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Bioinformatics 2012 Stockholm June 11-14 2012

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Bioinformatics 2012 Stockholm June 11-14 2012 BIOINFORMATICS 2012 STOCKHOLM JUNE 11-14 2012 hp://socbin.org/bioinfo2012/ Welcome SocBiN in collaboration with Center for Biomembrane Research welcomes you to the 12th annual conference in bioinformatics. This year the conference will be held in beautiful Stockholm starting at lunch-time June 11 and ending at lunch on June 14. It will be held in the lecture hall "Berzelius" (Berzelius väg 3 / Tomtebodavägen at the bus stop for SL bus 69) Stockholm on the Karolinska Institutet campus, close to Science for Life Laboratory, Stockholm. We are looking forward to an exciting scientific program with 4 invited keynote speakers and 5 sessions (Molecular Machines, Using next generation sequence data, Data analysis of proteomics assays, Bioinformatics of chemical biology and RNA bioinformatics). We wish you all very welcome The organization committee Arne Elofsson, Department of Biochemistry and Biophysics, Stockholm University, Erik Lindahl, Theoretical Physics, KTH and Bengt Persson, Linköping University SocBin SocBiN (Society for Bioinformatics in Northern Europe) is a non-profit organization for people working with and interested in bioinformatics and computational biology. The members of the organization are predominantly from the Nordic and Baltic countries, but others are also welcome. We are grateful for the help of our session chairs • Arne Elofsson,Science for Life Laboratory, Stockholm University,Sweden • Lukas Käll, Science for Life Laboratory, KTH,Sweden • Anders Andersson, Science for Life Laboratory, KTH,Sweden • Jens Carlsson, Center for Biomembrane Research, Stockholm University, Sweden • Janusz Bujnicki, International Institute of Molecular and Cell Biology in Warsaw, Poland Program Mon 11 Data Analysis of Proteomics Assays 13:45- Arne Elofsson Welcome 14:00 14:00- Ruedi Searching and Mining of Proteomic SWATH-MS datasets 14:30 Aebersold 14:30- Lennart Snakes and ladders: where do proteomics assays fail and how 15:00 Martens can we fix them? 15:00- The Triform algorithm: improved sensitivity and specificity in Finn Drabløs 15:15 ChIP-Seq peak finding Coffee 15:45- Edward Insights from proteomics into protein organization, evolution, and 16:15 Marcotte genetic disease 16:15- Roman Pathway Analysis in Expression Proteomics 16:45 Zubarev 16:45- Paul Horton MoiraiSP: a novel mitochondrial cleavage site predictor 17:00 17:00- Reception and poster session (Presentation by odd numbers) 19:00 Tue June 12 RNA Bioinformatics 09:30- Bob Darnell 10:00 10:00- Jan Gorodkin Towards the search for RNA-RNA interaction based networks 10:30 10:30- Mihaela A biophysical model to infer canonical and non-canonical 10:45 Zavolan microRNA-target interaction Coffee 11:15- The Detection of the Architectural Modules of RNA and Recent Eric Westhof 11:45 Progress in RNA Modelling 11:45- Samuel Flores A structural and dynamical model of human telomerase 12:15 12:15- Nanjiang Shu Computational analysis of membrane protein topology evolution 12:30 LUNCH Keynotes Session 13:30- Anders Krogh On the accuracy of short read mapping 14:30 14:30- Kerstin 15:30 Lindblad-Toh Coffee 16:00- Genome-Scale Metabolic Models: A Bridge between Bioinformatics Jens Nielsen 17:00 and Systems Biology 17:00- Paul Horton Excavating human NUMTs 18:00 18:00- olving the Recalcitrant Crystal Structure of Group II Chaperonin Michael Levitt 19:00 TRiC/CCT by Mass Spectrometry and Sentinel Correlation Analysis 19:30- Conference Dinner 24:00 Wed 13 Bioinformatics of chemical biology 09:30- Gert Vriend What can we (not yet) learn from 70 GPCR structures 10:00 10:00- Raymond Understanding Human G-protein Coupled Receptor Structural 10:30 Stevens Diversity and Modularity 10:30- Chemogenomic Discovery of Allosteric Antagonists at the GPRC6A David Gloriam 10:45 Receptor Coffee 11:15- Helgi Schiöth The origin of GPCRs, the largest family of membrane bound proteins 11:45 11:45- Andreas Using Chemogenomics Approaches to Modulate Biological Systems 12:15 Bender 12:15- PoSSuM: a database of known and potential ligand-binding sites in Kentaro Tomii 12:30 proteins Using Next generation sequence data 14:00- Metagenomics data analysis: from the oceans to the human Jeroen Raes 14:30 microbiome 14:30- Christopher Extracting ecological signal from noisy microbiomics data 15:00 Quince Comprehensive Analysis of Antibiotic Resistance Genes in River 15:00- Johan Sediment, Well Water and Soil Microbial Communities Using 15:15 Bengtsson Metagenomic DNA Sequencing 15:15- Daniel Allele specic expression changes after induction of inflammation 15:30 