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Program
Sunday, May 17, 2009
Monday, May 18, 2009
Tuesday, May 19, 2009
Wednesday, May 20, 2009
Thursday, May 21, 2009
Click here for a pdf of the RECOMB2009 program
Sunday, May 17, 2009
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8:30 AM-
6:30 PM
Optional Tours -Meet in the hotel lobby to join the tours to the Arizona-Sonora Desert Museum or Biosphere 2. For more information
2:00 PM-
5:00 PM

Tour the BIO5 Institute at The University of Arizona
Free. Transportation provided. Visit the Institute's new, state-of-the-art facility on the UA campus. Researchers from the the iPlant Collaborative, Arizona Genomics Institute, and Arizona Research Lab's Genomics Analysis Technology Core, Biotechnology Computing Core, and Human Origins Genotyping Laboratory will present. More information about the program. To sign up, send email to < This e-mail address is being protected from spambots. You need JavaScript enabled to view it > listing subject as "BIO5 Tour."

2:00 PM-
7:00 PM
Registration
The RECOMB 2009 registration desk is located in the resort's lobby foyer.
6:30 PM-
8:30 PM
Welcome Reception and Exhibits Open
Show your conference credentials for access to the kickoff reception.
Monday, May 18, 2009
[top]
7:30 AM-
8:30 AM
Continental Breakfast
7:30 AM-
5:30 PM
Registration
The RECOMB 2009 registration desk is located in the resort's lobby foyer.
The welcome and all keynote, paper, and poster presentations will be in the Grand Ballroom.
8:30 AM-
8:45 AM
Conference Welcome - Laurence Hurley, Associate Director, BIO5 Institute, The University of Arizona
8:45 AM -
10:35 AM
Session Ron Pinter, Chair
8:45 AM-
9:45 AM
KEYNOTE: Mark Gerstein
Large Scale Analysis of Protein Interaction Networks (Stanislav Ulam Computational Biology Lecture)
9:45 AM-
10:10 AM
Paper Presentation
Topology-Free Querying of Protein Interaction Networks
S. Bruckner, F. Hűffner, R.M. Karp, R. Shamir, R. Sharan
10:10 AM-
10:35 AM
Paper Presentation
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks
M. Lavallee-Adam, B. Coulombe, M. Blanchette
10:35 AM-
11:00 AM
Break
11:00 AM-
11:25 AM
Paper Presentation
Detecting the Presence and Absence of Causal Relationships Between Expression of Yeast Genes with Very Few Samples
E.Y. Kang, I. Shpitser, H.M. Kang, C.Ye, E. Eskin
11:25 AM-
11:50 AM
Paper Presentation
Evaluating Between-Pathway Models with Expression Data
B. Hescott, M. Leiserson, L. Cowen, D. Slonim
11:50 AM-
12:15 PM
Paper Presentation
Cross Species Expression Analysis of Innate Immune Response
Y. Lu, R. Rosenfeld, G. Nau, Z. Bar-Joseph
12:15 PM-
1:30 PM
Lunch
12:15 PM -
5:00 PM
Poster Setup for Session A
12:15 PM-
7:30 PM
Exhibits are open
1:30 PM -
2:30 PM
Session Pavel Pevzner, Chair
1:30 PM-
2:30 PM
KEYNOTE 2: Pardis Sabeti
Natural Selection in Humans and Pathogens
2:30 PM-
2:55 PM
Paper Presentation
Haplotype Inference in Complex Pedigrees
B. Kirkpatrick, J. Rosa, E. Halperin, R.M. Karp
2:55 PM-
3:20 PM
Paper Presentation
Deep Sequencing of a Genetically Heterogeneous Sample: Haplotype Reconstruction and Read Error Correction
O. Zagordi, L. Geyrhofer, V. Roth, N. Beerenwinkel
3:20 PM-
3:45 PM
Paper Presentation
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data
S. Sindi and B. Raphael
3:45 PM-
4:15 PM
Break
3:45 PM -
5:50 PM
Session Michael Brent, Chair
4:15 PM-
4:40 PM
Paper Presentation
Storage and Retrieval of Individual Genomes
V. Makinen, G. Navarro, J. Siren, N. Valimaki
4:40 PM-
5:05 PM

