Dear Delegates,History of Productive Scientiﬁc Discussions of New Challenging Ideas and Participants Contributing from a Wide Range of Interdisciplinary ﬁelds

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 mission is to develop the next generation of computational biologists. We would like to thank and acknowledge our sponsors and the ISCB organisers for their crucial support. The SCS3 provides an exciting 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 successful 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 organizing 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 student 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 conference 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 discussion 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 promote 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 opportunities 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. For instance, she is Medical Informatics MEDIN- and development. She is now FO’92 Gold Medal and a currently coordinating BioSa- Professor of Biochemistry at piens, a European-Union- member of the exclusive “La Sapienza” University in funded Network of Excel- World Technology Network Rome where she continues to lence. Janet Thornton is a (2001) as one of 450 top sci- Fellow of the Royal Society, a pursue her scientiﬁc interests entists, entrepreneurs ﬁnan- Member of the European Mo- on protein structure predic- ciers, journalists, academics lecular Biology Organization, tion and analysis. She was an and policy makers world a Foreign Associate of the US ISCB Vice President and she wide. He is also entrepreneu- National Academy of Sci- won the Marotta Prize of the rial, having spun off or been ences and a Commander of National Academy of Science involved with several compa- the British Empire. in 2001. nies.

4 3rd IS CB S t u d en t Cou n cil S ymp os iu m

PANELIST PANEL DISCUSSION MODERATOR CLOSING REMARKS Rita Casadio Thomas Lengauer Reinhard Schneider Professor, University of Bolo- Director, Max Planck Institute Team Leader, EMBL Heidel- gna, Italy for Informatics, Germany berg, Germany

After her undergraduate de- Thomas Lengauer is Director Reinhard Schneider com- gree in Physics in 1973, Rita at the Max-Planck Institute for pleted his PhD in Biology at Casadio obtained a resear- Informatics in Saarbrucken, the University of Heidelberg ch fellowship at the University Germany. His background is and the European Molecular of Bologna. In 1978 - 1979 in Mathematics (PhD Berlin) Biology Laboratory (EMBL) she spent some time at and Computer Science (PhD followed by postdoctoral re- the Cardiovascular Research Stanford). He has been en- search at EMBL Heidelberg. Institute of the University of gaged in research in Compu- He is an entrepreneur and California, San Francisco, tational Biology since the be- has co-founded many com- where she worked on the ginning of the 1990s. His ma- panies such as LION biosci- characterization of bacteri- jor focuses of research are ence AG, OnScale solutions, orhodopsin, a light-driven protein bioinformatics, com- Certon Systems and was the transmembrane proton putational drug screening and Chief Information Officer of pump. She was the recipient design and bioinformatics for LION bioscience AG, Ger- of an EMBO fellowship to understanding and curing many, Chief Executive Officer work on the characterization diseases. Previously, he held of LION bioscience Research of the conformational the positions of a full profes- Inc., Cambridge, MA, USA changes of the proton ATP- sor at the University of Pad- and Xapien GmbH, Heidel- ase in bacterial membranes erborn, Germany and of a berg, Germany. He has also at the University of Osn- Director of the Institute for provided consulting services abruck, Germany. Back in Algorithms and Scientific to research-based compa- Italy, she worked at the Uni- Computing at the German nies. Since 2004 he has been versity of Bologna as a re- National Research Center for a Team Leader at EMBL Hei- searcher in Biophysics and Computer Science. Thomas delberg. His group’s prime was involved in different pro- Lengauer is a founding mem- goal is to develop a compre- jects aimed at the characteri- ber of the ISCB and he hensive knowledge platform zation of the water- headed the steering board of for the life sciences, focusing membrane interface in bio- the ECCB conference series on the biology-driven re- logical membranes. Since since its foundation in 2002 search areas. The group 1993 she is group leader of until 2005. In 2003 he re- deals with advanced data the Biocomputing Unit at the ceived the Konrad Zuse mining, visualization, data Interdepartmental Centre for Medal of the German Infor- integration and knowledge Biotechnological Researches matics Society and the Karl management. Reinhard (CIRB) of the University of Heinz Beckurts Award. He is Schneider is currently a Vice Bologna, Italy. In 2001 Rita a member of the German President of the ISCB, mem- became full professor of Bio- Academy of Sciences Leo- ber of the ISCB Board of Di- physics at Bologna University. poldina. He is co-chair of rectors and chair of the Gov- ISMB/ECCB 2007. ernance Committee.

5 3rd IS CB S t ud ent Co uncil S ymp os ium

Welcome To The 3rd ISCB Student Council Symposium!

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 history of productive scientiﬁc discussions of new challenging ideas and participants contributing from a wide range of interdisciplinary ﬁelds. Such meetings have proved useful in providing students and postdocs innovative inputs and an increased network of potential collaborators.

We are extremely excited to have you here and the vibrant city of Vienna welcomes you to our SCS3 event.

A d ver t is emen t

6 3rd IS CB S t u d en t Cou n cil S ymp os iu m Agenda

Saturday, July 21st

Time Location

8:30 am Hall E1 WELCOME Opening Remarks Student Council Representative

8:40 am Hall E1 KEYNOTE Comparative Functional Genomics of Ageing Janet Thornton

9:20 am Hall E1 STUDENT PRESENTATIONS Semi-supervised class discovery using quantitative phenotypes - CVD as a case study Roy Navon

Genomic Scale Analysis of Lateral Gene Transfer in Apicomplexan Parasites: insights into early eukaryotic evolution, host-pathogen interaction and drug target development Lucia Peixoto

Towards interoperability between anatomy and phenotype ontologies Robert Hoehndorf

Variation of Geometrical and Physicochemical Properties in Protein Binding Pockets and their Ligands Abdullah Karhaman

10:40 am Hall E1 COFFEE BREAK

11:10 am Hall E1 STUDENT PRESENTATIONS What is the response? Identifying interesting behaviour in microarray time series data Katherine Lawler

ChIP-on-chip signiﬁcance analysis reveals ubiquitous transcription factor binding Adam Margolin

Mining expression-dependent modules in the human interaction network Elisabeth Georgii

Combining dissimilarity based classiﬁers for cancer prediction using gene expression proﬁles Angela Blanco

12:30 pm TBA LUNCH BREAK

1:10 pm TBA QUICKFIRE SESSION

1:30 pm TBA POSTER SESSION

3:00 pm Hall E1 SPECIAL SESSION BioWiki Contest: an Openfree Project for Bioknowledge Sharing Jong Bhak

3:20 pm Hall E1 KEYNOTE Structural Bioinformatics: Shortcuts and Pitfalls Anna Tramontano

4:00 pm Hall E1 AWARDS CEREMONY

4:10 pm Hall E1 PANEL DISCUSSION The Future of Bioinformatics Rita Casadio, Tan Tin Wee, Janet Thornton, Anna Tramontano and Thomas Lengauer (Moderator)

4:50 pm Hall E1 GOOD BYE Closing Remarks Reinhard Schneider

Panel Discussion own research. However, it is crucial to be aware One of the major goals of the Student Council is of the directions into which the ﬁeld is developing to promote the career development of students in order to make the right career decisions. As the and young researchers in Bioinformatics and ﬁeld grows several challenges become apparent: Computational Biology. In the early stages of a How are we going to integrate all the data we are career it is simple to get lost in the details of one's generating? How are we going to more effectively

7 3rd I S CB S t u d en t Co u n cil S ymp os iu m integrate in silico predictions with in vitro and in ute. If there are issues that you would like to raise vivo experiments? That's why the Student Coun- don't hesitate to ask. cil has invited a group of high-profile scientists to The panel discussion promises to be one of the join us for a panel discussion on "The Future of highlights of this year's Student Council Sympo- Bioinformatics". sium. Don't miss this chance to hear from current Rita Casadio and Tan Tin Wee will join keynote leaders in the field about the challenges the next speakers Janet Thornton and Anna Tramontano generation will be facing! to discuss the key issues that Bioinformaticians Quickfire Session and Computational Biologists will be facing in the years to come. Thomas Lengauer, Co-Chair for The Quickfire Session will give everyone who is ISMB/ECCB 2007, will moderate this session. interested up to 1 minute to introduce themselves The discussion will be interactive and the dele- and their poster to the other delegates at the gates will have plenty of opportunities to contrib- symposium. Please sign up during the first coffee break.

