David Haak

One of the goals of research in my lab is to understand how interactions at the genomic level impact organismal responses with an aim to improve productivity and sustainability of agricultural plants in the eastern United States.  We have several projects in this area including investigations of plant-microbe genomic interactions that enhance plant resistance to pathogens, epigenomic mechanisms that lead to the rapid evolution of stress tolerance, genomic responses to drought and herbivore stress, genomic regulation of plant-viral interactions, and finally, host-microbe-parasite genomic interactions in the honey bee gut that impact host health.  The development of genomic and bioinformatic resources is central to each of these projects.  Members of the lab have produced products such as new or improved reference genomes, bioinformatic tools that employ traditional and machine learning algorithms, and novel workflows for coupling existing genomic resources with advanced sequencing technologies.

• CSES 5844: Plant Genomics
• ALS 5224: Introduction to Genomic Data Science
• PPWS 5714: Molecular Biology for Applied Plant Science
• GRAD 6894: Introduction to Microbial Community Analysis

Associate Professor | 2022-Present
School of Plant and Environmental Sciences
Virginia Tech, Blacksburg, Va.

Assistant Professor | 2014-2022
School of Plant and Environmental Sciences
Virginia Tech, Blacksburg, Va.

Postdoctoral Fellow | 2010-2014
Department of Biology
Indiana University, Bloomington, In.

• National Science Foundation Graduate Research Program Fellow, 2007-2010
• Howard Hughes Medical Institute Research Fellowship, 2005
• North Carolina Governors' Outstanding Volunteer Award, 2003

1. Cui, C., Herlihy, J., Bombarely, A., McDowell, J.M. and Haak, D.C., 2019. Draft assembly of Phytophthora capsici from long-read sequencing uncovers complexity. Molecular Plant-Microbe Interactions, ppMPMI-04.
2. Hasing, T., Rinaldi, E.*, Manrique, S., Colombo, L., Haak, D.C., Zaitlin, D., and Bombarely, A., 2019.  Extensive phenotypic diversity in the cultivated Florist’s Gloxinia, Sinningia speciosa, (Lodd.) Hiern, is derived from the domestication of a single founder population. Plants People Planet, August 19.
3. Beam, S.C., Mirsky, S., Cahoon, C., Haak, D.C., and Flessner, M., 2019. Harvest weed seed control of Italian ryegrass [Lolium perenne L. ssp. multiflorum (Lam.) Husnot], common ragweed (Ambrosia artemisiifolia L.), and Palmer amaranth (Amaranthus palmeri S. Watson). Weed Technology, pp.1-6.
4. Barney, J.N., Schenk, T.E., Haak, D.C., Salom, S., Brown, B.L., Hotchkiss, E., (accepted 2018). Building Partnerships and Bridging Science and Policy to Address the Biological Invasions Crisis.  Invasive Plant Science and Management.
5. Tran, H., Zhu, H., Wu, X., Kim, G., Clarke, C.R., Larose, H., Haak, D.C., Askew, S.D., Barney, J.N., Westwood, J.H. and Zhang, L., (2018). Identification of Differentially Methylated Sites with Weak Methylation Effects. Genes, 9(2), p.75.
6. Soorni, A., Fatahi, R., Haak, D.C., Salami, S.A. and Bombarely, A., (2017). Assessment of Genetic Diversity and Population Structure in Iranian Cannabis Germplasm. Scientific reports, 7(1), p.15668.
7. Haak, D. C., Fukao, T., Grene, R., Hua, Z., Ivanov, R., Perrella, G., & Li, S. (2017). Multilevel regulation of abiotic stress responses in plants. Frontiers in Plant Science, 8, 1564.
8. Kim, G., Clarke, C., Larose, H., Tran, H., Haak, D.C., Zhang, L., Askew, S., Barney, J., Westwood, J. (2017). Herbicide injury induces dose-dependent DNA methylome reprogramming in Arabidopsis.  PeerJ, 5, e3560.
9. Soorni, A., Haak, D., Zaitlin, D., & Bombarely, A. (2017). Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data. BMC Genomics, 18(1), 49.
10. Peterson, B. A., Haak, D. C., Nishimura, M. T., Teixeira, P. J., James, S. R., Dangl, J. L., & Nimchuk, Z. L. (2016). Genome-Wide Assessment of Efficiency and Specificity in CRISPR/Cas9 Mediated Multiple Site Targeting in Arabidopsis. PLoS One, 11(9), e0162169.
11. Fricke, E. C., Haak, D. C., Levey, D. J., & Tewksbury, J. J. (2016). Gut passage and secondary metabolites alter the source of post-dispersal predation for bird-dispersed chili seeds. Oecologia, 181(3), 905–910.
12. Pease, J. B., Haak, D. C., Hahn, M. W., & Moyle, L. C. (2016). Phylogenomics reveals three sources of adaptive variation during a rapid radiation. PLoS Biology, 14(2), e1002379.
13. Haak, D.C., Ballenger, B.A. ^#, Moyle, L.C. (2014).  No evidence for phylogenetic constraint on natural defense evolution among wild tomatoes. Ecology, 95(6), 1633-1641.
14. HilleRisLambers, J., Ettinger, A. K., Ford, K. R., Haak, D. C., Horwith, M., Miner, B. E., et al. (2013). Accidental experiments: ecological and evolutionary insights and opportunities derived from global change. Oikos, 122(12), 1649–1661.
15. Haak, D.C., McGinnis, L.A., Levey, D.J., and Tewksbury, J.J. (2012). Why aren’t all chilies hot? A tradeoff limits pungency. Proceedings of the Royal Society B: Biological Sciences 279.1735.
16. Haak, D. C., J. HilleRisLambers, E. Pitre, and S. Freeman. (2011). Increased Structure and Active Learning Reduce the Achievement Gap in Introductory Biology. Science 332:1213.
17. Freeman, S., Haak, D., & Wenderoth, M. P. (2011). Increased course structure improves performance in introductory biology. Cell Biology Education, 10(2), 175–186.
18. Deutsch, C., Tewksbury, J., Huey, R., Sheldon, K., Ghalambor, C., Haak, D., & Martin, P. (2008). Impacts of climate warming on terrestrial ectotherms across latitude. Proceedings of the National Academy of Sciences, 105(18), 6668.
19. Tewksbury, J., Reagan, K., Machnicki, N., Carlo, T., Haak, D., Peñaloza, A., & Levey, D. (2008). Evolutionary ecology of pungency in wild chilies. Proceedings of the National Academy of Sciences, 105(33), 11808.
20. Tewksbury, J.J., Levey, D.J., Huizinga, M., Haak, D.C., and Travaset, A. (2008). Costs and benefits of capsaicin-mediated control of gut retention in dispersers of wild chilies.   Ecology 89(1):107-17.
21. Freeman, S., O'Connor, E., Parks, J., Cunningham, M., Hurley, D., Haak, D., et al. (2007). Prescribed active learning increases performance in introductory biology. CBE—Life Sciences Education, 6(2), 132.
22. Tewksbury, J.J., Manchego, C., Haak D.C., Levey, D.J.  (2006).  Where did the chili get its spice?  Biogeography of capsaicinoid production in ancestral wild chili species.  Journal of Chemical Ecology 32(3):547-564.