Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase
Sanchez-Vazquez, Patricia, Dewey, Colin N., Kitten, Nicole, Ross, Wilma, Gourse, Richard L.
Published in Proceedings of the National Academy of Sciences - PNAS (23.04.2019)
Published in Proceedings of the National Academy of Sciences - PNAS (23.04.2019)
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Journal Article
Evaluation of de novo transcriptome assemblies from RNA-Seq data
Li, Bo, Fillmore, Nathanael, Bai, Yongsheng, Collins, Mike, Thomson, James A, Stewart, Ron, Dewey, Colin N
Published in Genome biology (21.12.2014)
Published in Genome biology (21.12.2014)
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Journal Article
RNA-Seq gene expression estimation with read mapping uncertainty
Li, Bo, Ruotti, Victor, Stewart, Ron M., Thomson, James A., Dewey, Colin N.
Published in Bioinformatics (15.02.2010)
Published in Bioinformatics (15.02.2010)
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Journal Article
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Haas, Brian J, Papanicolaou, Alexie, Yassour, Moran, Grabherr, Manfred, Blood, Philip D, Bowden, Joshua, Couger, Matthew Brian, Eccles, David, Li, Bo, Lieber, Matthias, MacManes, Matthew D, Ott, Michael, Orvis, Joshua, Pochet, Nathalie, Strozzi, Francesco, Weeks, Nathan, Westerman, Rick, William, Thomas, Dewey, Colin N, Henschel, Robert, LeDuc, Richard D, Friedman, Nir, Regev, Aviv
Published in Nature protocols (01.08.2013)
Published in Nature protocols (01.08.2013)
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Journal Article
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive
Bernstein, Matthew N, Doan, AnHai, Dewey, Colin N
Published in Bioinformatics (Oxford, England) (15.09.2017)
Published in Bioinformatics (Oxford, England) (15.09.2017)
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Journal Article
Rbm20 regulates titin alternative splicing as a splicing repressor
Li, Shijun, Guo, Wei, Dewey, Colin N, Greaser, Marion L
Published in Nucleic acids research (01.02.2013)
Published in Nucleic acids research (01.02.2013)
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Journal Article
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
Larget, Bret R., Kotha, Satish K., Dewey, Colin N., Ané, Cécile
Published in Bioinformatics (15.11.2010)
Published in Bioinformatics (15.11.2010)
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Journal Article
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans
Begun, David J, Holloway, Alisha K, Stevens, Kristian, Hillier, Ladeana W, Poh, Yu-Ping, Hahn, Matthew W, Nista, Phillip M, Jones, Corbin D, Kern, Andrew D, Dewey, Colin N, Pachter, Lior, Myers, Eugene, Langley, Charles H
Published in PLoS biology (01.11.2007)
Published in PLoS biology (01.11.2007)
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Journal Article
Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema
Stewart, Ron, Rascón, Cynthia Alexander, Tian, Shulan, Nie, Jeff, Barry, Chris, Chu, Li-Fang, Ardalani, Hamisha, Wagner, Ryan J, Probasco, Mitchell D, Bolin, Jennifer M, Leng, Ning, Sengupta, Srikumar, Volkmer, Michael, Habermann, Bianca, Tanaka, Elly M, Thomson, James A, Dewey, Colin N
Published in PLoS computational biology (01.03.2013)
Published in PLoS computational biology (01.03.2013)
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Journal Article
Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis
Sedykh, Irina, Yoon, Baul, Roberson, Laura, Moskvin, Oleg, Dewey, Colin N., Grinblat, Yevgenya
Published in Developmental biology (01.09.2017)
Published in Developmental biology (01.09.2017)
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Journal Article
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments
Leng, Ning, Li, Yuan, McIntosh, Brian E, Nguyen, Bao Kim, Duffin, Bret, Tian, Shulan, Thomson, James A, Dewey, Colin N, Stewart, Ron, Kendziorski, Christina
Published in Bioinformatics (15.08.2015)
Published in Bioinformatics (15.08.2015)
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Journal Article
RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis
Mehta, Charu, Fraga de Andrade, Isabela, Matson, Daniel R, Dewey, Colin N, Bresnick, Emery H
Published in Nucleic acids research (20.09.2021)
Published in Nucleic acids research (20.09.2021)
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Journal Article
Fast statistical alignment
Bradley, Robert K, Roberts, Adam, Smoot, Michael, Juvekar, Sudeep, Do, Jaeyoung, Dewey, Colin, Holmes, Ian, Pachter, Lior
Published in PLoS computational biology (01.05.2009)
Published in PLoS computational biology (01.05.2009)
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Journal Article
PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways
Su, Shengqin, Chhabra, Gagan, Ndiaye, Mary A, Singh, Chandra K, Ye, Ting, Huang, Wei, Dewey, Colin N, Setaluri, Vijayasaradhi, Ahmad, Nihal
Published in Molecular cancer therapeutics (01.01.2021)
Published in Molecular cancer therapeutics (01.01.2021)
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Journal Article
Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome
Hewitt, Kyle J., Kim, Duk Hyoung, Devadas, Prithvia, Prathibha, Rajalekshmi, Zuo, Chandler, Sanalkumar, Rajendran, Johnson, Kirby D., Kang, Yoon-A., Kim, Jin-Soo, Dewey, Colin N., Keles, Sunduz, Bresnick, Emery H.
Published in Molecular cell (02.07.2015)
Published in Molecular cell (02.07.2015)
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