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In-Silico Analysis of Proteins

Celebrating the 20th anniversary of Swiss-Prot

July 30 - August 04, 2006 : Fortaleza, Brazil

Confirmed Speakers:

Ron Appel

Proteomics Informatics Group (PIG), Swiss Institute of Bioinformatics, Geneva, Switzerland

Rolf Apweiler

Sequence Database Group, European Bioinformatics Institute (EBI), Hinxton, UK

Michael Ashburner

Department of Genetics, University of Cambridge

Michael Ashburner is Professor of Biology in the University of Cambridge and one-time Research Programme Coordinator and Joint-Head of the EMBL-European Bioinformatics Institute. He is a founder of FlyBase and of the Gene Ontology Consortium.

Terri Attwood

Faculty of Life Sciences and School of Computer Sciences, University of Manchester, Manchester, UK

We have specialised in protein sequence analysis, particularly using "fingerprinting" to provide functional, structural and evolutionary insights into various kinases, tubulins, ion channels, G protein-coupled receptors, and so on - this led to the creation of the PRINTS fingerprint database, a founding partner of InterPro. We have also developed software tools, like CINEMA and Ambrosia, to allow 3D visualisation of fingerprints, and have also developed automatic annotation and text-mining tools, like PRECIS, METIS and BioIE, to facilitate manual annotation of protein families.

For more details, see umber.sbs.man.ac.uk/dbbrowser/ and utopia.cs.man.ac.uk.

Amos Bairoch

Swiss-Prot Group, Swiss Institute of Bioinformatics, Geneva, Switzerland

Amos Bairoch is the founder and group leader of Swiss-Prot, the largest, manually annotated protein database, which is now part of UniProt. Swiss-Prot provides extensive information on proteins and at present includes over 210'000 fully annotated proteins from more than 1'500 different species.

Alex Bateman

Wellcome Trust Sanger Institute, Hinxton, UK

The goal of the Bateman group is to infer biological knowledge and accurately transfer this information to large data sets such as complete genomes. These are primarily through model based resources such as Pfam and Rfam.

More info on http://www.sanger.ac.uk/Teams/faculty/bateman/

Lionel Binns

Hewlett-Packard

Ewan Birney

Ensembl Group, European Bioinformatics Institute (EBI), Hinxton, UK

Ewan Birney is the Head of the Ensembl project, one of the leading ways to view and use the Human Genome. Ensembl (www.ensembl.org) provides user-friendly views of many vertebrate genomes and supports the work of thousands of researchers worldwide.

Judith Blake

The Jackson Laboratory, Bar Harbor ME

Judith Blake's research at over the last 10 years has focused on the development of bioinformatics systems essential for functional genomics and genetics research particularly in mammalian systems. She is a leader in efforts to bring semantic standards and data integration methodologies for genomic, genetic and phenotypic information to the biological research community. Judith is one of the founders and principal investigators of the Gene Ontology (GO) Consortium; an international project that develops and provides ontologies for molecular biology and that supports functional annotation and analysis efforts using the GO. She is also one of the principal investigators and developers of the Mouse Genome Informatics (MGI) database resource that integrates genetic, genomic and phenotypic information about the laboratory mouse for comparative use in the study of human biology and disease.

Peer Bork

Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

Philip E. Bourne

Department of Pharmacology, University of California San Diego, La Jolla CA, USA

Our laboratory aims to serve the community through the provision of resources like the RCSB Protein Data Bank (PDB; in collaboration with Rutgers University) and the Immune Epitope Database (IEDB; in collaboration with The La Jolla Institute for Allergy and Immunology and others). Our research focuses on the use of these resources with emphasis on structural bioinformatics. Of particular interest of late are evolution studied through protein structure, protein motion, protein-protein and protein ligand interactions and novel methods and software for exploiting sequence-structure-function space.

Details can be found at http://www.sdsc.edu/pb.

