HiCOMB 2009

HiCOMB 2009
Eighth IEEE International Workshop on High Performance Computational Biology

Monday, May 25, 2009
Rome, Italy

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

Advance Program for HiCOMB 2009

Register Online

(Please note that the IPDPS 2009 registration includes access to this workshop, and that there is no separate workshop registration).

HiCOMB 2009 Keynote Talk

De Novo Modeling of GPCR Class A Structures

Charles L. Brooks III
University of Michigan, Ann Arbor

Abstract:
In this talk I will describe recent work to develop novel methods to model GPCR structures from their sequence information and statistically significant side chain contacts within a "template" structure. Our approach utilizes methods of bioinformatics to identify likely high confidence side chain side chain TM helical contacts and then reconstitutes the seven TM helical domain through a simulated annealing protocol with refinement using replica exchange and an implicit solvent/implicit membrane sampling scheme. Results will be presented for de novo prediction of the b2 adenergic receptor, the adenine receptor and a number of other amine receptors.

Speaker Biography:
Charles L. Brooks III is the Warner-Lambert Professor of Chemistry and Professor of Biophysics at the University of Michigan. Prior to moving to Michigan in 2008, Professor Brooks was professor of Molecular Biology at The Scripps Research Institute since 1994 and professor of Chemistry at Carnegie Mellon University until 1993, where he began as an assistant professor in 1985. Professor Brooks received his undergraduate training in chemistry, physics and mathematics from Alma College. He studied chemical physics at Purdue University, where he received his Ph.D. in 1982, and was a postdoctoral fellow at Harvard University from 1982-85. Professor Brooks' research focuses on the applications of statistical mechanics, quantum chemistry, and computational methods to solve chemically and physically oriented problems in biology.

Papers to be presented at HiCOMB 2009:

Parallel Reconstruction of Neighbor-Joining Trees for Large Multiple Sequence Alignments using CUDA
Yongchao Liu, Bertil Schmidt, and Douglas Maskell
Accelerating Error Correction in High-Throughput Short-Read DNA Sequencing Data with CUDA
Haixiang Shi, Bertil Schmidt, Weiguo Liu, and Wolfgang Mueller-Wittig
Parallel Monte Carlo Study on Caffeine-DNA Interaction in Aqueous Solution
Michael Kalugin and Alexandr Teplukhin
Dynamic Parallelization for RNA Structure Comparison
Eric Aubanel, Patricia Evans, and Eric Snow
HMMer Acceleration Using Systolic Array Based Reconfigurable Architecture
Yanteng Sun, Peng Li, Guochang Gu, Yuan Wen, Yuan Liu, and Dong Liu
A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications
Yaohang Li, Dougalas Wardell, and Vincent Freeh
Exploring FPGAs for Accelerating the Phylogenetic Likelihood Function
Nikolaos Alachiotis, Euripides Sotiriades, Apostolos Dollas, and Alexandros Stamatakis
Long Time-scale Simulations of in vivo Diffusion using GPU Hardware
Elijah Roberts, John Stone, Leonardo Sepulveda, Wen-Mei Hwu, and Zaida Luthey-Schulten
An Efficient Implementation Smith Waterman Algorithm on GPU using CUDA, for Massively Parallel Scanning of Sequence Databases
Lukasz Ligowski and Witold Rudnicki
A Novel Framework for Modeling Ion Channels
May Siksik and Vikram Krishnamurthy
High-throughput Protein Structure Determination using Grid Computing
Jason W. Schmidberger, Blair Bethwaite, Colin Enticott, Mark A. Bate, Steve G. Androulakis, Noel Faux, Cyril F. Reboul, Jennifer M. N. Phan, James C. Whisstock, Wojtek J. Goscinski, Slavisa Garic, David Abramson, and Ashley M. Buckle
Folding@home: Lessons From Eight Years of Volunteer Distributed Computing
Adam L. Beberg, Guha Jayachandran, Siraj Khaliq, Vijay S. Pande

HiCOMB 2009 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 30, 2008 (Extended Deadline)
Author Notification:	December 25, 2008
Camera-ready Paper Due:	February 15, 2009

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
Email:

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

Program Chair

Michela Taufer
Dept. of Computer and Information Sciences
University of Delaware
103 Smith Hall
Newark, DE 19716 USA
Phone: +1.302.831.0071
Email:

Program Committee

Dmitry A. Afonnikov, Institute of Cytology and Genetics SB RAS,
Novosibirsk and Novosibirsk State University (Russia)
Pratul K. Agarwal, Oak Ridge National Laboratory (USA)
Nancy Amato, Texas A&M University (USA)
Roger Armen, University of Michigan at Ann Arbor (USA)
Georg Fuellen, Ernst-Moritz-Arndt-University Greifswald (Germany)
Concettina Guerra, Georgia Tech (USA) and University of Padova (Italy)
Ming-Ying Leung, University of Texas at El Paso (USA)
Mark Miller, San Diego Supercomputer Center (USA)
Aiichiro Nakano, University of South California (USA)
Sandeep Patel, University of Delaware (USA)
Geppino Pucci, University of Padova (Italy)
Jacques Rougemont, EPFL (Switzerland)
Alexandros Stamatakis, Ludwig-Maximilians-University Munich (Germany)
Bertil Schmidt, Nanyang Technological University (Singapore)
Heiko Schroder, RMIT University (Australia)
John Stone, University of Illinois at Urbana-Champaign (USA)
Wing-Kin Sung, National University of Singapore (Singapore)
Jim Tisdall, DuPont (USA)
Chau-Wen Tseng, University of Maryland, College Park (USA)

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

HiCOMB Online Proceedings