Parametric Alignment of Drosophila Genomes. - Colin N. Dewey; Peter Huggins; Kevin Woods; Bernd Sturmfels; Lior Pachter (PLoS Comput. Biol., 2006)

Reconstructing latent periods in genome sequences with insertions and deletions. - Raman Arora; Colin N. Dewey; William A. Sethares (GENSiPS, 2009)

Fast Statistical Alignment. - Robert K. Bradley; Adam Roberts; Michael E. Smoot; Sudeep Juvekar; Jaeyoung Do; Colin N. Dewey; Ian H. Holmes; Lior Pachter (PLoS Comput. Biol., 2009)

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. - Bret R. Larget; Satish K. Kotha; Colin N. Dewey; Cécile Ané (Bioinform., 2010)

RNA-Seq gene expression estimation with read mapping uncertainty. - Bo Li 015; Victor Ruotti; Ron M. Stewart; James A. Thomson; Colin N. Dewey (Bioinform., 2010)

Positional orthology: putting genomic evolutionary relationships into context. - Colin N. Dewey (Briefings Bioinform., 2011)

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. - Bo Li 015; Colin N. Dewey (BMC Bioinform., 2011)

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data. - Dongjun Chung; Pei Fen Kuan; Bo Li 015; Rajendran Sanalkumar; Kun Liang 001; Emery H. Bresnick; Colin N. Dewey; Sündüz Keles (PLoS Comput. Biol., 2011)

Sequence Surveyor: Leveraging Overview for Scalable Genomic Alignment Visualization. - Danielle Albers; Colin N. Dewey; Michael Gleicher (IEEE Trans. Vis. Comput. Graph., 2011)

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. - Laura H. LeGault; Colin N. Dewey (Bioinform., 2013)

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema. - Ron M. Stewart; Cynthia Alexander Rascón; Shulan Tian; Jeff Nie; Chris Barry; Li-Fang Chu; Hamisha Ardalani; Ryan J. Wagner; Mitchell D. Probasco; Jennifer M. Bolin; Ning Leng; Srikumar Sengupta; et al. (PLoS Comput. Biol., 2013)

EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. - Ning Leng; Yuan Li; Brian E. McIntosh; Bao Kim Nguyen; Bret Duffin; Shulan Tian; James A. Thomson; Colin N. Dewey; Ron M. Stewart; Christina Kendziorski (Bioinform., 2015)

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. - Xin Zeng; Bo Li 015; Rene Welch; Constanza Rojo; Ye Zheng; Colin N. Dewey; Sündüz Keles (PLoS Comput. Biol., 2015)

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. - Matthew Bernstein; AnHai Doan; Colin N. Dewey (Bioinform., 2017)

A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP). - Huishi Toh; Atefeh Bagheri; Colin N. Dewey; Ron M. Stewart; Lili Yan; Dennis Clegg; James A. Thomson; Peng Jiang (Comput. Biol. Chem., 2023)