Steven Brenner

Computational Genomics Research Group, University of California, Berkeley CA, USA

The Brenner research group uses evolutionary principles and computational methods to understand genome information. We have longstanding interest in protein function prediction and in analysis of protein   RNA structures. Our laboratory is undertaking experimental and computational studies of nonsense-mediated decay and its relationship to alternative splicing, especially their combined use as a regulatory mechanism. Most recently, we have engaged in environmental and medical metagenomic studies.

S°ren Brunak

BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark

The Center for Biological Sequence Analysis has obtained important results from bioinformatics research within the past 10 years. Starting in 1993, we have been able to create one of the largest, multi-disciplinary basic research groups within bioinformatics in academia in Europe. The aim and scope of the work at the center has allowed for a considerable amount of basic research in new methods and approaches. The center works in seven specialist research groups, has a highly multi-disciplinary profile (molecular biologists, biochemists, medical doctors, physicists and computer scientists) with a ratio of 2:1 of bio-to-nonbio backgrounds.

S°ren Brunak, Ph.D., is professor of bioinformatics at the Technical University of Denmark. Prof. Brunak is the current Director of the Center for Biological Sequence Analysis. His research has in particular addressed machine learning approaches for elucidation of the structure, localization and function of biological macromolecules. His focus is now integrative biology and systems biology, in particular in relation to cell cycle modelling and simulation.

More about his research group can be found at www.cbs.dtu.dk and www.cbs.dtu.dk/staff/show-staff.php?id=514.

Philipp Bucher

Swiss Institute of Bioinformatics and, Swiss Institute for Experimental Cancer Research, Epalinges, Switzerland

Philipp Bucher, originally trained as a molecular biologist, has devoted a large part of his research efforts on the computational characterization of eukaryotic promoters. The Eukaryotic Promoter Database EPD, which also celebrates its 20th anniversary this year, is a byproduct of these efforts. Current research activities of his group address various problems related to the interpretation of gene regulatory regions, with a specific focus on Cancer-relevant pathways.

Julio Collado-Vides

Laboratorio de BiologÝa Computacional, Centro de Investigaciˇn sobre Fijaciˇn del Nitroacutegeno, Cuernavaca, Morelos, Mexico

Director of the Center of Genomic Sciences, National Autonomous University of Mexico. Works in computational biology of gene regulation. His lab curates RegulonDB and regulation in EcoCyc, describing the best known regulatory networ, that of E.coli K-12. This has enabled us to implement for several computational predictive methods (for binding sites, promoters, operons and functional associations), as well as for biological integrative analyses (See: http://www.ccg.unam.mx/Computational_Genomics/ComputationalGenomics.php).

Antoine Danchin

Genetics of Bacterial Genomes, Institut Pasteur, Paris, France

Michael Dunn

Biochemistry Department, University of California at Riverside, Riverside CA, USA

My laboratory is engaged in the study of protein structure-function relationships for the protein hormone, insulin, and for pyridoxylphosphate requiring enzymes, with the emphasis placed on the tryptophan synthase bienzyme complex. A significant part of this effort in recent years has been to explore the allosteric properties of the insulin hexamer, and allosteric site-site communication in the regulation of substrate channeling of the tryptophan synthase bienzyme complex. For more details, see www.biochemistry.ucr.edu/faculty/dunn.html

Ernest Feytmans

Director of the Swiss Institute of Bioinformatics

Takashi Gojobori

National Institute of Genetics, Research Organization of Information and Systems, Shizuoka, Japan

The Center for Information Biology was established in April 1995, as a center of information biology in Japan, and reorganized as the Center for Information Biology and DNA Data Bank of Japan in April 2001. The center consists of five laboratories where researchers conduct research on genetic information by an extensive use of computers. The DNA Data Bank of Japan (DDBJ) is also housed in the center. In collaboration with EMBL-Bank and GenBank, DDBJ plays worldwide a pivotal role in the collection, annotation, management, publication and distribution of DNA sequence data.

