Google Scholar

Link Year Citation
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