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Magnet Group

Biographies

Abel L. Packer - Bireme

Abel Laerte Packer is Director of the Latin American and Caribbean Center on Health Sciences Information (BIREME/PAHO/WHO) in São Paulo, Brazil, since -1999. Brazilian, of nationality, he holds a Bachelor of Science degree and a Master’s degree in Library Science from Syracuse University in New York.

He joined BIREME/PAHO/WHO in September 1986, where he has been in charge of the information systems development for more than 10 years. He has actively participated in the design, development and operation of major BIREME projects, such as the Latin American and Caribbean System on Health Sciences Information, the LILACS database (referencing the Health Sciences literature from Latin American and Caribbean coun tries), the LILACS/CD-ROM (launched in 1987), the SciELO project – Scientific Electronic Library Online (launched in 1997) and the Virtual Health Library, the current LA & C framework for the technical cooperation in health-related scientific and technical information led by BIREME.
He is the author and co-author of several articles in his specialty.

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Amos Bairoch - SIB

Amos Bairoch mainly works in the field of protein sequence analysis and more particularily in the development of databases and software tools for this purpose. His first project as a Ph.D student was the development of PC/Gene, an MS-DOS based software package for the analysis of protein and nucleotide sequences. PC/Gene was commercialized, first by a Swiss company (Genofit) then by Intelligenetics in the US which was later bought by Oxford Molecular.

While working on PC/Gene he started to develop an annotated protein sequence database which became SWISS-PROT. It was first released in July 1986. From 1988 onward it has been a collaborative project with the Data Library group of the EMBL which has now became the European Bioinformatics Institute (EBI). SWISS-PROT has grown both in size, in its scope and in the amount of work and people necessary to produce it.

In 1988, Amos started to develop PROSITE, a database of protein families and domains. A little while later he created ENZYME, a nomenclature database on enzymes as well as SeqAnalRef, a sequence analysis bibliographic reference database.

In collaboration with Ron Appel he initiated, in August 1993, the first molecular biology WWW server, ExPASy. What was intended as a prototype grew rapidely into a major site that provides access to the many databases produced partially or completely in Geneva as well as many tools for the analysis of proteins (proteomics).

In the last four years he was involved with colleagues in Geneva and Lausanne in setting-up the Swiss Institute of Bioinformatics (SIB), whose mission is to establish in Switzerland a center of excellence in the field of bioinformatics with an emphasis on research, education, services and the developments of databases and tools. He is currently one of the six group leaders of the SIB.

In November 1997, together with Ron Appel and Denis Hochstrasser he founded GeneBio (Geneva Bioinformatics SA), a company involved in biological knowledge.

In April 2000, the above persons with Keith Rose and Robin Offord founded GeneProt (Geneva Proteomics), a high throughput proteomics company.

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Barend Mons - Concept Web Alliance/NBIC

Prof. dr. Barend Mons (1957, The Netherlands) obtained his MSc. (1981) and his PhD. (1986) at the University of Leiden, The Netherlands, majoring in Cell and Molecular Biology. He was appointed Professor in Biosemantics at the Leiden University Medical Center.

After 15 years of fundamental research in Malaria and three years at the European Commission Research programme, he returned to The Netherlands. Since 2002 Barend is Associate Professor in Bio-Semantics at the Department of Medical Informatics, Erasmus Medical Centre, University of Rotterdam and (since 2005) at the Department of Human Genetics at the Leiden University Medical Centre, both in The Netherlands. However, he remained involved in International Scientific Management and Networking at various levels. He initiated the wikiprofessional approach to enable community annotation of biological information.

His present research activities mainly focus on international networking to realise a new form of computer-assisted distributed annotation and on-line knowledge discovery, in close collaboration between his academic groups in Rotterdam and Leiden, and recenty also in the scope of the Netherlands Bioinformatics Centre (NBIC) a co-organiser of the Concept Web Alliance meeting. He is also one of the founders of Knewco and an inventor of the KnowletTM technology.

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Carole Goble - MyGrid

Carole Goble is a Full Professor in the School of Computer Science. She is co-leader of the Information Management Group of some 60 researchers including 13 academic staff, 27 research staff, 3 Visiting / Honorary Researchers, and 29 research students. She has a leading role in the Semantic Web, e-Science and the Semantic Grid. She applies technical advances in knowledge technologies and workflow systems to solve information management problems for Life Scientists and other scientific disciplines. She is the director of the large UK e-Science myGrid/Taverna programme of work for workflow based middleware for Life Scientists. myGrid uses semantic technologies for service and workflow discover and metadata management of workflow-based experiments. myGrid is now part of the Open Middleware Infrastructure Institute UK. Taverna is now used in over 340 organisations world-wide. Carole was the founding chair of this Institute (of 40+ software developers) which has been funded to harden and support developments from the UK’s e-Science programme. She is also the co-Director of the myExperiment initiative, bringing social networking and social computing approaches to Virtual Research Environments for Scientists, with 1400+ users worldwide sharing scientific workflows. She is also a PI on the BioCatalogue project, jointly with the EBI, which is building a socially curated catalogue of bio-web services for the community. Carole is also the technical director of the SysMO-DB initiative to build a data exchange and sharing infrastructure for the European SysMO (systems biology for microorganisms) consortium.