http://www.ddbj.nig.ac.jp/Welcome-e.html

http://www.cib.nig.ac.jp/dda/en/index.html

Michael Gribskov

Department of Biological Sciences, Purdue University, USA

Winston Hide

National Bioinformatics Institute, University Western Cape, Bellville, South Africa

Win Hide is the founder and Director of the National Bioinformatics Institute situated at the University of Western Cape, Cape Town, South Africa. He holds the appointment of Professor of genomics at UWC. Work at the Institute has centered on generating transcript representations of genes in the human genome, with a focus upon cancer gene discovery. He leads a pathogen bioinformatics unit of the SA Medical Research Council and is responsible for the bioinformatics of the current Tsetse Fly Genome Project. In collaboration with the European 6th Framework Programme, the US Department of Energy, the Brazilian genome project and the International Human Genome Consortium, Hide has developed several systems for disease gene discovery. Collaborators include Stanford, Harvard, Yale, Oxford, Cambridge, University of Tokyo, and Pasteur Institute. An International Kerr Programme Fellow of the Ludwig Institute for Cancer research, Hide has established Africa?s first World Health Organisation African Regional Training Centre for Bioinformatics, National Bioinformatics Network, large scale bioinformatics for HIV programme, accredited graduate programme in Bioinformatics and has founded the African Society for Computational Biology and Bioinformatics. He was the first African to be elected to the board of the International Society for Computational Biology. His experience is evolutionary biology and genomics, development of high performance tools for the analysis of the genome, and in implementations of genomics in biotechnology. Hide was a Keck Computational Fellow in the USA at Baylor College of Medicine Department of Molecular Genetics and also a fellow at the Smithsonian National Museum of Natural History in Washington DC. He has been director of Genomics at MasPar Computer Corporation, in Silicon Valley, and is a doctoral graduate of Temple University in Philadelphia.

Des Higgins

UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland

The main activity of the laboratory is in sequence alignment software and algorithms. We are involved in collaborations to develop and maintain the Clustal and T-Coffee packages. We are also interested in the application of multivariate analysis methods to analyse gene expression, transcription factor binding sites and microRNA data.

Victor Jongeneel

Transcriptome Analysis, Swiss Institute of Bioinformatics, and Ludwig Institute for Cancer Research, Lausanne, Switzerland

Victor Jongeneel was trained as a microbiologist. He became involved with computers while doing his PhD and a post-doc in the United States. After returning to Switzerland, he spent much of his "spare" time introducing the researchers at ISREC and the Ludwig Institute to the wonders of bioinformatics. Since 1998, he has turned his hobby into a job. His research in centered around the exploitation of sequence-based transcriptome data (ESTs, SAGE, MPSS) for the discovery of cancer-specific expression patterns.

Daniel Kahn

Laboratoire de BiomÚtrie et Biologie Evolutive, Lyon1 University, Lyon, France
INRIA HELIX project, www-helix.inrialpes.fr

Daniel Kahn is the founder of the ProDom database of protein domain families ( www.toulouse.inra.fr/prodom.html). He also designed the PRIAM methodology for metabolic inference. Daniel Kahn has had a long-standing interest in understanding the modularity of regulatory systems and of regulatory proteins. His current research deals with the evolution of protein modularity, the evolution of metabolism and the integrated modelling of metabolic and gene regulation.

Minoru Kanehisa

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan

Minoru Kanehisa is Director and Professor at the Bioinformatics Center of Kyoto University, and also Professor at the Human Genome Center of the University of Tokyo. He is the founder of KEGG, which just celebrated its 10th anniversary.

Jack Leunissen

Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands

Barend Mons

Knewco, Inc.

Nasri Nahas

GeneBio, Geneva, Switzerland

Kenta Nakai

Laboratory of Functional Analysis in silico,Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan

My laboratory is named: functional analysis in silico. I am interested in the interpretation of genetic information, such as transcriptional regulatory information, encoded in genome sequences of various organisms.

See http://fais.hgc.jp/index.html.en for more info.

