7th iscb student council symposium · 2011. 7. 25. · 5 with the intention of making the 7th...
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7thISCBStudentCouncilSymposium
Vienna,July15th2011
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ContentsWelcome 4
Agenda 6
Program
Scientific Speed Dating 10
Keynote Speakers 10
Research and Industry Partners Session 13
Accepted Abstracts 17
Awards 25
ISCB Student Council Travel Fellowships 26
Acknowledgements 27
Sponsors 28
Regional Student Groups Initiative 30
Other Student Council Activities at ISMB/ECCB 2011
Art and Science Exhibition 33
ISCB Student Council Open Business Meeting and Awards Ceremony 34
Student Council Career Central 35
Student Council Social HQ 36
Social Event: Blast your Brain! 37
Committees
Chairs 38
Organizing Committee 39
Program Committee 39
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Welcometothe7thISCBStudentCouncilSymposium!
Dear Student Council Symposium attendees,
It is our great pleasure to welcome you all to the 7th ISCB Student Council
Symposium taking place in Vienna, Austria. Our previous Symposiums in Boston (2010),
Stockholm (2009), Toronto (2008), Vienna (2007), Fortaleza (2006) and Madrid (2005) were
a great success. We are therefore thrilled to continue our efforts in Vienna this year. As in
previous years, our goal is to create an opportunity for students to meet their peers from all
over the world, promoting the exchange of ideas and networking. This year we managed to
secure funds to organize the Symposium, give poster and oral presentation awards and,
most importantly, provide 12 travel fellowships for Symposium delegates.
We are honored to have Dr. Curtis Huttenhower (Harvard School of Public Health),
Dr. Ivet Bahar (University of Pittsburgh), and Dr. Chad Myers (University of Minnesota) as
keynote speakers at this year’s Symposium. Their keynotes promise to be inspiring
presentations of exceptional work relevant to everyone in the field.
We will start the Symposium with the recent tradition of Scientific Speed Dating: a
chance to meet colleagues in an informal and friendly way. Throughout the day we will hear
oral presentations from a selection of 12 outstanding student abstracts spanning a wide‐
range of research areas. In the evening, the poster session will offer exciting science in
various domains, and give everybody a chance to discuss their research topics in more
depth.
Everyone involved in the organization of this Symposium contributed significantly
to make this event happen. Our volunteers have spent many months preparing all aspects
of this Symposium ranging from the invitation of keynote speakers, fundraising, advertising,
organizing the peer‐review process and the speed dating session to such mundane things as
maintaining a website. This year, our team has managed to secure more funds than ever
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with the intention of making the 7th Student Council Symposium even better than before.
We wish to continue this unique and well‐received event as judged by registration and
submission numbers.
Now it is up to you to make the most out of this opportunity. Talk to the other
delegates, ask your questions and show enthusiasm about your research if you are
presenting! You can make this Symposium a starting point for fruitful future collaborations
and another step towards a successful career in computational biology. Do not forget to
check out other Student Council events during ISMB/ECCB 2011, such as the Career
Central/Student Council Lounge (Booth 4), our Open Business Meeting, the Art and Science
Exhibition and, of course, our Social Events.
Enjoy your time in Vienna!
Lorena Pantano Rubino, Student Council Symposium Chair Pedro Lopes, Student Council Symposium Co‐Chair Geoffrey John Macintyre, Student Council Chair
PS: This booklet went into print in early June. Please check http://Symposium.iscbsc.org for
the latest updates and announcements.
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Agenda
Time Item Details on Page 08:00 Registration
08:30 Scientific Speed Dating 10
09:30 Keynote: Systems‐Level Insights from Large‐Scale Combinatorial Perturbation
Experiments in Yeast, Dr. Chad Myers 11
10:15 Coffee Break
10:45 Student Presentations Session 1: Sequence Analysis 17
Bacteriophage Evolution Drives Pseudomonas Aeruginosa PAO1 Biofilm Diversification Kerensa McElroy, University of New South Wales, Randwick, Sydney, AU
Efficient branch‐and‐bound techniques for two‐locus association mapping Karin Klotzbuecher, Max Planck Institutes, Tübingen, DE
Genome‐Wide Association Study of Tb in the South African Colored Population: Comprehensive Gene and Pathway‐Based Association Emile R. Chimusa, University of Cape Town, Cape Town, ZA
Variant Detection and the Autism Sequencing Project Orion Buske, Toronto, Toronto, CA
11:45 Research and Industry Partners Session
Training and Career opportunities at EMBL‐EBI Johannes Griss and Dr. Jennifer MacDowell, EBI 13
A Snap‐Shot of Bioinformatics at NICTA Dr. Izhak Haviv, NICTA 16
12:15 Lunch Break
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13:30 Keynote: Protein Dynamics: Learning from Computations and Experiments
Dr. Ivet Bahar 11
14:15 Internship Program – Testimonial
14:30 Student Presentations Session 2: Bioinformatics Tools 17
Resolving Atomic Interaction Networks to Understand GPCR Conformational Switching AJ Venkatakrishnan, University of Cambridge / MRC Laboratory of Molecular Biology, Cambridge, UK
Oqtans: A Galaxy‐Integrated Workflow for Quantitative Transcriptome Analysis from NGS Data Sebastian Schultheiss, Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, DE
Replication of Epistatic DNA Loci in Two Case‐Control GWAS studies using OPE algorithm Benjamin Goudey, University of Melbourne and NICTA, Melbourne, AU
An Integrative Bioinformatics Predictor of Protein Sub‐Cellular Localization in Malaria Ben Woodcroft, Bio21 Molecular Science and Biotechnology, Melbourne, AU
15:30 Coffee Break
16:00
Student Presentations Session 3: Transcriptomics, Data Management and Phylogeny
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Profiling Transcription Initiation in Human Aged Brain Using Deep‐CAGE Margherita Francescatto, Vrije Universiteit Medical Center and University of Porto, Amsterdam, NL
The Development of an Open‐Access Database for Human Transcriptional Regulation Interactions Luiz Bovolenta, Instituto de Biociências de Botucatu, Unesp‐Univ Estadual Paulista, Botucatu, BR
Computational Purification of Tumor Gene Expression Data Amit Deshwar, University of Toronto, Toronto, CA
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Markov Models to Delineate Evolutionary and Codon Usage Patterns amoung Malpighiales Mehedi Hassan, University of Glamorgan, Pontypridd, UK
17:00
Keynote: Functional Metagenomics and the Human Microbiome
Dr. Curtis Huttenhower 10
17:45
Closing Remarks
18:00 Poster Session 19
19:30 Symposium Ends
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Program
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ScientificSpeedDating We are continuing the speed‐dating event introduced at last year’s Symposium! No,
we are not going to help you find your life partner (even though it may be a side effect), we are talking about scientific speed dating to chat with your colleagues and break the ice in a convivial atmosphere.
