SocBiN Bioinformatics 2014, Oslo, 11 to 13 June, 2014

Detailed programme

The programme consists of keynotes and lectures by invited scientists, oral presentations based on selected submitted abstracts, as well as poster presentations. All lectures are held in the Simula auditorium.

To submit an abstract for oral presentation in the plenary sessions, please register and then log in with the supplied password. For more details, please see the information for presenters.

The programme is preliminary as of 10 June 2014 and is subject to change.

Wednesday 11 June

08.30 Registration (lobby)
09.30 Session 1 - Comparative genomics and phylogeny
Chair: Torbjørn Rognes, University of Oslo and Oslo University Hospital, Norway
09.30 Keynote: Fredrik Ronquist, Swedish Museum of Natural History, Stockholm, Sweden
Teaching computers phylogenetic models
Abstract S1
10.15 Invited Speaker: Alexandros Stamatakis, Heidelberg Institute for Theoretical Studies, Germany
Inference and post-analysis of huge phylogenies
Abstract S2
10.45 Coffee break (lobby)
11.15 Invited Speaker: Jens Stoye, University of Bielefeld, Germany
Family-Free Genome Comparison
Abstract S3
11.45 Oral presentations selected from submitted abstracts
11.45 Mikko Arvas
Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species
Abstract T1
12.00 Ole Herman Ambur
Evolutionary inferences of the DNA Uptake Sequences from genomics in the Neisseriaceae
Abstract T2
12.15 Hilde Vinje
A systematic search for discriminating sites in the 16S ribosomal RNA gene
Abstract T3
12.30 Lunch (canteen)
13.30 Session 2 - Metagenomics
Chair: Nils Peder Willasen, University of Tromsø, Norway
13.30 Keynote: Frank Oliver Glöckner, MPI for Marine Microbiology, Germany
Environmental Bioinformatics - with a focus on "Marine"
Abstract S4
14.15 Invited Speaker: Peter Sterk, Oxford e-Research Centre, University of Oxford, Oxford, UK and EMBL-EBI, Hinxton, UK
The metagenomics resource at the European Bioinformatics Institute
Abstract S5
14.45 Invited Speaker: Nicola Segata, Laboratory of Computational Metagenomics, University of Trento, Italy
Strain-level microbiome characterization with shotgun metagenomics
Abstract S6
15.15 Coffee break (lobby)
15.45 Oral presentations selected from submitted abstracts
15.45 Andres Veidenberg
Wasabi: a web-based platform for evolutionary sequence analysis
Abstract T4
16.00 Runar Stokke
Metagenomic study of a filamentous microbial mat from the Loki’s Castle Vent Field
Abstract T5
16.15 Tomasz Szczepanski
Virulence prediction of Shiga toxin-producing Escherichia coli (STEC) using computational genome analysis
Abstract T6
16.30 Sinan Uğur Umu
Harnessing the power of comparative RNA-seq to illuminate uncharacterised RNA families across Bacteria and Archaea
Abstract T7
16.45 Konika Chawla
Identification of genes coding for R3 and Z surface proteins of Streptococcus agalactiae
Abstract T8
17.00 Håkon Dahle
Use of metatranscriptomics, amplicon pyrosequencing and thermodynamics to assess how microbial communities are shaped by energy availability
Abstract T9
17.15 Michael Dondrup
LiceBase - Building a model organism database and functional genomics tools for the sea lice research community
Abstract T10
17.30 Get-together (Escape)
22.00 End

