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Sunday, May 17, 2009 Monday, May 18, 2009 Tuesday, May 19, 2009 Wednesday, May 20, 2009 Thursday, May 21, 2009
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Click here for a pdf of the RECOMB2009 program
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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 |
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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." |
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2:00 PM- 7:00 PM | Registration The RECOMB 2009 registration desk is located in the resort's lobby foyer. |
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6:30 PM- 8:30 PM | Welcome Reception and Exhibits Open Show your conference credentials for access to the kickoff reception.
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7:30 AM- 8:30 AM | Continental Breakfast
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7:30 AM- 5:30 PM | Registration The RECOMB 2009 registration desk is located in the resort's lobby foyer.
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| | The welcome and all keynote, paper, and poster presentations will be in the Grand Ballroom.
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8:30 AM- 8:45 AM | Conference Welcome - Laurence Hurley, Associate Director, BIO5 Institute, The University of Arizona |
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8:45 AM - 10:35 AM
| Session Ron Pinter, Chair
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8:45 AM- 9:45 AM | KEYNOTE: Mark Gerstein Large Scale Analysis of Protein Interaction Networks (Stanislav Ulam Computational Biology Lecture)
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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
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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
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10:35 AM- 11:00 AM | Break
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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
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11:25 AM- 11:50 AM | Paper Presentation Evaluating Between-Pathway Models with Expression Data B. Hescott, M. Leiserson, L. Cowen, D. Slonim
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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
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12:15 PM- 1:30 PM | Lunch
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12:15 PM - 5:00 PM
| Poster Setup for Session A
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12:15 PM- 7:30 PM | Exhibits are open |
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1:30 PM - 2:30 PM
| Session Pavel Pevzner, Chair |
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1:30 PM- 2:30 PM | KEYNOTE 2: Pardis Sabeti Natural Selection in Humans and Pathogens
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2:30 PM- 2:55 PM | Paper Presentation Haplotype Inference in Complex Pedigrees B. Kirkpatrick, J. Rosa, E. Halperin, R.M. Karp
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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
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3:20 PM- 3:45 PM | Paper Presentation Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data S. Sindi and B. Raphael
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3:45 PM- 4:15 PM | Break
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3:45 PM - 5:50 PM
| Session Michael Brent, Chair
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4:15 PM- 4:40 PM | Paper Presentation Storage and Retrieval of Individual Genomes V. Makinen, G. Navarro, J. Siren, N. Valimaki
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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 |
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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 |
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6:00 PM- 7:00 PM | RECOMB Business Meeting - Grand Ballroom
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6:30 PM- 8:00 PM | Poster Session A - Sonoran Room (Light refreshments)
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7:30 AM- 8:30 AM | Breakfast
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7:30 AM- 5:30 PM | Posters from Session A remain up - Sonoran Room
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10:00 AM - 5:30 PM
| Exhibits are open
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| | All keynote and paper presentations will be in the Grand Ballroom.
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8:45 AM - 10:35 AM
| Session Terry Speed, Chair
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8:45 AM- 9:45 AM | KEYNOTE: Carlos Bustamante Population Genetics in the Personal Genome Era |
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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
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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
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10:35 AM- 11:00 AM | Break
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10:35 AM - 12:15 PM
| Session Bonnie Berger, Chair
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11:00 AM- 11:25 AM | Paper Presentation Spatial Clustering of Multivariate Genomic and Epigenomic Information A. Tanay, R. Jaschek
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11:25 AM- 11:50 AM | Paper Presentation Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation T. Raveh-Sadka, M. Levo, E. Segal
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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
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12:15 PM- 1:30 PM | Lunch |
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1:30 PM- 2:55 PM
| Session Eleazar Eskin, Chair |
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1:30 PM- 2:30 PM | KEYNOTE: Steve Quake Single Molecule Sequencing of an Individual Human Genome (Distinguished Technology Lecture)
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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
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2:55 PM- 3:15 PM | Break |
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3:15 PM- 6:15 PM
| Session Serafim Batzoglou, Chair
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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 |
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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?