Who are the other people who will spend the day with you? Where are they working? What are their research interests? Are they Ph.D. students? Is this the first time they attended the Symposium? Are they here to present a poster? Will they attend ISMB? Getting to know people during this event might help you make the most of your Student Council Symposium experience. And there is always lunch and coffee breaks to follow up on interesting beginnings.
Don’t miss the speed‐dating event!
KeynoteSpeakersCurtisHuttenhowerHarvard School of Public Health, Boston, MA, USA
Dr. Curtis Huttenhower is an Assistant Professor in the Department of Biostatistics at the Harvard School of Public Health. He received his Ph.D. from Princeton University in the lab of Dr. Olga Troyanskaya, where he also performed his postdoctoral research at the Lewis‐Sigler Institute. His lab focuses on computational metagenomics and the human microbiome, particularly in terms of scalable methods for characterizing microbial populations, their molecular and metabolic functionalities, and their impacts on human health. He chairs the Metabolic Reconstruction group in the Human Microbiome Project
and co‐chairs the Whole‐Genome Shotgun metagenomic analysis group, and his lab has produced a microbiome‐wide map of microbial functional activity as part of this effort. In past lives, he studied computational linguistics at Carnegie Mellon University and worked as a developer in the software industry.
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IvetBaharUniversity of Pittsburgh, Pittsburgh, PA, USA
Dr. Ivet Bahar is currently the Founding Chair of the Department of Computational and Systems Biology (CSB), the University of Pittsburgh at the School of Medicine. She received her Ph.D. in Chemistry in 1986 from Istanbul Technical University. She then joined the Chemical Engineering Department at Bogazici University, Istanbul,
Turkey where she served as an Assistant (1986‐87), Associate (1987‐93) and Full (1993‐2001) Professor, while also being a regular visiting scientist at the Molecular Structure Division of the Laboratory of Experimental & Computational Biology, NIH, Bethesda, USA, and the Laboratoire de Physique et Chimie Structurale et Macromoleculaire, Paris. She moved to the University of Pittsburgh in 2001, where she established a new Center for Computational Biology and Bioinformatics (2001‐05) which led to her current department, and she served as the Director of the Carnegie Mellon‐U Pitt Joint Ph.D. program in Computational Biology (2005‐09). Her research area is molecular biophysics and computational biology, with focus on the dynamics of proteins and their assemblies, and modeling and simulations of complex biomolecular interactions at multiple scales. She is an elected member of the European Molecular Biology Organization (EMBO), and a Principal Member of the Turkish Academy of Sciences.
ChadMeyersUniversity of Minnesota, Minneapolis, MN, USA
Dr. Chad Myers received his Ph.D. from the Department of Computer Science at Princeton University in 2007, working with Dr. Olga Troyanskaya in the Lewis‐Sigler Institute for Integrative Genomics. In 2008, he began his current position as an Assistant Professor in the Department of Computer Science and Engineering at the University of Minnesota. Dr. Myers’s research emphasis includes computational methods for analysis and interpretation of large‐scale genetic
interaction networks and methods for integration of diverse genomic data to predict gene function or infer biological networks. His lab is developing approaches for analyzing and leveraging interaction networks to answer biological questions in a variety of systems including yeast, plants (Arabidopsis and maize), worm and human.
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ResearchandIndustryPartnersSessionJohannesGrissEuropean Bioinformatics Institute, Hinxton, UK
Johannes Griss is a Database Application Developer for the proteomic
services team at the EMBL‐European Bioinformatics Institute, which is part
of the European Molecular Biology Laboratory (EMBL‐EBI). Johannes
undertook his degree in medicine at Medical University of Vienna and is
currently doing a Ph.D. there. Johannes’s role at the EMBL‐EBI involves the
development of tools and the development of data standards for the
proteomics community as well as doing research on large proteomics datasets.
Abstract of talk
Life as a Developer at EMBL‐EBI
The multidisciplinary, collaborative environment of the EMBL‐EBI gives you the possibility to work
with excellent people from all over the world and to be at the heart of bioinformatics research in
Europe. The EBI’s primary objective is to make biological data freely available and accessible to
researchers, and the proteomics services are a big part of that. We develop resources and tools for a
broad range of users, and try to make this data as easily accessible and reusable as possible.
