| link |
2019 |
Bell J, Larson M, Kutzler M, Bionaz M, Löhr CV, Hendrix D. miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs. PLoS computational biology. 2019 Oct;15(10). |
| link |
2019 |
Jespersen N, Estelle A, Waugh N, Davey NE, Blikstad C, Ammon YC, Akhmanova A, Ivarsson Y, Hendrix DA, Barbar E. Systematic identification of recognition motifs for the hub protein LC8. Life science alliance. 2019 Aug 1;2(4):e201900366. |
| link |
2019 |
Huang L, Zhang H, Deng D, Zhao K, Liu K, Hendrix DA, Mathews DH. LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search. Bioinformatics. 2019 Jul 5;35(14):i295-304. |
| link |
2019 |
Zhang Z, Garzotto M, Davis EW, Mori M, Stoller WA, Farris PE, Wong CP, Beaver LM, Thomas GV, Williams DE, Dashwood RH. Sulforaphane Bioavailability and Chemopreventive Activity in Men Presenting for Biopsy of the Prostate Gland: A Randomized Controlled Trial. Nutrition and cancer. 2019 May 30:1-4. |
| link |
2018 |
Danaee, P., Rouches, M., Wiley, M., Deng, D., Huang, L., & Hendrix, D. (2018). bpRNA: large-scale automated annotation and analysis of RNA secondary structure. Nucleic acids research, 46(11), 5381-5394. |
| link |
2018 |
Hill, S. T., Kuintzle, R. C., Teegarden, A., Merrill, E., Danaee, P., & Hendrix, D. A. (2017). A Deep Recurrent Neural Network Discovers Complex Biological Rules to Decipher RNA Protein-Coding Potential. Nucleic acids research, |
| link |
2017 |
Sall, K., Hendrix, D., Sekine, T., Katsuragawa, Y., Koyari, R., & Nonogaki, H. (2017). Transcriptomics of nine-cis-epoxycarotenoid dioxygenase 6 induction in imbibed seeds reveals feedback mechanisms and long non-coding RNAs. Seed Science Research, 27(4), 251-261. |
| link |
2017 |
Henning, J. A., Gent, D. H., Townsend, M. S., Woods, J. L., Hill, S. T., & Hendrix, D. (2017). QTL analysis of resistance to powdery mildew in hop (Humulus lupulus l.). Euphytica, 213(4), 98. |
| link |
2017 |
LM Beaver, R Kuintzle, A Buchanan, MW Wiley, ST Glasser, CP Wong, GS Johnson, JH Chang, CV Löhr, DE Williams, RH Dashwood, DA Hendrix, E Ho Long non-coding RNAs and sulforaphane: a target for chemoprevention and suppression of prostate cancer., Journal of Nutr. Biochem 42() 72-83. |
| link |
2017 |
GR Garcia, BC Goodale, MW Wiley, JK La Du, DA Hendrix, RL Tanguay In vivo characterization of an AHR-dependent long non-coding RNA required for proper Sox9b expression. Mol Pharm mol. 117.108233 |
| link |
2017 |
RC Kuintzle, ES Chow, TN Westby, BO Gvakharia, JM Giebultowicz, DA Hendrix Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging. Nature Communications 8: 14529 |
| link |
2017 |
JA Henning, DH Gent, MS Townsend, JL Woods, ST Hill, D Hendrix QTL analysis of resistance to powdery mildew in hop (Humulus lupulus L.). Euphytica 213(4) 98. |
| link |
2017 |
J Henning, S Hill, P Darby, D Hendrix QTL examination of a bi-parental mapping population segregating for “short-stature” in hop (Humulus lupulus L.). Euphytica 213(3) 77 |
| link |
2016 |
P Danaee, R Ghaeini, DA Hendrix A Deep Learning Approach for Cancer Detection and Relevant Gene Identification. (2016) Pac Symp Biocomput. 22: 219-229. |
| link |
2016 |
ST Hill, J Coggins, A Liston, D Hendrix, JA Henning Genomics of the hop pseudo-autosomal regions. (2016) Euphytica. 209(1) 171-179. |
| link |
2016 |
K Bekelis, JS Kerley-Hamilton, A Teegarden, CR Tomlinson, R Kuintzle, N Simmons, RJ Singer, DW Roberts, M Kellis, and DA Hendrix MicroRNA and gene expression changes in unruptured human cerebral aneurysms. (2016) Journal of Neurosurgery. 125(6) 1390-1399. |
| link |
2015 |