Monday, July 23rd

Time Location

12:15 pm Hall A/B/C EVERYBODY WELCOME Student Council Open Meeting Student Council Representatives

9:00 pm Xpress127 NETWORKING Social Event at Xpress127 Students at ISMB/ECCB 2007

Student Council Open Meeting Xpress127 Dance Club, Café, Restaurant & Pub. The aim of this meeting is to understand the There will be plenty of opportunities for meeting needs of the global and local student communi- other students from around the world attending ties and to provide an environment that fosters the Student Council Symposium and ISMB/ the development of new networking opportunities ECCB 2007. Xpress127 offers inside and outside and projects for those interested in the commu- seating areas, several bars and a selection of nity. food. A DJ will be spinning Latino and Disco mu- For this event the Student Council is very eager to sic. There won’t be a cover at the door but please invite students, postdocs and researchers in gen- note that you will be responsible for your own bill. eral. Some initiatives that the Student Council is keen to hear from and to collaborate with involve outreach activities of research institutions and LOCATION companies, recruitment openings and educa- Xpress127 tional programs. Handelskai 127 We recognize we are the premier international 1200 Wien student network in the ﬁeld and hope to encour- TELEPHONE age lively discussions on how to deliver more ef- +43-133-20777 fectively our current services to Student Council WEB members and the general student community. http://www.xpress127.at An overview of the past year’s achievements in terms of our mission and projects is on the GETTING THERE FROM ISMB/ECCB 2007 agenda as well as introduction of Student Council Walk to subway stop Kaisermühlen-VIC leaders and acknowledgment of their contribu- Get on subway U1 → Reumannplatz tions. The largest part of the meeting will be set Exit at Vorgartenstraße for discussion time and suggestions from the Transfer to Bus 11a → Heiligenstadt audience. Exit at Engerthstraße/Innstraße Walk to Handelskai 127 (~ 2 min) Social Event at Xpress127 GETTING THERE FROM ELSEWHERE The Student Council invites you to attend a net- http://efa.vor.at/wvb/index_en.htm working and social event on Monday night at the

8 3rd IS CB S t u d en t Cou n cil S ymp os iu m Student Presentation Abstracts

(1) BIOINFORMATICS OF HEALTH AND DISEASE (5) ARRAYS Semi-supervised class discovery using What is the response? Identifying interesting quantitative phenotypes - CVD as a case behaviour in microarray time series data study Katherine Lawler, Alvis Brazma Roy Navon, Israel Steinfeld, Zohar Yakhini, Diego European Bioinformatics Institute, United King- Ardigo, Ivana Zavaroni dom Agilent Technologies / Tel Aviv University, Israel Microarray studies frequently produce short time series of Genomic studies typically focus on comparing disease to healthy population. In our work, various parameters were fewer than 20 timepoints for thousands of genes. It remains a stratified solely from healthy subjects including expression challenging problem to make statistically sound inferences profiling of their PBM cells. We present a semi-supervised from these short time series. Here we ask: given a microarray class discovery, constraining the search space to patterns timecourse experiment, which genes are showing a response, that respect an order induced by the rich quantitative annota- and what is that response? tions. (6) ARRAYS (2) EVOLUTION ChIP-on-chip significance analysis reveals Genomic Scale Analysis of Lateral Gene ubiquitous transcription factor binding Transfer in Apicomplexan Parasites: insights Adam Margolin, Teresa Palomero, Adolfo Fer- into early eukaryotic evolution, host- pathogen interaction and drug target devel- rando, Andrea Califano, Gustavo Stolovitzky opment Columbia University, United States Lucia Peixoto, David Roos We present a novel statistical method for inferring significance University of Pennsylvania, United States of transcription factor / target interactions measured by ChIP- The phylum Apicomplexa comprises >5000 species, including on-chip experiments. We infer an order of magnitude more Toxoplasma gondii and Plasmodium parasites responsible for interactions than traditional methods, and predictions are malaria. Lateral Gene Transfer (LGT) is believed to have been confirmed by ChIP / qPCR experiments, binding site enrich- an important force driving apicomplexan evolution. Whole ment analysis, and gene expression profiling upon TF inhibi- genome phylogenetic analyses for T. gondii and P. falciparum tion. were performed; results suggest LGT as a prominent force in parasite evolution. (7) SYSTEMS BIOLOGY & NETWORKS Mining expression-dependent modules in (3) ONTOLOGIES Towards interoperability between anatomy the human interaction network and phenotype ontologies Elisabeth Georgii, Sabine Dietmann, Koji Tsuda Robert Hoehndorf, Janet Kelso, Frank Loebe, MPI for Biological Cybernetics, Friedrich Miescher Heinrich Herre Laboratory of the Max Planck Society, Germany Max Planck Institute for Evolutionary Anthropol- We present a novel approach for detecting functional modules ogy, Germany by integrating static information from protein interaction net- Achieving interoperability between biomedical ontologies is a works with gene expression data. Our method discovers sets highly desired state of affairs. We identify a major problem for of interacting proteins that occur specifically in subsets of the interoperability between biomedical ontologies. The com- cellular conditions. The enumerative algorithm based on item- mon use of anatomy ontologies together with phenotype set mining allows to integrate several heterogeneous data ontologies may lead to inconsistencies. We provide a solution sets. to this problem through the use of an extended logical framework for representing ontologies. (8) MACHINE LEARNING Combining dissimilarity based classifiers for (4) STRUCTURE AND FUNCTION PREDICTION Variation of Geometrical and Physicochemi- cancer prediction using gene expression cal Properties in Protein Binding Pockets profiles and their Ligands Angela Blanco, Manuel Martin-Merino, Javier De Abdullah Kahraman, Richard J. Morris, Roman A. Las Rivas Laskowski, Janet M. Thornton Universidad Pontificia de Salamanca, Spain European Bioinformatics Institute, United King- Machine learning techniques allow to identify cancerous tis- dom sues using gene expression profiles. However, the techniques The variation of the ligand and binding pocket shape together proposed in the literature fail to identify cancerous tissues with the variation of the hydrophobicity, van-der-Waals and (false negative errors) which is a serious drawback. To over- electrostatic potential on the ligand surface were analysed in come this problem we present a new classification scheme different proteins. A correlation between ligand and binding that combines different dissimilarities to reduce particularly site could be detected only for shape and hydrophobicity indicating their importance for molecular recognition. false negative errors.

9 3rd I S CB S t u d en t Co u n cil S ymp os iu m Awards

Like in previous years the Student Council has Student Council Travel Fellowships teamed up with sponsors to award prizes for The winners of the travel fellowships were se- presentations and posters of outstanding quality. lected by a committee based on the abstracts For the ﬁrst time in the history in the ISCB Stu- they had submitted and based on their CVs. Due dent Council Symposium we were able to give to funding restrictions only students from EU- and away 5 travel fellowships to undergraduate and EMBC countries were eligible. master’s level students to come to the symposium and to ISMB/ECCB 2007. VALUE OF AWARD Best Presentation Award £400 (~$780)

All student presenters are eligible for this award (1) SPONSOR and the winner will be selected by the delegates European Bioinformatics Institute and a jury.

VALUE OF AWARD £200 (~$390)

(1) SPONSOR Oxford Journals Bioinformatics The winners of the 2007 ISCB Student Council Travel Fellowships are: Maital Ashkenazi The Hebrew University Jerusalem, Israel

PREVIOUS WINNERS Pavol Hanus, 2006 TU Munich, Germany Javier Carrera Universidad Politecnica Valencia, Best Poster Award Spain All posters that have been accept through peer- review are eligible for this award and the winner and runner-up will be selected by the delegates and a jury. Inigo Ortiz de Mendibil Ayuso University of Navarra, Spain VALUE OF AWARD £200 (~$390) £100 (~$195), Runner-Up

(1) SPONSOR BMC Bioinformatics Teresa Szczepinska VU University Amsterdam, The Netherlands and Warsaw University, Poland

Nurcan Tuncbag Koc University, Turkey PREVIOUS WINNERS Feng Chen, 2006 University of Pennsylvania, USA

10 3rd IS CB S t u d en t C ou ncil S ymp os ium

Welcome To The 3rd ISCB Student Council Symposium!

We are extremely excited to have you here and the vibrant city of Vienna welcomes you to our SCS3 event.

A d ver t is emen t

11 3rd I S CB S t u d en t Co u n cil S ymp os iu m Accepted Poster Abstracts

Arrays (5) ARRAYS ChIP-on-chip significance analysis reveals (1) ARRAYS ubiquitous transcription factor binding GEO Import Adam Margolin, Teresa Palomero, Adolfo Fer- Faisal Rezwan, Helen Parkinson, Alvis Brazma rando, Andrea Califano, Gustavo Stolovitzky European Bioinformatics Institute, United King- Columbia University, United States dom We present a novel statistical method for inferring significance To analyze data in GEO (Gene Expression Omnibus) at Na- of transcription factor / target interactions measured by ChIP- tional Center for Biotechnology Information (NCBI) and design on-chip experiments. We infer an order of magnitude more a set of rules how data can be mapped to ArrayExpress (at interactions than traditional methods, and predictions are European Bioinformatics Institute, EMBL-EBI) infrastructure, in confirmed by ChIP / qPCR experiments, binding site enrich- particular the data warehouse and the repository and to im- ment analysis, and gene expression profiling upon TF inhibi- port some GEO data tion. (6) ARRAYS (2) ARRAYS What is the response? Identifying interesting An Optimized Oligonucleotide Array Design behaviour in microarray time series data for ChIP-on-chip Katherine Lawler, Alvis Brazma Fiona Nielsen, Stefan Graef, Xinmin Zhang, Ste- European Bioinformatics Institute, United King- fan Kurtz, Sergei Denisov, Roland Green, Ewan dom Birney, Paul Flicek, Martijn Huynen, Henk Stun- Microarray studies frequently produce short time series of nenberg fewer than 20 timepoints for thousands of genes. It remains a NCMLS, Radboud Universiteit Nijmegen, Nether- challenging problem to make statistically sound inferences lands from these short time series. Here we ask: given a microarray timecourse experiment, which genes are showing a response, We have developed a new oligonucleotide array design algo- and what is that response? rithm using a novel approach to evaluate sequence unique- ness. Using this algorithm, we have tested the performance of different designs in order to optimise the design parameters Bioinformatics of Health & Disease towards minimal noise and maximal genome coverage. (7) BIOINFORMATICS OF HEALTH AND DISEASE (3) ARRAYS Virtual Screening on HIV-1 Reverse Tran- Meta-analysis of six Thyroid Tumor Microar- scriptase Inhibitors ray Datasets: a one-gene Classifier (SERPI- Jyotika Singh, Sudhir Kumar NA1) for Papillary Thyroid Carcinoma Indian Agricultural Research Institute, India Klemens Vierlinger, Martin Lauss, Christa Nˆham- Acquired Immunodeficiency Syndrome (AIDS) epidemic has mer, Klaus Kaserer, Bruno Niederle, Friedrich affected human lives in both developed and developing coun- Leisch tries equally. The causative agent for this dreaded disease is a virus called HIV (Human Immunodeficiency Virus). The enzyme ARCS, Austria reverse transcriptase (RT) plays an important role in its activity. A Microarray meta-analysis approach revealed a large abun- High-throughput screening (HTS) has been advantageous dance of discriminative genes between papillary thyroid dis- over traditional methods of screening in ease and benign thyroid across 4 distinct datasets. After data integration using DWD, even a single gene (SERPINA1) could (8) BIOINFORMATICS OF HEALTH AND DISEASE correctly identify 99% of thyroid samples. T2DM-GeneMiner a web resource for meta- analysis and marker identification for type 2 (4) ARRAYS puma: a Bioconductor package for Propa- diabetes mellitus Axel Rasche, Ralf Herwig gating Uncertainty in Microarray Analysis Richard Pearson, Xuejun Liu, Guido Sanguinetti, MPI Molecular Genetics, Germany Marta Milo, Neil Lawrence, Magnus Rattray Multiple functional genomics data for type 2 diabetes mellitus we joined in a meta-analysis approach for scoring genes. We University of Manchester, United Kingdom derived a set of 213 disease relevant genes, whereon func- Most analyses of microarray data are based on point esti- tional information on cellular networks is extrapolated. A web mates of expression levels and ignore the uncertainty of such interface allows screening of a gene in the underlying data. estimates. By propagating uncertainty to downstream analyses we can improve results. For the first time, the puma package makes a suite of uncertainty propagation methods freely available to a general audience.

