David Hendrix

Assistant Professor
Computer Science

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 Interests: 

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.

Washietl, S., S. Will, D. Hendrix, L. A. Goff, J. L. Rinn, B. Berger, and M. Kellis, "Computational analysis of noncoding RNAs", Wiley Interdisciplinary Reviews: RNA, vol. 3, issue 6, pp. 759 - 778, 11/2012. Abstract
Shi, W., D. Hendrix, M. Levine, and B. Haley, "A distinct class of small RNAs arises from pre-miRNA–proximal regions in a simple chordate", Nature Structural & Molecular Biology, vol. 16, issue 2, pp. 183 - 189, 02/2009. Abstract
Hong, J. - W., D. Hendrix, D. Papatsenko, and M. S. Levine, "How the Dorsal gradient works: insights from postgenome technologies.", Proceedings of the National Academy of Sciences of the United States of America, vol. 105, issue 51, pp. 20072-6, 12/2008. Abstract
Hong, J. - W., D. Hendrix, and M. S. Levine, "Shadow Enhancers as a Source of Evolutionary Novelty", Science, vol. 321, issue 5894, pp. 1314 - 1314, 09/2008. Abstract
Haley, B., D. Hendrix, V. Trang, and M. Levine, "A simplified miRNA-based gene silencing method for Drosophila melanogaster", Developmental Biology, vol. 321, issue 2, pp. 482 - 490, 09/2008. Abstract
Hendrix, D., J. - W. Hong, J. Zeitlinger, D. S. Rokhsar, and M. S. Levine, "Promoter elements associated with RNA Pol II stalling in the Drosophila embryo", Proceedings of the National Academy of Sciences, vol. 105, issue 22, pp. 7762 - 7767, 05/2008. Abstract
Hendrix, D., and C. Jarzynski, "A “fast growth” method of computing free energy differences", The Journal of Chemical Physics, vol. 114, issue 14, pp. 5974, 04/2001. Abstract