Carole has over 130 publications in Semantics and e-Science, and is a popular keynote speaker, giving keynotes in the major conferences in Grid Computing, Web, Semantics, Digital Libraries and Bioinformatics.

She sits on 15 national and international oversight committees concerning e-Science, Bioinformatics, Semantic technologies and Grid Computing, including membership of the BBSRC Strategic Advisory Board.

She was co-PC chair of WWW2006 and was the EIC of the Elsevier’s Journal of Web Semantics for its first 7 years.

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Frank van Harmelen - Free University of Amsterdam

Frank van Harmelen (1960) is a professor in Knowledge Representation & Reasoning in the AI department (Faculty of Science) at the Vrije Universiteit (Free University) Amsterdam. After studying mathematics and computer science in Amsterdam, he moved to the Department of AI in Edinburgh, where he was awarded a PhD in 1989 for his research on meta-level reasoning. While in Edinburgh, he co-developed a logic-based toolkit for expert systems, and worked with Prof. Alan Bundy on proof planning for inductive theorem proving. After his PhD research, he moved back to Amsterdam where he worked from 1990 to 1995 in the SWI Department under Prof. Wielinga, on the use of reflection in expert systems, on the formal underpinnings of the CommonKADS methodology for Knowledge-Based Systems. In 1995 he joined the AI research group at the Vrije Universiteit Amsterdam, where he co-lead the On-To-Knowledge project, on of the first Semantic Web projects. He was appointed full professor in 2002, and is leading the Knowledge Representation and Reasoning Group. He was one of the co-designers of the OWL Web Ontology Language. He is currently scientific director the LarKC project, aiming to develop the Large Knowledge Collider, a platform for very large scale semantic web reasoning. His interests include Approximate reasoning, Semantic Web and Medical Protocols.

He has published three books (on meta-level inference, on knowledge-based systems, and on the Semantic Web) and over 100 research papers, most of which can be found on-line.

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Frederique Lisacek - SIB

(Frederique Lisacek was standing in for Amos Bairoch at the meeting on May 8th in New York)

Her group develops proteomics software and databases, in particular the renowned Melanie 2-D gel electrophoresis analysis software and the SWISS-2DPAGE database. Further development of tools is currently underway for the identification and characterisation of proteins using mass spectrometry. The group is co-responsible for ExPASy, the world’s first Web site dedicated to protein molecular biology.

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Gert-Jan van Ommen - LUMC

Prof. dr. Gert-Jan B. van Ommen, PhD, (1947) is head of the Department of Human Genetics of Leiden University Medical Center (LUMC) and founder of the Leiden Genome Technology Center (LGTC), a principal genomics facility in the Netherlands. He has as major research interests neuromuscular and neurodegenerative diseases (with a focus on Duchenne Muscular Dystrophy, DMD, and Huntington Disease); development and application of genome research and diagnostic technology for disease study, diagnosis, therapy and prevention, including the societal aspects of genetic advances. He is past president of HUGO, the European Society of Human Genetics and the Dutch Society of Human Genetics and Editor-in-chief of the European Journal of Human Genetics. He is member of several National, EU and HUGO committees in the fields of Genetics, Innovative Health Care, Genomics, Bioinformatics, Biobanking, Ethics and IP issues. He is Director of the Center for Medical Systems Biology, CMSB, one of four Centers of Excellence of the Netherlands Genome Initiative. It is a joint initiative of Leiden University Medical Center, Leiden University, Free University Amsterdam and its Medical Center, Erasmus MC Rotterdam and TNO Leiden, aiming to improve diagnosis, therapy and prevention of common diseases and rare variants thereof.

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Henning Hermjakob - EBI

Henning Hermjakob joined the EBI in September 1997. After working in the production and maintenance of TrEMBL, he is contributing to the development of data representation standards in the HUPO Proteomics Standards Initiative and the implementation of these standards, in particular in the IntAct and PRIDE databases.

In the years 1991 to 1996 he studied Bioinformatics at the Department of Computer Science of the University of Bielefeld. In the acedemic year 1994/1995 he studied at the University of Bordeaux in the framework of the european exchange programm ERASMUS.

In his master’s thesis he developed the RIFLE system, a fast and reliable tool for the 16S rDNA-based identification of microorganisms without sequencing. After his diploma, he worked at the National Research Center for Biotechnology in Braunschweig, Germany in the Transfac team.