Paper Presentation
A Statistical Framework for the Functional Analysis of Metagenomes
I. Sharon, A. Pati, V. Markowitz, R. Pinter

5:10 PM-
5:50 PM

Selected Poster Presentations - Grand Ballroom
Model-Based Dissection of Transcriptional Deregulation

E. Szczurek, F. Markowetz, I. Gat-Viks, P. Biecek, J. Tiuryn, M. Vingron

An Ensemble Model of Competitive Multi-factor Binding of the Genome
T. Wasson, A. Hartemink

Discovery of Copy Number Variation Using Next Generation Sequencing
P. Medvedev, M. Fiume, T. Smith, A. Dalca, S. Lee, M. Brudno

Low Frequency Oscillations in Single-Nucleotide Content Play a Role in Nucleosome Positioning in H. Sapiens
S. Reynolds, J. Bilmes, W. Stafford Noble

6:00 PM-
7:00 PM
RECOMB Business Meeting - Grand Ballroom
6:30 PM-
8:00 PM
Poster Session A - Sonoran Room (Light refreshments)
Tuesday, May 19, 2009
[top]
7:30 AM-
8:30 AM
Breakfast
7:30 AM-
5:30 PM
Posters from Session A remain up - Sonoran Room
10:00 AM -
5:30 PM
Exhibits are open
All keynote and paper presentations will be in the Grand Ballroom.
8:45 AM -
10:35 AM
Session Terry Speed, Chair
8:45 AM-
9:45 AM
KEYNOTE: Carlos Bustamante
Population Genetics in the Personal Genome Era
9:45 AM-
10:10 AM
Paper Presentation
COE: A General Approach for Efficient Genome-Wide Two-Locus Epistatic Test in Disease Association Studies
X. Zhang
10:10 AM-
10:35 AM
Paper Presentation
An Adaptive and Memory Efficient Algorithm for Genotype Imputation
H.M. Kang, N. Zaitlen, B. Han, E. Eskin
10:35 AM-
11:00 AM
Break
10:35 AM -
12:15 PM
Session Bonnie Berger, Chair
11:00 AM-
11:25 AM
Paper Presentation
Spatial Clustering of Multivariate Genomic and Epigenomic Information
A. Tanay, R. Jaschek
11:25 AM-
11:50 AM
Paper Presentation
Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation
T. Raveh-Sadka, M. Levo, E. Segal
11:50 AM-
12:15 PM
Paper Presentation
On the Relationship Between DNA Periodicity and Local Chromatin Structure
S. Reynolds, J. Bilmes, W. Stafford Noble
12:15 PM-
1:30 PM
Lunch
1:30 PM-
2:55 PM
Session Eleazar Eskin, Chair
1:30 PM-
2:30 PM
KEYNOTE: Steve Quake
Single Molecule Sequencing of an Individual Human Genome (Distinguished Technology Lecture)
2:30 PM-
2:55 PM
Paper Presentation
Optimizing PCR Assays for DNA Based Cancer Diagnostics
A. Bashir, Q. Lu, B. Raphael, D. Carson, Y.-T. Liu, V. Bafna
2:55 PM-
3:15 PM
Break
3:15 PM-
6:15 PM
Session Serafim Batzoglou, Chair
3:15 PM-
6:30 PM
3:15 – 3:40 Mostafa Ronaghi, CTO Illumina and NextBIO, The New Era of Genomics
3:40 – 4:05 Rade Drmanac, Complete Genomics, Revolutionizing Human Genome Sequencing
4:05 – 4:30 Ilya Kupershmidt, NextBio, Ontology-Based Meta-Analysis of Global Collections of Public and Internal Large Scale Data
4:30 – 4:55 Eran Halperin, Tel Aviv University (formerly of Navigenics), Current Challenges in Personalized Medicine
4:55 – 5:20 Joanna Mountain, 23andMe, Consumers, Genomes and Research
5:20 – 6:30 Panel Discussion, Pardis Sabeti, Moderator
7:00 PM-
10:00 PM

Off-Site Dinner & Tour: The Arizona Journey
During this exclusive event, you'll enjoy dinner and behind-the-scenes glimpses of the world's largest collection of Southwest Indian pottery at the Arizona State Museum, an affiliate of the Smithsonian Institute. See the sacred Eagle and Hoop dances presented by the Redhouse family and a featured live performance by Native American artist and two-time Grammy Nominee, Vince Redhouse.