12 3rd IS CB S t u d en t Cou n cil S ymp os iu m

(9) BIOINFORMATICS OF HEALTH AND DISEASE (13) BIOINFORMATICS OF HEALTH AND DISEASE PIDexpert decision support system for im- A network of protein domains that are pre- munodeficiencies sent in chimeric tyrosine-kinase proteins in Crina Samarghitean, Kirsi Varpa, Kati Iltanen, cancer Merja Helminen, Mauno Vihinen Inigo Ortiz de Mendibil Ayuso, Jose Luis Vizma- Institute of Medical Technology, University of nos, Francisco Novo Tampere, Finland University of Navarra (UNAV), Spain PIDexpert is a medical expert system, which help physicians Because of the presence of fusion proteins, with TK activity, in the diagnosis and treatment of primary immunodeficiencies. implicated in different types of tumors,a collection of gene- It gives the diagnostic picture based on clinical history, physi- mapped translocation breakpoints was created, called TICdb. cal findings and laboratory tests. PIDexpert includes a knowl- Using TICdb, a network of genes translocated in cancer was edge base, a query base, a knowledge acquisition system, an also created focused on the part of this network that includes inference engine and a user interface. genes coding for TKs.

(10) BIOINFORMATICS OF HEALTH AND DISEASE (14) BIOINFORMATICS OF HEALTH AND DISEASE Large-scale design of primers for genes A method for estimating the number of from atypical plants peaks in liquid chromatography-mass spec- Imen Riani trometry data sets Institut Pasteur de Tunis, Tunisia Teresa Szczepinska, Sander Piersma, Marius Co- Abstract: Salinity is one of the principal barriers in the intensiﬁ- drea, Jaap Heringa, Elena Marchiori cation of the cultivation of cereals. Currently several genes VU University Amsterdam, Netherlands involved in the tolerance with salinity were characterized We propose a method for estimating the number of peaks in Arabidopsis,whereas little is known about these genes in LC-MS data, to be used in algorithms for simultaneous peak cereals and others monocotyledones because of the lack of detection and alignment based on clustering. The method can sequence data. We propose here the protocol for systematic be embedded as a part of a computational tool for disease bioinformatic analysis of the orthologs of Arabidopsis thaliana, biomarker detection. Oryza sativa (abundantly studied) and Populus trichocarpa genes in plants (maize, tomato, citrus, olives, and dates), and to store the results in a database freely available via the Web. (15) BIOINFORMATICS OF HEALTH AND DISEASE In silico knock out screening of the meta- (11) BIOINFORMATICS OF HEALTH AND DISEASE bolic network of Plasmodium falciparum to A procedure to decompose high resolution yield Potential Drug Targets mass spectra Segun Fatumo, Ezekiel Adebiyi Nicola Barbarini, Paolo Magni, Riccardo Bellazzi Covenant University, Nigeria University of Pavia, Italy Plasmodium falciparum is responsible for nearly all malaria- In the present work, we will propose a novel strategy to de- related deaths. We constructed the metabolic network and compose high resolution SELDI/MALDI-TOF mass spectra developed a tool which analyzes metabolic pathways of plas- obtained from a mixture of pepitdes/proteins by grouping modium falciparum and then identify essential reactions/ together the mass/charge ratios corresponding to the same enzymes that may be considered as drug targets. Some reac- protein, exploiting the available knowledge on MS technique, tions were identiﬁed as essential for survival or growth of the chemistry of proteins and statistical considerations. organism.

(16) BIOINFORMATICS OF HEALTH AND DISEASE (12) BIOINFORMATICS OF HEALTH AND DISEASE Computational Cancer Genomics from a A Systematic Strategy for Large-Scale Systems-Biologic Perspective: From Se- Analysis of Genotype-Phenotype Correla- quence and Function to Pathways and Net- tions works Paul Fisher, Cornelia Hedeler, Katherine Wolsten- Jimmy Lin, Bert Vogelstein, Ken Kinzler, Laura croft, Helen Hulme, Harry Noyes, Stephen Kemp, Wood, Nickolas Papadopoulos, Will Parsons, Robert Stevens, Andrew Brass Sian Jones, Susan Zhang, Tobias Sjoblom, Victor Univeristy of Manchester, United Kingdom Velculescu, Giovanni Parmigiani, Christine Gan It is increasingly common to combine Quantitative Trait Loci Johns Hopkins Medical Institutions, United States and Microarray data to aid in the search for candidate genes responsible for phenotypic variation. Workﬂows provide a We present a comprehensive systems-biologic analysis of the means for systematically processing these large datasets and breast and colorectal cancer genomes (Sjˆblom et al. 2006). represent a framework for the re-use and the explicit declara- We identiﬁed top candidate sequence similarity clusters, pro- tion of experimental methods. tein domains, functional groups, protein-protein networks, interactome hubs, and pathways, that are likely to play a role in carcinogenesis and malignant progression.

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(17) BIOINFORMATICS OF HEALTH AND DISEASE (21) DATABASES Semi-supervised class discovery using Multimedia based diagnostic tools for lepi- quantitative phenotypes - CVD as a case dopterous insect pests identification of study vegetables Roy Navon, Israel Steinfeld, Zohar Yakhini, Diego Rajesh Kumar Rajesh, V.V. Ramamurthy, Neeraj Ardigo, Ivana Zavaroni Kumar, Gaurav Sharma, Vishal Mittal Agilent Technologies / Tel Aviv University, Israel Indian Agricultural Research Institute, India Genomic studies typically focus on comparing disease to Biosystematic studies lead to the illustration of taxonomic healthy population. In our work, various parameters were characters of major lepidopterous pest species occurring in stratified solely from healthy subjects including expression vegetable agroecosystems. The order Lepidoptera consists of profiling of their PBM cells. We present a semi-supervised butterflies and moths, their immature stages are more de- class discovery, constraining the search space to patterns structive to agricultural crops. These identification keys first that respect an order induced by the rich quantitative annota- tabulated in MS-Access format then suitably programmed tions. with visual basic.

Biophysics (22) DATABASES g:Profiler - A web-based toolset for func- (18) BIOPHYSICS tional profiling of gene lists from large-scale The Role of Long and Short Range Interac- experiments tions on the Denatured State of Peptide Juri Reimand, Jaak Vilo Oligomers University of Tartu, Estonia Ozge Engin, Mehmet Sayar, Burak Erman g:Profiler is a web toolkit for characterising high-throughput Koc University, Turkey gene lists. It retrieves statistically significant Gene Ontology terms, biological pathways, and Transfac motifs to genes, The relative contributions of long and short range interactions proteins or microarray probes, allows ranked lists analysis, on the denatured state of peptide oligomers are investigated multiple testing corrections, interactive visualisation, etc. The with the rotational isomeric states model. A coarse-grained toolkit also provides ID conversions, ortholog mappings and model based on a modified Markov assumption for peptides expression similarity search. is developed,which captures the conformations of short peptide oligomers successfully. (23) DATABASES HotSprint: Database of Computational Hot Comparative Genomics Spots at Protein Interfaces Emre Guney, Nurcan Tuncbag, Attila Gursoy, (19) COMPARATIVE GENOMICS Computational identification of fungal ge- Ozlem Keskin nomes by an innovative methodology. Koc University, Turkey Sudheer Menon, Gopal Prasad Agarwal HotSprint is a database of computational hot spots at protein Indian Institute of Technology - Delhi, India interfaces extracted from the multi-chain structures in Protein Data Bank (PDB). Hot spots are predicted based on sequence conservation and solvent accessibility of interface residues. The predicted hot spots are observed to correlate Databases with the experimental hot spots. (20) DATABASES Ecosystems & Ecology SAALSA, a UniProtKB/Swiss-Prot curator assistant for structural data integration (24) ECOSYSTEMS & ECOLOGY Fabrice David, Fabrice P.A. David, Anne-lise Toxin mediated interactions in view of the Veuthey, Yum Lina Yip Rock Paper Scissors game Swiss Institute of Bioinformatics, Switzerland Gunter Neumann SAALSA (Semi-Automatic Annotation from Local Structural Numerical Mathematics, Germany Analysis) is a web-based interface designed to help annota- Starting from biological ground principles, we determine evo- tion of proteins in UniProtKB/Swiss-Prot using structural data. lutionary stable states or pathways in the space of traits in This application gathers and crosschecks the information bacteria interacting with bacteriocines. As target dynamics we available from different structures Built-in annotation rules and get Zeeman class 33. This implies that all toxin mediated sequence to structure mappings enforce the consistency in interactions tend to a stable coexistive fixed point, if reason- lines describing protein features. able biological relations between the parameters are as- sumed.

