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BioLINK 2009


About the Organizers

        

   Christian Blaschke is Chief Scientific Officer and leader of the text mining projects in bioalma, Madrid, Spain. He obtained his PhD in the Group of Alfonso Valencia and was part of the organization of BioLINK SIG meetings starting in 2002. His academic work has been focused on text mining applied to molecular biology and biomedicine where he contributed in the areas of protein-protein interactions, DNA array analysis and automatic ontology learning. Christian Blaschke was also one of the organizers of the BioCreAtIvE (Critical Assessment of Information Extraction for Biology) challenge carried out in 2004.

   Lynette Hirschman is Chief Scientist and Director, Biomedical Informatics for the Information Technology Center at the MITRE Corporation in Bedford, MA, USA. She has been one of the organizers of the BioLINK SIG on Text Mining in Biology for ISMB starting in 2002, and an organizer of the 2004 and 2005 workshops on Text Mining in Biology for the ACL (Association for Computational Linguistics). Dr. Hirschman has also been a founder of BioCreAtIvE, (Critical Assessment of Information Extraction for Biology), the first Challenge Evaluation for text mining applied to biological applications held first in 2003-2004 and again in 2007-2008. She is currently working with the Genome Standards Consortium to improve capture of metadata for whole genome and metagenomics sequences using text mining and linguistic analysis.

    Hagit Shatkay is the head of the Computational Biology and Machine Learning Lab in the School of Computing, at Queen's University, Kingston, Ontario. Her research is in the area of machine learning as it applies to biomedical data mining. She has been an active member of the bio-text research community since its early days (1999), where her work focuses primarily on biomedical information retrieval, and on the integration of text and images into the biological data mining process. Recent major projects in her lab include SherLoc ¡V protein subcellular location prediction by integrating text and sequence data, and F-SNP ¡V a comprehensive system for ranking SNPs by potential deleterious effects. She has been on the organizing committee of the BioLINK SIG at ISMB since 2005, and on the steering committee for the TREC Genomics Track since 2003. Prior to joining Queen's University, she was an Informatics Research scientist with the Informatics Research group at Celera/Applied Biosystems. She holds a BSc and MSc in Computer Science from the Hebrew University in Jerusalem, and a PhD in Computer Science from Brown University.

    Alfonso Valencia is the director of the Structural and Computational Biology Programme of the Spanish National Cancer Research Centre and Director of the Spanish Bioinformatics Institute. His group works in the development and application of Computational Biology methods for the study of problems related with the evolution of molecular interactions. In the field of text mining his group developed new approaches for the detection of protein function and interactions in biological text and a number of applications combining text mining with other genomic resources. Dr. Valencia is co-executive editor of the journal "Bioinformatics", member of EMBO, co-organizer of ECCB 05, chair of the text mining/Biological networks areas of ISMB (03-07) and founder, former VP, and member of the board of directors of ISCB. Dr. Valencia has been part of the organization of BioLINK (Text Mining in Biology) since 2001 and co-organizer of the Critical Assessment of Information Extraction for Biology (BioCreAtIvE 2003-4 and 2006-07).

   Scott Markel is the Principal Bioinformatics Architect in Accelrys' R & D group. In this role he is responsible for the design and implementation of Pipeline Pilot¡¦s bioinformatics f unctionality. He is a member of the Board of Directors of the International Society for Computational Biology and was recently appointed a Vice President. Scott is on the editorial boards of Briefings in Bioinformatics and PLoS Computational Biology. He was most recently a Research Fellow and Principal Software Architect at LION bioscience, where he was responsible for providing architectural direction in the development of software for the life sciences. He has a Ph.D. in mathematics from the University of Wisconsin¡VMadison. He is a co-author, with Darryl Leon, of Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases. Scott is a co-editor, also with Darryl, of In Silico Technology in Drug Target Identification and Validation and a co-author, with Ewan Birney and Jason Stajich, of the forthcoming Using BioPerl.

    Robert F. Murphy is the Ray and Stephanie Lane Professor of Computational Biology and Director of the Lane Center for Computational Biology at Carnegie Mellon University. He is also Professor of Biological Sciences, Biomedical Engineering, and Machine Learning and directs (with Ivet Bahar) the joint CMU-Pitt Ph.D. Program in Computational Biology. He served as the first full-term chair of NIH¡¦s Biodata Management and Analysis Study Section, was named a Fellow of the American Institute for Medical and Biological Engineering in 2006, and received an Alexander von Humboldt Foundation Senior Research Award in 2008. Dr. Murphy has co-edited two books and published over 150 research papers. He is President of the International Society for Advancement of Cytometry and is on the Editorial Boards of Cytometry and the Journal of Proteome Research. Dr. Murphy¡¦s group pioneered the application of machine learning methods to high-resolution fluorescence microscope images depicting subcellular location patterns in the mid 1990¡¦s. He currently leads NIH-funded projects for proteome-wide determination of subcellular location in 3T3 cells and continued development of the SLIF system for automated extraction of information from text and images in online journal articles.








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