Furthermore, we are actively involved in the development of new data and reporting standards for
the field. One can work at the EBI in any number of ways: in our team we benefit from the
contributions of visiting scientists, postdocs and Ph.D. students, who are with us for anywhere
between a week and several years.
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JenniferMcDowallEuropean Bioinformatics Institute, Hinxton, UK
Dr. Jennifer McDowall is a Bioinformatics Outreach Officer for the EMBL‐European Bioinformatics Institute. Jennifer has created hands‐on
courses on the UniProt protein sequence database, the European
Nucleotide Archive, the InterPro protein function database and in the use
of sequence search and analysis tools, including the use of these
databases and tools for patent searching. She has provided training at
over 30 institutes worldwide. Jennifer has worked in a wide range of roles at EMBL‐EBI, including
as a Senior Database Curator for InterPro, curating protein signatures for the functional
classification of proteins.
Abstract of talk
Training and Career Opportunities at EMBL‐EBI
EMBL‐EBI is a world‐leading bioinformatics center, and makes biological data freely available to
the scientific community through an extensive array of services. EMBL‐EBI offers a stimulating
environment for training and career progression for early‐stage researchers. In addition to
developing user services, the EBI is active in research, training and working closely with industry.
Our research groups use computational approaches to address a broad range of biological
questions and often work in collaboration with a service team at the EBI or experimental
researchers. Two postdoctoral programs and individual group vacancies offer a variety of
opportunities for researchers to join the EBI and work at the forefront of bioinformatics.
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AssociateProfessor IzhakHavivNICTA and the Department of Pathology, The University of Melbourne
Izhak completed his his Ph.D. at the Weizmann Institute of Science and post doctoral fellowship at R. Tjian’s lab in UC Berkeley, as a Howard Hughes medical institute fellow, working on genome‐scale analyses to monitor global transcriptional responses. In the Peter MacCallum Cancer Centre, Izhak took part in the first steps of utilizing the microarrays to analyze ovarian and gastric patient specimens. Over the past ten years, Dr. Haviv has focused his career in the interface between genome‐wide profiling of pathological human samples, model systems and functional assays, and bioinformatics. Dr. Haviv has been a founding member and contributed to the establishment of (1) the Peter Mac
profiling facility, (2) VCFG, and (3) Baker IDI Omics facility. He has developed multiple approaches to determine the role of cancer stroma in virulent phenotype of the cancer cases, such as metastasis and drug resistance. More recently, Izhak has been developing methods to analyse a minute number of cells from tissue microtome section on Massively Parallel Sequencing, at the level of mRNA, CpG methylation, and histone‐modification‐specific chromatin immunoprecipitation. Izhak is particularly interested in the establishment of analysis pipelines for epigenetic profiling datasets (such as DNA methylation, chromatin immunopreciupitation, etc) that are generated via Massively parallel sequencing, in R‐bioconductor (Robinson, 2010), and in Galaxy environments. In Baker IDI, Dr. Haviv assisted in the foundation of the Victorian centre for functional genomics (shRNA and siRNA screening) and an integrated systems biology scale profiling facility, including an Illumina GAII sequencer, iSCAN microarray, and three mass spectrometry platforms focusing on small molecules and proteins (LC‐MS). His work in integrated genomics is contributing to the ENCODE, TCGA, ICGC, and NIH epigenetic roadmap projects, specifically in investigating how transcription factor binding affects transcription of genes, positioned at distant locations, and consequently, this work contributes to our understanding of unclassified disease‐associated SNPs. Abstract of talk Next generation sequencing and targeted drug development are in the cross roads of the maturation of personalized medicine. We have developed a series of tools for genomic data analysis. Our unique niche emphasis is on reduced computational hardware requirements and consequent accelerated performance. We focus on expanding the fraction of the genome, which is annotated with functional roles, and using a number of models for gene‐gene interactions and epigenetic gene control, we enhance the interpretation of unclassified genomic variations. To demonstrate the accelerated performance of our algorithms, during the presentation we will perform three analyses that would each typically requiring hours to carry out. We will focus on the MHC locus of the genome, which is critical to many auto‐immune diseases. We will assemble (Conway, Bioinformatics, 2011) and determine the genotype of Agilent Sure‐select target enriched sequencing of the locus, performed on indexed six individual multiplexes. SNPs that are intergenic, which normally cannot be assigned functional impact, will be analyzed for their effect on the potential binding of transcription factors, and their superimposition on known cis‐regulatory modules (Macintyre, Bioinformatics, 2010). Epistasis and other modes of gene‐gene synergy will be assessed, using our newly developed algorithm (Kowalczyk, in preparation), and compared to existing datasets on protein‐protein interaction networks (KEGG, Biocarta, etc), and sets of coexpressed genes (MSigDB). Using this set of analyses on prostate acquired castration resistance, show that the identification of targets of AR binding in the genome regulates prostate cell survival and patient performance.
