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 |
0.584 |
|
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 |
0.494 |
|
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 |
0.578 |
|
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 |
0.595 |
|
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 |
0.581 |
|
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 |
0.607 |
|
2011 |
Dewey CN. Positional orthology: putting genomic evolutionary relationships into context. Briefings in Bioinformatics. 12: 401-12. PMID 21705766 DOI: 10.1093/Bib/Bbr040 |
0.568 |
|
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 |
0.503 |
|
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 |
0.672 |
|
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 |
0.572 |
|
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 |
0.788 |
|
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 |
0.774 |
|
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 |
0.765 |
|
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 |
0.318 |
|
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 |
0.679 |
|
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 |
0.786 |
|
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 |
0.781 |
|
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