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February 20-21, 2004
Mellon Institute Auditorium
Carnegie Mellon University
Pittsburgh, PA
See text version
Online
Registration Form
The recent availability of large-scale genotype data has created
new possibilities for tracking down genetic risk factors of complex
diseases. Extensive data on human genetic variability in healthy
and diseased individuals, predominantly in the form of single
nucleotide polymorphisms (SNPs), is giving us the raw material
we will need to locate genes and genetic variants that are associated
with disease. At the same time, though, finding the faint statistical
signals in the growing mass of SNP data poses formidable cross-disciplinary
challenges. Much recent attention has focused on the use of haplotypes
-- evolutionarily conserved sets of contiguous polymorphisms --
as a way of exploiting regularities in the data sets to reduce
the dimensionality of the problem. Many questions remain about
the nature of this haplotype conservation, how best to use it
in disease inference studies, and how effective it will prove
in practice. Important areas of active research include developing
new methods to gather SNP and haplotype data, characterizing the
haplotype structure of the human genome, improving the design
of disease association studies, and enhancing their statistical
power. Promising approaches to these problems are currently emerging
from a combination of new methods for gathering genetic polymorphism
data, better understanding of the biological basis of genome structure,
sophisticated statistical techniques for finding meaning within
these data, and advanced computational methods for inferring genetic
structure and applying it to various related analysis problems.
SCOPE
This meeting will focus on current research at the intersection
of genetics, computer science, statistics, and related fields
in gathering and analyzing SNP and haplotype data and applying
it to problems in medicine and basic research. We plan to build
on the success of the first RECOMB Satellite Meeting on Computational
Methods for SNPs and Haplotypes in bringing together leading participants
from widely divergent backgrounds to share their expertise and
results. The recent availability of large-scale genotype data
has created new possibilities for tracking down the currently
elusive genetic risk factors of many complex diseases. Extensive
data on human genetic variability in healthy and diseased individuals,
predominantly in the form of single nucleotide polymorphisms (SNPs),
is giving us the raw material we will need to locate genes and
genetic variants that are associated with disease. Much recent
attention has focused on the use of haplotypes --- evolutionarily
conserved sets of contiguous polymorphisms --- as a way of exploiting
regularities in the data sets to reduce the magnitude of the problem.
Many questions remain about the nature of this haplotype conservation,
how best to use it in disease inference studies, and how effective
it will prove in practice.
TOPICS
Original research papers (including significant work-in-progress)
or state-of-the-art surveys are solicited in all aspects of SNP
and haplotype analysis and applications to medicine, including,
but not limited to: - New methods for gathering genetic polymorphism
data. - Understanding of the biological basis of genome structure.
- Statistical techniques for the analysis of the data. - Computational
methods for inferring genetic structure. - Applications to disease
association and to medicine. - New genotype and haplotype data
sets and their analysis.
Any questions regarding this workshop should be emailed
to 
recomb-workshop@lists.andrew.cmu.edu.
RECOMB Satellite
Workshop Schedule [Tentative]
| Friday,
February 20 |
| 7:30-8:00 |
Continental breakfast |
| 8:00-8:20 |
Opening remarks
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| 8:20-8:45 |
Andrew Clark |
| 8:45-9:10 |
"The Incomplete
Perfect Phylogeny Haplotype Problem" by Gad Kimmel
and Ron Shamir |
| 9:10-9:35 |
David Schwartz |
| 9:35-10:00 |
"Empirical Evaluation
of Genetic and Environmental Interactions in Complex Disease"
by John Maindonald and Susan Wilson |
| 10:00-10:20 |
Coffee break |
| 10:20-10:45 |
David Clayton |
| 10:45-11:10 |
"On the Complexity
of Haplotyping Via Perfect Phylogeny" by Jens
Gramm, Till Nierhoff, Roded Sharan, and Till Tantau |
| 11:10-11:35 |
Mark Daly |
| 11:35-12:00 |
Discussion |
| 12:00-1:30 |
Lunch |
| 1:30-1:55 |
Kathryn Roeder |
| 1:55-2:20 |
“Optimally Phasing
Long Genomic Regions using Local Haplotype Predictions"
by Eleazar Eskin, Eran Halperin, and Roded Sharan |
| 2:20-2:45 |
Rasmus Nielsen |
| 2:45-3:10 |
Sorin Istrail |
| 3:10-3:30 |
Coffee Break |
| 3:30-3:55 |
Goncalo Abacasis |
| 3:55-4:20 |
"A Note on Conditional
Haplotyping Method in Pedigrees" by Guimin Gao
and Ina Hoeschele |
| 4:20-4:45 |
Discussion |
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Saturday
February 21 |
| 7:30-8:00 |
Continental breakfast |
| 8:00-8:25 |
Peter Donnelly |
| 8:25-8:50 |
"Incremental Haplotype
Inference, Phylogeny and Almost Bipartite Graphs"
by Peter Damaschke |
| 8:50-9:15 |
Francisco de la Vega |
| 9:15-9:40 |
"Comparison of Four
Computational Methods for Haplotype Inference Problem"
by Yan Zhang, Yiyu Jia, Chee Keong Kwoh, and Jianjun Liu |
| 9:40-10:05 |
Jeffrey Wall |
| 10:05-10:25 |
Coffee break |
| 10:25-10:50 |
Ron Shamir |
| 10:50-11:15 |
Tianhua Niu (substituting for Jun Liu) |
| 11:15-11:40 |
"A Branch-and-Bound
Algorithm for the Chromosome Tagging Problem"
by Itsik Pe'er, Paul de Bakker, Jeffery C. Barrett, David
Altshuler, and Mark J. Daly |
| 11:40-12:05 |
Magnus Nordborg |
| 12:05-1:45 |
Lunch |
| 1:45-2:10 |
Carlos Bustamante |
| 2:10-2:35 |
"Bayesian Haplotype
Inference via the Dirichlet Process" by Eric P.