Partha Pratim Das*, David A. Hendrix*, Effie Apostolou, Alice H. Buchner, Matthew C. Canver, Semir Beyaz, Damir Ljuboja, Rachael Kuintzle, Woojin Kim, Rahul Karnik, Zhen Shao, Huafeng Xie, Jian Xu, Alejandro De Los Angeles, Yingying Zhang, Junho Choe, Don Leong Jia Jun, Xiaohua Shen, Richard I. Gregory, George Q. Daley, Alexander Meissner, Manolis Kellis, Konrad Hochedlinger, Jonghwan Kim, Stuart H. Orkin PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. (2015) Cell Reports. 12(9) 1456-1470. |
| link |
2013 |
Phillip Grote, Lars Wittler*, David Hendrix*, Frederic Koch*, Sandra Währisch, Arica Beisaw, Karol Macura, Gaby Bläss, Manolis Kellis, Martin Werber, Bernhard G Herrmann The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse. (2013) Developmental Cell 24(2) 206-214. |
| link |
2012 |
Stefan Washietl, Sebastian Will, David A Hendrix, Loyal A Goff, John L Rinn, Bonnie Berger, Manolis Kellis Computational analysis of noncoding RNAs. (2012) Wiley Interdisciplinary Reviews: RNA 3(6) 759-778 |
| link |
2012 |
ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. (2012) Nature 489, 57–74
|
| link |
2011 |
Valerie Hilgers, Michael W Perry, David Hendrix, Alexander Stark, Michael Levine, Benjamin Haley Neural-specific elongation of 3' UTRs during Drosophila development. (2011) Proc Nat Acad Sci 108(38):15864-15869 |
| link |
2011 |
VS Chopra*, DA Hendrix*, LJ Core, C Tsui, JT Lis, M Levine The Polycomb Group Mutant esc Leads to Augmented Levels of Paused Pol II in the Drosophila Embryo.. (2011) Mol Cell |
| link |
2010 |
D Hendrix, M Levine, W Shi miRTRAP, a computatational method for the systematic identification of miRNAs from high throughput sequencing data. (2010) Genome Biology 11:R39 |
| link |
2010 |
Uffe Hellsten, Richard M. Harland, Michael J. Gilchrist, David Hendrix, Jerzy Jurka, Vladimir Kapitonov, Ivan Ovcharenko, Nicholas H. Putnam, Shengqiang Shu, Leila Taher, Ira L. Blitz, Bruce Blumberg, Darwin S. Dichmann, Inna Dubchak, Enrique Amaya, John C. Detter, Russell Fletcher, Daniela S. Gerhard, David Goodstein, Tina Graves, Igor V. Grigoriev, Jane Grimwood, Takeshi Kawashima, Erika Lindquist, Susan M. Lucas, Paul E. Mead, Therese Mitros, Hajime Ogino, Yuko Ohta, Alexander V. Poliakov, Nicolas Pollet, Jacques Robert, Asaf Salamov, Amy K. Sater, Jeremy Schmutz, Astrid Terry, Peter D. Vize, Wesley C. Warren, Dan Wells, Andrea Wills, Richard K. Wilson, Lyle B. Zimmerman, Aaron M. Zorn, Robert Grainger, Timothy Grammer, Mustafa K. Khokha, Paul M. Richardson, Daniel S. Rokhsar The Genome of the Western Clawed Frog Xenopus tropicalis. (2010) Science 328: 633-636, April 30
|
| link |
2009 |
W Shi*, D Hendrix*, M Levine, B Haley A distinct class of small RNAs arises from pre-miRNA proximal regions in a simple chordate. (2009) Nat Struct Mol Biol 6(2):183-9 |
| link |
2008 |
B Haley, D Hendrix, V Trang, M Levine A simplified miRNA-based gene silencing method for Drosophila melanogaster. (2008) Dev Biol 321(2):482-90 |
| link |
2008 |
D Hendrix*, JW Hong*, J Zeitlinger, DS Rokhsar, MS Levine Promoter elements associated with RNA Pol II stalling in the early Drosophila embryo. (2008) Proc Nat Acad Sci 105(22): 7762-7767 |
| link |
2008 |
JW Hong, D Hendrix, M Levine Shadow Enhancers as a source for evolutionary novelty. (2008) Science 321(5894): 1314 |
| link |
2008 |
JW Hong, D Hendrix, D Papatsenko, M Levine How the dorsal gradient works: insights from postgenome technologies. (2008) Proc Natl Acad Sci USA 23;105(51):20072-6 |
| link |
2005 |
S Mahony, D Hendrix, TJ Smith, A Golden Self-Organizing Maps of Position Weight Matrices for Motif Discovery in Biological Sequences. (2005) AI Review 24:397-413 |
| link |
2005 |
S Mahony, D Hendrix, A Golden, TJ Smith, DS Rokhsar. Transcription factor binding site identification using the Self-Organizing Map. (2005) Bioinformatics 21(9):1807-14 |
| link |
2001 |
D Hendrix, C Jarzynski. A 'fast growth' method of computing free energy differences. (2001) The Journal of Chemical Physics 114, 5974 |