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7:30 AM- 8:30 AM | Breakfast |
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10:00 AM - 5:30PM | Exhibits are open (Arizona Foyer)
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| | All keynote, paper, and poster presentations are in the Grand Ballroom.
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8:45 AM - 10:35 PM
| Session John Kececioglu, Chair
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8:45 AM- 9:45 AM | KEYNOTE: Michael Hammer DNA and Human Origins
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9:45 AM- 10:10 AM | Paper Presentation The Multi-State Perfect Phylogeny Problem with Missing and Removable Data D. Gusfield
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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
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10:35 AM- 11:00 AM | Break |
| | Posters from Session A should be taken down- Sonoran Room |
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11:00 AM - 12:15 PM
| Session Bill Noble, Chair
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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
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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
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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
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12:15 PM- 1:30 PM | Lunch |
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12:15 PM - 5:30 PM
| Poster B Setup - Sonoran Room
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1:30 PM - 3:45 PM
| Session Sorin Istrail, Chair |
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1:30 PM- 2:30 PM | KEYNOTE: Mikhail Gelfand Alternative Splicing as a Playground of Evolution
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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 |
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2:55 PM- 3:20 PM | Paper Presentation Learning Models for Aligning Protein Sequences with Predicted Secondary Structure E. Kim, T. Wheeler, J. Kececioglu
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3:20 PM- 3:45 PM | Paper Presentation Lifting Prediction to Alignment of RNA Pseudoknots M. Mohl, S. Will, R. Backofen
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3:45 PM- 4:15 PM | Break
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4:15 PM - 6:00 PM
| Session Colin Dewey,Chair |
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4:15 PM- 4:40 PM | Paper Presentation Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep C. Daskalakis, E. Mossel, S. Roch
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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
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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
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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 |
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6:15 PM- 7:45 PM | Poster Session B - Sonoran Room (Light refreshments)
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7:30 AM- 8:30 AM | Breakfast |
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7:30 AM- 3:00 PM | Exhibits are open - Arizona Foyer
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7:30 AM- 3:00 PM | Posters from Session B remain up
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| | All keynote and paper presentations and the awards ceremony are in the Grand Ballroom.
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8:45 AM - 10:35 PM
| Session Michael Waterman, Chair |
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8:45 AM- 9:45 AM | KEYNOTE: Mike Snyder Analyzing Genomes and Regulatory Networks Using Omics Technologies (Distiguished Biology Lecture)
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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
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10:10 AM- 10:35 AM | Paper Presentation Overlapping Pools for High Throughput Targeted Resequencing S. Prabhu, I. Pe'er
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10:35 AM- 11:00 AM | Break |
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11:00 AM - 12:15 PM
| Session Mona Singh, Chair
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11:00 AM- 11:25 AM | Paper Presentation Searching Protein 3-D Structures in Linear Time T. Shibuya
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11:25 AM- 11:50 AM | Paper Presentation Boosting Protein Threading Accuracy J. Peng, J. Xu
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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
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12:15 PM- 1:30 PM | Lunch |
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1:30 PM - 2:45 PM
| Session Vineet Bafna, Chair |
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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
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1:55 PM- 2:20 PM | Paper Presentation Prediction of Novel Modifications by Unrestrictive Search of Tandem Mass Spectra S. Na, E. Paek
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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
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2:45 PM- 3:15 PM | Break
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| | Posters from Session B should be taken down
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3:15 PM - 4:05 PM
| Session John Kececioglu, Chair
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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
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3:40 PM- 4:05 PM | Paper Presentation A Probabilistic Graphical Model for Ab Initio Folding F. Zhao, J. Peng, J. Xu
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4:05 PM- 4:30 PM | Awards Ceremony - Grand Ballroom
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| 4:30 PM | Conference Adjourns |