Stockholm Bioinformatics Centre Annual Report 2007 Director’s summary 2007 was a stable year for SBC – no major positions were vacated or filled, nor did any major relocations or other big environment changes occur. A steady production of science resulted in 33 publications, including important contributions in top journals such as Nature, Science, and PNAS. Four PhD theses were defended (Elias, Melén, Viklund, Granseth), and at the Frescati campus one workshop and one symposium were organized. Collaborations with experimental groups at KTH School of Biotechnology and SU Department of Biochemistry and Biophysics (DBB) are on-going. SBC is involved in several grant applications with external groups at KTH and SU, notably two Linnaeus grants at VR. A new web server machine was set up at SBC during 2007 in order to relieve the main www server, and eleven virtual servers were installed on it. These include bioinformation databases (InParanoid, FunCoup, Pfam, Humanoid), protein function/structure prediction servers (Phobius, Sfinx, GPCRHMM), sequence analysis tools (jSquid, Sfixem, MSA), and DAS services for protein transmembrane topology prediction (See Computer Infrastructure). In total about 40 web servers are now hosted, which makes the SBC a major contributor of bioinformatics resources internationally. As a result of the Bologna process, the SBC has been involved in developing Master programmes in bioinformatics and computational biology. Building on existing courses and 1 adding new ones (see Courses), two programmes have been set up. At KTH for a Master in Computational and Systems Biology, and at SU for a Master in Bioinformatics. The KTH programme will start in the fall of 2008 while the SU programme started in the fall of 2007. Here fourteen students, all of foreign nationality, were registered and have been learning bioinformatics techniques both via lectures and hands-on work in a new computer lab with twelve Linux workstations. Although this is a small start, we hope that it marks the beginning of a blossoming curriculum that will provide a steady stream of talented bioinformaticians for the future. The KTH and SU programmes have different focus, but several courses are common. The SBC thus serves as a hub to find synergies and cross-fertilize the bioinformatics education and research between the two universities. Personnel during 2007: Prof. Arne Elofsson Åsa Björklund PhD student Diana Ekman PhD student Olivia Eriksson PhD student Johannes Frey-Skött PhD student Linnea Hedin PhD student Kristoffer Illergård PhD student Per Larsson PhD student Håkan Viklund* PhD student Erik Granseth* PhD student Prof. Jens Lagergren Öjvind Johansson Post-doc Ali Tofigh PhD student Örjan Åkerborg PhD student Isaac Elias* PhD student Ass. Prof. Erik Lindahl Anna Johansson PhD student Aron Hennerdal PhD student Pär Bjelkmar PhD student Jenny Falk PhD student Yana Vereshchaga Post-doc Prof. Gunnar von Heijne Andreas Bernsel PhD student Karin Melen* PhD student Prof. Erik Sonnhammer (Director of the SBC) Andrey Alexeyenko Post-doc Olof Karlberg* Post-doc Mats Lindskog* Post-doc Kristoffer Forslund PhD student Anna Henricson PhD student Gabriel Östlund PhD student Bengt Sennblad Assistant professor 2 Lars Arvestad Senior scientist Olof Emanuelsson Research associate Karin Julenius Assistant professor Erik Sjölund System administrator *) Left during 2007 Collaboration partners SU Molecular Biology & Functional Genomics (Prof. Marie Öhman) KTH Biotechnology (Prof. Tuula Teeri, Prof. Peter Savolainen, and Prof. Mathias Uhlén) KI CMM (Prof. Gunnar Norstedt) Center for Biological Sequence Analysis, Danmarks Tekniska Universitet (Prof. Søren Brunak & Dr. Anders Gorm Pedersen) Bioinformatics Center, Köpenhamns Universitet (Prof. Anders Krogh) Bioinformatics Laboratory, BioInfoBank Institute, Poznan (Dr. Leszek Rychlewski) Institut Pasteur, Paris (Dr. Marc Delarue) Stanford University (Prof. Michael Levitt, Prof. Vijay S. Pande, Prof. James Trudell) Uppsala University (Dr. van der Spoel) University of Wyoming (Dr. David Liberles) McGill Centre for Bioinformatics (Dr. Mike Hallett) University of British Columbia (Dr. Wyeth Wasserman). Yale University, New Haven, CT. (Dr. Mark Gerstein) University of Buffalo (Dr. Daniel Fischer) Cornell University, Ithaca, NY. (Dr. Klaas van Wijk) The Pfam database consortium (Dr. Richard Durbin, Sanger Institute; Prof. Sean Eddy, Janelia farm, VA, USA) University of Valencia, Spain (Dr. Gustavo Camps-Valls) University of Rochester Medical Center (Dr. Fred Hagen) University of Paris René Descartes (Prof. Jean-Laurent Casanova) LU Clinical Genetics (Mattias Höglund) Max Planck Inst. für Genetik, Berlin. (Alexander Schliep) EU bioinformatics network Biosapiens EU bioinformatics network Embrace EU bioinformatics network Genefun Scientific publications 2007 was a very fruitful year for SBC in terms of publications. Papers were published in top journals such as Nature, Science, PNAS, and Genome Research. Many of them represent collaborations with experimental groups, testifying to SBC's ability to apply new computational techniques to real-world biological problems. Being part of the ENCODE consortium for detailed analysis of the genome adds competence to the SBC that is valuable to many neighboring experimental groups, for instance KTH-biotechnology. From http://www.sbc.su.se/publications: Hessa, T., Meindl-Beinker, N.M., Bernsel, A., Kim, H., Sato, Y., Lerch-Bader, M., Nilsson, I., White, S.H. and von Heijne, G. (2007) Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature 450 (7172) : 1026-1030. 