Cedric Notredame

Structural and Genetic Information, CNRS, Marseille, France

Christine Orengo

Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, London, England

Christos Ouzounis

Center for Research and Technology Hellas (CERTH) Thermi, Thessaloniki, Greece

William Pearson

Department of Biochemistry, University of Virginia, Charlottesville VA, USA

We have a long-standing interest in exploiting protein sequence information, both for understanding better how new protein sequences arise and for understanding the relationship between protein sequence and protein structure. Since the description of the FASTP program in 1985, our group has been developing more effective methods for identifying distantly related protein sequences. Over the past 10 years, state-of-the-art methods have improved to where proteins that have diverged from a common ancestor in the past billion years are likely to be detected by sequence similarity searching. We hope to push back that threshold to beyond 2 billion years (near the time when prokaryotes and eukaryotes diverged), but already it is possible to identify novel proteins that are likely to have emerged in the last 500 - 800 million years. If we can identify proteins that emerged in the last 100 - 250 million years, it may be possible to identify the mechanisms by which new proteins are formed.

More info on http://www.people.virginia.edu/~wrp/

Manuel Peitsch

Informatics and Knowledge Management, Novartis Institutes for BioMedical Research, Basel, Switzerland

Rich Roberts

New England Biolabs, Cambridge MA, USA

Burkhard Rost

Dept Biochemistry & Mol Biophysics, CUBIC, Columbia University, New York NY, USA

The function of most proteins in the human genome remains obscure and target for extensive and expansive investigations. Protein function is a rather intuitive concept, yet it is neither a well-defined term, nor is there a generic descriptor for all aspects of function. This has hampered the progress in the development of general methods that predict function directly from sequence. Our group has been developing many, unique template-based and de novo prediction methods. Our special edge is the combination of evolutionary information and machine learning. One particular challenge that we have been addressing over the last years with our CS colleague Yechiam Yemini is the design of a semantic modeling server to integrate access and manipulations of diverse, distributed biological resources. This modeling server is based on an extended object-relationship network model for correlating and manipulating biological resources.

Our long-term goal is the contribution to the development of a comprehensive system that models three aspects of function particularly in multi-cellular organisms: where is a molecule located most of the time, what does it interact with, and when does the interaction occur. In my talk, I will focus on three particular topics pertaining to the first of these three objectives. Firstly, I will describe one of our methods for the de novo prediction subcellular localization. Secondly, I will sketch our first steps toward de novo predictions of protein-protein and protein-DNA interactions. Lastly, I will briefly sketch the idea behind our most recent, preliminary improved method for database searches employed for the selection of targets in the context of large-scale structural genomics. One goal of structural genomics is to determine one experimental protein structure for each representative protein family. Experimental structures have been determined for over 200 of the proteins selected by us by our experimental colleagues. In this context, I shall present some of our recent findings about the organization of sequence/structure space.

Kenneth Rudd

Dept. of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami FL, USA

The EcoGene database of Escherichia coli K-12 genes and gene products now has an open source relational database implementation with dynamic page rendering using a new MySQL backend DB design and a customized PHP-Nuke interface (ecogene.org). The new EcoGene 2.0 interface includes web applications for the MapSearch restriction map alignment program and the PrintMap PDF map drawing software. Other new features include SQL-based gene and reference querying (EcoSearch), live data downloads, daily literature and function updates, new GeneMaps on the GenePages, pre-run BLAST results, InterGene tables and gene-flanking sequence retrieval, and EcoBlast, a local Blast server. New directions include TopicPages to cluster and complement the information on GenePages, an expanding EcoTeam of outside co-curators, and the in-house experimental validation of sRNA and protein starts. EcoGene also includes pseudogene and prophage gene identification and classification.

