Colin N. Dewey, Ph.D. - Publications

Affiliations: 
2006 University of California, Berkeley, Berkeley, CA 

35 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
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  0.92
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: 10.15252/embr.201541465  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2013 Zhang Y, Cooke A, Park S, Dewey CN, Wickens M, Sheets MD. Bicaudal-C spatially controls translation of vertebrate maternal mRNAs. Rna (New York, N.Y.). 19: 1575-82. PMID 24062572 DOI: 10.1261/rna.041665.113  0.92
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  0.92
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  0.92
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  0.92
2013 Li S, Guo W, Dewey CN, Greaser ML. Rbm20 regulates titin alternative splicing as a splicing repressor. Nucleic Acids Research. 41: 2659-72. PMID 23307558 DOI: 10.1093/nar/gks1362  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2011 Dewey CN. Positional orthology: putting genomic evolutionary relationships into context. Briefings in Bioinformatics. 12: 401-12. PMID 21705766 DOI: 10.1093/bib/bbr040  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2007 Dewey CN. Aligning multiple whole genomes with Mercator and MAVID. Methods in Molecular Biology (Clifton, N.J.). 395: 221-36. PMID 17993677 DOI: 10.1385/1-59745-514-8:221  0.92
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  0.92
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  0.92
2006 Dewey CN, Rogozin IB, Koonin EV. Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns. Bmc Genomics. 7: 311. PMID 17156453 DOI: 10.1186/1471-2164-7-311  0.92
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  0.92
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  0.92
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  0.92
2005 Dewey C, Woods K. Parametric sequence alignment Algebraic Statistics For Computational Biology. 193-205. DOI: 10.1017/CBO9780511610684.011  0.92
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  0.92
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  0.92
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  0.92
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