for microRNA Studies  
   
Parallel session 2, Theme: Proteomics & Structures  
Morris Swertz (University Medical Center Groningen)  
Towards a MOLGENIS based data analysis framework for proteomics  
Hanka Venselaar (CMBI, UMC St. Radboud Nijmegen)  
Project HOPE: Providing the last piece of the puzzle….  
Robbie Joosten (NKI – AVL)  
Preparing the PDB for structural bioinformatics at wARP 7.1  
Rene Pool (Centre for Integrative Bioinformatics VU (IBIVU))  
Modeling the Effective Interaction Between Proteins - A Coarse-Grained Approach  
   
Coffee & tea & poster session  
   
Parallel project presentations, based on abstract submission:  
   
Parallel session 3, Theme: Sequence annotation  
Jumamurat Bayjanov (CMBI, UMC St. Radboud Nijmegen)  
Gene-trait matching in Lactococcus lactis strains  
Bernd Brandt (Vrije Universiteit Amsterdam)  
Multi-Harmony: detecting functional specificity from sequence alignment  
Marnix Medema (University of Groningen)  
Genome sequencing of Streptomyces clavuligerus ATCC 27064 reveals a 1.8-Mb linear megaplasmid packed with secondary metabolite gene clusters  
   
Parallel session 4, Theme: Text Mining  
Peter-Bram ‘t Hoen (Leiden University Medical Center)  
A New Statistical Framework for Gene Expression Data Interpretation Based on the Scientific Literature  
Herman van Haagen (Leiden University Medical Center)  
Predicting disease causing genes via implicit links in text and non textual information  
Ernest van Ophuizen (Wageningen University)  
Matching anatomical ontologies; evaluating UMLS, FMA-OBO and WordNet as references  
   
Lunch & poster session  
   
Parallel workshops:  
Workshop 1: Quality of software code  
Workshop 2: Work Smart and Save Time (pdf-file 7.3 MB)  
Workshop 3: Translating science to the general public  
   
Coffee & tea break & poster session  
   
Parallel project presentations, based on abstract submission:  
   
Parallel session 5, Theme: Networks & Pathways  
Philip Lijnzaad (UMC Utrecht)  
Mechanisms of signaling pathway redundancy and connectivity: modules for combinatorial control  
Miranda Stobbe (AMC Amsterdam)  
Integration of human metabolic pathway databases: a critical assessment  
Willem Ligtenberg (Eindhoven University of Technology)  
Reverse Engineering of Gene regulation Networks by dual Thresholding  
Yiannis Kourmpetis (Wageningen University & Research Center)  
Computational prediction of protein function in Arabidopsis thaliana by integrating network and sequence data  
   
Parallel session 6, Theme: Systems Bioinformatics  
Hannes Hettling (Vrije Universiteit Amsterdam)  
Estimating the importance of the "Photophocreatine shuttl" in heart muscle by multiscale 'sloppy' modeling  
Anand Gavai (Vrije Universiteit Amsterdam)  
BiGGR - Flux Distribution Analysis: An open source package for constraint based metabolic network modeling in R  
Kuan Yan (Leiden Institute of Advanced Computer Science (LIACS))  
Quantification and Function Analysis of Extracellular Matrix Dynamics using High-throughput Time-lapse Image Sequence in Cytometry Study  
Han Rauwerda (University of Amsterdam)  
Integrating genome and transcriptome resources for microarray design; the Zebrafish example  
   
Drinks, poster session & conference dinner  
   
Presentation of awards for best lecture & best poster  
   
NBIC Cafe