Colin N. Dewey

16 papers Journal 15Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
IsoBayes: a Bayesian approach for single-isoform proteomics inference.
Bioinform.
Jordy Bollon, Michael R. Shortreed, Erin Jeffery, Ben T. Jordan, Rachel Miller, Andrea Cavalli, Lloyd M. Smith, Colin N. Dewey, Gloria M. Sheynkman, Simone Tiberi
2023 J jnl
A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP).
Comput. Biol. Chem.
Huishi Toh, Atefeh Bagheri, Colin N. Dewey, Ron M. Stewart, Lili Yan, Dennis Clegg, James A. Thomson, Peng Jiang
2017 J jnl
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.
Bioinform.
Matthew Bernstein, AnHai Doan, Colin N. Dewey
2015 J jnl
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.
Bioinform.
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
2015 J jnl
Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping.
PLoS Comput. Biol.
Xin Zeng, Bo Li, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keles
2013 J jnl
Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema.
PLoS Comput. Biol.
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, Michael Volkmer, Bianca Habermann, Elly M. Tanaka, James A. Thomson, Colin N. Dewey
2013 J jnl
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.
Bioinform.
Laura H. LeGault, Colin N. Dewey
2011 J jnl
Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data.
PLoS Comput. Biol.
Dongjun Chung, Pei Fen Kuan, Bo Li, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin N. Dewey, Sündüz Keles
2011 J jnl
Positional orthology: putting genomic evolutionary relationships into context.
Briefings Bioinform.
Colin N. Dewey
2011 J jnl
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
BMC Bioinform.
Bo Li, Colin N. Dewey
2011 J jnl
Sequence Surveyor: Leveraging Overview for Scalable Genomic Alignment Visualization.
IEEE Trans. Vis. Comput. Graph.
Danielle Albers, Colin N. Dewey, Michael Gleicher
2010 J jnl
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis.
Bioinform.
Bret R. Larget, Satish K. Kotha, Colin N. Dewey, Cécile Ané
2010 J jnl
RNA-Seq gene expression estimation with read mapping uncertainty.
Bioinform.
Bo Li, Victor Ruotti, Ron M. Stewart, James A. Thomson, Colin N. Dewey
2009 J jnl
Fast Statistical Alignment.
PLoS Comput. Biol.
Robert K. Bradley, Adam Roberts, Michael E. Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian H. Holmes, Lior Pachter
2009 — conf
Reconstructing latent periods in genome sequences with insertions and deletions.
GENSiPS
Raman Arora, Colin N. Dewey, William A. Sethares
2006 J jnl
Parametric Alignment of
PLoS Comput. Biol.
Colin N. Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter