Accepted Papers for RECOMB 2014

The conference proceedings (Lecture Notes in Computer Science Volume 8394, 2014) are now online.

  • Jianzhu Ma, Sheng Wang, Zhiyong Wang and Jinbo Xu. MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
  • Siavash Mirarab, Nam-Phuong Nguyen and Tandy Warnow. PASTA: ultra-large multiple sequence alignment
  • Wen-Yun Yang, Farhad Hormozdiari, Eleazar Eskin and Bogdan Pasaniuc. A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation
  • Emily Berger, Deniz Yorukoglu and Bonnie Berger. HapTree: A novel Bayesian framework for single individual polyplotyping using NGS data
  • Ngan Nguyen, Glenn Hickey, Daniel Zerbino, Brian Raney, Dent Earl, Joel Armstrong, David Haussler and Benedict Paten. Building a Pangenome Reference for a Population
  • Zhanyong Wang, Jae-Hoon Sul, Sagi Snir, Jose A. Lozano and Eleazar Eskin. Gene-Gene Interactions Detection Using A Two-stage Model
  • Arne Reimers, Frank Bruggeman, Brett Olivier and Leen Stougie. Fast Flux Module Detection using Matroid Theory
  • Shaun Mahony, Matthew Edwards, Esteban Mazzoni, Richard Sherwood, Akshay Kakumanu, Carolyn Morrison, Hynek Wichterle and David Gifford. An integrated model of multiple-condition ChIP-seq data reveals predeterminants of Cdx2 binding
  • Rui Wang and Scott Schmidler. Bayesian Multiple Protein Structure Alignment
  • Jianling Zhong, Todd Wasson and Alexander Hartemink. Learning protein-DNA interaction landscapes by integrating experimental data through computational models
  • Ewa Szczurek and Niko Beerenwinkel. Modeling mutual exclusivity of cancer mutations
  • Marinka Zitnik and Blaz Zupan. Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion
  • Hamidreza Chitsaz and Mohammad Aminisharifabad. Exact Learning of RNA Energy Parameters From Structure
  • Shutan Xu, Shuxue Zou and Lincong Wang. A geometric clustering algorithm and its applications to structural data
  • Armin Töpfer, Tobias Marschall, Rowena A Bull, Fabio Luciani, Alexander Schönhuth and Niko Beerenwinkel. Viral quasispecies assembly via maximal clique enumeration
  • Yana Safonova, Anton Bankevich and Pavel Pevzner. DipSPAdes: Assembler for Highly Polymorphic Diploid Genomes
  • Jan Hoinka, Alexey Berezhnoy, Zuben E. Sauna, Eli Gilboa and Teresa Przytycka. AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application
  • Mingfu Shao, Yu Lin and Bernard Moret. An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes
  • Kelley Harris, Sara Sheehan, John Kamm and Yun S. Song. Decoding Coalescent Hidden Markov Models in Linear Time
  • Chen-Ping Fu, Vladimir Jojic and Leonard Mcmillan. An Alignment-Free Regression Approach for Estimating Allele-Specific Expression using RNA-Seq Data
  • Henry C.M. Leung, S.M. Yiu and Francis Chin. IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information
  • Arun Konagurthu, Parthan Kasarapu, Lloyd Allison, James Collier and Arthur Lesk. On sufficient statistics of least-squares superposition of vector sets
  • Yu Zheng and Louxin Zhang. Reconciliation with Non-binary Gene Trees Revisited
  • Keith Noto, Carla Brodley, Saeed Majidi, Diana Bianchi and Donna Slonim. CSAX: Characterizing Systematic Anomalies in eXpression Data
  • Adrian Guthals, Christina Boucher and Nuno Bandeira. The generating function approach for peptide identification in spectral networks
  • Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin, Colin Collins, Gholamreza Haffari and S. Cenk Sahinalp. HIT.nDRIVE: Multi-Driver Gene Prioritization based on Hitting Time
  • Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau and Alexander Schoenhuth. WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads
  • Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared Simpson and Paul Medvedev. On the representation of de Bruijn graphs
  • Adam Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael Jordan, David Patterson, Bin Yu and Yun Song. Changepoint Analysis for Efficient Variant Calling
  • Y. William Yu, Deniz Yorukoglu and Bonnie Berger. Traversing the k-mer landscape of NGS read datasets for quality score sparsification
  • Hetu Kamisetty, Bornika Ghosh, Christopher James Langmead and Chris Bailey-Kellogg. Learning Sequence Determinants of Protein:protein Interaction Specificity with Sparse Graphical Models
  • Ben Raphael and Fabio Vandin. Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data
  • Shay Zakov and Vineet Bafna. Reconstructing Breakage Fusion Bridge architectures using noisy copy numbers
  • Derek Aguiar, Eric Morrow and Sorin Istrail. Tractatus: an exact and subquadratic algorithm for inferring identity-by-descent multi-shared haplotype tracts
  • Hua Wang, Heng Huang and Chris Ding. Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency