Monday, March 26, 2007
Renaissance Long Beach Hotel,
Long Beach, California, USA
(Held in conjunction with the International Parallel and
Distributed Processing Symposium)
Abstract:
A new technology, optical mapping, is used to infer the genome map of
the location of short sequence patterns called restriction sites. The
technology, developed by David Schwartz, allows the visualization of
the maps of randomly located single molecules of length from one-half
to one million base pairs. The genome map is constructed from
overlapping these shorter maps. The substantial mathematical and
computational challenges come from modeling the measurement errors and
from the process of map assembly. We will report on our experience
with assembling the maize genome.
Speaker Biography:
Michael Waterman holds an Endowed Associates Chair at USC. He came to USC in 1982 after positions at Los Alamos National Laboratory and Idaho State University. He has a bachelors in Mathematics from Oregon State University, and a Ph.D. in Statistics and Probability is from Michigan State University. He was named a Guggenheim Fellow (1995), was elected to the American Academy of Art and Sciences (1995), and was elected to the National Academy of Sciences (2001). Also he is a Fellow of the American Association for the Advancement of Science and Fellow of the Institute of Mathematical Statistics. He has held visiting positions at the University of Hawaii (1979-80), the University of California at San Francisco (1982), Mt. Sinai Medical School (1988), Chalmers University (2000), and in 2000-2001 he held the Aisenstadt Chair at University of Montreal. He is Professor-at-large at the Keck Graduate Institute of Life Sciences and in fall 2000 he became the first Fellow of Celera Genomics In 2002 he received a Gairdner Foundation International Award and in 2005 he was elected to the French Acadimie des Sciences.
Beginning Fall 2003, Professor Waterman became Faculty Master of Parkside International Residence College. PIRC is a residental college that is home to over 600 undergraduates and serves as a center for internationally oriented culutral, academic and social events.
Professor Waterman works in the area of Computational Biology, concentrating on the creation and application of mathematics, statistics and computer science to molecular biology, particularly to DNA, RNA and protein sequence data. He is the co-developer of the Smith-Waterman algorithm for sequence comparison and of the Lander-Waterman formula for physical mapping. He is a founding editor of Journal of Computational Biology, is on the editorial board of seven journals, and is co-author of the texts Computational Genome Analysis: An Introduction and Introduction to Computational Biology: Maps, Sequences and Genomes.
Computational Biology is fast emerging as an important discipline for academic research and industrial application. The large size of biological data sets, inherent complexity of biological problems and the ability to deal with error-prone data all result in large run-time and memory requirements. The goal of this workshop is to provide a forum for discussion of latest research in developing high-performance computing solutions to problems arising from molecular biology. We are especially interested in parallel algorithms, memory-efficient algorithms, large scale data mining techniques, and design of high-performance software. The workshop will feature contributed papers as well as invited talks from reputed researchers in the field.
Topics of interest include but are not limited to:
Papers reporting on original research (both theoretical and
experimental) in all areas of bioinformatics and computational biology
are sought. Surveys of important recent results and directions are
also welcome. To submit a paper, upload a postscript or PDF copy of the
paper here.
The paper should not exceed 12 single-spaced pages
(US Letter or A4 size) in 11pt font or larger. All papers will be
reviewed. IEEE CS Press will publish the IPDPS symposium and workshop
abstracts as a printed volume. The complete symposium and workshop
proceedings will also be published by IEEE CS Press on CD-ROM and will
also be available in the IEEE Digital Library.
| Workshop Paper Due: | Extended to November 27, 2006, 10PM EST |
| Author Notification: | December 18, 2006 |
| Camera-ready Paper Due: | January 22, 2007 |
|
Srinivas Aluru Dept. of Electrical & Computer Engg. and Lawrence H. Baker Center for Bioinformatics & Biological Statistics Iowa State University 3227 Coover Hall Ames, IA 50011, USA Phone: +1.515.294.3539 Fax: +1.515.294.8432 email: aluru@iastate.edu |
David A. Bader College of Computing Georgia Institute of Technology Atlanta, GA 30332 USA Phone: +1.404.894.3152 Email: |
|
Shankar Subramaniam Dept. of Bioengineering Dept. of Chemistry and Biochemistry San Diego Supercomputing Center University of California at San Diego 9500 Gilman Drive La Jolla, CA 92093 Phone: +1 (858) 822-0986 Fax: +1 (858) 822-3752 Email: shankar@sdsc.edu |
Ananth Grama Purdue University Department of Computer Sciences 305 N. University Street West Lafayette, Indiana, 47907-2107 Phone: +1 (765) 494-6964 Fax: +1 (765) 494-0739 Email: ayg@cs.purdue.edu |
For up-to-date information about this workshop, please visit
http://www.hicomb.org/.