RECOMB 2007

The conference proceedings for RECOMB 2007 is published by Springer, in the series Lecture Notes in Bioinformatics.

8:30am-5:30pm

Optional Tours

12:30-6:30

Affymetrix Low Level Analysis Workshop 2007
Sponsored by the Affymetrix Developers' Network

2:00pm-7:00pm

Registration

6:30pm-8:30pm

Welcome Reception

7:30am-8:30am

Continental Breakfast

7:30am-5:30pm

Registration Open

8:30am-8:45am

Conference Welcome

8:45am-9:10am

QNet: A Tool for Querying Protein Interaction Networks
Authors: Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan

9:10am-9:35am

Pairwise Global Alignment of Protein Interaction Networks By Matching Neighborhood Topology
Authors: Rohit Singh, Jinbo Xu, Bonnie Berger

9:35am-10:00am

Reconstructing the Topology of Protein Complexes
Authors: Allister Bernard, David Vaughn, Alexander J. Hartemink

10:00am-10:25am

Network Legos: Building Blocks of Cellular Wiring Diagrams
Authors: T. M. Murali, Corban G. Rivera

10:25am-10:50am

Break

10:50am-11:15am

An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in-silico Gene Perturbation Experiments
Authors: Abhishek Garg, Ioannis Xenarios, Luis Mendoza, Giovanni DeMicheli

11:15am-11:40am

A Feature-Based Approach to Modeling Protein-DNA Interactions
Authors: Eilon Sharon, Eran Segal

11:40pm-12:35pm

Elizabeth Blackburn

12:35pm-2:00pm

Lunch

2:00pm-2:55pm

Pat Brown

12:30pm-7:30pm

Exhibits Open

2:55pm-3:20pm

Network Motif Discovery Using Subgraph Enumeration and Symmetry- Breaking
Authors: Joshua A. Grochow, Manolis Kellis

3:20pm-3:45pm

Nucleosome Occupancy Information Improves de novo Motif Discovery
Authors: Alexander J Hartemink, Raluca Gordan, Leelavati Narlikar

3:45pm-4:10pm

Break

4:10pm-4:35pm

Framework for Identifying Common Aberrations in DNA Copy Number Data
Authors: Amir Ben-Dor, Doron Lipson, Anya Tsalenko, Mark Reimers, Lars O. Baumbusch, Michael M. Barrett, John N. Weinstein, Anne-Lise Borresen-Dale, Zohar Yakhini

4:35pm-5:00pm

Estimating Genome-wide Copy Number using Allele Specific Mixture Models
Authors: Wenyi Wang, Benilton Carvalho, Aravinda Chakravarti, Rafael A. Irizarry

5:00pm-5:25pm

GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH Data
Authors: Yanxin Shi, Fan Guo, Wei Wu, Eric P. Xing

5:30pm-7:30pm

Poster Session A

7:30am-8:30am

Continental Breakfast

7:30am-7:00pm

Poster Session A Continued

8:30am-9:25am

Abby Dernburg

9:25am-9:50am

Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions
Authors: Hiroyuki Kuwahara, Chris J. Myers

9:50am-10:15am

Shift Invariant Adaptive Double Threading: Learning MHC II - peptide binding
Authors: Noah Aaron Zaitlen, Manuel Reyes-Gomez, David Heckerman, Nebojsa Jojic

10:00am-5:30pm

Exhibits Open

10:15am-10:40am

Break

10:40am-11:05am

Reconstructing the Phylogeny of Mobile Elements
Authors: Sean O'Rourke, Noah Zaitlen, Nebojsa Jojic, Eleazar Eskin

11:05am-11:30am

Beyond Galled Trees - Decomposition and Computation of Galled Networks
Authors: Daniel H Huson, Tobias H Kloepper

11:30am-11:55am

Variational Upper Bounds for Probabilistic Phylogenetic Models
Authors: Ydo Wexler, Dan Geiger

11:55am-12:20pm

Heuristics for the Gene-duplication Problem: An $\Omega(n)$ Speed-up for the Local Search
Authors: Mukul Subodh Bansal, Oliver Eulenstein, AndrÈ Wehe, Gordon Burleigh

