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David Hendrix

Assistant Professor

ALS 2077A
541-737-6224

Education

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

Research

The Hendrix Lab employs a broad range of computational approaches, from machine learning to data mining, to investigate questions concerning genomics and gene regulatory systems. We seek to use computational biology and bioinformatics to uncover new mechanisms of gene regulation, as well as validate known biology. We develop motif-finding algorithms and pipelines to understand how promoters and regulatory elements operate, as well as creating new approaches for the analysis of deep-sequencing data to increase knowledge of the principles underlying transcription initiation, transcriptional gene silencing, post-transcriptional gene silencing and Polymerase stalling/pausing. 

One major objective of our lab includes furthering the understanding of the structure, function and mechanisms of action of noncoding RNAs, both large and small. The past decade has seen the discovery of numerous non-coding RNAs whose functions are largely unknown. We aim to discover new non-coding RNAs and gain insight into the roles of these molecules in gene regulation by developing novel computational approaches for the integration of structural predictions, genome-wide sequence analysis, and deep sequencing data.

Selected Publications

 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.