Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 33

1.

GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia.

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.

Dev Cell. 2017 Aug 7;42(3):213-225.e4. doi: 10.1016/j.devcel.2017.07.009.

2.

Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis.

Sedykh I, Yoon B, Roberson L, Moskvin O, Dewey CN, Grinblat Y.

Dev Biol. 2017 Sep 1;429(1):92-104. doi: 10.1016/j.ydbio.2017.07.003. Epub 2017 Jul 6.

PMID:
28689736
3.

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.

Bernstein MN, Doan A, Dewey CN.

Bioinformatics. 2017 Sep 15;33(18):2914-2923. doi: 10.1093/bioinformatics/btx334.

4.

Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.

Jiang P, Nelson JD, Leng N, Collins M, Swanson S, Dewey CN, Thomson JA, Stewart R.

Dev Biol. 2017 Jun 15;426(2):143-154. doi: 10.1016/j.ydbio.2016.05.024. Epub 2016 Jul 28.

5.

Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq.

Liu P, Sanalkumar R, Bresnick EH, Keleş S, Dewey CN.

Genome Res. 2016 Aug;26(8):1124-33. doi: 10.1101/gr.199174.115. Epub 2016 Jul 12.

6.

Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation.

Tanimura N, Miller E, Igarashi K, Yang D, Burstyn JN, Dewey CN, Bresnick EH.

EMBO Rep. 2016 Feb;17(2):249-65. doi: 10.15252/embr.201541465. Epub 2015 Dec 23.

7.

Cis-regulatory mechanisms governing stem and progenitor cell transitions.

Johnson KD, Kong G, Gao X, Chang YI, Hewitt KJ, Sanalkumar R, Prathibha R, Ranheim EA, Dewey CN, Zhang J, Bresnick EH.

Sci Adv. 2015 Sep 4;1(8):e1500503. doi: 10.1126/sciadv.1500503. eCollection 2015 Sep.

8.

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping.

Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN, Keleş S.

PLoS Comput Biol. 2015 Oct 20;11(10):e1004491. doi: 10.1371/journal.pcbi.1004491. eCollection 2015 Oct.

9.

Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome.

Hewitt KJ, Kim DH, Devadas P, Prathibha R, Zuo C, Sanalkumar R, Johnson KD, Kang YA, Kim JS, Dewey CN, Keles S, Bresnick EH.

Mol Cell. 2015 Jul 2;59(1):62-74. doi: 10.1016/j.molcel.2015.05.020. Epub 2015 Jun 11.

10.

EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.

Leng N, Li Y, McIntosh BE, Nguyen BK, Duffin B, Tian S, Thomson JA, Dewey CN, Stewart R, Kendziorski C.

Bioinformatics. 2015 Aug 15;31(16):2614-22. doi: 10.1093/bioinformatics/btv193. Epub 2015 Apr 5.

11.

Evaluation of de novo transcriptome assemblies from RNA-Seq data.

Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN.

Genome Biol. 2014 Dec 21;15(12):553. doi: 10.1186/s13059-014-0553-5.

12.

Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo.

Gao X, Johnson KD, Chang YI, Boyer ME, Dewey CN, Zhang J, Bresnick EH.

J Exp Med. 2013 Dec 16;210(13):2833-42. doi: 10.1084/jem.20130733. Epub 2013 Dec 2.

13.

Bicaudal-C spatially controls translation of vertebrate maternal mRNAs.

Zhang Y, Cooke A, Park S, Dewey CN, Wickens M, Sheets MD.

RNA. 2013 Nov;19(11):1575-82. doi: 10.1261/rna.041665.113. Epub 2013 Sep 23.

14.

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.

LeGault LH, Dewey CN.

Bioinformatics. 2013 Sep 15;29(18):2300-10. doi: 10.1093/bioinformatics/btt396. Epub 2013 Jul 11.

15.

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

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, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A.

Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11.

16.

Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.

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, Thomson JA, Dewey CN.

PLoS Comput Biol. 2013;9(3):e1002936. doi: 10.1371/journal.pcbi.1002936. Epub 2013 Mar 7.

17.

Rbm20 regulates titin alternative splicing as a splicing repressor.

Li S, Guo W, Dewey CN, Greaser ML.

Nucleic Acids Res. 2013 Feb 1;41(4):2659-72. doi: 10.1093/nar/gks1362. Epub 2013 Jan 9.

18.

Genomic variation in natural populations of Drosophila melanogaster.

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, Song YS, Hahn MW, Begun DJ.

Genetics. 2012 Oct;192(2):533-98. doi: 10.1534/genetics.112.142018. Epub 2012 Jun 5.

19.

Whole-genome alignment.

Dewey CN.

Methods Mol Biol. 2012;855:237-57. doi: 10.1007/978-1-61779-582-4_8. Review.

PMID:
22407711
20.

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Li B, Dewey CN.

BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323.

21.

Positional orthology: putting genomic evolutionary relationships into context.

Dewey CN.

Brief Bioinform. 2011 Sep;12(5):401-12. doi: 10.1093/bib/bbr040. Epub 2011 Jun 24. Review.

22.

BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.

Larget BR, Kotha SK, Dewey CN, Ané C.

Bioinformatics. 2010 Nov 15;26(22):2910-1. doi: 10.1093/bioinformatics/btq539. Epub 2010 Sep 21.

PMID:
20861028
23.

RNA-Seq gene expression estimation with read mapping uncertainty.

Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN.

Bioinformatics. 2010 Feb 15;26(4):493-500. doi: 10.1093/bioinformatics/btp692. Epub 2009 Dec 18.

24.

Fine-scale phylogenetic discordance across the house mouse genome.

White MA, Ané C, Dewey CN, Larget BR, Payseur BA.

PLoS Genet. 2009 Nov;5(11):e1000729. doi: 10.1371/journal.pgen.1000729. Epub 2009 Nov 20.

25.

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M.

Nature. 2007 Nov 8;450(7167):219-32.

26.

Aligning multiple whole genomes with Mercator and MAVID.

Dewey CN.

Methods Mol Biol. 2007;395:221-36.

PMID:
17993677
27.

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.

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.

PLoS Biol. 2007 Nov 6;5(11):e310.

28.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, 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, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

29.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

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, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A.

Genome Res. 2007 Jun;17(6):760-74.

30.
31.

Parametric alignment of Drosophila genomes.

Dewey CN, Huggins PM, Woods K, Sturmfels B, Pachter L.

PLoS Comput Biol. 2006 Jun 23;2(6):e73. Epub 2006 Jun 23.

32.

Evolution at the nucleotide level: the problem of multiple whole-genome alignment.

Dewey CN, Pachter L.

Hum Mol Genet. 2006 Apr 15;15 Spec No 1:R51-6. Review.

PMID:
16651369
33.

A genome-wide map of conserved microRNA targets in C. elegans.

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.

Curr Biol. 2006 Mar 7;16(5):460-71. Epub 2006 Feb 2.

Supplemental Content

Loading ...
Support Center