KEYNOTES

Robert Huber,
Max-Planck-Institut fuer Biochemie, Germany.
http://nobelprize.org/nobel_prizes/chemistry/laureates/1988/huber-autobio.html

Biosketch: Robert Huber was born in 1937 in Munich. He studied chemistry at the Technische Universität München (TUM), where he also completed his Ph.D. and habilitation. Since 1972, he has been a member of the Max-Planck-Gesellschaft and Director at the Max-Planck-Institut für Biochemie until his retirement in 2005. Since 1976, he also serves at the TUM as a Professor. He holds appointments as Guest Professor at the Universität Duisburg-Essen (Germany), the Cardiff University (Great Britain), the Universidad Autonoma de Barcelona (Spain), and the Seoul National University (Korea). He serves as a member of the Board and/or Scientific Advisory Board of a number of pharmaceutical and crop science companies, and he is co-founder of two companies, Proteros and Suppremol, located in Martinsried and offering services for drug discovery and development and for the development of novel therapies for autoimmune diseases, respectively. Huber has made major contributions to the understanding of the structure and function of biological macromolecules. He has studied proteases and their natural and synthetic inhibitors, metalloenzymes (iron, nickel, molybdenum, copper), proteins of the immune system (antibodies and antibody receptors), protein hormones and their receptors, protein kinases, enzymes of amino acid biosynthesis, enzymes of cofactor and vitamin biosynthesis and proteins of energy and electron transfer. In addition, he has contributed to the development of instruments for data collection and to methods in protein crystallography, particularly Patterson methods, graphic methods, and refinement, to the use of electron rich metal clusters, and most recently to the methods and instruments for crystal improvement. He has been honoured by numerous honorary doctorates, professorships, memberships in learned societies and awards, including the Otto-Warburg Medal, the Emil von Behring Medal, the Sir Hans Krebs Medal, the The Linus Pauling Medal, Max Tishler Prize and, in 1988, the Nobel Prize for Chemistry together with H. Michel and J. Deisenhofer.

Title: Proteins and their structures, basic science and application PPT DIR

Abstract: Protein crystallography experienced in the last twenty years a rapid development in methods and instrumentation, allowing the determination of very large and complex protein structures, particularly when combined with electron microscopy. These structures document an unlimited versatility and adaptability of the proteins4 architecture, but reveal also unexpected relationships. The structures are a basis for understanding their binding specificities and catalytic properties (chemistry), their spectral and electron transfer properties (physics), and their roles in physiological systems (biology and medicine). They allow design and development of specific ligands of target proteins opening novel ways for plant protection. Examples are given for important therapeutic targets in medicine and targets for the development of herbicides and fungicides in crop protection.

Chris Sander,
Director,
Memorial Sloan-Kettering Cancer Center's Computational Biology Center, USA.

Biosketch: Chris Sander is currently the director of the Memorial Sloan-Kettering Cancer Center's Computational Biology Center and Chairman of the Sloan-Kettering Institute's Computational Biology Program. His computational biology research team at Memorial Sloan-Kettering Cancer Center aims to analyze and simulate biological processes at different levels of organization, predict the results of interventions in biological systems, and improve the prevention, diagnosis, prognosis, and therapy of cancer. Current areas of research in the Sander group include: identification of oncogenically altered pathways from genomic and molecular profiling in cancer, algorithms for the analysis of cancer genomics data, design of combinatorial cancer therapy, drug target identification, knowledge representation of biological pathways, protein evolution, specificity in protein networks, and the function of small RNAs. Sander is also the editor of the journal Bioinformatics and he advises the US National Institutes of Health, the Mayo Clinic Genomic Center and the IBM Deep Computing Initiative. He previously worked as chief information science officer with Millennium Pharmaceuticals and at the European Bioinformatics Institute.

Title: Systems biology of cancer cells and the Cancer Genome Atlas PPT

The talk will present the complexity and diversity of cancer genotypes from hundreds of patient samples profiled as part of The Cancer Genome Atlas; and, a new approach to modelling cell biology and designing combination therapy based on systematic perturbation experiments and rich observation of the state of signaling molecules. (1) We present a novel method for deriving network models from molecular profiles of perturbed cellular systems. The network models aim to predict quantitative outcomes of combinatorial perturbations, such as drug pair treatments or multiple genetic alterations. (2) The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of various genome analysis technologies. More than two hundred primary glioblastoma samples have so far been analyzed for changes in DNA copy number, mRNA expression, miRNA expression, DNA methylation, as well as for germ-line and somatic mutations in protein-coding genes. Our analysis efforts focus on three main aspects: 1) identification of recurrent regions of DNA copy number loss and gain using our new computational method, RAE; 2) prediction of the functional impact of mutations using our Online Mutation Assessor (OMA) tool; and 3) identification of altered signaling pathways, based on data obtained from our (with G. Bader, University of Toronto) Pathway Commons resource (http://www.pathwaycommons.org/). By mapping DNA copy number changes and mutations to known biological pathways, we have identified recurrent altered signaling processes. Classification of alterations in particular tumors by sub-pathways is likely to facilitate the development of sub-type specific therapies.



