HiCOMB 2006

HiCOMB 2006
Fifth IEEE International Workshop on High Performance Computational Biology

Tuesday, April 25, 2006
Rodos Palace Resort Hotel & Convention Center, Rhodes Island, Greece

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

Advance Program for HiCOMB 2006

Register Online

(Please note that the IPDPS 2006 registration includes access to this workshop, and that there is no separate workshop registration).

Papers to be presented at HiCOMB 2006:

Bio-Sequence Database Scanning on a GPU
Weiguo Liu, Bertil Schmidt, Gerrit Voss, Andre Schroder, Wolfgang Muller-wittig
Some Initial Results on Hardware BLAST Acceleration with a Reconfigurable Architecture
Euripides Sotiriades, Christos Kozanitis, Apostolos Dollas
Phylospaces: Reconstructing Evolutionary Trees in Tuple Space
Marc L. Smith, Tiffani L. Williams
Parallel Implementation of a Quartet-Based Algorithm for Phylogenetic Analysis
B. B. Zhou, D. Chu, M. Tarawneh, P. Wang, C. Wang, A. Y. Zomaya, R. P. Brent
Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective
Alexandros Stamatakis
Parallel Multiple Sequence Alignment with Local Phylogeny Search by Simulated Annealing
Jaroslaw Zola, Denis Trystram, Andrei Tchernykh, Carlos Brizuela
MT-ClustalW: Multithreading Multiple Sequence Alignment
Kridsadakorn Chaichoompu, Surin Kittitornkun, Sissades Tongsima
Parallel Implementation of the Replica Exchange Molecular Dynamics Algorithm on Blue Gene/L
M. Eleftheriou, A. Rayshubski, J. W. Pitera, B. G. Fitch, R. Zhou, R. S. Germain
Application Re-Structuring and Data Management on a GRID Environment: a Case Study for Bioinformatics
Giovanni Ciriello, Matteo Comin, Concettina Guerra
A Method to Improve Structural Modeling Based on Conserved Domain Clusters
Fa Zhang, Lin Xu, Bo Yuan
An Experimental Study of Optimizing Bioinformatics Applications
Guangming Tan, Lin Xu, Shengzhong Feng, Ninghui Sun

HiCOMB 2006 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:

Bioinformatic databases
Computational genomics
Computational proteomics
DNA assembly, clustering, and mapping
Gene expression and microarrays
Gene identification and annotation
Parallel algorithms for biological analysis
Parallel architectures for biological applications
Molecular evolution
Molecular sequence analysis
Phylogeny reconstruction algorithms
Protein structure prediction and modeling
String data structures and algorithms

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:	November 15, 2005
Author Notification:	December 19, 2005
Camera-ready Paper Due:	January 21, 2006

Workshop Co-Chairs

David A. Bader
College of Computing
Georgia Institute of Technology
Atlanta, GA 30332 USA
Phone: +1.404.894.3152
Email:

Srinivas Aluru
Dept. of Electrical & Computer Engg. and
Lawrence H. Baker Center for Bioinformatics
& Biological Statistics
Iowa State University
3218 Coover Hall
Ames, IA 50011, USA
Phone: +1.515.294.3539
Fax: +1.515.294.8432
email: aluru@iastate.edu

Program Chair

Chau-Wen Tseng
Dept. of Computer Science
University of Maryland
College Park, MD 20742
Phone: +1 (301) 405-8010
Fax: +1 (301) 405-6707
Email: tseng@cs.umd.edu

Program Committee

Mike Cummings, University of Maryland
Art Delcher, University of Maryland
Nathan Edwards, University of Maryland
Wu-Chun Feng, Los Alamos National Laboratory
Guang Gao, Univerity of Delaware
Attila Gursoy, Koc University
Sorin Istrail, Brown University
Luay Nakhleh, Rice University
Jan Prins, University of North Carolina at Chapel Hill
Joel Saltz, Ohio State University
Alejandro A. Schäffer, National Institutes of Health
Alexandros Stamatakis, FORTH-ICS
Michela Taufer, University of Texas at El Paso
Thomas Wu, Genentech
Albert Y. Zomaya, University of Western Australia

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

HiCOMB Online Proceedings