Thursday 12 June

09.00 Session 3 - Post-ENCODE bioinformatics
Chair: Eivind Hovig, University of Oslo and Oslo University Hospital, Norway
09.00 Invited Speaker: Stein Aerts, Katholieke Universiteit Leuven, Belgium
Reverse engineering the Drosophila eye network by large-scale transcriptome perturbations and motif discovery
Abstract S7
09.30 Invited speaker: Morten B. Rye, Norwegian University of Science and Technology and St. Olavs Hospital, Trondheim, Norway
Chromatin data integrated with a human reference atlas of experimentally defined promoters reveal repressed promoters located in active chromatin
Abstract S8
10.00 Invited Speaker: Geir Kjetil Sandve, University of Oslo, Norway
The Genomic HyperBrowser - a comprehensive solution for downstream genomic analysis
Abstract S9
10.30 Coffee break (lobby)
11.00 Oral presentations selected from submitted abstracts
11.00 Pubudu Samarakoon
Identification and verification of exonic copy number variants (CNVs) and analysis of CNVs and SNVs using interaction networks
Abstract T11
11.15 Ines Heiland
Improving the analysis of high throughput time course data using modelling based approaches
Abstract T12
11.30 Christof Winter
WGS-based reconstruction of exact fusion sequences at chromosomal rearrangements in cancer samples for their detection in patient blood by PCR
Abstract T13
11.45 Kanthida Kusonmano
Identification of differentially expressed gene modules from protein-protein interactions and transcriptional correlations in endometrial cancer
Abstract T14
12.00 Bjørn Fjukstad
Kvik: Interactive Exploration of Multi-Omics Data from the NOWAC Postgenome Biobank
Abstract T15
12.15 Matúš Kalaš
BioXSD - A data model proposal for integrative bioinformatics
Abstract T16
12.30 Lunch (canteen)
13.30 Session 4 - Gene regulation
Chair: Finn Drabløs, Norwegian University of Science & Technology, Trondheim, Norway
13.30 Keynote: Gary Stormo, Washington University
Improved experimental and computational methods for motif modeling
Abstract S10
14.15 Invited Speaker: Tom Whitington, Karolinska Institutet
Characterisation of regulatory variants in complex disease using functional genomics
Abstract S11
14.45 Invited Speaker: Albin Sandelin, Copenhagen University
An atlas of enhancers and promoter activity across the human body
Abstract S12
15.15 Coffee break (lobby)
15.45 Invited Speaker: Guillaume Filion, Centre for Genomic Regulation (CRG), Barcelona
A colorful TRiP into the Drosophila chromatin
Abstract S13
16.15 Oral presentations selected from submitted abstracts
16.15 Junbai Wang
Result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence
Abstract T17
16.30 Vilde D. Haakensen
Pathways deregulated in breast cancer progression from normal to benign breast tissue, DCIS and invasive cancers – a meta-analysis
Abstract T18
16.45 Marcin Wojewodzic
Seeking for Transgenerational Effects of Diet Quality in Clones – Ecophysiological and RNA-seq approaches
Abstract T19
17.00 Morten Muhlig Nielsen
Regmex: A flexible motif discovery tool for ranked sequence lists
Abstract T20
17.15 Takaya Saito
The Precision-Recall plot is more informative than the ROC plot when evaluating binary classifiers on imbalanced datasets
Abstract T21
17.30 Poster session (Smalltalk)
Abstracts P1-P20
19.00 Break
20.00 Conference dinner (Sporten)

Friday 13 June

09.00 Session 5 - Marine genomics
Chair: Dag Inge Våge, Norwegian University of Life Sciences, Ås, Norway
09.00 Invited Speaker: Felicity Jones, Max Planck, FML, Tübingen, Germany 
How does the genomic recombination landscape shape loci underlying adaptation and speciation?
Abstract S14
09.30 Invited Speaker: Jason Rafe Miller, J. Craig Venter Institute, USA
De Novo Genome Assembly with PacBio Reads
Abstract S15
10.00 Invited Speaker: Bronwen Aken, Wellcome Trust Sanger Institute, Cambridge, UK
Ensembl resources: data and tools
Abstract S16
10.30 Coffee break (lobby)
11.00 Invited Speaker: Kristian Vlahoviček, Department of Molecular Biology, Faculty of Science, Zagreb, Croatia
Genomic complexity of basal metazoans, lessons learned from sponges
Abstract S17
11.30 Invited Speaker: Görel Sundström, Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
Architecture and evolution of Neopterygii genomes
Abstract S18
12.00 Oral presentations selected from submitted abstracts
12.00 Ole Kristian Tørresen
A new, high quality reference genome assembly for Atlantic cod
Abstract T22
12.15 Harald Grove
Use of genetic linkage data to improve genome assemblies in marine species
Abstract T23
12.30 Lunch (canteen)
13.30 Session 6 - Tools and technologies for integrative bioinformatics
Chair: Inge Jonassen, University of Bergen, Norway
13.30 Keynote: Steve Pettifer, The Advanced Interfaces Group, The University of Manchester, UK
Stories that persuade with data: the role of scientific article as an integrative tool
Abstract S19
14.15 Oral presentations selected from submitted abstracts
14.15 Sabry Razick
The eGenVar data management system for cataloguing and sharing sensitive data and metadata for life sciences
Abstract T24
14.30 Maria Francesca Iozzi
TSD: a Secure and Scalable Service for Sensitive Data and eBiobanks
Abstract T25
14.45 Katerina Michalickova and Nikolay Vazov
Lifeportal - web portal to high performance computing resources at University of Oslo
Abstract T26
15.00 Edvard Pedersen
Enabling incremental updates for bioinformatics workflows
Abstract T27
15.15 Final remarks


Norwegian University of Life Sciences
University of Tromsø
Norwegian University of Science and Technology
University of Oslo
Research Council of Norway
Elixir Norway
University of Bergen