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AcceptedAbstractsOralPresentationsSequenceAnalysis Bacteriophage Evolution Drives Pseudomonas Geruginosa PAO1 Biofilm Diversification Kerensa McElroy, University of New South Wales, Randwick, Sydney, AU We deep‐sequenced a P. aeruginosa PAO1 biofilm model of lung infection (P. aeruinosa is the leading cause of death for Cystic Fibrosis patients). Surprisingly, PAOI exhibited negligible genetic diversity. In contrast, its bacteriophage underwent ongoing diversification. Statistical haplotype reconstruction revealed superinfective phage emergence, possibly driving PAO1 biofilm phenotypic diversification. Efficient Branch‐and‐Bound Techniques for Two‐Locus Association Mapping Karin Klotzbuecher, Max Planck Ins tutes Tübingen, Tübingen, DE We present two different approaches to efficiently determine pairs of interacting SNPs , which are strongly associated with a phenotype. First, we use a branch‐and‐bound strategy to prune away insignificant pairs. Secondly, we apply prior biological knowledge in the form of candidate genes and interactions to reduce the search space. . Genome‐Wide Association Study of TB in the South African Colored Population: Comprehensive Gene and Pathway‐Based Association Study Emile R. Chimusa, University of Cape Town, Cape Town, ZA The admixed Coloured population in South Africa has the highest incidence of tuberculosis in Africa. Understanding of the genetic basis of the TB susceptibility and of its multiple genetic factors is critical for informing the development of novel interventions. New paradigms of Genome‐wide association study were conducted on this population.
Variant detection and the Autism Sequencing Project Orion Buske, University of Toronto, Toronto, CA In collaboration with SickKids, we are sequencing the exomes of 1000 individuals with autism to discover associated genetic variants. We present our current sequencing and analysis pipeline, along with the tools we have developed for alignment, variant detection, and visualization of next‐generation sequencing data. BioinformaticsTools Resolving Atomic Interaction Networks to Understand GPCR Conformational Switching AJ Venkatakrishnan, University of Cambridge/MRC Laboratory of Molecular Biology, Cambridge, IN G‐protein coupled receptors (GPCRs) are membrane proteins vital in health and disease. A detailed structural understanding of GPCR functioning is still unclear. We have developed a novel network based framework to study protein structure conformational changes and applied it to understand roles of residues and residue interactions in GPCR activation. Oqtans: A Galaxy‐Integrated Workflow for Quantitative Transcriptome Analysis from NGS Data Sebastian Schultheiss, Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, DE We demonstrate how a complete quantitative RNA‐seq analysis can be performed easily and effectively in
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Replication of Epistatic DNA Loci in Two Case‐Control GWAS studies Using OPE Algorithm Benjamin Goudey, University of Melbourne and NICTA, Melbourne, AU In this paper, we validate robustness of a novel algorithm known as Optimal Pairwise Epistasis (OPE) for exhaustively examining all pairwise interactions. We have tested our approach over 2 independent GWAS studies of Celiac disease and demonstrate the high level of replication achieved An Integrative Bioinformatics Predictor of Protein Sub‐Cellular Localization in Malaria Ben Woodcroft, Bio21 Molecular Science and Biotechnology, Melbourne, AU Prediction of protein sub‐cellular localization in the malarial parasite Plasmodium falciparum remains a biologically relevant and unsolved bioinformatic question. We present Plasmarithm, the first global localisation predictor for Plasmodium that uses genomic, transcriptomic and other systems biology data. For training and testing, experimental annotation was manually curated from >700 publications.
Transcriptomics,DataManagementandPhylogeny Profiling Transcription Initiation in Human Aged Brain Using Deep‐CAGE Margherita Francescatto, Vrije Universiteit Medical Center and University of Porto, Amsterdam, NL The aim of this study was to characterize transcription start sites in different areas of human aged brain and correlate expression with methylation and structural genomic variation. We present here our findings on alternative promoters and antisense transcription.
The Development of an Open‐Access Database for Human Transcriptional Regulation interactions Luiz Bovolenta, Instituto de Biociências de Botucatu, Unesp ‐Univ Estadual Paulista, Botucatu, BR In an effort to provide researchers with a repository of TF‐TG interactions from which such interactions can be directly extracted, we present here the human transcriptional regulation interactions database (HTRIdb), an open‐access database of experimentally validated interactions among human TFs and their respective TGs. Computational Purification of Tumor Gene Expression Data Amit Deshwar, University of Toronto, Toronto, CA An integrative bioinformatic strategy was developed to identify peptidic antigens with low cross‐reactivity in the pathogen's genome, based on a number of attributes such as protein disorder, tandem repeats, subcellular localization, codon usage, sequence similarity against human and related pathogens, etc. Peptide microarray technology was used to validate predictions Markov Models to Delineate Evolutionary and Codon Usage Patterns among Malpighiales Mehedi Hassan, University of Glamorgan, Pnotypridd, UK This presentation is about our recent work where a comparative study of codon usage patterns of chloroplast genes in Jatropha curcas and Manihot esculenta was performed using multivariate statistical analysis and correlation analysis. Our models placed Jatropha curcasas sister to Manihot esculenta on the emerging biofuel‐model.