12:20pm-2:00pm

Lunch

12:30-2:00

Birds of a Feather Discussion: Algorithms for next-generation sequencing applications

2:00pm-2:55pm

Jay Keasling

2:55pm-3:20pm

Support Vector Training of Protein Alignment Models
Authors: Chun-Nam John Yu, Thorsten Joachims, Ron Elber, Jarek Pillardy

3:20pm-3:45pm

Tools for Simulating and Analyzing RNA Folding Kinetics
Authors: Xinyu Tang, Shawna Thomas, Nancy M. Amato

3:45pm-4:10pm

Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences
Authors: Yue Lu, Sing-Hoi Sze

4:10pm-4:35pm

Break

4:35pm-5:00pm

Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data
Authors: Joel R Pradines, Vlado Dancik, Alan Ruttenberg, Victor Farutin

5:00pm-5:25pm

Multivariate Segmentation in the Analysis of Transcription Tiling Array Data
Authors: Antonio Piccolboni

5:25pm-5:50pm

A Bayesian Model that Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements
Authors: Anitha Kannan, Andrew Emili, Brendan J Frey

6:00pm-7:00pm

RECOMB Business Meeting

7:30am-8:30am

Continental Breakfast

8:30am-9:25am

Jennifer Graves

9:25am-9:50am

Rearrangements in Genomes with Centromeres — Part I: Translocations
Authors: Michal Ozery-Flato, Ron Shamir

9:50am-10:15am

Identification of Deletion Polymorphisms from Haplotypes
Authors: Erik Corona, Benjamin Raphael, Eleazar Eskin

10:00am-5:00pm

Exhibits Open

10:15am-10:40am

Break

10:40am-11:05am

Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation
Authors: Hetunandan Kamisetty, Eric P. Xing, Christopher James Langmead

11:05am-11:30am

Minimizing and Learning Energy Functions for Side-Chain Prediction
Authors: Chen Yanover, Ora Schueler-Furman, Yair Weiss

11:30am-11:55am

Protein Conformational Flexibility Analysis with Noisy Data
Authors: Anshul Nigham, David Hsu

11:55am-12:20pm

Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules
Authors: Yuval Inbar, Dina Schneidman-Duhovny, Oranit Dror, Ruth Nussinov, Haim J. Wolfson

12:20pm-2:00pm

Lunch

2:00pm-2:55pm

Harry Noller

2:55pm-3:20pm

Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments
Authors: Anthony A. Philippakis, Aaron M. Qureshi, Michael F. Berger, Martha L. Bulyk

3:30pm-5:30pm

Poster Session B

6:30-8:30pm

Reception

7:30am-8:30am

Continental Breakfast

8:30am-9:25pm

Yishi Jin

7:30am-3:00pm

Poster Session B Continued

7:30am-3:00pm

Exhibits Open

9:25am-9:50am

Improved Ranking Functions for Protein and Modification-Site Identifications
Authors: Marshall Bern, David Goldberg

9:50am-10:15am

Peptide Retention-Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions
Authors: Aaron A. Klammer, Xianhua Yi, Michael J. MacCoss, William Stafford Noble

10:15am-10:40am

A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data
Authors: Ole Schulz-Trieglaff, Rene Hussong, Clemens Groepl, Andreas Hildebrandt, Knut Reinert

10:40am-11:05am

Break

11:05am-11:30am

Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms
Authors: Yufeng Wu

11:30am-11:55am

An Efficient and Accurate Graph-based Approach to Detect
Population Substructure
Authors: Srinath Sridhar, Satish Rao, Eran Halperin

11:55am-12:20pm

RB-Finder: An Improved Distance-based Sliding Window Method to Detect Recombination Breakpoints
Authors: Wah Heng Lee, Wing Kin Sung

12:20pm-1:30pm

Lunch

1:30pm-2:25pm

Aviv Regev

2:25pm-2:50pm

Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs
Authors: Cyrus L. Harmon, Parvez Ahammad, Ann Hammonds, Richard Weiszmann, Susan E. Celniker, S. Shankar Sastry, Gerald M. Rubin

2:50pm-3:30pm

Awards Ceremony

3:30pm

Adjourn