14 3rd IS CB S t u d en t Cou n cil S ymp os iu m Evolution Genomics

(25) EVOLUTION (29) GENOMICS Genomic Scale Analysis of Lateral Gene Overlapping Alternative Donor Splicing Sites Transfer in Apicomplexan Parasites: insights Ekaterina Ermakova, Ramil Nurtdinov, Mikhail into early eukaryotic evolution, host- Gelfand pathogen interaction and drug target devel- Institute for Information Transmission Problems opment (Kharkevich Institute), Russian Academy of Sci- Lucia Peixoto, David Roos ences, Russia University of Pennsylvania, United States Overlapping alternative donor and acceptor sites may have The phylum Apicomplexa comprises >5000 species, including different functional roles: alternative splicing of overlapping Toxoplasma gondii and Plasmodium parasites responsible for acceptor sites mainly leads to microvariations in protein se- malaria. Lateral Gene Transfer (LGT) is believed to have been quences, whereas alternative donor sites often lead to frame- an important force driving apicomplexan evolution. Whole shifts and thus either yield major differences in protein se- genome phylogenetic analyses for T. gondii and P. falciparum quence and structure, or generate NMD-inducing mRNA were performed; results suggest LGT as a prominent force in isoforms. parasite evolution. (30) GENOMICS (26) EVOLUTION Improved prediction of conserved exon Changes in Transcriptional Enhancer Activity skipping using Bayesian Networks of the Second-Fastest Evolving Human Ge- Rileen Sinha, Ulrike Gausmann, Michael Hiller, nomic Region Rainer Pudimat, Stefan Schuster, Matthias Courtney Onodera, Sara Sowko, Bryan King, Ar- Platzer, Rolf Backofen men Shamamian, Matthew Weirauch, Sofie Leibniz Institute Institute for Age Research - Fritz Salama, David Haussler Lipman Institute, Germany University of California, Santa Cruz, United States We used Bayesian Networks, a state of the art machine learn- We demonstrate the second-fastest-evolving human genomic ing tool, to accurately distinguish between alternative and region, HAR2, exhibits transcriptional enhancer activity in constitutive human exons. Using a combination of previously mouse embryonic stem cells given a luciferase reporter; fur- described features and novel ones, we were able to achieve a ther, the chimpanzee and human versions show differing ac- performance competitive with the state of the art from the tivities. We attempt to reconstitute human-like activity in literature. chimpanzee HAR2 with site-directed mutagenesis informed by transcription factor binding site analysis. (31) GENOMICS Tag-Based Approaches for the Detection of Gene Prediction Cis-Encoded Antisense Transcription Anca Petrescu, Marco Marra, Allen Delaney (27) GENE PREDICTION Universiy Of British Columbia, Canada Gene analysis of a newly isolated lassa virus To create a genome-wide catalog of accurate gene expres- strain sion profiles for mammalian sense-antisense transcripts, we Lawrence Okoror, Fred Esumeh, Hilary Alaiya analyzed over 200 publicly available LongSAGE libraries and Ambrose Alli University, Nigeria one Solexa-SAGE library. We found that more than half of the EnsEMBL genes have evidence for antisense transcription Lassa virus is the cause of morbidity and mortality in parts of throughout mouse development. West Africa with yearly out breaks. We analyse the gene of a newly isolated strain Ng04-02 using global alignment, multiple sequence alignment, gene ontology (amigo), genscan, fge- Machine Learning nesh, geneid. From this we suggest that the yearly out break new strains which evade circulating antibodies. (32) MACHINE LEARNING Modeling substrate specificity of human (28) GENE PREDICTION dipeptidyl-peptidase III using Random For- Defining The Secretome: A Gene Model Ex- ests tender For Secreted Proteins Fran Supek, Marija Abramic, Tomislav Smuc Zhongqiang Chen, Amit Bahl, Axel Bernal, Qian Rudjer Boskovic Institute, Croatia Liu, Manami Nishi, Bo Wu, Fernando Pereira, Substrate specificity of the human dipeptidyl-peptidase III has David Roos been modeled using Random Forests on representations of University of Pennsylvania, United States amino acids by three general physicochemical properties. Site Successful identification of secreted proteins (the secretome) P1 has a strong impact on peptide binding affinity, but does requires accurate gene model prediction, particularly for the not affect cleavage. A hydrophobic amino acid at site P1í is first exon, which encompasses most signal peptides. We favorable for both processes. have developed an automated method for correcting gene predictions to identify coding exons containing secretory (or other) signals, utilizing both inter-species (comparative genomics) and intra-species information.

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(33) MACHINE LEARNING Other Combining dissimilarity based classifiers for cancer prediction using gene expression (37) OTHER profiles Analysis of mass spectrometry data using Angela Blanco, Manuel Martin-Merino, Javier De sub-spectra and wavelets Las Rivas Wouter Meuleman, Marcel Reinders, Lodewyk Universidad Pontificia de Salamanca, Spain Wessels Machine learning techniques allow to identify cancerous tis- Netherlands Cancer Institute / Delft University of sues using gene expression profiles. However, the techniques Technology, Netherlands proposed in the literature fail to identify cancerous tissues SELDI mass spectra are constructed from single-shot sub- (false negative errors) which is a serious drawback. To over- spectra, exhibiting varying noise and signal levels. We analyse come this problem we present a new classification scheme these sub-spectra separately using wavelets and combine that combines different dissimilarities to reduce particularly findings afterwards. This approach provides statistical mean- false negative errors. ing to found peaks, increases sensitivity and specificity, and removes the need for ad hoc noise removal methods. (34) MACHINE LEARNING Using Gene Regulatory Networks to Study (38) OTHER Gene Interactions in Human Liver Cancer Rapid prototyping of a docking algorithm Ibrahim Emam, Rasha Mokhtar, Ashraf Abdelbar using the BALL library The American University in Cairo, Egypt Christine Hedderich, Oliver Kohlbacher, Andreas A Bayesian network model was used to build two gene net- Hildebrandt works for a set of proliferation genes to compare gene inter- Saarland University, Germany actions in normal liver tissue versus Human Hepatocellular Carcinoma(HCC) caused by HCV. Results provided valid bio- In this work, we report on an implementation and extension of logical hypotheses about tumor development in HCC, which the Stochastic Roadmap-approach to protein docking (Apay- might lead to new drug targets. din et al.), performed as the first author's master's thesis. Our work demonstrates that the Biochemical ALgorithms Library, BALL, significantly reduces development time and gives easy (35) MACHINE LEARNING access to a wide range of molecular modelling functionality. Learning Yeast Functional Upstream Open Reading Frames from Heterogeneous Data (39) OTHER Sources Pck, a software for pockets detection and Selpi, Christopher Bryant, Graham Kemp, Marija analysis Cvijovic, Per Sunnerhagen, Olle Nerman, Erik Benjamin Schwarz, Jean-Marie Wurtz Kristiansson, Janeli Sarv, Alexandra Jauhiainen IGBMC, France The Robert Gordon University, United Kingdom We present a software to detect pockets and ease their While identifying functional upstream open reading frames analysis through a VMD Plugin. It is based on computational (uORFs) is important in understanding uORF's roles in gene geometry for molecular description and pocket detection, and regulation, laboratory experiments are expensive. Our logic- introduces novel functionalities and descriptions for their based approach to predicting functional uORFs in Saccharo- analysis. myces cerevisiae uses knowledge derived from sequence data, expression data, and GO annotations. The method gives 81% sensitivity, and simple-interpretable hypotheses. Population Genetics & Variation

(40) POPULATION GENETICS AND VARIATION Ontologies Genetic basis for Anopheles arabiensis refractoriness to Plasmodium falciparum in (36) ONTOLOGIES Towards interoperability between anatomy rice cultivating zones in central and western and phenotype ontologies Kenya Robert Hoehndorf, Janet Kelso, Frank Loebe, Damaris Matoke Heinrich Herre Kenya Medical Research Institute, Kenya Max Planck Institute for Evolutionary Anthropol- Anopheles arabiensis mosquitoes are amongst the most important malaria vectors in sub-tropical Africa. Itís predominant ogy, Germany in areas of rice agriculture. Refractoriness to malaria parasites Achieving interoperability between biomedical ontologies is a has been known to occur in Anopheles mosquitoes. This highly desired state of affairs. We identify a major problem for study seeks to determine basis of refractoriness and QTLs the interoperability between biomedical ontologies. The com- controlling refractoriness to Plasmodium falciparum in mon use of anatomy ontologies together with phenotype Anopheles arabiensis. ontologies may lead to inconsistencies. We provide a solution to this problem through the use of an extended logical framework for representing ontologies.

