RECOMB'seq 2013 Accepted Papers

Jie Zhu, Yufang Qin, Taigang Liu, Xiaoqi Zheng and Jun Wang. Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles
Christine Lo, Sangwoo Kim, Shay Zakov and Vineet Bafna. Evaluating Genome Architecture of a Complex Region via Generalized Bipartite Matching
Matthew Hayes and Jing Li. Bellerophon: a hybrid method for detecting interchromosomal rearrangements at base pair resolution using next-generation sequencing data
Evgeny Kapun and Fedor Tsarev. De Bruijn Superwalk with Multiplicities Problem is NP-hard
Yi Li and Xiaohui Xie. A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues
Christopher Whelan and Kemal Sonmez. Cloudbreak: A MapReduce Algorithm for Detecting Genomic Structural Variation
David Tse, Guy Bresler and Ma'Ayan Bresler. Optimal Assembly for High Throughput Shotgun Sequencing
Haitham Ashoor, Aurélie Hérault, François Radvanyi, Vladimir B. Bajic, Emmanuel Barillot and Valentina Boeva. HMCan – a tool to detect chromatin modifications in cancer samples using ChIP-seq data
Xi Wang and Murray J. Cairns. Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing
Chi-Long Li, Kun-Tze Chen and Chin Lung Lu. Assembling Contigs in Draft Genomes Using Reversals and Block-Interchanges
Roy Lederman. A Random-Permutations-Based Approach to Fast Read Alignment
Jing Zhang, C.-C. Jay Kuo and Liang Chen. WemIQ: a weighted-log-likelihood expectation maximization method for isoform quantification from RNA-Seq data
Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi and Veli Mäkinen. A Novel Min-Cost Flow  Method for Estimating Transcript Expression with RNA-Seq
Yongchu Liu, Jiangtao Guo, Gangqing Hu and Huaiqiu Zhu. Gene Prediction in Metagenomic Fragments Based on the SVM Algorithm
Gary Benson, Yevgeniy Gelfand, Joshua Loving and Yozen Hernandez. VNTRseek -- A Computational Pipeline to Detect Tandem Repeat Variants in Next-Generation Sequencing Data: Analysis of the 454 Watson Genome
Li Song and Liliana Florea. CLASS: Constrained Transcript Assembly of RNA-seq Reads
Christina Ander, Ole Schulz-Trieglaff, Jens Stoye and Anthony Cox. metaBEETL: high-throughput analysis of heterogeneous  microbial populations from shotgun DNA sequences
Yu Zhang. Inferring Population Stratification and Admixture in Sequencing Data with Little Ancestry Information
Jacob Biesinger, Yuanfeng Wang and Xiaohui Xie. Discovering and Mapping Chromatin States Using a Tree Hidden Markov Model
Sheng Li, Francine Garrett-­bakelman, Altuna Akalin, Paul Zumbo, Ross Levine, Ari Melnick and Christopher Mason. eDMR: An optimized algorithm for detecting and annotating regional differential methylation
Seunghak Lee, Aurelie Lozano, Prabhanjan Kambadur and Eric Xing. Detecting SNP-SNP Interactions With Piecewise Independence Screening
Manuel Allhoff, Alexander Schoenhuth, Marcel Martin, Ivan G. Costa, Sven Rahmann and Tobias Marschall. Discovering Context-Specific Sequencing Errors
Eric Bareke, Jean-Francois Spinella, Ramon Vidal, Jasmine Healy, Daniel Sinnett and Miklos Csuros. Joint genotype inference with germline and somatic mutations