Download Proposal for a track at the 2002 ACM Symposium on Applied

Track Proposal for SAC 2008
Name of the Track:
Bioinformatics
Track Chairs:
Mathew Palakal
School of Informatics
Indiana University Purdue University Indianapolis, USA
[email protected]
William Perrizo
Department of Computer Science
North Dakota State University, USA
[email protected]
Track Motivation and Description:
The publishing of the draft of the human genome marked a major step in the
advancement of understanding how the human body works at a molecular level by giving
biologists the potential genes from which all proteins and molecular interactions can be
derived. The genome sequence has ushered in a new era of rapid and exponential growth
of data related to how organisms function at a molecular level. DOE's Genomes to Life
program for example, will make important contributions in the quest to venture beyond
characterizing such individual life components as genes and other DNA sequences
toward a more comprehensive, integrated view of biology at a whole-systems level. This
track will address research issues related to these challenges.
A large part of the information to support biology and biomedical research is available on
large number of heterogeneous databases in both structured and unstructured formats.
The challenge is to obtain information and knowledge from these databases using
innovative computational approaches to support and promote biomedical research. One
example of such a computational challenge is in identifying biological pathways using
data, information, and knowledge scattered over heterogeneous databases. Computational
tools using system-theoretic approaches are needed to model metabolic pathways, signaltransduction pathways, genetic regulatory circuits and biological systems modeling.
By comparing the genomes and pathways of several species at a high level, we hope to
understand how stable biological systems have evolved. Over the last few years,
microarray data have provided many insights into the transcriptome and into cellular
function. These data are now increasingly complemented by mass spectrometry data of
the proteome, whose analysis poses new computational challenges.
There are no other tracks at SAC that will overlap with this track. This track distinguishes
itself from the other major conferences in bioinfomatics / computational biology
(RECOMB, ISMB, ECCB, WABI) by its focus on data integration and whole-systems
bioinformatics. RECOMB and ISMB have their roots in the combinatorics and AI
communities and, as does WABI, used to focus, on theoretical research and proof-ofconcept implementations. The SAC’08 BIO track, in contrast, provides a forum for
integrative work.
Track Topics:
1. Use of natural language processing techniques and/or artificial intelligence techniques
to automatically extract multiple biological objects such as gene names, protein
names, drugs, organisms, disease, etc., from free-text.
2. Information and knowledge extraction such as object-object interactions (ex: protein
interactions, functions, etc.).
3. Software systems to support biological research that integrates multi-format and
multi-type data from heterogeneous databases.
4. Information visualization techniques for integrated biological systems.
5. Clustering of very large dimensional data such as microarray and mass-spectrometry
data.
6. Clustering algorithms having application in biological and biomedical informatics.
7. Classification algorithms having application in biological and biomedical informatics.
8. Network models and simulations of various pathways.
9. Visualization techniques for network simulations
10. Pathway estimation from genomic data.
11. Computational methods that model cellular mechanisms, the protein machine, and
regulatory networks.
12. Algorithms for processing and interpreting large-scale mass-spectrometry data
13. Comparative genomics and genome dynamics (i.e., evolution of whole genomes, e.g.,
by translocations, reversals, duplications, etc.)
Proposed Process of Soliciting Quality Submissions:
In addition to the standard alternatives such as bulletin boards, newsgroups, and websites,
we plan to personally encourage our colleagues to submit papers. Both the track chair and
co-chairs have been active in this field and they do have a long list of notable
acquaintances. We have already developed a web site to manage the activities of the
track, and electronically advertise in the specialized user groups and research networks
and institutions. This system also allows to collect, review, select and put together an
attractive program solely through the electronic media. We plan to form a small but
distinguished track program committee for the purpose of reviewing submissions and
developing an attractive track program.
Mathew Palakal and William Perrizo will serve as chair and co-chairs of the track and act
as co-organizers. Collectively, this team has expertise in different aspects of the
Bioinformatics field and they bring in contacts from both academia and industry. Mathew
Palakal also has significant experiences in organizing and managing extremely successful
SAC Bioinformatics Track of 2003, 2004, 2005, 2006, and 2007 so he is well aware of
the mechanics of SAC submissions and reviewing process. William Perrizo served as the
Co-Chair for the SAC Bioinformatics in 2006. He is the founder, conference chair and
program committee member for the National Science Foundation Funded Virtual
Conferences on Genomics and Bioinformatics (held in September of 2001,
2002 http://www.ndsu.nodak.edu/virtual-genomics/conference_2002.htm, 2003
http://www.ndsu.nodak.edu/virtual-genomics/conference_2003.htm,
2004 http://www.virtualgenomics.org/conference_2004.htm. He has been Conference
Chair, Program Chair, Publicity Chair and Session Chair for many other conference
sponsored by the ACM, IEEE and ISCA organizations.
Dr. Mathew Palakal’s research interests include artificial intelligence and bioinformatics.
He has published over 70 articles in leading Journals and presented at numerous
conferences. He received over 30 research and teaching grants including grants from NSF
and Eli Lilly & Co., for his bioinformatics research. He is the Director of Informatics
Research Institute at IUPUI that primarily focuses on all aspects cutting edge research in
information and knowledge management. Please see Dr. Palakal’s home page at
www.cs.iupui.edu/~mpalakal for more information.
Dr. William Perrizo is a Full Professor of Computer Science at North Dakota State
University. He has been a Research Scientist at the IBM Advanced Business Systems
Division and the U.S. Air Force Electronic Systems Division. His areas of expertise are
Data Mining, Bioinformatics, Knowledge Discovery, Database Systems, Distributed
Database Systems, High Speed Computer and Communications Networks and Precision
Agriculture. He is a member of ACM, IEEE, IAAA, ISCA, and AAAS.