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(41) POPULATION GENETICS AND VARIATION (46) SEQUENCE ANALYSIS Evaluation of in silico Single Nucleotide VAMSAS: Bridging the gaps between the Polymorphisms Discovery in Expressed Se- analysis of DNA, Protein Sequences and quence Tags Protein Structure Erika Souche, Bart Hellemans, Jeroen Van Houdt, Jim Procter, Andrew Waterhouse, Pierre Margue- Adelino Canario, Sven Klages, Richard Reinhardt, rite, Dominik Lindner, Iain Milne, Tom Oldﬁeld, Kim Filip Volckaert Henrick, Frank Wright, David Marshall, David Laboratory of Aquatic Ecology, Belgium Martin, Geoff Barton Three in silico Single Nucleotide Polymorphisms (SNPs) dis- University of Dundee, United Kingdom covery tools are tested on the same Expressed Sequence Tag Visualization and Analysis of Molecular Sequences and Struc- (EST) dataset. Randomly chosen SNP candidates are vali- tures (VAMSAS) is an extensible mechanism for storing and dated by direct sequencing. Comparing algorithms and results dynamically exchanging sequences, alignments, trees and of each tool can reveal the factors that are essential for an structures between three freely available interactive graphical accurate in silico SNP discovery. applications: TOPALi, Jalview and AstexViewer@MSD-EBI.

Regulation (47) SEQUENCE ANALYSIS Multiple alignment and structure prediction (42) REGULATION of non-coding RNAs Functional transcription factor binding mo- Stinus Lindgreen, Paul Gardner, Anders Krogh tifs have a strong location bias towards the University of Copenhagen, Denmark transcription start sites of human and We present a novel approach to the problem of simultaneous mouse genes alignment and structure prediction for multiple RNA se- Yuval Tabach quences. Using simulated annealing and a scoring system Weizmann Institute of Science, Israel combining covariation, basepair probabilities and the log- likelihood of the alignment, we sample alignments and struc- We present a novel way of finding functional transcription- ture for unaligned sequences. We compare our results to factor binding-sites, allowing a "flexible" threshold and con- other programs. sidering location bias and GC content. We perform a comprehensive analysis of 134 biological groups and 412 motifs. Supported with experimental evidence we show that gener- (48) SEQUENCE ANALYSIS ally, binding-sites located 200bp upstream to the TSS are Synchronization Properties of Protein Bind- functional. ing Sites Pavol Hanus (43) REGULATION TU Muenchen, Germany Detecting cis-regulatory motifs for coopera- Protein-DNA and protein-RNA binding sites recognition often tively binding proteins corresponds to sequence specific one-dimensional diffusion. Liesbeth van Oeffelen, Yves Moreau, Bart De Techniques to study a similar problem of frame synchroniza- Moor tion in communications engineering are adopted to the biological scenario and used to study the synchronization proper- KULeuven, Belgium ties of different binding sites (promoters, splice sites, etc.). To find regulatory motifs in DNA, one usually determines a position weight matrix (PWM) based on observed binding sequences and predicts regulatory motifs by scoring the up- Structure & Function Prediction stream region of each gene. However, this method assumes that only one protein copy is involved, and adaptations are (49) STRUCTURE AND FUNCTION PREDICTION required for cooperatively binding proteins. Variation of Geometrical and Physicochemi- cal Properties in Protein Binding Pockets Sequence Analysis and their Ligands Abdullah Kahraman, Richard J. Morris, Roman A. (44) SEQUENCE ANALYSIS Laskowski, Janet M. Thornton Alternative Transcription Start Sites: Core European Bioinformatics Institute, United King- Promoters and Spatiotemporal Regulatory dom Signatures The variation of the ligand and binding pocket shape together Elizabeth Rach, Uwe Ohler with the variation of the hydrophobicity, van-der-Waals and Duke University, United States electrostatic potential on the ligand surface were analysed in different proteins. A correlation between ligand and binding site could be detected only for shape and hydrophobicity (45) SEQUENCE ANALYSIS indicating their importance for molecular recognition. Improved and automated residue function determination from multiple sequence alignment Kai Ye, Gert Vriend, Adriaan IJzerman Leiden University, Netherlands

17 3rd I S CB S t u d en t Co u n cil S ymp os iu m Structure Prediction Systems Biology & Networks

(50) STRUCTURE PREDICTION (54) SYSTEMS BIOLOGY & NETWORKS Predicting local structure using sequence The QTL-Shielding Test (QST): a Novel Tech- information nique for Genetic Network Discovery in a Huzefa Rangwala, George Karypis Microarray/Marker Dataset University of Minnesota, Twin Cities, United Christine Duarte, Zhao-Bang Zeng States Nature Source Genetics, United States Motivated by the alignment requirements of comparative We present a technique for inferring genetic relationships from modeling approaches and the operational characteristics of the analysis of an e-QTL or Expression-Quantitative Trait Loci protein structure alignment algorithms, we estimate the RMSD dataset in which marker and microarray data are collected in value between a pair of protein fragments by considering only an experimental cross. The QST has been applied to yeast sequence-derived information. For protein pairs with low se- and eucalyptus datasets to find key regulators involved in a quence similarity (<12%), these new structural features lead to number of important pathways. improved alignments. (55) SYSTEMS BIOLOGY & NETWORKS (51) STRUCTURE PREDICTION Automatic design of functional genetic net- Homology Modeling of a Voltage-gated Po- works tassium channel (Human Kv7.1) Javier Carrera, Guillermo Rodrigo, Alfonso Jara- Alexandr Goncearenco, Yasmin Karimi-Nejad, millo Konrad Koehler Departamento Matematica Aplicada, Universidad Cologne University Bioinformatics Center, Ger- Politecnica Valencia, Spain many The use of forward-engineering techniques allows generating Homology models of Long QT Syndrome related KCNQ1 new protein networks with targeted behaviours. Using an potassium channel were built and assessed using experimen- automated evolutionary design procedure, we explore the tal data. Proof-of-principle for their use in a virtual screening space of all possible transcriptional regulation networks to find protocol is given. It is suggested that conformational changes the optimal circuit with specified behaviour (e.g. Boolean logic could be induced to improve blockade predictions. A PyMOL functions or oscillators) and to study the evolution of genetic plugin is proposed. networks

(52) STRUCTURE PREDICTION (56) SYSTEMS BIOLOGY & NETWORKS Modelling Co-translational Protein Folding MetabolomeExplorer: Inferring Metabolic Rhodri Saunders, Charlotte Deane Networks From High Resolution Mass Spec- University of Oxford, United Kingdom trometry Data Under co-translational folding a protein folds sequentially from Richard Scheltema, Richard Scheltema1, Frans the N-terminus as it is translated. We use simplified models to Stellaard, Ritsert Jansen, Michael Barrett identify the characterisitics of co-translationally folded struc- University of Groningen, Netherlands tures. Significant differences are observed between co- translatinal folders and all others. We are now investigating The new generation mass spectrometers, separating complex these characteristics in real protein structures. mixtures at high resolution and mass accuracy, gave metabo- lomics a powerful tool. To harness the overwhelming information abundance generated, novel bioinformatics solutions are (53) STRUCTURE PREDICTION needed. As a showcase the MetabolomeExplorer was devel- Membrane Protein Structure Prediction: In- oped, implementing new concepts for normalizing and analyz- fluence of Distance Constraints on the Effi- ing ultra-high resolution mass spectrometry data. ciency of the Conformational Search with Monte Carlo Simulation (57) SYSTEMS BIOLOGY & NETWORKS Claire Gervais, Zhong Chen, Ying Xu PRISM: A Web Server for Prediction and University of Georgia, United States Visualization of Protein-Protein Interactions We present our approach for ab initio prediction of alpha-helix Nurcan Tuncbag, Emre Guney, Mehmet Cengiz transmembrane structures. Monte Carlo simulations are car- Ulubas, Ozlem Keskin, Attila Gursoy ried out using the Wang-Landau algorithm. We show how to Koc University, Turkey include experimental data (e.g. in form of distance constraints) PRISM is a web server for the querying, visualization and in the conformational search procedure in order to increase analysis of the protein interfaces and putative protein-protein the overall efficiency of the algorithm. interactions derived from known PDB structures. Interactions are predicted by considering shape complementarities and evolutionary conservation of protein interfaces. PRISM, with its graphical features, is a valuable resource for analyzing protein- protein interactions.

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(58) SYSTEMS BIOLOGY & NETWORKS (62) SYSTEMS BIOLOGY & NETWORKS Finding genes involved in plants response to Mining expression-dependent modules in drought the human interaction network Maital Ashkenazi, Menachem Moshelion Elisabeth Georgii, Sabine Dietmann, Koji Tsuda The Hebrew University of Jerusalem, Israel MPI for Biological Cybernetics, Friedrich Miescher We create networks of genes with correlated expression pat- Laboratory of the Max Planck Society, Germany terns in response to various water deficit situations. By inter- We present a novel approach for detecting functional modules secting these networks we can locate cliques enriched with by integrating static information from protein interaction net- water stress specific genes. We try to suggest a role in plants works with gene expression data. Our method discovers sets response to drought for the unknown genes in these cliques. of interacting proteins that occur specifically in subsets of cellular conditions. The enumerative algorithm based on item- (59) SYSTEMS BIOLOGY & NETWORKS set mining allows to integrate several heterogeneous data Logical Modelling and Analysis of the Bud- sets. ding Yeast Cell cycle Adrien Faure, Claudine Chaouiya, Andrea Cilib- (63) SYSTEMS BIOLOGY & NETWORKS erto, Denis Thieffry Gene- and pathway-centric approaches to INSERM, France the measurement of similarities between different cell states Leaning on a logical framework, we are developing a modular modelling approach of the budding Yeast cell cycle, building Martina Koeva upon a model of the core cell cycle engine and progressively University of California, Santa Cruz, United States aggregating specific regulatory modules. The present com- We are interested in the comparison between different stem munication focuses on the integration of the morphogenesis cell populations, as well as tissues, based on gene expression control checkpoint. data. I have developed several measures for the assessment of similarities between cell states, using both a gene- and (60) SYSTEMS BIOLOGY & NETWORKS pathway-centric approaches and have applied them to sev- Non-Genetic Individuality in the Host-Phage eral publicly available datasets. Interaction Sivan Pearl, Chana Gabay, Nathalie Balaban, (64) SYSTEMS BIOLOGY & NETWORKS Amos Oppenheim RegAlign: An Algorithm for the Alignment of Hebrew University, Israel Gene Regulatory Networks George Davidescu Persistent bacteria are protected from stresses such as anti- biotics, due to non-genetic heterogeneity of growth rates. As University of New Brunswick, Canada phages represent a common stress bacteria encounter, we RegAlign is a new tool which produces a global alignment of studied the effect of persistence on the interaction between two given regulatory networks while taking into account the E.coli and phage lambda. We observed non-genetic individu- similarity of both the networksí nodes and their structures. The ality in bacterial response to phages, which might alter popu- project also aims to propose a standardized system of repre- lation dynamics. senting regulatory network data.

