Colin N. Dewey

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 2

Top Topics

Gene Expression

Top Venues

PLoS Comput. Biol.

Comput. Biol. Chem.

Publications

Huishi Toh, Atefeh Bagheri, Colin N. Dewey, Ron M. Stewart, Lili Yan, Dennis Clegg, James A. Thomson, Peng Jiang
A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP). Comput. Biol. Chem. 102 (2023)
Matthew Bernstein, AnHai Doan, Colin N. Dewey
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. Bioinform. 33 (18) (2017)
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
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. Bioinform. 31 (16) (2015)
Xin Zeng, Bo Li, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keles
Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. PLoS Comput. Biol. 11 (10) (2015)
Laura H. LeGault, Colin N. Dewey
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. Bioinform. 29 (18) (2013)
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
Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema. PLoS Comput. Biol. 9 (3) (2013)
Danielle Albers, Colin N. Dewey, Michael Gleicher
Sequence Surveyor: Leveraging Overview for Scalable Genomic Alignment Visualization. IEEE Trans. Vis. Comput. Graph. 17 (12) (2011)
Colin N. Dewey
Positional orthology: putting genomic evolutionary relationships into context. Briefings Bioinform. 12 (5) (2011)
Bo Li, Colin N. Dewey
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 12 (2011)
Dongjun Chung, Pei Fen Kuan, Bo Li, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin N. Dewey, Sündüz Keles
Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data. PLoS Comput. Biol. 7 (7) (2011)
Bo Li, Victor Ruotti, Ron M. Stewart, James A. Thomson, Colin N. Dewey
RNA-Seq gene expression estimation with read mapping uncertainty. Bioinform. 26 (4) (2010)
Bret R. Larget, Satish K. Kotha, Colin N. Dewey, Cécile Ané
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinform. 26 (22) (2010)
Robert K. Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian H. Holmes, Lior Pachter
Fast Statistical Alignment. PLoS Comput. Biol. 5 (5) (2009)
Raman Arora, Colin N. Dewey, William A. Sethares
Reconstructing latent periods in genome sequences with insertions and deletions. GENSiPS (2009)
Colin N. Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter
Genomes. PLoS Comput. Biol. 2 (6) (2006)