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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
136082012
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
10272013
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
8882010
Shadow enhancers as a source of evolutionary novelty
JW Hong, DA Hendrix, MS Levine
Science 321 (5894), 1314-1314, 2008
5612008
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
3632017
A “fast growth” method of computing free energy differences
DA Hendrix, C Jarzynski
The Journal of Chemical Physics 114 (14), 5974-5981, 2001
2222001
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
1972008
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
1682009
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
1632011
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
1462008
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
1292018
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
1242010
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
1202019
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), 14529, 2017
972017
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
962008
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
922017
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
872005
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
862018
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
712015
The lncRNA locus handsdown regulates cardiac gene programs and is essential for early mouse development
N Ritter, T Ali, N Kopitchinski, P Schuster, A Beisaw, DA Hendrix, ...
Developmental cell 50 (5), 644-657. e8, 2019
702019
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