(61) SYSTEMS BIOLOGY & NETWORKS Text Mining Analysis of gene expression data on metabolic networks (65) TEXT MINING Anna-Lena Kranz, Thorsten Bonato, Marcus Os- Text Mining in predicting gene cancer rela- wald, Hanna Seitz, Gerhard Reinelt, Heiko Runz, tionships Johannes Zschocke, Roland Eils, Rainer Koenig Aischarya Brahma University of Heidelberg/Institute for Pharmacy Vellore Institute of Technology University, India and Molecular Biotechnology, Germany This paper motivates the need for a concerted effort in the When analysing microarray expression data, it is often not area of integration of biological knowledge, both by outlining enough to examine single genes but rather groups of genes. the genes related to a particular type of cancer and also vari- We invented a novel method that determines significant ex- ous types of cancer related to a particular gene. pression patterns of topologically associated genes and thereby identifies functionally relevant central components in (66) TEXT MINING the network with respect to different conditions of interest. Mining of methodological choices in phylogenetic workflows and why your supervisor may not have all the answers James Eales, John Pinney, Robert Stevens, David Robertson University of Manchester, United Kingdom We have developed a methodology for mining phylogenetic methodologies from full text journal articles. This methodology provides a vital improvement in the communication of experimental workflows between researchers.

19 3rd I S CB S t u d en t Co u n cil S ymp os iu m The ISCB Student Council

The Student Council is the student-led section of Computational Biology. We are committed to the International Society for Computational Biol- achieving this ambitious goal through a variety of ogy (ISCB). Our aim is to facilitate opportunities ways. We will offer a series of activities and career for development and growth to young members development sessions which are now being dis- of ISCB while nurturing the next generation of cussed. These activities will include educational computational biologists. The Student Council webinars, the development of the Regional Stu- continually thrives to provide opportunities for dent Groups throughout the world, the creation of networking, career enhancement and soft skills. a new centralized portal that will include a mod- erated database of announcements that can be posted by all members, and many others which CHAIR Manuel Corpas we will announce as they are firmed up. University of Manchester, UK Our agenda is open, full of activities and opportunities. Our liaisons within the ISCB Board of Di- VICE CHAIR rectors, Michal Linial and Rita Casadio, have Sarath Chandra Janga given their support to us, and the ISCB has pro- Universidad Autonoma de Mexico, Mexico vided all the resources and contacts that we need SECRETARY to succeed. There is only one more thing that is Milana Frenkel-Morgenstern required for the success of the Student Council, Weizmann Institute of Science, Israel and that is your involvement! If you think our efforts can be beneficial to you, and you, in turn, REPRESENTATIVE TO ISCB BOARD OF DIRECTORS can assist in our efforts, then you should be a Vijaya Parthiban member of the Student Council. Cologne Univ. Bioinformatics Center, Germany Becoming A Member MEMBERS 425 If you are or plan to become a student or post doc member of ISCB, signing up for the Student WEB Council is a very simple process. Within your http://www.iscbsc.org membership registration form just mark the check CONTACT box for “Student Council” on the list of commit- [email protected] tees you are interested in serving. If you already registered for ISCB membership but neglected to mark that checkbox, or cannot remember if you We have had the chance to openly discuss our did or not, simply login on the membership page ideas both formally and informally with members and select “Edit Personal Information” to update of the ISCB Board of Directors as well as among or verify your record. Once the checkbox is ourselves, creating an atmosphere of mutual marked you will be enrolled as an Student Coun- learning and scientific growth. Creativity and cil member within seven days. It's that simple! communication of ideas has been a constant characteristic of our internal email forum where Becoming A Leader everyone has a voice to contribute with whatever If you just not want to be a member but also a idea may enhance our plan of becoming truly a leader of the Student Council, we are always resource for the new generation of leaders in the looking for highly motivated and ambitious stu- field of Computational Biology. dents. The simplest way to become an Student Some of the highlights during the 12 months Council leader is to get involved with one of our have been the creation of five affiliated Regional current activities. If you want to hear more about Student Groups: Singapore, India, Africa, Den- our current opportunities, or simply have fresh mark and Canada. Each one of them has had its ideas that you would like us to work on, do not own challenges and outcomes. The 3rd ISCB hesitate, just drop us a line to [email protected] Student Council Symposium at ISMB/ECCB and we will get you started. We invite you to rein- 2007 represents for us the highlight of the year force your own professional development by after many months of dedicated efforts to organ- committing yourself to the Student Council. The ize this event. next level of your research might just involve con- The road ahead looks more exciting than ever, tacts you make through the Student Council with our main goal of consolidating as the premier community. organization for young researchers in the area of

20 3rd IS CB S t u d en t C ou ncil S ymp os ium

Welcome To The 3rd ISCB Student Council Symposium!

We are extremely excited to have you here and the vibrant city of Vienna welcomes you to our SCS3 event.

A d ver t is emen t

21 3rd I S CB S t u d en t Co u n cil S ymp os iu m The Student Council Goes Local - Regional Student Groups

Over the past year ISCB Student Council leaders RSGs are not authorized to collect membership have researched the possibility of setting up Re- fees of any kind and hence it might be necessary gional Student Groups (RSGs) in countries and beneficial for RSGs to have a partnership around the world to better serve local student with a local organization that is willing to support communities. The goal is to conduct events, the activities of the group. which will be beneficial to the professional development of Bioinformatics and Computational Bi- Committee ology students on a local level. Further, opportu- The RSG Committee (http://www.iscbsc.org/rsg) nities need to be created for students to interact is responsible for worldwide coordination of the with local industry and organizations. Regional Student Groups affiliated with the Stu- A request for setting up RSGs was submitted to dent Council. the ISCB Board of Directors and their approval was given in the fall of 2006. Talks were held with CHAIR student groups in several countries and the Stu- Saraswathi Sundararajan dent Council got a positive response from them to partner in future activities pertaining to stu- FOUNDING MEMBERS dents in their region. Saraswathi Sundararajan The Student Council has so far successfully es- Manuel Corpas tablished three affiliated RSGs in Singapore, India Vijaya Parthiban and Africa and is reviewing proposals from REGIONAL STUDENT GROUP PRESIDENTS groups in Denmark and Canada. Amr Abu-zeid Segun Fatumo Joining A Regional Student Group Angela Jean If you are interested in joining a RSG, please send Abhishek Pratap the group an email expressing your interest (con- Prashanth Suravajhala tact details given below). Generally, there is no membership fee for becoming an RSG member CONTACT locally. If you plan to compete for an official posi- [email protected] tion such as President or Secretary you should become a member of the ISCB and the Student The committee is responsible for: Council. Membership dues for the ISCB vary de- pending on your country of residence and Stu- ‣ RSG leaders report to the Chair of the RSG dent Council membership is included for free. Committee and carry out the activities within Starting A New Regional Student Group their local groups. The Chair of the RSG Committee and its members report the pro- If you do not find an established RSG in your gress and updates of all the RSGs to the country or region you are invited to propose the ISCB. formation of a new RSG. Please contact the RSG ‣ Assignment of various tasks to RSG and shar- Committee of the Student Council (contact de- ing the expertise of the Student Council to tails given below) if you are interested. The com- organize symposiums, job fairs and confer- mittee will help you to start an RSG in your coun- ences locally. try. You will receive a document listing the terms ‣ Coordination of professors and researchers and conditions for starting a new RSG and advice (also non-RSG members) and RSG members on how to proceed. to execute (virtual) Bioinformatics projects lo- Generally, an RSG can be formed by a group of cally. students led by a President and a Secretary and ‣ Acting as a bridge to enable and encourage who have the support of a local faculty sponsor interaction between two or more independent who is willing to oversee the group’s activities and RSGs. report its progress to the Student Council once a ‣ Initiation of ties with established Bioinformatics year. The officers or at least the President of the societies (locally and globally) and collabora- RSG are expected to be Student Council mem- tion with them. bers.

