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Accepted Papers & Short Talks

RECOMB-Seq
 

Inferring Viral Spectrum from 454 Pyrosequencing Reads
Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion Mandoiu, Peter Balfe and Alex Zelikovsky

Assembly of non-unique insertion content using next-generation sequencing
Nathaniel Parrish, Farhad Hormozdiari and Eleazar Eskin

A Hidden Markov Model for Copy Number Variant Prediction from Whole Genome Resequencing Data
Yufeng Shen, Yiwei Gu and Itsik Pe'Er

Genotyping common and rare variation using overlapping pool sequencing
Dan He, Noah Zaitlen, Bogdan Pasaniuc, Eleazar Eskin and Eran Halperin

Contig graph mining for duplication breakpoints
Jurgen F. Nijkamp, Jean-Marc Daran, Marcel J.T. Reinders and Dick De Ridder

Modeling and automation of sequencing-based determination of RNA structure
Sharon Aviran, Cole Trapnell, Julius Lucks, Stefanie Mortimer, Shujun Luo, Gary Schroth, Jennifer Doudna, Adam Arkin and Lior Pachter

A Whole-Genome Probe Design for Massively Parallel Variant Validation using Selective Circularization
Daniel Newburger, Georges Natsoulis, Hua Xu, Sue Grimes, John Bell and Hanlee Ji

TavernaPBS: Custom Next-Generation Sequence Analysis Workflows using High-Performance Computing Resources with Taverna and PBS
Mark Lawson, Paul Shuber and Aaron Mackey

Counting k-mers with a Bloom Filter
Pall Melsted and Jonathan Pritchard

Improved Variant Discovery and Allele Frequency Estimation from Pooled DNA Resequencing with Bayesian Latent Class Analysis and Compositional Bias Models
Shom Paul and Aaron Mackey

Accurate Estimation of Gene Expression Levels from DGE Sequencing Data
Marius Nicolae and Ion Mandoiu

Constrained traversal of repeats with paired sequences
Sébastien Boisvert, Élénie Godzaridis, François Laviolette and Jacques Corbeil

Separating Metagenomic Data into Genomes via Clustering
Olga Tanaseichuk and Tao Jiang

Finding Deletions with Exact Break Points from Noisy Low Coverage Paired-end Short Sequence Reads
Jin Zhang and Yufeng Wu

mTiM: margin-based transcript mapping from RNA-seq
Georg Zeller, Nico Goernitz, Gunnar Raetsch, Jonas Behr, Andre Kahles, Soeren Sonnenburg and Pramod Mudrakarta

 

RECOMB-CCB
 

Analyzing the genome of the Tasmanian Devil and its transmissible cancer
Ole Schulz-Trieglaff, Elizabeth Murchison, Zemin Ning, Wendy Wong, Markus Bauer, Jennifer Becq, Anthony J. Cox, Matthew Hims, Sean Humphray, Sergii Ivakhno, Irina Khrebtukova, Ludmil Alexandrov, Shujun Luo, Lisa Murray, Richard Shaw, Philip Tedder, Dirk Evers, Niall Gormley, Gary Schroth, Geoffrey Smith, David Bentley and Mike Stratton

RNA-Seq profiling of prostate tumors identify subtype specific splice signatures and metastasis associated splice patterns
Anna Lapuk, Chunxiao Wu, Jamie Rosner, Sonal Brahmbhatt, Shawn Anderson, Stas Volik, Robert Bell, Anne Haegert, Ladan Fazli, Antonio Hurtado-Coll, Yongjun Zhao, Marco Marra, Martin Gleave and Colin Collins

Sequence-Based Profiling of Prostate Tumours
Stanislav Volik, Anna Lapuk, Chunxiao Wu, Andrew Mcpherson, Martin Gleave, Yuzhuo Wang, Antonio Hurtado-Coll, Ladan Fazli, Sonal Brahmbhatt, Anne Haegert, Robert Bell, Shawn Anderson, Martin Hirst, Yongjun Zhao, Steven Jones, Sohrab Shah, Fereydoun Hormozdiari, Marco Marra, Cenk Sahinalp and Colin Collins

Predicting Chemotherapeutic Response Using Optimally Discriminative Subnetworks
Kendric Wang, Phuong Dao, Martin Ester, Collin Collins, Anna Lapuk and Cenk Sahinalp

Computational purification of tumor gene expression profiles leads to predictive models of patient outcome
Gerald Quon, Syed Haider, Ang Cui, Paul Boutros and Quaid Morris

AInferring Candidate Somatic Deletions using Short-Reads Combined from Normal and Mixed Samples
Roland Wittler and Cedric Chauve

A Bayesian approach for sensitive detection of somatic genomic alterations from next-generation sequencing of clinical cancer specimens
Roman Yelensky, Doron Lipson, Alex Parker, Mirna Jarosz, Christine Sheehan, Frank Juhn, Zac Zwirko, Kristina Brennan, Troy Bloom, Sean Downing, John Curran, Jeffrey Ross and Maureen Cronin

Accurate somatic point mutation prediction using supervised machine learning algorithms
Jiarui Ding, Andrew Roth, Ryan Giuliany, Sam Aparicio and Sohrab Shah

Detecting Somatic Mutations In Tumour/Normal Paired Sample Sequence Data
Andrew Roth, Anamaria Crisnan, Samuel Aparicio and Sohrab Shah

Reconstructing Cancer Genome Organization from Paired End Sequencing
Layla Oesper, Sarah J. Aerni, Ryan Drebin and Benjamin J. Raphael

A systematic assessment of associations among chromosomal aberrations in cancer karyotypes
Ron Shamir, Michal Ozery-Flato, Chaim Linhart, Luba Trachtenbrot and Shai Izraeli

Statistical approaches for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data
Christopher Yau and Christopher C. Holmes

deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data
Andrew Mcpherson, S. Cenk Sahinalp, David Huntsman and Sohrab Shah