Tim Hubbard,
Head of Informatics,
Wellcome Trust Sanger Institute, UK.
http://www.sanger.ac.uk/Teams/faculty/hubbard/

Biosketch: Tim Hubbard graduated with a BA in Biochemistry from University of Cambridge in 1985 and a PhD in Protein Design from the Department of Crystallography, Birkbeck College, London in 1988. In 1997 he joined the Sanger Institute to became Head of Human Genome Analysis. He has been Head of Informatics since 2007. Before joining the Sanger Institute he worked mainly on protein folding, classification and design. In 1994 he co-founded SCOP (the Structural Classification of Proteins database) and used it to calibrate the reliability of sequence alignment methods. He was a co-organiser of the CASP (Critical Assessment of Structure Prediction) protein structure prediction competition 1996-2007. At the Sanger Institute he was a member of the strategy group that organised the sequencing of the human genome. In 1999 he developed an automatic annotation system which evolved into the Ensembl project with Michele Clamp and Ewan Birney at EBI. Since 2007 he has been the PI of GENCODE, a programme of the ENCODE project, which brings together Havana, Ensembl and seven external groups to generate the reference geneset for the human genome. He is also Sanger PI of the Genome Reference Consortium which is responsible for reference genome sequences of human and mouse. Along side these large scale projects, he has a research group which uses machine learning approaches to develop ab initio algorithms for vertebrate genome annotation such as large scale motif discovery. The group has also developed components of bioinformatics infrastructure, including the popular biojava open source framework and components of the Distributed Annotation System (DAS) including the SPICE client, the Dazzle Server and the DAS registry. Tim serves on many national and international advisory boards including those involved in open access publishing (ukPMC) and infrastructure for uk patient medical records research. In his private capacity he is also significantly involved in international policy discussions around innovation, intellectual property and public health.

Title: Ten years of Human Genome Bioinformatics: the vanguard of data driven biology Not Available

Abstract: Ten years ago, human genome sequence started to flood into public databases. Handling it was a big jump in scale for a young bioinformatics field, which was only just getting to grips with the thirty times smaller worm genome. At the Wellcome Trust Genome Campus the Ensembl project was started from scratch to handle this data and address the huge demand from biologists for access to the genome. Ensembl became a system to store the genome data in an RDBMS; pipelines to generate pre-computed sets of analysis; APIs to provide both web and programmatic access. Almost 10 years on, Ensembl now integrates more than forty vertebrate genomes, making a new release every ~2 months. Through it consistent gene annotation is provided, generated for the reference genomes of human, mouse and zebrafish by integrated approach combining curation and computation, under projects such as GENCODE. It has recently been joined by a sister database EnsemblGenomes at EBI which aims to present genomes of the rest of biology using the same software system. We are now facing a new jump in data scale and complexity: in vertebrates from genome to genomes (1000 genomes project, International Cancer Genome Consortium) and from a single reference functional annotation towards a map of the differences in functional state between cell types; developmental stages and genotypes (transcriptomics and ChiP-seq based assay data). A representation of the human genome that captures these new dimensions of annotation will be required to optimally interpret the growing abundance of human genetics data.

Ensembl is one of a number of genome browsers and just one of 1000s of biological databases. More broadly, its time to recognise that data scales associated with the human genome are now the norm for biology. The amount of raw sequence data being transferred between centres in the 1000 Genomes Project and other initiatives is becoming comparable to that generated by large high-energy physics experiments such as the Large Hadron Collider at CERN. Biology is transforming itself into a data rich discipline. This growth needs to be reflected in terms of investment in national and international bioinformatics infrastructure, as the value of the data is maximised through broad access and use. This will means more resources, but also more scrutiny of both bioinformatics and computational biology, as they become more central to the process of biological discovery.

Vladimir Bajic,
Director,
Computational Bioscience Research Center,
King Abdullah University of Science and Technology, Saudi Arabia.

