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Colin N. Dewey, Ph.D. - Publications

Affiliations: 
2006 University of California, Berkeley, Berkeley, CA, United States 
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45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Toh H, Bagheri A, Dewey C, Stewart R, Yan L, Clegg D, Thomson JA, Jiang P. A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP). Computational Biology and Chemistry. 102: 107795. PMID 36436489 DOI: 10.1016/j.compbiolchem.2022.107795  0.462
2020 Liu P, Soukup AA, Bresnick EH, Dewey CN, Keles S. PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. Genome Research. PMID 32958497 DOI: 10.1101/Gr.252445.119  0.376
2020 Nolte MJ, Jing P, Dewey CN, Payseur BA. Giant Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic Organs. Genome Biology and Evolution. PMID 32531054 DOI: 10.1093/Gbe/Evaa118  0.42
2019 Dewey CN. Whole-Genome Alignment. Methods in Molecular Biology (Clifton, N.J.). 1910: 121-147. PMID 31278663 DOI: 10.1007/978-1-4939-9074-0_4  0.522
2019 Sanchez-Vazquez P, Dewey CN, Kitten N, Ross W, Gourse RL. Genome-wide effects on transcription from ppGpp binding to its two sites on RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America. PMID 30971496 DOI: 10.1073/Pnas.1819682116  0.395
2017 Hewitt KJ, Katsumura KR, Matson DR, Devadas P, Tanimura N, Hebert AS, Coon JJ, Kim JS, Dewey CN, Keles S, Hao S, Paulson RF, Bresnick EH. GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia. Developmental Cell. 42: 213-225.e4. PMID 28787589 DOI: 10.1016/J.Devcel.2017.07.009  0.317
2017 Bernstein MN, Doan A, Dewey CN. MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. Bioinformatics (Oxford, England). PMID 28535296 DOI: 10.1093/Bioinformatics/Btx334  0.406
2016 Jiang P, Nelson JD, Leng N, Collins M, Swanson S, Dewey CN, Thomson JA, Stewart R. Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability. Developmental Biology. PMID 27475628 DOI: 10.1016/J.Ydbio.2016.05.024  0.412
2016 Liu P, Sanalkumar R, Bresnick EH, Keleş S, Dewey CN. Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq. Genome Research. PMID 27405803 DOI: 10.1101/Gr.199174.115  0.364
2015 Tanimura N, Miller E, Igarashi K, Yang D, Burstyn JN, Dewey CN, Bresnick EH. Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation. Embo Reports. PMID 26698166 DOI: 10.1182/Blood.V126.23.161.161  0.301
2015 Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN, Keleş S. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. Plos Computational Biology. 11: e1004491. PMID 26484757 DOI: 10.1371/Journal.Pcbi.1004491  0.586
2015 Hewitt KJ, Kim DH, Devadas P, Prathibha R, Zuo C, Sanalkumar R, Johnson KD, Kang YA, Kim JS, Dewey CN, Keles S, Bresnick EH. Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome. Molecular Cell. 59: 62-74. PMID 26073540 DOI: 10.1016/J.Molcel.2015.05.020  0.35
2015 Leng N, Li Y, McIntosh BE, Nguyen BK, Duffin B, Tian S, Thomson JA, Dewey CN, Stewart R, Kendziorski C. EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. Bioinformatics (Oxford, England). PMID 25847007 DOI: 10.1093/Bioinformatics/Btv193  0.376
2015 Hewitt K, Johnson KD, Kim D, Devadas P, Prathibha R, Zuo C, Dewey C, Sanalkumar R, Kim J, Keles S, Bresnick EH. Cistrome Control of Hematopoieitic Stem/Progenitor Cell Function Blood. 126: 43-43. DOI: 10.1182/Blood.V126.23.43.43  0.358
2014 Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biology. 15: 553. PMID 25608678 DOI: 10.1186/S13059-014-0553-5  0.495
2013 Gao X, Johnson KD, Chang YI, Boyer ME, Dewey CN, Zhang J, Bresnick EH. Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo. The Journal of Experimental Medicine. 210: 2833-42. PMID 24297994 DOI: 10.1084/Jem.20130733  0.341
2013 LeGault LH, Dewey CN. Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. Bioinformatics (Oxford, England). 29: 2300-10. PMID 23846746 DOI: 10.1093/Bioinformatics/Btt396  0.424
2013 Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, ... ... Dewey CN, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols. 8: 1494-512. PMID 23845962 DOI: 10.1038/Nprot.2013.084  0.58
2013 Stewart R, Rascón CA, Tian S, Nie J, Barry C, Chu LF, Ardalani H, Wagner RJ, Probasco MD, Bolin JM, Leng N, Sengupta S, Volkmer M, Habermann B, Tanaka EM, ... ... Dewey CN, et al. Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema. Plos Computational Biology. 9: e1002936. PMID 23505351 DOI: 10.1371/Journal.Pcbi.1002936  0.458
