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Items: 1 to 20 of 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.

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