3rd IS CB S t u d ent Co u ncil S ymp os ium Welcome To The 3rd ISCB Student Council Symposium! Welcome to the Student Council Symposium 3 (SCS3) in Vienna. The ISCB Student Council's mis- sion is to develop the next generation of computa- tional biologists. We would like to thank and ac- knowledge our sponsors and the ISCB organisers for their crucial support. The SCS3 provides an ex- citing environment for active scientific discussions and the opportunity to learn vital soft skills for a successful scientific career. In addition, the SCS3 is the biggest international event targeted to students in the field of Computational Biology. We would like to thank our hosts and participants for making this event educative and fun at the same time. Student Council meetings have had a rich Dear Delegates,history of productive scientific discussions of new challenging ideas and participants contributing from a wide range of interdisciplinary fields. Such meet- We are very happy to welcomeings have you proved all touseful the in ISCBproviding Student students Council and postdocs Symposium innovative inputsin Vienna. and an Afterincreased the network suc- cessful symposiums at ECCBof potential 2005 collaborators. in Madrid and at ISMB 2006 in Fortaleza we are determined to con- tinue our efforts to provide an event for students and young researchers in the Computational Biology community. Like in previousWe ar yearse extremely our excitedintention to have is toyou crhereatee and an the opportunity vibrant city of Vforienna students welcomes to you meet to our their SCS3 event. peers from all over the world for exchange of ideas and networking. With Janet Thornton and .Anna Tramontano we have invited two high-profile keynote speakers who have been involved in Computational Biology since its beginnings. Their keynotes promise to be a rich source of insight relevant to everyone in the field. Exciting new research results will be presented by 8 student authors who submitted outstanding work to the symposium. Overall we are pleasantly surprised by the quality and the number of abstracts that we received. A wide range of topic areas is covered and the poster session will offer exciting science for any kind of interest. While science clearly is a key aspect of the ISCB Student Council Symposium, our major goal is to foster career development of Computational Biologists. Our field is growing and expanding rapidly and this situation won’t change anytime soon. It is not straightforward for students and researchers early in their career to make the right decisions in times where there are seemingly endless opportunities. We hope that the program of the symposium will provide some clues on how to successfully navigate this entan- gled web of dead ends and promising career paths. In particular our panel discussion on “The Future of Bioinformatics” is intended to equip you with guidance, advice and ideas from top people in the field. We have panelists from a great diversity of backgrounds and careers such as Rita Casadio, Tan Tin Wee, Janet Thornton, Anna Tramontano and as moderator of the discussion Thomas Lengauer, Chair of ISMB/ ECCB 2007. Everyone involved in the organization of this symposium has made a significant effort to make this event happen. Our volunteers have spent many months preparing all aspects of this symposium ranging from the invitation of keynote speakers over fundraising, advertising, organization of the peer-review process and the panel discussion to such mundane things as maintaining a website. Most people on the organiz- ing committee have never met in person and email was the primary means of communication. Nonethe- less, our team has managed to create a unique event that so far has been very well received by the stu- dent community according to registration and submission numbers. Now it is up to you to make the most out of this opportunity. Talk to other delegates, ask your questions during the panel discussion and show enthusiasm about your research if you are presenting! You can 1 make this symposium a starting point for fruitful future collaborations and another step onto a successful career path in Computational Biology. Enjoy your time in Vienna! Nils Gehlenborg Manuel Corpas Conference Chair Conference Chair & ISCB Student Council Chair PS. This booklet went into print in early July. Please check http://www.iscbsc.org/scs3 for the latest updates and announcements. 