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PosterPresentations 1. Mapping of Genome‐Wide Expression Data in Biologically Coherent Ordered List of Genes Integrated Networks Marcio Acencio, Universidade Estadual Paulista ‐ Instituto de Biociências de Botucatu, Botucatu, BR 2. Predicting Protein Associations with Long Noncoding RNAs Federico Agostini, Centre for Genomic Regulation, Barcelona, ES 3. Minimum Curvilinearity to Address High‐Throughput Protein‐Protein Interaction Experiments Gregorio Alanis‐Lobato, King Abdullah University of Science and Technology, Thuwal, SA 4. Explanation of Helicobacter Pylori Virulence and Adaptation Based on Proteogenomic Analysis Dmitry Alexeev, Russian Institute Of Physico‐Chemical Medicine, Moscow, RU 5. A Unified View on Regulatory Genomics Sonja Althammer, Universitat Pompeu Fabra, Barcelona, ES 6. In Silico Phenotype Prediction of Ionizing‐Radiation‐Resistant Bacteria by Extraction of Discriminative Motifs Sabeur Aridhi, Blaise Pascal University, Clermont Ferrand, FR 7.Curation and Analysis of Polyketide Metabolism in Mycobacterium Tuberculosis Anshu Bhardwaj, Council of Scientific and Industrial Research, New Delhi, IN 8. Structural Comparison of Erwinase and E. Coli L‐Asparaginase to Facilitate Rational Rngineering of a Cancer Drug Mainá Bitar, Technische Universität München, Garching, DE
9. Maximizing the Number of Aligned Reads from RNA‐Seq Data Thomas Bonfert, Ludwig‐Maximilians‐University Munich, Munich, DE 10. Discovery of Novel Causes of Oncogenic Pathway Activation with REVEALER Olga Botvinnik, Broad Institute, Cambridge, US 11. Distribution and Influence of Cation‐pi Interactions between Native and Mutant Prions George Priya Doss C, VIT University, Vellore, IN 12. Using Large‐Scale Phylogenomics to Assess the Evolutionary Position of Elusive Taxa: the Case of the Microsporidian Pathogens Salvador Capella‐Gutierrez, Centre for Genomic Regulation, Barcelona, ES 13. Finding Consistent Explanations for Observations from Genome‐Wide Mutant Assays Deborah Chasman, University of Wisconsin‐Madison, Madison, US 14. Nonparametric Estimation of an Unknown Probability Distribution Using Maximum Likelihood and Bayesian Approaches: Application to CNV Analysis Alona Chubatiuk, University of Southern California, Los Angeles, US 15. Comparative proteomic Analysis of Cerebrospinal Fluid of Patients with Viral and Bacterial Meningitis Ana Cordeiro, Oswaldo Cruz Foundation, Belo Horizonte, BR 16. Combinatorial Approach to Discovering Biomarkers for Disorders of the Eye Jigisha Darbha, University of Geneva, Geneva, CH
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17. A Semantic Web Infrastructure for Bioinformatics of Staphylococcus Aureus Cândida Delgado, Instituto de Tecnologia Química e Biológica, Oeiras, PT 18. A Comparative Study of HMM Classifier on Protein Sequence Classification Wajdi Dhifli, LIMOS ‐ Blaise Pascal University, Aubière, FR 19. A Generalized Linear Model for Large‐Scale Metalloproteins Identification in Bacterial Proteomes Johan Estellon, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Grenoble, FR 20. Finding Active Subnetworks in Diseases by Using Integrated Biological Networks Raj Gaire, University of Melbourne, Carlton, AU 21. mTIM: margin‐based Transcript Identification from RNA‐Seq Nico Goernitz, Technical University Berlin & MPI Tuebingen, Berlin, DE 22. Predict Subcellular Localization for Proteins in All Kingdoms Tatyana Goldberg, Technische Universität München, Garching, DE 23. Analysis of Trypanosoma Cruzi Gene Expression in Response to Ionizing Radiation Priscila Grynberg, Universidade Federal de Minas Gerais, Belo Horizonte, BR 24. Toward PWAS: Discovering Pathways Associated with Human Disorders Emre Guney, Pompeu Fabra University, Barcelona, ES 25. Cholesterol‐‐Responsive Gene Network Reconstruction from Hypercholesterolemic Mice Transcriptome Data Gustavo Hime, Freiburg Institute For Advanced Studies, Freiburg, DE
26. Web‐based Interactive Protein Contact Maps with PConPy2 Hui Kian Ho, University of Melbourne, Carlton, AU 27. Multi‐Access Module for the Identification of Trees of Gujarat State Minal Jani, Sardar Patel University, Anand, IN 28. The Relevance of HIV‐1 Pol, Gag and Vif T‐cell Epitopes Based Vaccine Across Kenyan Population HLA Class 1 Diversity Muriira Karau, Kenya Bureau of Standards, Nairobi, KE 29. Computational Analysis of DNA Replicases in Double‐Stranded DNA Viruses: Relationship with the Genome Size Darius Kazlauskas, Vilnius University, Vilnius, LT 30. The MAP Interactome in Drosophila: an Integrative Systems Biology Quest for New Mitotic Proteins Faisal Khan, University of Oxford, Exeter, UK 31. System‐Level Analysis of Cell Line Data for Targeted Drug Discovery Nayoung Kim, Sookmyung Women's University, Seoul, KR 32. Spectral Classification of Short Numerical Exon and Intron Sequences Benjamin Kwan, University of Ottawa, Ottawa, CA 33. A Knowledge Federation Strategy for Integrating Genotype‐to‐Phenotype Data Pedro Lopes, University of Aveiro 34. Computational Analysis of Genetic Network Related to Pancreatic Cancer in Human Mrinal Mishra, VIT University, Vellore, IN