2013 Gao X, Johnson KD, Chang Y, Boyer ME, Dewey CN, Zhang J, Bresnick E. Genetic Basis For Hematopoietic Stem Cell Generation In The Mammalian Embryo Blood. 122: 3667-3667. DOI: 10.1182/Blood.V122.21.3667.3667  0.338
2012 Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, Pool JE, Langley SA, Suarez C, Corbett-Detig RB, Kolaczkowski B, Fang S, Nista PM, Holloway AK, Kern AD, Dewey CN, et al. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 192: 533-98. PMID 22673804 DOI: 10.1534/Genetics.112.142018  0.514
2012 Dewey CN. Whole-genome alignment. Methods in Molecular Biology (Clifton, N.J.). 855: 237-57. PMID 22407711 DOI: 10.1007/978-1-61779-582-4_8  0.596
2011 Albers D, Dewey C, Gleicher M. Sequence surveyor: Leveraging overview for scalable genomic alignment visualization Ieee Transactions On Visualization and Computer Graphics. 17: 2392-2401. PMID 22034360 DOI: 10.1109/Tvcg.2011.232  0.447
2011 Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. Bmc Bioinformatics. 12: 323. PMID 21816040 DOI: 10.1186/1471-2105-12-323  0.582
2011 Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, KeleÅŸ S. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. Plos Computational Biology. 7: e1002111. PMID 21779159 DOI: 10.1371/Journal.Pcbi.1002111  0.608
2011 Dewey CN. Positional orthology: putting genomic evolutionary relationships into context. Briefings in Bioinformatics. 12: 401-12. PMID 21705766 DOI: 10.1093/Bib/Bbr040  0.569
2010 Larget BR, Kotha SK, Dewey CN, Ané C. BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics (Oxford, England). 26: 2910-1. PMID 20861028 DOI: 10.1093/Bioinformatics/Btq539  0.309
2010 Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics (Oxford, England). 26: 493-500. PMID 20022975 DOI: 10.1093/Bioinformatics/Btp692  0.505
2010 Ané C, Dewey CN, Kotha SK, Larget BR. Gene tree reconciliation: new developments in Bayesian concordance analysis with BUCKy Nature Precedings. DOI: 10.1038/Npre.2010.4625.1  0.305
2009 White MA, Ané C, Dewey CN, Larget BR, Payseur BA. Fine-scale phylogenetic discordance across the house mouse genome. Plos Genetics. 5: e1000729. PMID 19936022 DOI: 10.1371/Journal.Pgen.1000729  0.442
2009 Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. Fast statistical alignment. Plos Computational Biology. 5: e1000392. PMID 19478997 DOI: 10.1371/Journal.Pcbi.1000392  0.673
2009 Arora R, Sethares WA, Dewey C. Reconstructing latent periods in genome sequences with insertions and deletions 2009 Ieee International Workshop On Genomic Signal Processing and Statistics, Gensips 2009. DOI: 10.1109/GENSIPS.2009.5174377  0.47
2007 Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, ... ... Dewey CN, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/Nature06340  0.747
2007 Dewey CN. Aligning multiple whole genomes with Mercator and MAVID. Methods in Molecular Biology (Clifton, N.J.). 395: 221-36. PMID 17993677 DOI: 10.1007/978-1-59745-514-5_14  0.573
2007 Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. Plos Biology. 5: e310. PMID 17988176 DOI: 10.1371/Journal.Pbio.0050310  0.746
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Dewey CN, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.783
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307  0.789
2006 Dewey CN, Huggins PM, Woods K, Sturmfels B, Pachter L. Parametric alignment of Drosophila genomes. Plos Computational Biology. 2: e73. PMID 16789815 DOI: 10.1371/Journal.Pcbi.0020073  0.775
2006 Dewey CN, Pachter L. Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Human Molecular Genetics. 15: R51-6. PMID 16651369 DOI: 10.1093/Hmg/Ddl056  0.766
2006 Lall S, Grün D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N. A genome-wide map of conserved microRNA targets in C. elegans. Current Biology : Cb. 16: 460-71. PMID 16458514 DOI: 10.1016/J.Cub.2006.01.050  0.656
2005 Dewey C, Woods K. Parametric sequence alignment Algebraic Statistics For Computational Biology. 193-205. DOI: 10.1017/CBO9780511610684.011  0.319
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Dewey C, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/Science.1105136  0.734
2004 Dewey C, Wu JQ, Cawley S, Alexandersson M, Gibbs R, Pachter L. Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Research. 14: 661-4. PMID 15060007 DOI: 10.1101/Gr.1939804  0.68
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Dewey C, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426  0.787
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Dewey C, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  0.782
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