Nobel Laureate Keynote
Max-Planck Institut f. Biochemistry, Germany.
Featured InCoB 2009 Distinguished Speaker
Max-Planck-Institut fuer Biochemie,
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.
Proteins and their structures, basic science and application PPT DIR
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
A*STAR Bioinformatics Institute Distinguished Speakers
Memorial Sloan-Kettering Cancer Center's Computational Biology Center, USA.
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.
Head of Informatics,
Wellcome Trust Sanger Institute, UK.
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
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
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.
NUS School of Computing Distinguished Speaker
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.
NUS Department of Biochemistry Distinguished Speaker
NUS Life Sciences Institute,
NUS Department of Biochemistry,
NUS Office of Deputy President (Research and Technology)
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
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
Title: Thinking about genetic variation and biomedical
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.
AMBIS Distinguished Speakers
Senior Group Leader,
Structural and Computational Biology Unit,
Biosketch: Peer Bork, PhD, is senior group leader and joint coordinator of the Structural and
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).
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
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
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
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.
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.
Duke-NUS Graduate Medical School Singapore.
Genome Institute of Singpore,
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
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.