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35. Birla Institute of Technology,Mesra, Hyderabad, IN Identification of Functionally Important Residues Rowards Substrate Stabilization in Family 11 Microbial Xylanases Karthik Mvk, Birla Institute of Technology,Mesra, Hyderabad, IN 36. Cross Genome Analysis of Histone Orthologs and Chromosomal Networks in Nucleosomes Across Species Preetam Nayak, SASTRA University, Thanjavur, IN 37. Integrated Molecular Biology and Bioinformatics approaches in Identification of Putative Reservoirs/Hosts of Rift Valley Fever Virus (RVF) in Kenya David Ouma, icipe‐African Isect Science for Food and Health, Nairobi, KE 38. Mining Gene Ontology Data with AGENDA Guvanch Ovezmyradov, University of Goettingen, Goettingen, DE 39. Cryptosporidium Species, Gastroenteric Pathogens and CD4 Counts in North Central Nigeria Victoria Pam, National Veterinary Research Institute,Vom,Plateau State,Nigeria, Jos, NG 40. A Non‐Biased Framework for the Annotation and Classification of the Non‐miRNA Small RNA Transcriptome Lorena Pantano, Center for Genomic Regulation, Spain 41. Comparative Genome‐Wide Analysis of transcription Initiation and Promoter Architecture in Eukaryotes R. Taylor Raborn, University of Iowa, Iowa City, US 42. Transcriptome of a Climacteric Fruit Species Diospyros Kaki Thunb for Functional Genomics Farzana Rahman, University of Glamorgan, Treforest, UK
43. A Method to Separate Function and Fold Specific Residues in Proteins Mohd Rehan, Jawaharlal Nehru University, New Delhi, IN 44. Falsifying Signalling Pathway Models in System Biology Mohammad Javad Sadeh, Institute of Functional Genomics Computational Diagnostics Group University of Regensburg, Regensburg, DE 45. A Novel Therapeutic Drug Targeting Surface Protein of Nipah Virus Using Computational Techniques Manzur Sayeem, University of Dhaka, Dhaka, BD 46. Antimony Resistance in Visceral Leishmaniasis Might be a Possible Consequence of Serial Mutations in ABC Transporters of Leishmania Species During Evolution Sukrat Sinha, University of Allahabad, ALLAHABAD, IN 47. Probabilistic Reconstruction of Protein Interaction Histories Using a Simple Measure of Interaction Affinity Ryan Topping, Imperial College, London, UK 48. Are Protein Disordered Regions Equal to Loops? Esmeralda Vicedo, Technische Universität München, Garching, DE 49. DMB: a Novel Tool for Logic Data Mining in Bioinformatics Emanuel Weitschek, Università degli Studi Roma Tre, Rome, IT 50. On Sequence Conservation Space of RNA‐Recognizing Residues in Protein Sequences Li Xue, Iowa State University, Ames, US
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Note: The above abstracts are ordered by the presenting author’s last name.
The information in the above section has been printed as provided by the authors.
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AwardsThe outstanding poster and oral presentation of the 7th ISCB Student Council Symposium will
be recognized and awarded with the support of our sponsors. All awards this year have been made
possible by the sponsorship of Oxford University Press.
We thank Oxford University Press for their continued support of the Student Council Symposium. BestPresentationAward
This award will acknowledge the Best Oral presentation by a Student at the Symposium. All
Symposium delegates will be asked to vote for their favorite presentation. The winner will be
determined by the vote and the opinions of a jury composed of ISCB Student Council leaders. The
Best presentation award this year is sponsored by Oxford University Press journal Bioinformatics.
Value of the award: 500 USD
Previous winners:
2010 – Geoff Macintyre
2009 – Nils Gehlenborg
2008 – Surya Saha
BestPosterAward
The best poster of the Symposium will be chosen through voting by the delegates at the
Symposium and by the opinions of a jury of ISCB Student Council leaders. In addition to the Best
Poster award, a Best Poster Runner‐Up award will also be given out. The Best poster awards have
been made possible by Oxford University Press journal Nucleic Acids Research.
Value of the Best Poster Award: 350 USD
Value of the Runner‐Up Award: 125 USD
Previous winners:
2010 – Mark McDowall and Wouter Meuleman (Runner‐Up)
2009 – Jose Caldas
2009 – Inken Wohlers and Nikolay Samusik (Runner‐Up)
2008 – Lixia Yao
2008 – Sebastian Pechman and Bridget Chukualim (Runners up)
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ISCBStudentCouncilTravelFellowships The ISCB Student Council has teamed up with this year’s sponsors to give more students
the opportunity to attend the 7th ISCB Student Council Symposium and ISMB/ECCB 2011 in
Vienna, Austria. Thanks to generous support from our sponsors, we were able to award 12
Travel Fellowships this year.
R. Taylor Raborn University of Iowa, USA
Benjamin Kwan University of Ottawa, Canada
Amit Deshwar Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada
Maina Bitar Department for Bioinformatics and Computational Biology ‐ Fakultät für Informatik, Technische Universität München
Farzana Rahman Computational Biology Group, Applied Mathematics and Statistics Research Unit, University of Glamorgan, Pontypridd, Wales, UK
Benjamin Woodcroft Department of Biochemistry & Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
Salvador Capella‐Gutierrez Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), UPF, Barcelona (Spain)
Emre Guney Pompeu Fabra University, Barcelona, Spain
Sonja Althammer Universitat Pompeu Fabra, Barcelona, Spain
Darius Kazlauskas Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
Emanuel Weitschek Department of Informatics and Automation, Università degli Studi Roma Tre, Rome, Italy
Mohd Rehan School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
Congratulations to all the Travel Fellowship awardees!
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AcknowledgementsThe 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 explicitly:
Without the logistical support and invaluable advice of ISCB Executive Administrator BJ
Morrison McKay and ISMB/ECCB 2011 conference organizer Steven Leard, the 7th ISCB
Student Council Symposium would not have been possible. We deeply appreciate their
continued support of the ISCB Student Council and the Symposium.
