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