Biosketch: Vladimir Bajic earned a graduate degree in Electrical Engineering and a master’s degree of Electrical Engineering Sciences from the University of Belgrade, Serbia, followed by a doctorate of Engineering Sciences in Electrical Engineering from the University of Zagreb, Croatia. He has previously worked in industry and has extensive experience with academic research institutions across the globe, including Vinca Nuclear Science Institute in Yugoslavia and the Institute for Infocomm Research in Singapore, where he was Head of the Knowledge Extraction Laboratory. Dr. Bajic is an elected member of the Academy of Nonlinear Sciences (Russia), has been a registered Professional Engineer in South Africa, and was awarded the only South African Research Chair in Bioinformatics and Human Health. He has served on the editorial boards of several international journals and currently serves on the Advisory Boards of a number of research institutes. He was an elected role model of the Institute for Infocomm Research (I2R), Singapore, in 2002. He is currently appointed as the Director of the Computational Bioscience Research Center and Professor of Applied Mathematics and Computational Science in the Mathematical and Computer Sciences and Engineering Division at King Abdullah University of Science and Technology (KAUST). Across various fields, he has authored or co-authored more than 360 research publications, edited volumes, software products and invention disclosures. His work in modeling and artificial intelligence has resulted in several promoter recognition tools and knowledge discovery platforms that are currently commercial products.

Title: Deeper insights from text-mining: Dragon Exploratory System PPT

Abstract: We present Dragon Exploratory System (DES) for mining textual data from biomedical literature. DES allows for multifaceted insights into biomedical information contained in text such as: ranked generation of hypotheses based on the A-B-C and A-B-C-D paradigms, automated extraction of topical information based on user definable sentence templates, and variety of information on association of biomedical entities identified in the documents. DES is interlinked with a number of public databases from where it gathers additional associated information. It also contains precompiled human promoter annotation. DES allows for linkages of concepts identified in the literature with inferred pathway information, transcription regulation, and inferred linkages to SNP data. We believe it represents a useful tool for extraction of biomedical knowledge and should provide a strong support for researchers in the field.

Peter Little,
Professor,
NUS Life Sciences Institute,
NUS Department of Biochemistry,
NUS Office of Deputy President (Research and Technology)
Biosketch:

Peter F. R. Little is presently Director of the Life Sciences Institute, Research Director and Professor in the Department of Biochemistry, National University of Singapore; he was previously Director of Research, UNSW Asia, Professor of Medical Biochemistry, UNSW and Reader in Molecular Genetics, Imperial College. He is a present member of Editorial Board of Genome Research, Comparative & Functional Genomics, Briefings in Functional Genomics and Proteomics. Prof. Little has extensive experience in scientific research management of national and private agencies and of consultancy work in genomic and non- genomic fields, working with major pharmaceutical, biotechnology and legal companies. He has authored or co-authored ~120 papers and have written a popular science book on genetics, Genetic Destinies, that was translated into 3 languages.

Title: Thinking about genetic variation and biomedical research PPTX

Abstract: The past decade has seen an explosion of variation data demonstrating that diversity of both protein-coding sequences, and of regulatory elements of protein coding genes, is common and of functional importance. In this presentation, I will argue that genetic diversity can no longer be ignored in studies of human biology, even those without ostensible genetic outcomes, and that this knowledge can, and must, inform research. Singapore is positioned at the population junctions of Asia, India, and Malaysia but is also a substantial contributor to global biomedical research interests which are mainly oriented towards the populations of the Western hemisphere. We have unique opportunities to bridge the resulting East - West gap in research. My talk will focus upon both my own research and that of the rich research skills of the NUS and NUS Life Science Institute.

Peer Bork,
Senior Group Leader,
Structural and Computational Biology Unit,
EMBL, UK.
http://www.embl.de/~bork/

Biosketch: Peer Bork, PhD, is senior group leader and joint coordinator of the Structural and Computational Biology unit at EMBL, a European research organisation with headquarters in Heidelberg. He also holds an appointment at the Max-Delbrueck-Center for Molecular Medicine in Berlin. Dr Bork received his PhD in Biochemistry (1990) and his habilitation in Theoretical Biophysics (1995). He works in various areas of computational biology and systems analysis with focus on function prediction, comparative analysis and data integration. He published ca 400 research articles in international, peer-reviewed journals, among them 40 in Nature, Science or Cell. According to ISI (analyzing the last 10 years), Dr. Bork is currently the most cited European researcher in Molecular Biology and Genetics. He is on the editorial board of a number of journals including Science and PloS Biology, and functions as senior editor of the journal Molecular Systems Biology. Dr Bork co-founded four biotech companies, two of them went public. More than 25 of his former associates hold now professorships or other group leader positions in prominent places all over the world. For his achievements in nurturing and stimulating young scientists he received the Nature award for creative mentoring.

