ISCB Newsletter v.5.2

Stephen Altschul is a major figure in the development of sequence searching techniques. He has written papers on the appropriate statistical approaches to evaluating sequence alignments. Altschul developed the immensely powerful and flexible sequence searching program BLAST as well as variations on the central idea of BLAST that have improved the sensitivity of the searching process: PHI-BLAST and PSI-BLAST. He is currently a Senior Investigator with the Computational Biology Branch of the National Center for Biotechnology Information (NCBI).

Michael Ashburner has been one of the pre eminent researchers in the study of Drosophila melanogaster throughout his career. With the advent of the Drosophila genome sequencing initiative, he developed FLYBASE, a powerful annotation platform that integrated new genome sequence data with the corpus of knowledge of genetic, developmental and physiological mechanisms amassed over the last century. Most recently he has been a pivotal player in the development of the Gene Ontology project. He is currently a professor in the Department of Genetics at Cambridge University and a Senior Researcher at the European Bioinformatics Institute (EBI).

Ford Doolittle has studied evolution from a molecular perspective for most of his scientific career. He has been studying evolutionary origins of prokaryotes and eukaryotes, and this includes wrestling with the role of lateral gene transfer between single-celled organisms in evolution and the problems that this lateral transfer raises for current methods of phylogenetic reconstruction. Doolittle is a professor of biochemistry at Dalhousie University and director of the Canadian Institute of Evolutionary Biology.

Terry Gaasterland is a leading figure in the field of automated genome annotation. While at the Argonne National Laboratory and the University of Chicago she developed the MAGPIE annotation system. Since moving to the Rockefeller University, where she is currently an assistant professor, she has initiated development of several other annotation tools. These include HERON, TANGO, EGRET and SANDPIPER, all based on logic-based queries for manipulating semantic information. She is applying these tools to microarray data, phylogenetic inference, and structural biology projects.

Barry Honig has developed many computational tools for studying and modeling protein three dimensional structure. His extensive theoretical treatments of molecular energetics and dynamics are providing new insights into the mechanisms of protein structure, protein-protein interactions, and protein-membrane interactions. As high-throughput structure prediction methods are being developed, Honig’s work is at the leading edge of method development and investigating mechanisms of membrane targeting by peripheral proteins and the detailed dynamics of protein-protein association. He is a professor of biochemistry and molecular biophysics at Columbia University.

John Reinitz, associate professor at State University, New York (SUNY) Stonybrook, applies techniques of information theory to the systematic study of embryonic development in Drosophila melanogaster. His theoretical treatments of this complex phenomenon are based on experimental determination of the changing concentrations of maternally-derived signaling gene products as the hierarchy of determination develops in the syncytial blastoderm. His efforts have transformed the descriptive analyses of the patterns of individual gene expression into a well-defined, predictive model of information flow during the development of the fundamental body plan.

Isidore Rigoutsos is the manager of the Bioinformatics and Pattern Discovery group at IBM’s Computational Biology Center. He developed the Teiresias algorithm, a generalized method for unsupervised pattern discovery. He and his collaborators have implemented this algorithm for a number of biological pattern identification problems and categorization problem covering most of the questions that are current in computational biology. This software initiative is a major part of the IBM BlueGene project in computational
biology.