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B.S. Applied Mathematics, B.S Physics, Georgia Institute of Technology • Ph.D. Physics, University of California, Berkeley • Postdoc, University of California, Berkeley • Postdoc, Massachusetts Institute of Technology CSAIL
The primary focus of our lab is to understand the structure, function and mechanisms of action of non-coding RNAs, both large and small. The past decade has seen the discovery of numerous non-coding RNAs whose function is largely unknown. We will employ structure prediction, genome-wide sequence analysis and deep sequencing data to uncover the roles of these molecules in gene regulation.
In addition, our lab develops algorithms and computational approaches to understand many different areas of computational biology. Our lab develops and utilizes motif finding algorithms to understand how promoters and regulatory elements operate. We develop computational approaches, incorporating structural predictions and deep sequencing data, to discover new regulatory RNAs and their functions. We develop new methods of analysis for deep sequencing data to help understand the principles of transcription, which will include transcription initiation, transcriptional gene silencing, post-transcriptional gene silencing and Polymerase stalling/pausing.
P. Grote, L. Wittler, D. Hendrix, F. Koch, S. Währisch, A. Beisaw, K. Macura, G. Bläss, M. Kellis, M. Werber, B.G. Herrmann "The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse.", Dev Cell, 24 (2013), pp. 206–214
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
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,42(6):837-844, June 24
Uffe Hellsten, Richard M. Harland, Michael J. Gilchrist, David Hendrix et al. "The Genome of the Western Clawed Frog Xenopus tropicalis." (2010) Science, 328: 633-636, April 30.
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. Published April 6, 2010.
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. Epub 2009 Jan 18.
JW Hong, D Hendrix, M Levine: "Shadow Enhancers as a source for evolutionary novelty." (2008) Science 321(5894): 1314.
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.