Title: Biological discoveries via data integration: From chemicals to ecosystems PPT

Abstract: Biological systems range from small biomolecules to entire ecosystems. We integrate heterogeneous data to uncover functional aspects of diverse biological systems at different spatial scales. I will illustrate our approach with examples from small-molecule-protein network analysis (e.g. how to use human phenotypic side effects to predict drug targets), from the systemic analysis of a small bacterium (e.g. how to bridge from biochemical complex purifications to an atomic model of a cell) and from environmental genomics (e.g. how to predict ecological parameters from metagenomics samples using satellite data).

Alessandro Sette,
Head,
Division of Vaccine Discovery,
La Jolla Institute for Allergy and Immunology, USA.

Biosketch: Alessandro Sette is currently a member of of the La Jolla Institute for Allergy and Immunology and head of its Division of Vaccine Discovery. He also chairs the institute's initiative for Emerging Infectious Diseases and Biodefense. Dr. Sette's research focus is on developing disease intervention strategies based on the specificity of immune responses. Dr. Sette graduated in Biological Sciences with a maximum cum laude degree from the University of Rome. He began his postdoctoral work at the Laboratory of Pathology, C.R.E. Casaccia, Rome. He remained there for five years before continuing his postdoctoral work at the National Jewish Center for Immunology and Respiratory Medicine in Denver, Colorado. In 1988, Dr. Sette left Colorado to join with Howard Grey, M.D. at the newly founded biotechnology company, Cytel, in La Jolla, California, and was also appointed as an adjunct assistant professor in Immunology at The Scripps Research Institute. He became director of immunology at Cytel in 1994, a position he held until he left in 1997 to found Epimmune, where he served both as vice president of research and chief scientific officer. He joined LIAI in 2002. Dr. Sette is an editorial board member and peer review consultant for numerous publications and is recognized as an Institute for Scientific Information highly cited investigator.

Title: The Immune Epitope Database and Analysis Resource (IEDB) AVI

Abstract: Over the last twenty years, the amount of information related to epitopes recognized in the course of T and B cell-mediated immune responses has dramatically increased. As of June 2004, a PubMed search using the word "epitope", reveals a total of 5,173 records prior to 1975 and 17,088 records in 1975-1984 period. The number of records jumps to 30,948 for 1985-1994, and has already reached 32,154 for the 1995-2004 period (with a large fraction of the 2004 records still to come).

Epitope-based techniques are utilized by scientists involved in vaccine development to characterize immune responses in experimental settings, following infection, or in response to vaccination. The purpose of these evaluations is to develop correlates of immunity or therapy and guide the development of vaccines and drugs targeting infectious pathogens. Knowledge of the epitopes recognized in the course of natural infection or as a result of vaccination, is also key for our capacity to develop bioinformatic tools and accurate analyze, model and predict immune responses. Recent concerns over emerging diseases and bioterrorism emphasized the need for information regarding the key epitopes recognized by the immune system.

Despite this growing need, a centralized resource to store and access relevant information is not available. Our goal is the creation of the Immune Epitope Database and Analysis Resource (IEDB), a comprehensive knowledge center comprised of a repository of immune epitope data and associated analysis tools. The IEDB is sponsored by the National Institute for Allergy and Infectious Diseases (NIAID) and will host data relating to both B and T cell epitopes from infectious pathogens as well as experimental and self-antigens. Priority will be placed on class A-C pathogens and emerging diseases. Epitopes recognized in humans, non-human primates, rodent and other animal species are included. This resource center is now freely available on the Internet.

A crucial component of the project is to involve and solicit feedback from the scientific community in the design of the IEDB's scope and capability. In addition to responding to direct feedback from the community, the IEDB will be produced in a manner that encourages the incorporation of analytical tools and data derived by research labs at-large.

Herein, we present the main principles and considerations, both at the immunological and bioinformatic level, utilized in its design. In particular, we emphasize the specific immunological perspective and the bioinformatic, software and logical database concepts applied to the design of the IEDB, to solicit feedback from the immunological and bioinformatic communities.

Louis H.Y. Chen,
Tan Chin Tuan Centennial Professor,
Director, Institute for Mathematical Sciences,
National University of Singapore, Singapore.

