HiCOMB 2007
Sixth IEEE International Workshop on High Performance Computational Biology

Monday, March 26, 2007
Renaissance Long Beach Hotel, Long Beach, California, USA

(Held in conjunction with the International Parallel and Distributed Processing Symposium)


HiCOMB Online Proceedings

Advance Program for HiCOMB 2007

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(Please note that the IPDPS 2007 registration includes access to this workshop, and that there is no separate workshop registration).

HiCOMB 2007 Keynote Talk

Optical Mapping of the Maize Genome

Michael S. Waterman
University of Southern California

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.

Papers to be presented at HiCOMB 2007:

HiCOMB 2007 Call For Papers

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:

Submission guidelines:

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.

Important Dates

Workshop Paper Due: Extended to November 27, 2006, 10PM EST
Author Notification: December 18, 2006
Camera-ready Paper Due: January 22, 2007

Workshop Co-Chairs

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

Program Co-Chairs

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

Program Committee

For up-to-date information about this workshop, please visit http://www.hicomb.org/.

Call for Papers for HiCOMB 2007:

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