We are also greatly indebted to ISMB/ECCB 2011 conference chair Dr. Burkhard Rost and
vice‐chair Dr. Michal Linial for giving us the opportunity to have the 7th 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. The Student Council would also like to thank our
keynote speakers Dr. Curtis Huttenhower, Dr. Ivet Bahar, and Dr. Chad Myers. 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 his or her
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 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
7th ISCB Student Council Symposium would not have been possible.
Thank you all!
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Sponsors We thank our sponsors for sharing our vision and helping to make the 7th ISCB Student Council Symposium a success. Specifically, we wish to thank:
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RegionalStudentGroupsInitiative
The Student Council (SC) has always strived to reach out to
Students of Computational Biology and Bioinformatics around
the world and promote communication between them, to
create a vibrant global network of peers. To accomplish this
more effectively, in 2006 the SC conceptualized the setting up
of Regional Student Groups (RSGs). Regional Student Groups
work to fulfill the broad mission of the SC at their regional level
by organizing events and initiatives tailored to the requirements of the local student
community.
The RSGs initiative has turned out to be an extremely popular and successful initiative. In
the past five years, the RSG network has grown to include 20 RSGs from all over the world.
Our active RSG network has seen RSGs organize symposia, conduct workshops and contests,
initiate discussion groups and even work with each other on trans‐national collaborative
student projects. As supra‐institutional organizations, RSGs are perfectly placed to foster
inter‐institutional contacts and collaborations in their region and where possible, even serve
as a link between students and the local industry. Most RSGs have also formed their own
network of members using mailing lists, discussion forums or other means to ensure quick
and efficient dissemination of useful information within the community.
The minimal leadership team required to run an RSG are a President and a Secretary
working under the guidance of a Faculty coordinator. Since the RSGs are affiliated to the SC
membership to an RSG is free. Only the President, Secretary and the Faculty advisors are
required to hold an ISCB membership. Individual RSGs are of course free to put in place a
more elaborate administration team if needed. This uncomplicated administrative structure
and low operating costs associated with the RSGs has made it feasible for students in many
developing countries to begin and develop RSGs in their countries.
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As recognition of the importance of the RSGs to the Student Council’s overall mission, the
RSGs funding program was initiated last July, thanks to funding support by the ISCB. As a
part of this program, RSGs are invited to submit proposal for events and initiatives they plan
to organize and after a peer review process some of those proposals are selected to be
funded by the SC. So far, RSGs have utilized these funds to organize Workshops,
Hackathons, Discussion groups and more. Visit http://iscbsc.org/node/65/rsg‐funding to see
more details about the funding program.
Snapshots from RSG events organized with funding support from the SC
The success of the RSGs initiative is due only to the enthusiasm and commitment shown by
the RSG leaders and the support that they have received from faculty advisors and other
interested professors. And with these motivated students leading our RSGs, we only expect
to see this initiative grow from strength to strength in the coming days.
If you would like to find out more about the RSGs initiative or find out how you too can get
involved in this, please visit http://iscbsc.org/content/regional‐student‐groups or send an
email to rsg@iscbsc.org
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OtherStudentCouncilActivitiesatISMB/ECCB2011
ArtandScienceExhibition
ISMB/ECCB 2011 brings together scientists from a wide
range of disciplines, including biology, medicine, computer science,
mathematics and statistics. In these fields we are constantly dealing
with information in visual form: from microscope images and
photographs of gels to scatter plots, network graphs and phylogenetic trees, structural
formulae and protein models to flow diagrams; visual aids for problem‐solving are
omnipresent.
Often these visual aids are mundane and nothing more than a small clue to the
solution of the problem. But then there are special ones that make the whole more than the
sum of its parts. Ones that combine outstanding beauty and aesthetics with deep insight
that perfectly proves the validity of the scientific approach or goes beyond the problem's
solution. Ones that surprise and inspire us through the transition from science to art, ones
that open our eyes and minds to reflect on the work we are doing.
The Art & Science Exhibition at ISMB/ECCB 2011 presents images and videos that have been
generated as part of a research project and some artworks resulting from creative efforts
that involve scientific concepts or employ scientific tools and methods. The artworks will be
displayed during all conference days.
Website: http://Symposium.iscbsc.org/content/art‐science‐exhibition
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ISCBStudentCouncilOpenBusinessMeetingand
AwardsCeremony
Sunday, July 17th, 13:00‐14:20 (ISCB 13:00‐13:30, ISCBSC 13:30‐14:00, QA 14:00‐14:20) in Room E1
We are pleased to invite you to the annual ISCB Student Council Open Business
meeting. This meeting is for people who want to learn more about how the Student Council
operates, how they can get involved, get updates on current Student Council activities, and
find out where the Student Council will head in the future.
This year the Student Council Open Business meeting will be held in conjunction with
the ISCB Open Business meeting. We strongly encourage you to come along to both
meetings and learn how each of the organizations work.
Input and feedback from the community are very important to us and we hope that
you will join us for this meeting. For those interested in getting involved in ISCB Student
Council activities there will be mentors available that can answer your questions about the
ISCB Student Council, and discuss with you the options to contribute to our community.
Agenda:
Report from the ISCB Student Council Leadership ‐ Overview of recent developments
within the ISCB Student Council
Contributing to the SC – Learn about contributing to the ISCB Student Council
Regional Student Group initiative ‐ Presentations by Regional Student Groups members
7th ISCB Student Council Awards Ceremony ‐ Presentation of the winners of the Best Poster
and Best Presentation Awards as well as the recipients of the Student Council Travel
Fellowships.
