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David A Hendrix
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An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium
Nature 489 (7414), 57, 2012
119982012
The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse
P Grote, L Wittler, D Hendrix, F Koch, S Währisch, A Beisaw, K Macura, ...
Developmental cell 24 (2), 206-214, 2013
8952013
The genome of the Western clawed frog Xenopus tropicalis
U Hellsten, RM Harland, MJ Gilchrist, D Hendrix, J Jurka, V Kapitonov, ...
Science 328 (5978), 633-636, 2010
8042010
Shadow enhancers as a source of evolutionary novelty
JW Hong, DA Hendrix, MS Levine
Science 321 (5894), 1314-1314, 2008
4892008
A deep learning approach for cancer detection and relevant gene identification
P Danaee, R Ghaeini, DA Hendrix
Pacific symposium on biocomputing 2017, 219-229, 2017
2782017
A “fast growth” method of computing free energy differences
DA Hendrix, C Jarzynski
The Journal of Chemical Physics 114 (14), 5974-5981, 2001
2082001
Promoter elements associated with RNA Pol II stalling in the Drosophila embryo
DA Hendrix, JW Hong, J Zeitlinger, DS Rokhsar, MS Levine
Proceedings of the National Academy of Sciences 105 (22), 7762-7767, 2008
1832008
A distinct class of small RNAs arises from pre-miRNA–proximal regions in a simple chordate
W Shi, D Hendrix, M Levine, B Haley
Nature structural & molecular biology 16 (2), 183-189, 2009
1592009
Neural-specific elongation of 3′ UTRs during Drosophila development
V Hilgers, MW Perry, D Hendrix, A Stark, M Levine, B Haley
Proceedings of the National Academy of Sciences 108 (38), 15864-15869, 2011
1392011
How the Dorsal gradient works: insights from postgenome technologies
JW Hong, DA Hendrix, D Papatsenko, MS Levine
Proceedings of the National Academy of Sciences 105 (51), 20072-20076, 2008
1332008
miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data
D Hendrix, M Levine, W Shi
Genome biology 11 (4), 1-12, 2010
1212010
A simplified miRNA-based gene silencing method for Drosophila melanogaster
B Haley, D Hendrix, V Trang, M Levine
Developmental biology 321 (2), 482-490, 2008
932008
Transcription factor binding site identification using the self-organizing map
S Mahony, D Hendrix, A Golden, TJ Smith, DS Rokhsar
Bioinformatics 21 (9), 1807-1814, 2005
832005
Long noncoding RNAs and sulforaphane: a target for chemoprevention and suppression of prostate cancer
LM Beaver, R Kuintzle, A Buchanan, MW Wiley, ST Glasser, CP Wong, ...
The Journal of nutritional biochemistry 42, 72-83, 2017
792017
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
P Danaee, M Rouches, M Wiley, D Deng, L Huang, D Hendrix
Nucleic acids research 46 (11), 5381-5394, 2018
722018
Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging
RC Kuintzle, ES Chow, TN Westby, BO Gvakharia, JM Giebultowicz, ...
Nature Communications 8 (1), 1-10, 2017
722017
PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells
PP Das, DA Hendrix, E Apostolou, AH Buchner, MC Canver, S Beyaz, ...
Cell reports 12 (9), 1456-1470, 2015
682015
A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential
ST Hill, R Kuintzle, A Teegarden, E Merrill III, P Danaee, DA Hendrix
Nucleic acids research 46 (16), 8105-8113, 2018
652018
Computational analysis of noncoding RNAs
S Washietl, S Will, DA Hendrix, LA Goff, JL Rinn, B Berger, M Kellis
Wiley Interdisciplinary Reviews: RNA 3 (6), 759-778, 2012
632012
LinearFold: linear-time approximate RNA folding by 5'-to-3'dynamic programming and beam search
L Huang, H Zhang, D Deng, K Zhao, K Liu, DA Hendrix, DH Mathews
Bioinformatics 35 (14), i295-i304, 2019
562019
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Articles 1–20