Chris Sander

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York NY, USA

Chris Sander is Head of the Computational Biology Center at Memorial Sloan Kettering Cancer Center in New York and tri-institutional professor at Rockefeller and Cornell Universities. His principal research interests are in computational and systems biology, including predictive simulations of biological processes, integrated molecular profiling of disease states, gene regulation by small RNAs, structural genomics and the development of multiplex cancer therapy. He is a leader in community efforts to create Pathway Commons, an open-source information resource for biological pathways, based on the bioPAX pathway ontology.

Torsten Schwede

Protein Structure Bioinformatics, Swiss Institute of Bioinformatics, Basel, Switzerland

Joel Sussman

Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel

Janet Thornton

European Bioinformatics Institute (EBI), Hinxton, UK

Jean-Franšois Tomb

DuPont, USA

Vitek Tracz

Science Navigation Group

Gunnar von Heijne

Dept of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden

Gunnar von Heijne has worked in two areas of relevance to SwissProt: protein subcellular localization and membrane protein topology. He has been active in the development of predictors such as SignalP, TopPred, and TMHMM that have at one time or another been used in the SwissProt annotation pipeline. He was until recently director of Stockholm Bioinformatics Center and is currently director of the Center for Biomembrane Research at Stockholm University.

Owen White

The Institute for Genomic Research (TIGR) Rockville MD, USA

Owen White is the director of The Institute for Genomic Research's Bioinformatics department, which numbers over 60 analysts and engineers. By 2005, TIGR and its collaborators had completed the genome sequences of about 50 organisms or microbial strains as well as developed more than 100 databases on organisms that have been fully or partially sequenced. TIGR engineers are currently working on a wide range of bioinformatics software development projects to help identify genes, assemble sequences, and compare closely related genomes. TIGR's Bioinformatics department is leading the field in developing large-scale genome alignment software, automated closure software and a new generation of gene-finder to take advantage of similarities between two species. Notable scientific contributions produced by TIGR's Bioinformatics department are Pathema (a NIAID funded Bioinformatics Resource Center), the Comprehensive Microbial Resource, TIGRFams, Manatee and Sybil.

Edgar Wingender

BIOBASE Biological Databases, WolfenbŘttel, Germany

E. Wingender is founder and scientific director of BIOBASE (Germany/USA/India) and head of the department of bioinformatics of the Medical School of the University of Gottingen. In addition, he acts as Editor-in-Chief of "In Silico Biology". His major research interests are bioinformatic problems of gene regulation and regulatory pathway modeling.

Shoshana Wodak

Department of Biochemistry and Structural Biology, University of Toronto, Toronto, Canada

Some of her research interests include: computational structural biology and bioinformatics. Using the data on more than 30,000 known protein structures deposited in the PDB we have been investigating how energetic criteria can be combined with sequence information to predict functional sites on protein 3D structures that are involved in protein-protein interactions and ligand binding. In Bioinformatics, her main focus in this area has been the development of tools and approaches for deciphering genome sequence information in terms of biological function, the major challenge of the Post-Genomic era. Our approaches in this area are mainly based on a systems-level analysis.

http://biochemistry.utoronto.ca/wodak/bch.html

Cathy Wu

Protein Information Resource (PIR) Georgetown University Medical Center, Washington DC, USA

Dr. Cathy H. Wu is the Director of Protein Information Resource (PIR) and a Professor of Biochemistry and Molecular Biology at Georgetown University Medical Center. PIR is an integrated proteomic bioinformatics resource and a consortium member of UniProt-the Universal Protein Resource. Dr. Wu has conducted bioinformatics research since 1990, and led the development of large software systems and protein databases since 1999 at PIR. She serves on the HUPO Council, the PDB Scientific Advisory Board, the Advisory Committee of the NIH Protein Structure Initiative, and is a past member of the Board of Directors of the International Society for Computational Biology. Her research interests include protein family classification and functional annotation, biological data integration, and literature mining. She has published more than 100 peer-reviewed papers and three books, and given more than 80 invited lectures.

Ioannis Xenarios

Serono Pharmaceutical Research Institute, Geneva, Switzerland

Last modified on March 20, 2006 at 16:20 PM