22 3rd IS CB S t u d en t Cou n cil S ymp os iu m

The RSG committee is currently working on an Some of the projected activities in the near future extension of the Student Council website as a in Singapore for RSG are going to involve: central meeting place for all RSGs. ‣ Creation of a virtual network across many re- Singapore gional institutions, including young and senior researchers in academia and industry. PRESIDENT ‣ Organization of scientific and career events. Angela Jean The ELM Machine Learning Workshop, con- Nanyang Technological University, Singapore ducted at the National University of Singapore, was a first step. SECRETARY ‣ Establishment of a board with job opportuni- Kalyan Mynampatti ties and relevant business links associated to National University of Singapore, Singapore Computational Biology in the region. FACULTY SPONSOR Tan Tin Wee We hope that the students, universities and in- National University of Singapore, Singapore dustries in Singapore will support us in our ven- ture. We would like to extend special thanks to FOUNDING MEMBER Professor Tan Tin Wee of the National University Saraswathi Sundararajan Iowa State University, USA of Singapore, ISCB Executive Officer BJ Morrison McKay and AMBIS of Singapore for their support INAUGURATION in inaugurating RSG in Singapore. November 2006

CONTACT India [email protected] PRESIDENT WEB Abhishek Pratap http://www.google.com/group/iscb-rsg-sin VIT University, India gapore SECRETARY AJ Venkatakrishnan The Student Council has sought the establish- VIT University, India ment of a pilot RSG in Singapore in cooperation with AMBIS, The Association for Medical and Bio- FACULTY SPONSOR informatics – Singapore, with the blessings of the To Be Appointed ISCB. We can complement each others’ work FOUNDING MEMBER and create an environment which will help our Saraswathi Sundararajan students to excel in their ﬁelds. This partnership Iowa State University, USA will create a forum for the dissemination, ex- INAUGURATION change and analysis of information through edu- December 2006 cation and participation of RSG members, which are the main goals of AMBIS and the RSG in Sin- CONTACT gapore. [email protected] WEB Aims: http://www.google.com/group/rsg-india

‣ Serve the needs of student researchers in the field of Computational Biology. The Regional Student Group in India is a Student ‣ Provide an regional network of excellence for Council initiative serving as a national forum and young researchers. resource devoted to developing competence and ‣ Offer resources and events geared to the sci- expertise in Bioinformatics and Computational entific advancement of the next generation. Biology in India. ‣ Facilitate the development of the next genera- The RSG was initiated by Saraswathi Sundarara- tion of Computational Biologists. jan and established with the blessings of Michael ‣ Offer benefits that are specific to our local Gribskov (then ISCB President), the support of members. the ISCB Board of Directors and Student Council ‣ Ultimate goal is to bring together the scientific and the enthusiasm of numerous committed stu- communities and enable them to work to- dent delegates, during the 5th International Con- gether for mutual advancement. ference on Bioinformatics (INCOB 2006, Decem-

23 3rd I S CB S t u d en t Co u n cil S ymp os iu m ber 18th - 20th) held at The Ashok, New Delhi, Africa India. Although the group is still in its nascent stage, it is PRESIDENT one of the most rapidly growing RSGs and has Segun Fatumo already attracted 225 members in just a few Covenant University, Nigeria months since its establishment in December 2006. SECRETARY In its current form the RSG is looking forward to Lilian Wambua expand its member base and attain sustainability. Int. Livestock Research Institute, Kenya It has adopted the mission of the Student Council FACULTY SPONSOR to develop next generation pioneers in the ﬁeld of Winston Hide Computational Biology. It aims at bridging the SANBI, South Africa gap between academic and corporate sector. It invites students to promote group learning and to FOUNDING MEMBER keep them updated about Indian and worldwide Segun Fatumo Bioinformatics activities. Covenant University, Nigeria INAUGURATION Accomplishments: May 2007

CONTACT ‣ Active forum for discussion of problems faced [email protected] in projects and day to day research. ‣ Regular updates on job vacancies in the Bioin- formatics industry in India and abroad. RSG Africa was just inaugurated 31st May, 2007 ‣ Postings about conferences, seminars and during the international conference on Bioinfor- workshops held regionally and worldwide. matics for African Pathogens and Disease Vec- ‣ Access to details of relevant contacts and tors held in Nairobi, Kenya from 28th May to 2nd information of industries and research centers. June, 2007 with about 100 registered students across East, West, Central and North Africa. Planned Activities: In addition to the President and Secretary the following executive members have been elected ‣ The RSG will be on the lookout for training during the conference: Sheila Ommeh, Kenya opportunities in the form of college projects (East Africa Representative), Sorho Fatogoma, and internships for young enthusiasts in the Cote d’Ivore (West and Central Africa Represen- ﬁeld of Computational Biology. tative), Ouissem Souiai, Tunesia (North Africa ‣ Nurture a network of contacts among stu- Representative) and Kenneth Babu, Kenya dents with industries, academics and local (Webmaster). government that have an active interest in The members of RSG Africa proposed to estab- computational biology. lish a pool of mentors among our own senior sci- ‣ Aims to launch an interactive website which entists in Bioinformatics. The following scientists would provide personalized space to the were appointed to our mentorship list covering all members. of Africa. ‣ Plans to conduct a web based seminar - A live discussion, with an invited guest who will dis- ‣ Winston Hide, South Africa cuss the current topics in Bioinformatics. ‣ Jaco de Ridder, South Africa ‣ Daniel Mesiga, East Africa ‣ Beatrice Kilel, East Africa/USA ‣ Trushar Shah, East Africa ‣ Doumbia Seydou, West Africa ‣ Ezekiel Adebiyi, West Africa ‣ Raphael Isokpehi, West Africa/USA ‣ Alia Benkahla, North Africa ‣ Fidelis Cho-Ngwa, Central Africa ‣ Olivier Gascuel, International Adviser/France

We are glad to receive the support of our mentors to help our students. All our mentors have been duly communicated of this appointment.

24 3rd IS CB S t u d en t Cou n cil S ymp os iu m Since the inauguration of RSG Africa, we had one Canada student session during which decision were made on the proposed events and program of PRESIDENT RSG Africa. The meeting was during the confer- Amr Abu-zeid ence in Nairobi as stated above. Furthermore, a Queen's University, Canada collection of job, grant and scholarship opportunities have been posted to members of RSG Africa SECRETARY via email. Sara Mostafavi We are looking forward to creating a website University of Toronto, Canada where well coordinated events and opportunities FACULTY SPONSOR will be posted. Most importantly, we hope to build To Be Appointed a formidable RSG during the next year. Since RSG Africa is growing very fast, our intention is to FOUNDING MEMBER eventually break up RSG Africa into a minimum of Amr Abu-zeid 4 RSGs either by sub-regions or by countries. Queen's University, Canada We earnestly seek for your contributions and INAUGURATION comment in our upward events. Proposal Under Review

CONTACT Denmark [email protected]

PRESIDENT Prashanth Suravajhala Roskilde University, Denmark

SECRETARY Claus Desler Roskilde University, Denmark

FACULTY SPONSOR Lene Juel Rasmussen Roskilde University, Denmark

FOUNDING MEMBER Prashanth Suravajhala Roskilde University, Denmark

INAUGURATION Proposal Under Review

CONTACT [email protected]

WEB http://www.google.com/group/rsg-den mark

25 3rd I S CB S t u d en t Co u n cil S ymp os iu m Organizing Committee

CONFERENCE CHAIRS Nils Gehlenborg EMBL-EBI and University of Cambridge, UK Manuel Corpas University of Manchester, UK

Sarath Chandra Janga Crina Samarghitean Universidad Autonoma de Mexico, Mexico University of Tampere, Finland John Cumbers Venkata Satagopam Brown University, USA EMBL Heidelberg, Germany Milana Frenkel-Morgenstern Ole Schulz-Trieglaff Weizmann Institute of Science, Israel Free University Berlin, Germany Xu Gu Saraswathi Sundararajan University of Glasgow, UK Iowa State University, USA Vijaya Parthiban Prashanth Suravajhala Cologne University Bioinformatics Center, Germany Roskilde University, Denmark Abhishek Pratap Victor Weigman VIT University, India University of North Carolina, USA Lucia Peixoto University of Pennsylvania, USA

Manuel Nils Sarath Vijaya Saraswathi

Xu Venkata Victor John Ole

Milana Prashanth Abhishek Crina Lucia

26 3rd IS CB S t u d en t Cou n cil S ymp os iu m Program Committee

PROGRAM CHAIR Sarath Chandra Janga Universidad Autonoma de Mexico, Mexico

Kiran Kumar Battula Dimitri Perrin National Institute of Nutrition, India Dublin City University, Ireland Markus Brosch Abhishek Pratap The Wellcome Trust Sanger Institute, UK VIT University, India Manuel Corpas Ravindra Pushker University of Manchester, UK University College Dublin, Ireland Heidi Dvinge Angel-Carlos Roman European Bioinformatics Institute, UK University of Extremadura, Spain Segun Fatumo Aminael Sanchez Rodriguez Covenant University, Nigeria Institute of Plant Biotechnology, Cuba Nils Gehlenborg Venkata Satagopam EMBL-EBI and University of Cambridge, UK EMBL Heidelberg, Germany Angela Jean Ole Schulz-Trieglaff Nanyang Technological University, Singapore Free University Berlin, Germany Abdullah Kahraman Aswin Seshasaye European Bioinformatics Institute, UK European Bioinformatics Institute, UK Katherine Lawler Saraswathi Sundarajan European Bioinformatics Institute, UK Iowa State University, USA Margus Lukk Prashanth Suravajhala European Bioinformatics Institute, UK Roskilde University, Denmark Antonia Mayer Andrija Tomovic European Bioinformatics Institute, UK Friedrich Miescher Institute for Biomedical Re- Magali Michaut search, Switzerland Institute of Biology and Technologies of Saclay, Mallika Veeramalai France Burnham Institute for Medical Research, USA Pieter Monsieurs Victor Weigman K.U. Leuven, Belgium University of North Carolina, USA Lucia Peixoto Daniel Zerbino University of Pennsylvania, USA European Bioinformatics Institute, UK

27 3rd IS CB S t ud ent Co uncil S ymp os ium

Welcome To The 3rd ISCB Student Council Symposium!