Xing, Roded Sharan, and Michael I. Jordan |
| 2:35-3:00 |
Fengzhu Sun |
| 3:00-3:20 |
Coffee break |
| 3:20-3:45 |
Mark Shriver |
| 3:45-4:10 |
“Haplotype Association
Mapping by Density-Based Clustering in Case-Control Studies"
by Jing Li and Tao Jiang |
| 4:10-4:45 |
Discussion and closing
remarks |
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SUBMISSIONS
Questions and electronic submissions can be
sent by email to
recomb-workshop@lists.andrew.cmu.edu
Your submission must be received in electronic form by 11:59pm
(PDT) of December 6, 2003 for your submission to be considered.
Due to the short turnaround time for reviewers, we will
not be able to make exceptions to the deadline. Accepted
papers will be compiled for a volume of Lecture
Notes in Bioinformatics. Please prepare manuscripts
according to the LNBI
author specifications. Papers should be at most 10 pages
long, excluding title and abstract. If necessary, additional
clearly marked appendices can be included but may not be
read in review, at the discretion of the reviewers. |
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Registration and
Payment Information
Online
Registration Form
Registration is required. There is a $75 fee to attend this
workshop. (All funds are in US dollars.) Your registration
fee includes:
- Admission to all workshop sessions.
- Continental breakfast, lunch, and morning and afternoon
coffee breaks.
IMPORTANT DATES
Submission Deadline: December 6,
2003
Notifications to Authors: December
15, 2003
Workshop: February 20-21, 2004
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Confirmed
speakers: |
|  Goncalo
Abecasis, University of Michigan
David
Altshuler, Harvard Medical School & Whitehead
Institute
Carlos
Bustamante, Cornell University
Andrew
Clark, Cornell University
David
Clayton, Cambridge Institute for Medical Research
Mark
Daly, Whitehead Institute
Francisco
de la Vega, Applied Biosystems
Peter
Donnelly, University of Oxford
Stacey
Gabriel, Whitehead Institute
Sorin
Istrail Applied Biosystems
Jun
Liu, Harvard University
Rasmus
Nielsen, Cornell University
Magnus
Nordborg, University of Southern California
Kathryn
Roeder, Carnegie Mellon University
David
Schwartz, University of Wisconsin at Madison
Ron
Shamir, Tel Aviv University
Mark
Shriver, Penn State University
Jeffrey
Wall, University of Southern California
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Accepted Papers |
| 1.
"Incremental Haplotype Inference,
Phylogeny and Almost Bipartite
Graphs" by Peter Damaschke
2. "Optimally Phasing Long Genomic
Regions using Local Haplotype
Predictions" by Eleazar Eskin, Eran Halperin,
and Roded Sharan
3. "A Note on Conditional Haplotyping
Method in Pedigrees" by
Guimin Gao and Ina Hoeschele
4. "On the Complexity of Haplotyping
Via Perfect Phylogeny"
by Jens Gramm, Till Nierhoff, Roded Sharan, and Till Tantau
5. "The Incomplete Perfect Phylogeny
Haplotype Problem"
by Gad Kimmel and Ron Shamir
6. "Haplotype Association Mapping
by Density-Based Clustering in
Case-Control Studies" by Jing Li and Tao Jiang
7. "Empirical Evaluation of Genetic
and Environmental Interactions
in Complex Disease" by John Maindonald and Susan
Wilson
8. "A Branch-and-Bound Algorithm for
the Chromosome Tagging
Problem" by Itsik Pe'er, Paul de Bakker, Jeffery
C. Barrett,
David Altshuler, and Mark J. Daly
9. "Bayesian Haplotype Inference via
the Dirichlet Process"
by Eric P. Xing, Roded Sharan, and Michael I. Jordan
10. "Comparison of Four Computational
Methods for Haplotype
Inference Problem" by Yan Zhang, Yiyu Jia, Chee
Keong Kwoh, and
Jianjun Liu |
Hotel Accommodations
We are holding hotel rooms for out-of-town visitors at the Holiday
Inn Select, 100 Lytton Avenue, Pittsburgh, PA 15213. To take advantage
of the pre-negotiated rate of $95 per night ($108.30 including
taxes), you should call the Holiday Inn at 412-682-6200 by January
29th to make your reservations and be sure to ask for the RECOMB
haplotype meeting rate.
This meeting is being organized and sponsored
by the ALADDIN
Center at Carnegie Mellon University with generous support
from Applied
Biosystems
Poster
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CENTER
Carnegie
Mellon 
Aladdin