Edsgärd Coffee 16:00- Erik van Reconstructing transcription regulatory networks in mammals using 16:30 Nimwegen a combination of modeling and next-generation sequencing data 16:30- Joakim Sequencing and assembly of the largest and most complex genome 17:00 Lundeberg to date - the Norway spruce (Picea abies) 17:00- Ivo Gut High-resolution whole-genome analysis and cancer 17:30 17:30- Poster session (Presentation by even numbers) 19:00 Thu 14 Molecular machines 09:00- Martin Weigt From sequence variability to protein (complex) structure prediction 09:30 09:30- Burkhard Rost Evolution teaches protein prediction 10:00 10:00- Janusz If Thereʼs an Order in All of This Disorder…: Structural 10:15 Bujnicki Bioinformatics of the Human Spliceosomal Proteome 10:15- Joanna M PyRy3D: a software tool for modelling of large macromolecular 10:30 Kasprzak complexes Coffee 11:00- Ingemar André Design and Prediction of Protein Self-assembly 11:30 11:30- Rob Russel 12:00 12:00- Closing words 12:15 List of partcipants Conference "Bioinformatics 2012", June 11-14 at Karolinska Institutet, Stockholm Sweden First name Surname/Family name University/Organization Country E-mail address Ruedi Aebersold ETH Zurich SWITZERLAND [email protected] Rahul Agarwal Chalmers SWEDEN [email protected] Mehmood Alam Khan KTH SWEDEN [email protected] Raja Hashim Ali Kungliga Tekniska Hogskolan SWEDEN [email protected] Anders Andersson KTH SWEDEN [email protected] Ingemar André Lund University SWEDEN [email protected] Reidar Andreson University of Tartu ESTONIA [email protected] Lars Arvestad Stockholm University SWEDEN [email protected] Ahmad Barghash Saarland University GERMANY [email protected] Walter Basile SWEDEN [email protected] Johan Bengtsson University of Gothenburg SWEDEN [email protected] Jorrit Boekel Scilifelab Stockholm SWEDEN [email protected] Mikael Borg SWEDEN [email protected] Susanne Bornelöv Uppsala university SWEDEN [email protected] John Boss Karolinska Institutet SWEDEN [email protected] Fredrik Boulund Chalmers University of Technology SWEDEN [email protected] Christian Brüffer Lund University SWEDEN [email protected] Torben Brömstrup KTH SWEDEN [email protected] Janusz Bujnicki IIMCB POLAND [email protected] Ignas Bunikis Uppsala University SWEDEN [email protected] Jens Carlsson Stockholm University SWEDEN [email protected] Alexey Chernobrovkin IBMC RAMS RUSSIA [email protected] Anna Czerwoniec Adam Mickiewicz University POLAND [email protected] Robert Darnell The Rockefeller University UNITED STATES [email protected] Carsten Daub Karolinska Institutet and SciLifeLab SWEDEN [email protected] Ino De Bruijn Stockholm University SWEDEN [email protected] Finn Drablos Norwegian Univ of Science and Technology NORWAY [email protected] Lei Du Karolinska Institutet SWEDEN [email protected] Stanislaw Dunin-Horkawicz IIMCB POLAND [email protected] Daniel Edsgärd KTH, Science for Life Laboratory SWEDEN [email protected] Arne Elofsson Principal Investigator/Lab Head/Senior R SWEDEN [email protected] Olof Emanuelsson Kungliga Tekniska Högskolan SWEDEN [email protected] Hassan Foroughi Asl Karolinska Institutet SWEDEN [email protected] Oliver Frings SWEDEN [email protected] Mattias Frånberg Stockholms Universitet/Karolinska Instit SWEDEN [email protected] David Gloriam University of Copenhagen DENMARK [email protected] David Gomez-Cabrero BILS SWEDEN [email protected] Jan Gorodkin University of Copenhagen DENMARK [email protected] Viktor Granholm Stockholm University SWEDEN [email protected] Svenn Helge Grindhaug Uni Research NORWAY [email protected] Dimitri Guala SWEDEN [email protected] Ivo Gut Centro Nacional de Análisis Genómico SPAIN [email protected] Mohamed Hamed Saarland University GERMANY [email protected] Sampsa Hautaniemi University of Helsinki FINLAND [email protected] Sikander Hayat [email protected] Paul Horton AIST, Computational Biology Res. Ctr. JAPAN [email protected] Luisa Hugerth KTH SWEDEN [email protected] Lina Hultin Rosenberg Karolinska Institutet SWEDEN [email protected] Lukasz Huminiecki [email protected] Katherine Abigail Icay University of Helsinki FINLAND [email protected] Henrik Johansson Karolinska Institute SWEDEN [email protected] Anna Johnning University of Gothenburg SWEDEN [email protected] Viktor Jonsson University of Gothenburg SWEDEN [email protected] Sini Junttila University of Turku FINLAND [email protected] Mette Jørgensen University of Copenhagen DENMARK [email protected] Yvonne Kallberg Karolinska Institutet SWEDEN [email protected] Joanna Kasprzak Kasprzak Adam Mickiewicz University POLAND [email protected] Zeeshan Khaliq Uppsala University SWEDEN [email protected] Per Kraulis SWEDEN [email protected] Anders
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