We are extremely excited to have you here and the vibrant city of Vienna welcomes you to our SCS3 event.

A d ver t is emen t

28 3rd IS CB S t u d en t Cou n cil S ymp os iu m Delegates

Priit Adler Fabrice David IMCB / University Of Tartu Swiss Institute Of Bioinformatics Tartu, Estonia Geneva, Switzerland

Daniel Almonacid Anna Dehof University of Cambridge Saarland University Cambridge, United Kingdom Saarbruecken, Germany

Nicola Barbarini Christine Duarte University Of Pavia Nature Source Genetics Pavia, Italy Ithaca, United States

Hugo Bastos Isabel Duarte University Of Lisbon NCMLS - CMBI - Radboud University Lisbon, Portugal Nijmegen, Netherlands

Pascal Benkert James Eales Institute For Biochemistry, University Of Cologne University Of Manchester Cologne, Germany Manchester, United Kingdom

Andreas Bertsch Ekaterina Ermakova Tuebingen University Institute For Information Transmission Problems Tuebingen, Germany Moscow, Russian Federation

Kevin Bleakley Marco Fabbri Université Montpellier 2 Istituto Clinico Humanitas Montpellier, France Rozzano, Italy

Regina Bohnert Daniel Faria Friedrich Miescher Laboratory Faculty Of Sciences - Lisbon University Of The Max Planck Society Lisboa, Portugal Tuebingen, Germany Magdalena Feldhahn Wouter Boomsma University Of Tuebingen, ZBIT University Of Copenhagen Tuebingen, Germany Copenhagen, Denmark Nina Fischer Kevin Brick University Of Tuebingen, ZBIT Istituto Superiore Di Sanita Tuebingen, Germany Roma, Italy Paul Fisher Norbert Busch University Of Manchester University Of Applied Sciences Stralsund Manchester, United Kingom Stralsund, Germany Caroline Friedel Eduardo Capanema Ludwig-Maximilians-Universität München Universidade Federal De Minas Gerais München, Germany Belo Horizonte, Brazil Oliver Gaertner Zhongqiang Chen Saarland University University Of Pennsylvania Saarbrücken, Germany Philadelphia, United States Nils Gehlenborg Jianhuan Chen EMBL-EBI The Hong Kong University Of Science Cambridge, United Kingdom Hong Kong, Hong Kong Claire Gervais Manuel Corpas University Of Georgia University Of Manchester Athens, United States Manchester, United Kingdom

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Sandra Gesing Aleksejs Kontijevskis University Of Tuebingen Uppsala University Tuebingen, Germany Uppsala, Sweden

Mireille Gomes Anna-Lena Kranz Queen's University University Of Heidelberg Kingston, Ontario Institute For Pharmacy Heidelberg, Germany Alexandr Goncearenco Cologne University Bioinformatics Center Samuel Kojo Kwoﬁe Cologne, Germany National Bioinformatics Network Cape Town, South Africa Tiago Grego University Of Lisbon Philip Law Lisboa, Portugal University of Pretoria Pretoria, South Africa Pavol Hanus Technische Universität München Katherine Lawler München, Germany EMBL-EBI Cambridge, United Kingdom Troy Hawkins Purdue University Han Kuen Liang Lafayette, United States Academia Sinica Taipei, Taiwan Christine Hedderich Saarland University Stinus Lindgreen Saarbruecken, Germany University Of Copenhagen Copenhagen, Denmark Andreas Heinzel Fh-Hagenberg Peter Majek Salzburg, Austria Cornell University Ithaca, United States Andreas Hildebrandt Saarland University Wouter Meuleman Saarbrücken, Germany Netherlands Cancer Institute Delft University Of Technology Robert Hoehndorf Delft, Netherlands MPI For Evolutionary Anthropology/Onto-Med Leipzig, Germany Naila Mimouni Oxford University Sarath Chandra Janga Oxford, United Kingdom Center For Genomic Sciences Cuernavaca, Mexico Roy Navon Tel Aviv University Daniel Jurczak Ramat Gan, Israel Fh-Hagenberg Vienna, Austria Siu-Kin Ng The Hong Kong University Abdullah Kahraman of Science and Technology EMBL-EBI Clear Water Bay, Hong Kong Cambridge, United Kingdom Fiona Nielsen Benny Kneissl NCMLS - Radboud University Nijmegen Boehringer Ingelheim Pharma GmbH & Co. KG Nijmegen, Netherlands Biberach (Riß), Germany Jamiu Tanwa Nureni Riaan Koegelenberg Jeppe College Of Commerce And Computer College South Africa Johannesburg, South Africa

Martina Koeva Courtney Onodera University Of California, Santa Cruz University Of California, Santa Cruz Santa Cruz, United States Santa Cruz, United States

30 3rd IS CB S t u d en t Cou n cil S ymp os iu m

Iñigo Ortiz De Mendibil Ayuso Venkata P. Satagopam University Of Navarra EMBL Pamplona, Spain Heidelberg, Germany

Lucia Peixoto Rhodri Saunders University Of Pennsylvania University Of Oxford Philadelphia, United States Oxford, United Kingdom

Catia Pesquita Theresa Scharl University Of Lisbon Vienna University Of Technology Lisbon, Portugal Vienna, Austria

Anca Petrescu Sebastian J. Schultheiss Universiy Of British Columbia MPI for Developmental Biology Vancouver, Canada Tuebingen, Germany

Nico Pfeifer Selpi University Of Tuebingen The Robert Gordon University Tuebingen, Germany Aberdeen, United Kingdom

Alejandro Pironti Ruijun Shen Universität Des Saarlandes Bi Pharma GmbH & Co. KG Saarbrücken, Germany Biberach, Germany

Abhishek Pratap Wei-Chung Shia VIT University Feng Chia University Vellore, India Taichung, Taiwan

Jim Procter Rileen Sinha University Of Dundee Leibniz Institute For Age Research Dundee, United Kingdom Fritz Lipmann Institute Jena, Germany Kay Prüfer Max Planck Institute For Evolutionary Anthropology Nives Skunca Leipzig, Germany Faculty Of Food Technol. And Biotechnology Zagreb, Croatia Sara Rahmati Queen's University Erika Souche Kingston, Canada KULeuven Leuven, Belgium Axel Rasche MPI Molecular Genetics Henning Stehr Berlin, Germany Max-Planck-Institute For Molecular Genetics Berlin, Germany Juri Reimand University Of Tartu Israel Steinfeld Tartu, Estonia Tel Aviv University Tel Aviv, Israel Eduardo Righi Capanema Universidade Federal De Minas Gerais Fran Supek Belo Horizonte, Brazil Rudjer Boskovic Institute Zagreb, Croatia Marc Röttig Universität Tübingen Danielle Tiedt Tuebingen, Germany University of Pretoria Pretoria, South Africa Crina Samarghitean University of Tampere Nora Toussaint Tampere, Finland University Of Tuebingen, ZBIT Tuebingen, Germany Daniel Samarov UNC Chapel Hill Chapel Hill, United States

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Eivind Valen Imprint University Of Copenhagen Copenhagen, Denmark

Bart Van Houte EDITORS VU University Amsterdam Nils Gehlenborg Amsterdam, Netherlands Abhishek Pratap CONTRIBUTORS Klemens Vierlinger Manuel Corpas Austrian Research Centers GmbH - ARC Seibersdorf, Austria Saraswathi Sundararajan Segun Fatumo Hilde Vollan Rohit Reja Faculty Division Ahus, University Of Oslo Prashanth Suravajhala Lorenskog, Norway LAYOUT AND CONCEPT Sophie Weggler Nils Gehlenborg Saarland University WEB Saarbruecken, Germany http://www3rd.iscbsc.or IS CB S t u dg/scs3ent Cou n cil S ymp os ium

Victor Weigman CONTACT UniversityWelcome Of North Car Tolinao The [email protected] Chapel Hill, United States 3rd ISCB Student Council Symposium! Hendrik Weisser SaarlandWelcome University to the, Center Student For Bioinformatics Council Symposium 3 Saarbruecken,(SCS3) in V Germanyienna. The ISCB Student Council's mission is to develop the next generation of computa- Kai Ye tional biologists. We would like to thank and ac- Leiden/Amsterdam Center For Drug Research knowledge our sponsors and the ISCB organisers Leiden, Netherlands for their crucial support. The SCS3 provides an ex- Georcitingg Zeller environment for active scientific discussions Maxand Planck the Instituteopportunity to learn vital soft skills for a Tuebingen,successful Germany scientific career. In addition, the SCS3 is the biggest international event targeted to students Qihuiin theZhu field of Computational Biology. Peking University Beijing,We Chinawould like to thank our hosts and participants for making this event educative and fun at the same List oftime. delegates Student provided Council by Mondial meetings Congress have on Junehad 28th.a rich history of productive scientific discussions of new challenging ideas and participants contributing from a wide range of interdisciplinary fields. Such meetings have proved useful in providing students and postdocs innovative inputs and an increased network of potential collaborators. COPYRIGHT We are extremely excited to have you here and the vibrant© 2007 city ISCB of Vienna Student welcomes Council you andto our contrib SCS3 - event. uting authors. All rights reserved. This booklet maybe reproduced without permission in its . original form.

DISCLAIMER The ISCB Student Council has made all efforts to provide accurate information but does not guarantee the correctness of any information provided in this booklet. The ISCB Student Council is a committee of the International Society for Computational Biology (ISCB), which is incorporated as a 501 (c)(3) non-proﬁt corporation in the United States.