Biosketch: Louis H. Y. Chen received his bachelor's degree from the University of Singapore in 1964 and his PhD from Stanford University in 1971. He has been a faculty member of the National University of Singapore since 1972. He is currently Tan Chin Tuan Centennial Professor and has been the Director of the Institute for Mathematical Sciences since 2000. His research interests are mainly in probability theory focusing largely on probability approximations using Stein’s method. He is best known for his pioneering work in Poisson approximation which has diverse applications in such fields as random graphs, computer science, molecular biology, statistical physics, epidemiology, reliability theory, game theory, and financial mathematics. More recently he has worked on applications of probability to computational biology. He has received many honors and awards, which include the National Science and Technology Award in 1991, Excellence for Singapore Award in 1997, and Fellowship in the Institute of Mathematical Statistics in 1989 and in the Academy of Sciences for the Developing World in 2000. He was elected President of the Bernoulli Society for Mathematical Statistics and Probability in 1997-1999 and President of the Institute of Mathematical Statistics in 2004-2005.

Title: Calculating p-values in sequence analysis PDF

Abstract: I will discuss the ideas behind Poisson approximation, compound Poisson approximation and importance sampling and their applications to problems concerning word patterns in biomolecular sequence analysis.

Jagath Rajapakse,
Director,
BioInformatics Research Centre,
Nanyang Technological University, Singapore.

Biosketch: Jagath Rajapakse is a Professor of Computer Engineering and the Director of the BioInformatics Research Centre, Nanyang Technological University (NTU). He is also a Visiting Professor to the Department of Biological Engineering, Massachusetts Institute of Technology (MIT). He began his postgraduate studies at the University of Buffalo (USA) under the Fulbright Scholarship, where he received M.Sc. and Ph.D. degrees in Electrical and Computer Engineering. Before joining NTU, he obtained his post-doctoral training at the Max-Planck-Institute of Cognitive and Brain Sciences (Germany) and the National Institute of Mental Health (USA). Professor Rajapakse's research expertise are in the areas of machine learning, brain imaging, and computational and systems biology. He has authored over 210 research papers in refereed journals, books, and conference proceedings. He serves as Associate Editor for IEEE Transactions on Medical Imaging, IEEE Transactions on Computational Biology and Bioinformatics, and IEEE Transactions on Neural Networks, and in editorial boards of several other journals.

Title: Challenges in microarray analysis PPTX

Abstract: Microarrays enable collection of expressions of thousands genes simultaneously from biological samples. Selection of genes biologically relevant for different pathologicl conditions has recently attracted many computational scientists. When gene expressions are gathered over different experimental conditions or over time, it is possible to generate gene regulatory networks. We present an overview of techniques of gene selection and of building regulatory networks, and results of our research in these areas.

Patrick Tan,
Associate Professor,
Duke-NUS Graduate Medical School Singapore.
Group Leader,
Genome Institute of Singpore,
Principal Investigator,
National Cancer Centre, Singapore.

Biosketch: Patrick Tan holds a joint appointment as an Associate Professor at the Duke-NUS Graduate Medical School and a Group Leader at the Genome Institute of Singapore. He is a Program Leader in Genomic Oncology at the Cancer Science Institute of Singapore, National University of Singapore and a Research Associate Professor in the Institute of Genome Sciences and Policy at Duke University, USA. His research focuses the application of genomics to cancer and infectious disease. He received his B.A. (summa cum laude) from Harvard University and MD PhD degree from Stanford University, where he received the Charles Yanofsky prize for Most Outstanding Graduate Thesis in Physics, Biology or Chemistry. Locally, he has received the President’s Scholarship, Loke Cheng Kim foundation scholarship, Young Scientist Award (A-STAR), Singapore Youth Award (twice), and the Singhealth Investigator Excellence Award. He is an editorial board member of the journals Cancer Research, BMC Medical Genomics, PLOS One, and SGH Proceedings. He is a member of the Local Review Panel (LRP) to the National Medical Research Council and Biomedical Research Council, a member of Specialists Accreditation Board, Translational Medicine, and Bioethics Advisory Committee (BAC), a national body that provides advice to the Singapore government on ethical issues related to biomedical research.

Title: Integrative genomic approaches to personalized cancer therapy PPT

Abstract: Cancers in different patients are known to exhibit highly distinct patterns of disease development, progression, and response to therapies. In this talk, I will describe how we have applied genomic approaches to dissecting the heterogeneity of cancer, both to elucidate basic mechanisms of tumorigenesis and also to guide the use and selection of therapeutics.