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  Accepted Papers


Heuristics for the Gene-duplication Problem: A Q(n) Speed-up
for the Local Search

Authors: Mukul Subodh Bansal, Oliver Eulenstein, AndrÈ Wehe, Gordon Burleigh

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

Estimating Genome-wide Copy Number Using Allele Specific Mixture Models
Author: Nate Miller

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

Reconstructing the topology of protein complexes
Authors: Allister Bernard, David Vaughn, Alexander J. Hartemink

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

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

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

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

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

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

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

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

Free Energy Estimates of All-atom Protein Structures Using Generalized
Belief Propagation

Authors: Hetunandan Kamisetty, Eric P. Xing, Christopher James Langmead

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

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

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

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

Multiple Sequence Alignment Based on Profile Alignment of
Intermediate Sequences

Authors: Yue Lu, Sing-Hoi Sze

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

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

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

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

Design of Compact, Universal DNA Microarrays for Protein Binding
Microarray Experiments

Authors: Anthony A. Philippakis, Aaron M. Qureshi, Michael F. Berger, Martha L. Bulyk

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

Connectedness Profiles in Protein Networks for the Analysis of Gene
Expression Data

Authors: Joel R Pradines, Vlado Dancik, Alan Ruttenberg, Victor Farutin

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

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

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

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

An Efficient and Accurate Graph-based Approach to Detect
Population Substructure

Authors: Srinath Sridhar, Satish Rao, Eran Halperin

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

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

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

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

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

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

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