3rd I S CB S t u d en t Co u n cil S ymp os iu m Acknowledgments The success of an event the size of the ISCB Student Council Symposium depends on the commitment of many. We would like to thank everyone involved in the organization this year for their contribution, be it a 15 minute job or months of work. For some efforts we are extraordinarily grateful and they deserve to be mentioned explic- itly: ‣ Without the logistical support and invaluable advice of ISCB Executive Administrator BJ Morrison McKay and ISMB/ECCB 2007 con- ference organizer Steven Leard the 3rd ISCB Student Council Symposium would not have been possible. We deeply appreciate their continued support of the ISCB Student Coun- cil and the symposium. ‣ We are also greatly indebted to ISMB/ECCB 2007 conference chairs Thomas Lengauer, Burkhard Rost and Peter Schuster for inviting us to have the 3rd ISCB Student Council Symposium in Vienna. Further, we would like to acknowledge the support of the ISCB Board of Directors and their trust in our vision. Special thanks go to Rita Casadio and Michal Linial, our Student Council Board of Directors liaisons, for their enthusiastic commitment to the mission of the Student Council. ‣ The Student Council would also like to thank our keynote speakers and panelists Janet Thornton and Anna Tramontano, panelists Rita Casadio and Tan Tin Wee and panel discus- sion moderator Thomas Lengauer as well as Reinhard Schneider for delivering the closing remarks. They are all very busy people, yet they are volunteering their time to contribute to the success of the symposium and to pro- mote the next generation of Computational Biologists. ‣ Furthermore, we would like to thank everyone on the program committee for their time and effort. All of our reviewers did a fantastic job and it's due to them that we stayed within our set deadlines. ‣ We thank Carey Briggs at the ISCB for sup- porting the review process and the production of this program booklet. We are grateful for the support of Sonja Hutter at Mondial Con- gress who provided us with delegate lists. ‣ We are extremely grateful for the financial support that we received from our sponsors. Without their help many of the exciting oppor- tunities that we offer to the delegates at the 3rd ISCB Student Council Symposium would not have been possible. 2 3rd IS CB S t u d en t Cou n cil S ymp os iu m Table of Contents Invited Speakers And Panelists 4 Agenda 7 Saturday, July 21st 7 Monday, July 23rd 8 Student Presentation Abstracts 9 Awards 10 Accepted Poster Abstracts 12 Arrays 12 Bioinformatics of Health & Disease 12 Biophysics 14 Comparative Genomics 14 Databases 14 Ecosystems & Ecology 14 Evolution 15 Gene Prediction 15 Genomics 15 Machine Learning 15 Ontologies 16 Other 16 Population Genetics & Variation 16 Regulation 17 Sequence Analysis 17 Structure & Function Prediction 17 Structure Prediction 18 Systems Biology & Networks 18 Text Mining 19 The ISCB Student Council 20 The Student Council Goes Local - Regional Student Groups 22 Singapore 23 India 23 Africa 24 Denmark 25 Canada 25 Organizing Committee 26 Program Committee 27 Delegates 29 Imprint 32 3 3rd I S CB S t u d en t Co u n cil S ymp os iu m Invited Speakers And Panelists KEYNOTE SPEAKER & PANELIST KEYNOTE SPEAKER & PANELIST PANELIST Janet Thornton Anna Tramontano Tan Tin Wee Director, European Bioinfor- Professor, University of Rome Assoc. Professor, National matics Institute, UK “La Sapienza”, Italy Univ. of Singapore, Singapore Janet Thornton has been Di- Anna Tramontano was trained Tan Tin Wee was educated in rector of the European Bioin- as a physicist but she soon Cambridge, London and Ed- formatics Instiute (EBI) since became fascinated by the inburgh and is currently a October 2001. Her active complexity of biology and by Member of the Institute of research group focuses on the promises of computa- Biology. He is an Associate using computational ap- tional biology. She worked at Professor in the Department proaches to understand biol- the Department of Biochem- of Biochemistry, Faculty of ogy (especially proteins) at istry and Biophysics of UCSF Medicine at the National Uni- the molecular level, and her where she collaborated in the versity of Singapore (NUS). research combines the use of development of the very He has consistently received genomic, transcriptomic, popular molecular graphics national, regional and interna- structural and metabolomic tional recognition such as the data with the aim of discover- software “Insight”. Later she was a staff scientist in the Singapore Youth Award for ing how molecules interact to excellence (1994), Vaccine perform their functions, and Biocomputing Programme of the EMBL, where she studied Research Trust Annual Award how these functions evolved. (1989), Japan Chamber of Under her directorship, the the sequence structure rela- tionship in immunoglobulin Commerce and Industry EBI has expanded into sev- (JCCI) Education award molecules. In 1990 she eral new research areas and (1997), ASEAN Business Fo- has secured funding to pro- moved back to Italy in the rum’s ASEAN Achievement vide space for its burgeoning Merck Research Laboratories Award (1997), National Uni- staff base. She works tire- near Rome, where she was versity of Singapore Annual lessly to raise awareness of involved in protein structure the need for a stable Bioin- Staff Achievement Award modelling and design, and in (1998), World Congress for formatics infrastructure in drug and vaccine discovery Europe.