Outlook ‐ Overview of the plans for the coming months and a preview of the 8th ISCB
Student Council Symposium.
Feedback and Discussion ‐ An opportunity to voice your opinion about the efforts of the
ISCB Student Council and the direction it should be taking. The ISCB Student Council is
counting on your input!
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StudentCouncilCareerCentral
The ISCB Student Council is committed to
helping students to develop a successful career in
the field of Computational Biology and
Bioinformatics. Besides our Student Council
Symposium, now on its sixth year and the Regional
Student Group initiative, for the second year the Student Council will be having a booth in
the Exhibitor floor at ISMB dedicated specifically to helping students and post‐docs with
career development.
Please come visit us at Booth 4 in the exhibitor floor, were you will find a job posting
board and tons of advice on how to navigate the job market in this exciting new field. You
can also participate in our interactive job posting board, where you can sign‐up to meet
potential employers or supervisors who are also present at the conference. Don’t forget to
bring your CV. A recruitment seminar and career discussion panel associated with the booth
will take place in Room J241 from 17:30‐18:30 on Sunday July 17th. We look forward to
seeing you there!
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StudentCouncilSocialHQDo you feel like science is just so much easier while drinking a beer (or a coke, or two
beers)? Do you think the hectic conference site is not appropriate for an intimate scientific
discussion with one of your peers? Or do you just feel bummed by all those posters that
present the same stuff as you, but better?
Come and join us at the SC Social HQ, a friendly riverside pub in Donauinseln (islands
from the Danube), where you can relax after the day and meet other students from the
conference. And even better, it is only 5 minutes by subway from the conference venue!
Friday‐Tuesday: Social HQ (19:00 onwards) *Depending on the weather the place may
change. Please visit our twitter #scs2011, @sciscb or facebook group: student council
http://www.facebook.com/group.php?gid=2314371661
to get updates on Student activities during the Symposium and ISMB/ECCB 2011.
Monday: SC Social Event: BLAST your brain! (19:00 onwards) *see description on next page
Looking forward to meeting you at the SC Social HQ!
Donauinseln
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SocialEvent:
BLASTyourBrain!The ISCB Student Council invites you to attend a networking and social event on the evening
of Monday the 18th of July where you will walk around the lovely Vienna city, mingle with
other students attending the conference and enjoy a relaxed evening!
BLAST your Brain! Is your algorithm efficient enough?
In this year’s student social event, you will experience a completely new level of BLASTing!
With our special quiz, having the right answers is not enough; you will need a performance
as well!
Join us in for extra fun right before dinner! Hope to see you all there that night!
Agenda:
19h00: Meet up at ISMB/ECCB conference hall
19h15: Walking tour through Vienna’s classic and famous streets
20h30: Start “BLAST your Brain!” at a trendy pub in Naschmarkt
21h30: Social event dinner, 510 Naschmarkt, http://www.neni.at
During “BLAST your Brain!” a variety of finger foods and drinks will be served. Stop in
anytime for our special student event on the evening of Monday, July 18th.
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StudentCouncilSymposiumCommittee
Lorena Pantano Rubino, Student Council Symposium Chair Center of Genomic Regulation (CRG)
Barcelona, Spain
Pedro Lopes, Student Council Symposium Co‐Chair DETI/IEETA, University of Aveiro
Priscila Grynberg, Program Chair Departamento de Bioquímica e Imunologia
Universidade Federal de Minas Gerais, Brazil
Anupama Jigisha, Fundraising Chair University of Geneva‐Swiss Institute of Bioinformatics Switzerland
Alexander Goncearenco, Website Computational Biology Unit, Department of Informatics
University of Bergen, Norway
Thomas Abeel, Travel Fellowships Chair Broad Institute of MIT and Harvard, Cambridge, MA, USA VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
Avinash Shanmugam, Keynotes Center for Computational Medicine and Bioinformatics
University of Michigan, Ann Arbor, USA
Surya Saha, Publicity Chair, Department of Plant Pathology and Plant‐Microbe Biology Cornell University, NY, USA
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Cynthia Prudence, Conference Booklet Editor Division of Biological and Medical Physics, Physics Department
University of Rhode Island, Kingston, RI, USA
OrganizingCommittee Noura Chelbat Jeroen de Ridder Geoff Macintyre Magali Michaut Casey Overby
ProgramCommittee Vinicius Abreu Preeti Bais Virginie Bernard Ulrich Bodenhofer Jose Caldas Louise Cerdeira Slavica Dimitrieva Márcio Dorn Karen Dowell Segun Fatumo Nils Gehlenborg Tatyana Goldberg Arlan Goncalves Ana Carolina Ramos Guimarães Roberto Herai Venkatakrishnan A. J. Ney Lemke Hailton David Lemos Karina Machado Geoff Macintyre Vinicius Maracaja‐Coutinho Mariana Lima Boroni Martins Daniele Merico Olga Nikolova Casey Overby Alexandre Paschoal Ulisses Pereira Cynthia Prudence Jeroen de Ridder Francisco Roque Venkata Satagopam Miranda Stobbe Claudia Elizabeth Thompson Marie Vendettuoli Esmeralda Vicedo Ramon Vidal Adriano Velasque Werhli Ana Trindade Winck Fuxiao Xin
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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.
Copyright © 2011 ISCB Student Council and contributing authors. All rights reserved. This booklet may be
reproduced without permission in its original form.
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