3 Xie, K., Hessa, T., Seppala, S., Rapp, M., Heijne, G. and Dalbey, R.E. (2007) Features of transmembrane segments that promote the lateral release from the translocase into the lipid phase. Biochemistry 46 (51) : 15153-15161. Lundin, C., Kall, L., Kreher, S.A., Kapp, K., Sonnhammer, E.L., Carlson, J.R., Heijne, G. and Nilsson, I. (2007) Membrane topology of the Drosophila OR83b odorant receptor. FEBS Lett 581 (29) : 5601-5604. Hollich, V. and Sonnhammer, E.L. (2007) PfamAlyzer: domain-centric homology search. Bioinformatics 23 (24) : 3382-3383. Wallner, B. and Elofsson, A. (2007) Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 69 (S8) : 184-193. Granseth, E., Seppala, S., Rapp, M., Daley, D.O. and Von Heijne, G. (2007) Membrane protein structural biology - How far can the bugs take us? (Review). Mol Membr Biol 24 (5) : 329-332. Newstead, S., Kim, H., von Heijne, G., Iwata, S. and Drew, D. (2007) High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 104 (35) : 13936-13941. Ekman, D., Bjorklund, A.K. and Elofsson, A. (2007) Quantification of the elevated rate of domain rearrangements in metazoa. J Mol Biol 372 (5) : 1337-1348. Andersson, S.A. and Lagergren, J. (2007) Motif yggdrasil: sampling sequence motifs from a tree mixture model. J Comput Biol 14 (5) : 682-697. Lundin, C., Johansson, S., Johnson, A.E., Naslund, J., von Heijne, G. and Nilsson, I. (2007) Stable insertion of Alzheimer Abeta peptide into the ER membrane strongly correlates with its length. FEBS Lett 581 (20) : 3809-3813. Bertaccini, E.J., Trudell, J.R. and Lindahl, E. (2007) Normal-Mode Analysis of the Glycine Alpha1 Receptor by Three Separate Methods. J Chem Inf Model 47 (4) : 1572-1579. Wallner, B., Larsson, P. and Elofsson, A. (2007) Pcons.net: protein structure prediction meta server. Nucleic Acids Res 35 (suppl_2) : W369-W374. Stenberg, F., von Heijne, G. and Daley, D.O. (2007) Assembly of the Cytochrome bo(3) Complex. J Mol Biol 371 (3) : 765-773. Elofsson, A. and Heijne, G. (2007) Membrane Protein Structure: Prediction versus Reality. Annu Rev Biochem 76: 125-140. Euskirchen, G.M., Rozowsky, J.S., Wei, C.L., Lee, W.H., Zhang, Z.D., Hartman, S., Emanuelsson, O., Stolc, V., Weissman, S., Gerstein, M.B., Ruan, Y. and Snyder, M. (2007) Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies. Genome Res 17 (6) : 898-909. Gerstein, M.B., Bruce, C., Rozowsky, J.S., Zheng, D., Du, J., Korbel, J.O., Emanuelsson, O., Zhang, Z.D., Weissman, S. and Snyder, M. (2007) What is a gene, post-ENCODE? History and 4 updated definition. Genome Res 17 (6) : 669-681. von Heijne, G. (2007) Membrane proteins up for grabs. Nat Biotechnol 25 (6) : 646-647. von Heijne, G. (2007) The membrane protein universe: what's out there and why bother? J Intern Med 261 (6) : 543-557. Julenius, K. (2007) NetCGlyc 1.0: prediction of mammalian C-mannosylation sites. Glycobiology 17 (8) : 868-876. Zhang, L., Sato, Y., Hessa, T., von Heijne, G., Lee, J.K., Kodama, I., Sakaguchi, M. and Uozumi, N. (2007) Contribution of hydrophobic and electrostatic interactions to the membrane integration of the Shaker K+ channel voltage sensor domain. Proc Natl Acad Sci U S A 104 (20) : 8263-8268. Sennblad, B., Schreil, E., Berglund Sonnhammer, A.C., Lagergren, J. and Arvestad, L. (2007) primetv: a viewer for reconciled trees. BMC Bioinformatics 8: 148. Kall, L., Krogh, A. and Sonnhammer, E.L. (2007) Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res 35 (suppl_2) : W429-W432. Vogt, G., Vogt, B., Chuzhanova, N., Julenius, K., Cooper, D.N. and Casanova, J.L. (2007) Gain-of-glycosylation mutations. Curr Opin Genet Dev 17 (3) : 245-251. Emanuelsson, O., Brunak, S., von Heijne, G. and Nielsen, H. (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2 (4) : 953-971. von Heijne, G. (2007) Formation of Transmembrane Helices In Vivo--Is Hydrophobicity All that Matters? J Gen Physiol 129 (5) : 353-356. Kutzner, C., Van Der Spoel, D., Fechner, M., Lindahl, E., Schmitt, U.W., De Groot, B.L. and Grubmuller, H. (2007) Speeding up parallel GROMACS on high-latency networks. J Comput Chem 28 (12) : 2075-2084. Wang, H., Julenius, K., Hryhorenko, J. and Hagen, F.K. (2007) Systematic Analysis of proteoglycan modification sites in Caenorhabditis elegans by scanning mutagenesis. J Biol Chem 282 (19) : 14586-14597.