The museum's curators will share the stories of these fascinating artifacts and answer your questions. Demonstrations include tortilla making, desert-dwelling animals, and regional crafts. The museum's beautiful store "Native Goods" will be open and its knowledgeable staff on hand to offer cultural insights. A truly once-in-a-lifetime experience, designed especially for RECOMB attendees.

Diane Dittemore, Curator of Ethnographic Materials, has extensive knowledge of ASM's broad contemporary and historic Native American ethnographic collections. Diane will be providing tours of her exhibit entitled “SET IN STONE: 2000 Years of Gem and Mineral Trade in the Southwest.”

Davison Koenig, Exhibits Curator and National Endowment for the Humanities Principal Investigator for the ASM Virtual Vault Project, designed the Pottery Project Exhibit and has been investigating applications of profile modeling, an innovative technique enabling rapid, low-cost digitization of three-dimensional objects. This revolutionary method quickly creates photorealistic digital models of objects using photography rather than costly laser scans. Davison will present on ways that the Virtual Vault, a visual database, can convey a wealth of interpretive and contextual information not delivered by traditional exhibition mechanisms.

Martin Kim, Native Goods Museum Store Manager, is committed to supporting the native arts of this region by featuring contemporary Native artists and offering visitors unique, educational materials and arts and crafts for purchase. Martin is also a master storyteller who enjoys sharing stories about objects as he sells top quality Indian handicrafts. Martin educates visitors by highlighting connections between the artifacts in the exhibits and the authentic Native American merchandise—pottery, jewelry, baskets, textiles—for sale in Native Goods.

Some tickets are still available, but this event will sell out. Follow the conference confirmation link that was emailed to you to modify your conference registration and add this optional item.

*Cost per person $65.00 US. adults, $35.00 children

Questions? This e-mail address is being protected from spambots. You need JavaScript enabled to view it

 

Wednesday, May 20, 2009
[top]
7:30 AM-
8:30 AM
Breakfast
10:00 AM -
5:30PM
Exhibits are open (Arizona Foyer)
All keynote, paper, and poster presentations are in the Grand Ballroom.
8:45 AM -
10:35 PM
Session John Kececioglu, Chair
8:45 AM-
9:45 AM
KEYNOTE: Michael Hammer
DNA and Human Origins
9:45 AM-
10:10 AM
Paper Presentation
The Multi-State Perfect Phylogeny Problem with Missing and Removable Data
D. Gusfield
10:10 AM-
10:35 AM
Paper Presentation
Sorting Signed Permutations by Inversions in O(n log n) Time
K. Swenson, V. Rajan, Y. Lin, B. Moret
10:35 AM-
11:00 AM
Break
Posters from Session A should be taken down- Sonoran Room
11:00 AM -
12:15 PM
Session Bill Noble, Chair
11:00 AM-
11:25 AM
Paper Presentation
Parameter Synthesis in Nonlinear Systems: Applications to Systems Biology
A. Donze, G. Clermont, A. Legay, C. Langmead
11:25 AM-
11:50 AM
Paper Presentation
A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series
O. Stegle, K. Denby, D. Wild, Z. Ghahramani, K. Borgwardt
11:50 AM-
12:15 PM
Paper Presentation
Finding Biological Accurate Clusterings in Hierarchical Decompositions Using the Variation of Information
S. Navlakha, J. White, N. Nagarajan, M. Pop, C. Kingsford
12:15 PM-
1:30 PM
Lunch
12:15 PM -
5:30 PM
Poster B Setup - Sonoran Room
1:30 PM -
3:45 PM
Session Sorin Istrail, Chair
1:30 PM-
2:30 PM
KEYNOTE: Mikhail Gelfand
Alternative Splicing as a Playground of Evolution
2:30 PM-
2:55 PM
Paper Presentation
Simultaneous Alignment and Folding of Protein Sequences
Jerome Waldispuhl, C.W. O'Donnell, S. Will, S. Devadas, R. Backofen, B. Berger
2:55 PM-
3:20 PM
Paper Presentation
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure
E. Kim, T. Wheeler, J. Kececioglu
3:20 PM-
3:45 PM
Paper Presentation
Lifting Prediction to Alignment of RNA Pseudoknots
M. Mohl, S. Will, R. Backofen