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Jan Velterop - Concept Web Alliance/Knewco

Johannes (Jan) Velterop is a science publisher. Born in The Hague, The Netherlands, he was originally a marine geologist and became a science publisher in the mid 1970s. He started his publishing career at Elsevier in Amsterdam. After a few years out of the scientific field as the director of the Dutch regional newspaper De Twentsche Courant, he returned to international science publishing at Academic Press in London. After Academic Press he joined Nature as director for a short while, but moved quickly on to help get BioMed Central, the first commercial open access science publisher, off the ground.

Velterop was one of the small group of people who first defined ‘open access’ in 2001 in Budapest, a meeting resulting in the Budapest Open Access Initiative.

In 2005 he joined Springer Science+Business Media as Director of Open Access, based in Guildford, UK. Springer is the first mainstream STM (Science, Technology, Medicine) publisher to offer open access as an option for virtually all its scientific and scholarly journals. In 2008 Springer brought open access publishing to the mainstream by the acquisition of BioMed Central.

At the end of March, 2008, Velterop left Springer to join Knewco, a company that uses semantic technology to accelerate scientific discovery. 

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Katy Borner - Indiana University

Katy Börner is the Victor H. Yngve Associate Professor of Information Science at the School of Library and Information Science, Adjunct Associate Professor in the School of Informatics, Core Faculty of Cognitive Science, Research Affiliate of the Biocomplexity Institute, Fellow of the Center for Research on Learning and Technology, Member of the Advanced Visualization Laboratory, and Founding Director of the Cyberinfrastructure for Network Science Center at Indiana University.   Her research focuses on the development of data analysis and visualization techniques for information access, understanding, and management. She is particularly interested in the study of the structure and evolution of scientific disciplines; the analysis and visualization of online activity; and the development of cyberinfrastructures for large scale scientific collaboration and computation.  She is the co-editor of the Springer book on ‘Visual Interfaces to Digital Libraries’ and of a special issue of PNAS on ‘Mapping Knowledge Domains’ (April 2004).   Her new book ‘Atlas of Science: Guiding the Navigation and Management of Scholarly Knowledge’ will become available in 2010. She and her colleagues at the Cyberinfrastructure for Network Science Center serve the

For more information on her research agenda, teaching, and other activities, visit: http://ella.slis.indiana.edu/~katy.

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Mark Musen - Stanford NCBO

Dr. Musen is Professor of Medicine (Biomedical Informatics) and Computer Science (by courtesy) at Stanford University, where he is head of the Stanford Center for Biomedical Informatics Research. He holds an MD from Brown University and a PhD from Stanford.

Dr. Musen conducts research related to intelligent systems, the Semantic Web, reusable ontologies and knowledge representations, and biomedical decision support. His long-standing work on a system known as Protégé has led to an open-source technology now used by thousands of developers around the world to build intelligent computer systems and new computer applications for e-science and the Semantic Web. He is known for his research on the application of intelligent computer systems to assist health-care workers in guideline-directed therapy and in management of clinical trials. He is principal investigator of the National Center for Biomedical Ontology, one of the seven National Centers for Biomedical Computing supported by the NIH Roadmap.

In 1989, Dr. Musen received the Young Investigator Award for Research in Medical Knowledge Systems from the American Association of Medical Systems and Informatics. He received a Young Investigator Award from the National Science Foundation in 1992. In 2006, he was recipient of the Donald A. B. Lindberg Award for Innovation in Informatics from the American Medical Informatics Association. Dr. Musen sits on the editorial boards of several journals related to biomedical informatics and computer science. He is co-editor of the Handbook of Medical Informatics (Springer-Verlag, 1997) and co-editor-in-chief of the journal Applied Ontology.

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Mark Wilkinson - SADI/iCAPTURE

Dr. Wilkinson earned his Bachelors degree in genetics from the University of Alberta in Edmonton, 1990, with an emphasis on developmental genetics. In 1996 he received his Ph.D. from the University of British Columbia in Botany. He followed a post-doctoral program under the Human Frontiers Science Program at the Max Planck Institut fuer Zuechtungsforschung in Cologne Germany, during which he made a career shift from developmental and molecular biology into Bioinformatics. He pursued a second post-doctoral fellowship at the National Research Council of Canada’s Plant Biotechnology Institute emphasizing bioinformatic analysis. He then worked as a freelance bioinformatics consultant for one year, after which he joined the iCAPTURE Team, and now continues working in the area of bioinformatics, with a particular focus on data integration and machine-readable knowledge representation.

Visit the Wilkinson Lab Homepage for up-to-date information on our research activities. The Wilkinson Laboratory is interested in the problem of facilitating the interaction between a biologist and the data and analytical tools they require each day to make new discoveries. Our laboratory focuses on four main themes: Annotation, Interrogation, Integration, and Visualization.

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