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Items: 1 to 20 of 23

1.

A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential.

Hill ST, Kuintzle R, Teegarden A, Merrill E 3rd, Danaee P, Hendrix DA.

Nucleic Acids Res. 2018 Jul 9. doi: 10.1093/nar/gky567. [Epub ahead of print]

PMID:
29986088
2.

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.

Danaee P, Rouches M, Wiley M, Deng D, Huang L, Hendrix D.

Nucleic Acids Res. 2018 Jun 20;46(11):5381-5394. doi: 10.1093/nar/gky285.

3.

Transcription Factor CTIP1/ BCL11A Regulates Epidermal Differentiation and Lipid Metabolism During Skin Development.

Li S, Teegarden A, Bauer EM, Choi J, Messaddeq N, Hendrix DA, Ganguli-Indra G, Leid M, Indra AK.

Sci Rep. 2017 Oct 18;7(1):13427. doi: 10.1038/s41598-017-13347-7.

4.

HopBase: a unified resource for Humulus genomics.

Hill ST, Sudarsanam R, Henning J, Hendrix D.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax009.

5.

In Vivo Characterization of an AHR-Dependent Long Noncoding RNA Required for Proper Sox9b Expression.

Garcia GR, Goodale BC, Wiley MW, La Du JK, Hendrix DA, Tanguay RL.

Mol Pharmacol. 2017 Jun;91(6):609-619. doi: 10.1124/mol.117.108233. Epub 2017 Apr 6.

6.

Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging.

Kuintzle RC, Chow ES, Westby TN, Gvakharia BO, Giebultowicz JM, Hendrix DA.

Nat Commun. 2017 Feb 21;8:14529. doi: 10.1038/ncomms14529.

7.

Long noncoding RNAs and sulforaphane: a target for chemoprevention and suppression of prostate cancer.

Beaver LM, Kuintzle R, Buchanan A, Wiley MW, Glasser ST, Wong CP, Johnson GS, Chang JH, Löhr CV, Williams DE, Dashwood RH, Hendrix DA, Ho E.

J Nutr Biochem. 2017 Apr;42:72-83. doi: 10.1016/j.jnutbio.2017.01.001. Epub 2017 Jan 12.

8.

A DEEP LEARNING APPROACH FOR CANCER DETECTION AND RELEVANT GENE IDENTIFICATION.

Danaee P, Ghaeini R, Hendrix DA.

Pac Symp Biocomput. 2017;22:219-229. doi: 10.1142/9789813207813_0022.

9.

MicroRNA and gene expression changes in unruptured human cerebral aneurysms.

Bekelis K, Kerley-Hamilton JS, Teegarden A, Tomlinson CR, Kuintzle R, Simmons N, Singer RJ, Roberts DW, Kellis M, Hendrix DA.

J Neurosurg. 2016 Dec;125(6):1390-1399. Epub 2016 Feb 26.

10.

PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells.

Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, Choe J, Jun DL, Shen X, Gregory RI, Daley GQ, Meissner A, Kellis M, Hochedlinger K, Kim J, Orkin SH.

Cell Rep. 2015 Sep 1;12(9):1456-70. doi: 10.1016/j.celrep.2015.07.053. Epub 2015 Aug 20.

11.

The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse.

Grote P, Wittler L, Hendrix D, Koch F, Währisch S, Beisaw A, Macura K, Bläss G, Kellis M, Werber M, Herrmann BG.

Dev Cell. 2013 Jan 28;24(2):206-14. doi: 10.1016/j.devcel.2012.12.012.

12.

Computational analysis of noncoding RNAs.

Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M.

Wiley Interdiscip Rev RNA. 2012 Nov-Dec;3(6):759-78. doi: 10.1002/wrna.1134. Epub 2012 Sep 18. Review.

13.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

14.

Neural-specific elongation of 3' UTRs during Drosophila development.

Hilgers V, Perry MW, Hendrix D, Stark A, Levine M, Haley B.

Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15864-9. doi: 10.1073/pnas.1112672108. Epub 2011 Sep 6.

15.

The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo.

Chopra VS, Hendrix DA, Core LJ, Tsui C, Lis JT, Levine M.

Mol Cell. 2011 Jun 24;42(6):837-44. doi: 10.1016/j.molcel.2011.05.009.

16.

The genome of the Western clawed frog Xenopus tropicalis.

Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS.

Science. 2010 Apr 30;328(5978):633-6. doi: 10.1126/science.1183670.

17.

miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data.

Hendrix D, Levine M, Shi W.

Genome Biol. 2010;11(4):R39. doi: 10.1186/gb-2010-11-4-r39. Epub 2010 Apr 6.

18.

A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate.

Shi W, Hendrix D, Levine M, Haley B.

Nat Struct Mol Biol. 2009 Feb;16(2):183-9. doi: 10.1038/nsmb.1536. Epub 2009 Jan 18.

19.

How the Dorsal gradient works: insights from postgenome technologies.

Hong JW, Hendrix DA, Papatsenko D, Levine MS.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20072-6. doi: 10.1073/pnas.0806476105. Epub 2008 Dec 22. Review.

20.

Shadow enhancers as a source of evolutionary novelty.

Hong JW, Hendrix DA, Levine MS.

Science. 2008 Sep 5;321(5894):1314. doi: 10.1126/science.1160631. No abstract available.

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