3:45 PM-
4:15 PM
Break
4:15 PM -
6:00 PM
Session Colin Dewey,Chair
4:15 PM-
4:40 PM
Paper Presentation
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep
C. Daskalakis, E. Mossel, S. Roch
4:40 PM-
5:05 PM
Paper Presentation
How Many Bootstrap Replicates are Necessary?
N. Pattengale, M. Alipour, O. Bininda-Emonds, B. Moret, A. Stamatakis
5:05 PM-
5:30 PM
Paper Presentation
New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees
C. Chauve, N El-Mabrouk
5:30 PM-
6:00 PM

Select Poster Presentations - Grand Ballroom
What Can Theory Do For You? Insights and Applications to Assembling Next Generation Sequences
N. Nagarajan, M. Pop

Revealing Genomewide Methylation Patterns from High-Throughput Sequencing by Statistical Inference
M. Singer, D. Boffelli, J. Dhahbi, D.I.K. Martin, L. Pachter

A Statistical Approach for Prediction from Longitudinal Microarray Data
Y. Zhang, R. Tibshirani, W. Xiao, R. Davis

6:15 PM-
7:45 PM
Poster Session B - Sonoran Room (Light refreshments)
Thursday, May 21, 2009
[top]
7:30 AM-
8:30 AM
Breakfast
7:30 AM-
3:00 PM
Exhibits are open - Arizona Foyer
7:30 AM-
3:00 PM

Posters from Session B remain up

All keynote and paper presentations and the awards ceremony are in the Grand Ballroom.
8:45 AM -
10:35 PM
Session Michael Waterman, Chair
8:45 AM-
9:45 AM
KEYNOTE: Mike Snyder
Analyzing Genomes and Regulatory Networks Using Omics Technologies (Distiguished Biology Lecture)
9:45 AM-
10:10 AM
Paper Presentation
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes
F. Hormozdiari, C. Alkan, E.E. Eichler, S.C. Sahinalp
10:10 AM-
10:35 AM
Paper Presentation
Overlapping Pools for High Throughput Targeted Resequencing
S. Prabhu, I. Pe'er
10:35 AM-
11:00 AM
Break
11:00 AM -
12:15 PM
Session Mona Singh, Chair
11:00 AM-
11:25 AM
Paper Presentation
Searching Protein 3-D Structures in Linear Time
T. Shibuya
11:25 AM-
11:50 AM
Paper Presentation
Boosting Protein Threading Accuracy
J. Peng, J. Xu
11:50 AM-
12:15 AM
Paper Presentation
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
A. Ramanathan, P.K. Agarwal, M. Kurnikova, C. Langmead
12:15 PM-
1:30 PM
Lunch
1:30 PM -
2:45 PM
Session Vineet Bafna, Chair
1:30 PM-
1:55 PM
Paper Presentation
Shared Peptides in Mass Spectrometry Based Protein Quantification
B. Dost, V. Bafna, N. Bandeira, X. Li, Z. Shen, S. Briggs
1:55 PM-
2:20 PM
Paper Presentation
Prediction of Novel Modifications by Unrestrictive Search of Tandem Mass Spectra
S. Na, E. Paek
2:20 PM-
2:45 PM
Paper Presentation
Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification
Z. He, Ch. Yang, C. Yang, R.Z. Qi, J. P.-M. Tam, W. Yu
2:45 PM-
3:15 PM
Break
Posters from Session B should be taken down
3:15 PM -
4:05 PM
Session John Kececioglu, Chair
3:15 PM-
3:40 PM
Paper Presentation
Protein Fragment Swapping: a Method for Asymmetric Selective Site-Directed Recombination
W. Zheng, K.E. Griswold, C. Bailey-Kellogg
3:40 PM-
4:05 PM
Paper Presentation
A Probabilistic Graphical Model for Ab Initio Folding
F. Zhao, J. Peng, J. Xu
4:05 PM-
4:30 PM
Awards Ceremony - Grand Ballroom
4:30 PMConference Adjourns
 
 

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