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The 11th SocBiN Conference

SocBiN - Society for Bioinformatics in Northern Europe

 

 


Bioinformatics 2011 Program:

Tuesday May 10, 2011

9.00 - 10.00 Registration

10.00 - 10.15 Welcoming words

- Chaiman of the program committee Sampsa Hautaniemi
- Dean Risto Renkonen (Faculty of Medicine, University of Helsinki)
- Director Eero Vuorio (Biocenter Finland)

10.15 - SESSION 1: DATA INTEGRATION APPROACHES IN DISEASES
Chair Sampsa Hautaniemi

-Jesper Tegner, Karolinska Institute, Sweden
Decoding putative mechanisms of atherosclerosis by integrating
bioinformatics and computational modeling across different data sources

-Carsten Daub, RIKEN Yokohama Institute, Japan
Transcriptional responses of inflammation in human tissue reveal targets for treatment
-Poster presentation:
Suleiman Khan, Aalto University, Finland
Decomposing drug action mechanisms into relationships of chemical structure with genome wide drug responses

11.30 - 12.00 Coffee break

-Nuria Lopez-Bigas, University Pompeu Fabra, Spain
Integration and data-mining of multidimensional oncogenomic data
-David Gilbert, Brunel University, UK
BioModel Engineering - the multiscale challenge
-Poster presentation:
Tauno Metsalu, University of Tartu, Estonia
Statistical methods for estimating microRNA expression from targets’ expression data

13.30 - 14.30 Lunch

14.30 - SESSION 2: PREDICTION AND ANALYSIS OF MUTATION EFFECTS
Chair Mauno Vihinen

-Sean Mooney, Buck Institute of Aging, USA
Understanding the functional importance of genetic variation and its impact on human genetic disease
-Mauno Vihinen, University of Tampere, Finland
Effects of missense variations - bioinformatic approach
-Poster presentation:
Morten Johansen, Technical University of Denmark
Prediction of disease causing non-synonymous SNPs by the artificial neural network predictor NetDiseaseSNP

16.00 - 16.30 Coffee break

-Christina Kiel, Center for Genomic Regulation, Spain
Integration of networks with disease-linked mutations based on structure, function, and protein stability calculations
-Yana Bromberg, Rutgers, USA
SNAPpy annotation of protein functional sites using in silico mutagenesis
-Poster presentation:
Kirsti Laurila, University of Turku, Finland
SNP genotype effects on gene and transcript expression variation in human embryonic and induced pluripotent stem cells

19.00 Conference Dinner at Töölönranta restaurant

Wednesday May 11, 2011

8.30 - 9.00 Registration

9.00 - SESSION 3: MODELING OF CELLULAR NETWORKS
Chair Lars Juhl Jensen

-Peer Bork, European Molecular Biology Laboratory, Germany
Using environmental constraints to identify interactions in networks
-Orkun Soyer, University of Exeter, UK
Evolutionary systems biology of signalling networks
-Poster presentation:
Elena Czeizler, University of Helsinki, Finland
Identifying cancer subtypes based on network modules

10.30 - 11.00 Coffee break

-Christian von Mering, University of Zurich, Switzerland
Optimality and evolution of protein abundance levels in eukaryotes
-Rune Linding, Technical University of Denmark, Denmark
Integrative models of phosphorylation networks
-Poster presentation:
Antti Häkkinen, Tampere University of Technology, Finland
Evolving the kinetics of single gene expression

12.30 - 13.30 Lunch

SESSION 4: PROTEIN STRUCTURE, FUNCTION AND INTERACTIONS
Chair: Arne Elofsson

-Christine Orengo, UCL Institute of Structural and Molecular Biology, UK
Mining evolutionary and experimental data to find the hidden hubs in protein networks
-Johannes Söding, Gene Center Munich, Germany
Evolution of protein domains from modular fragments and the origin of outer membrane beta barrels
-Poster presentation:
Kristoffer Forslund, Stockholm University, Sweden
Domain architecture conservation in orthologs

15.00 - 15.30 Coffee break

-Jose Onuchic, University of California, USA
The energy landscape for proteins: from folding to biomolecular machines
-Ron Dror, D.E. Shaw Research laboratory, USA
Elucidating membrane protein function through long-timescale molecular dynamics simulations
-Poster presentation:
Babu A Manjasetty, European Molecular Biology Laboratory, France
Effect of experimental conditions on protein structures:
Criteria for conformational choice and structural variation

17.00 - 20.00 Poster session

Thursday May 12, 2011

8.30 - 9.00 Registration

9.00 - SESSION 5: HIGH-THROUGHPUT SEQUENCE DATA ANALYSIS
Chair Carsten Daub

-Albin Sandelin, University of Copenhagen, Denmark
Small RNAs from transcription initiation, splicing and termination
-Nikolaus Rajewsky, Max Delbruck Center for Molecular Medicine, Germany
Post-transcriptional gene regulation by small RNAs and RNA binding proteins
-Poster presentation:
Ari Löytynoja, University of Helsinki, Finland
Phylogenetic placement of RNA-seq data using a graph alignment algorithm

10.30 - 11.00 Coffee break

-Poster presentations:
Hendrik Edgren, FIMM, University of Helsinki, Finland
Paired-end RNA-sequencing based identification of 24 novel fusion genes in breast cancer
Anna Johnning, University of Gothenburg, Sweden

The genome of an extensively drug-resistant bacterium isolated from a wastewater treatment plant receiving effluent from antibiotic manufacturing
-Steven E. Brenner, University of California, USA
Ultraconserved nonsense: gene regulation by splicing and RNA surveillance

12.30 - 13.30 Lunch

13.30 - SESSION 6: BIOINFORMATICS OF METAGENOMICS
Chair Rainer Lehtonen

-Sanjay Vashee, J. Craig Venter Institute, USA
Lessons Learned from the Human Microbiome
-Janne Nikkilä, Finnish Red Cross, Finland
Analysis of multivariate, multi-organism and multi-source data sets
-Poster presentation:
Johan Bengtsson, University of Gothenburg, Sweden
METAXA: A software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

15.00 -15.30 Coffee break

-Petri Auvinen, University of Helisnki, Finland
Genomes and metagenomes of food spoilage
-Otso Ovaskainen, University of Helsinki, Finland
Combining metagenomics with fruit body surveys reveals contrasting life-history strategies in fungi
-Poster presentation:
Erik Kristiansson, Chalmers University of Technology, Sweden
Pyrosequencing of Antibiotic-Contaminated River Sediments Reveals High Levels of Resistance and Gene Transfer Elements

16.45 - Closing words

- Director Arne Elofsson (Society for Bioinformatics in Northern Countries)
- Chairman of the program committee Sampsa Hautaniemi

17.00 End of the program

Download the program as a PDF-file here:
SocBiN Bioinformatics 2011 program

Download the program with the poster abstracts here:
Socbin Bioinformatics 2011 program and abstract book

 

See also the Bioinformatics Day of the Finnish Society for Bioinformatics held in Helsinki on May 13, 2011, registration and more information here.

 

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