Lisa Stubbs

Institute for Genomic Biology
1206 W. Gregory Drive
Urbana IL 61801
Office: 217-244-4000

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Institute for Genomic Biology
1206 W. Gregory Drive
Urbana IL 61801
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Lisa Stubbs

Professor, Cell and Developmental Biology
Ph.D., University of California, San Diego (Biology)

Evolution of genome structure and regulatory networks; Mouse models for human neurodevelopmental disease

My group combines genetics with high-throughput genomics and comparative bioinformatics approaches to understand the function and evolution of cis- and trans-acting components of mammalian regulatory machinery. We are interested in aspects of regulatory biology that are deeply conserved between species, since these define the basic functions upon which lineage-specific mechanisms have been built. We are also interested in those components that have changed over evolutionary time and in using genetic approaches to tie these mechanisms to species-specific biology. Working against a background of deep conservation, these changing regulatory components hold potential to explain biological differences between species, but also between individuals in the same populations. Differences in the structure and function of regulatory elements, some of which are located at great distances from the affected genes, can play significant roles in crafting interpersonal differences including susceptibilities to disease. Locating these elements, analyzing their evolutionary histories, and tying their activities to specific genes are major thrusts of our work.

Collaborative Projects

My group is involved in a large collaborative project funded by the Simons Foundation, "Molecular Roots of the Social Brain", with the laboratories of Drs. Gene Robinson, Alison Bell, Saurabh Sinha, Dave Zhao, Jian Ma and Yoshi Oono.

Research Areas

Representative Publications

Rittschof, CC, Bukhari SA, Caetano-Anolles D, Cash-Ahmed A, Kent M, Lu X, Sanogo O, Sloofman L, Troy JM, Weinser PA, Zhang H, Bell AM, Sinha S, Robinson GE, Stubbs L. Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish and honey bee. Proc Acad Sci USA 111:17929-17934, 2014.

Bolt CC, Elso CM, Lu X, Pan F, Kispert A, and Stubbs L. A distant downstream enhancer directs essential expression of Tbx18 in urogenital tissues. Devel Biol 392: 483-493, 2014.

Liu H, Chang L-H, Sun Y, Lu X and Stubbs, L. Deep vertebrate roots for mammalian zinc-finger transcription factor subfamilies. Genome Biol Evol 6:510-525, 2014.

Elso C, Lu X, Thompson HL, Weisner PA, Skinner A, Carver EA, and Stubbs L. A reciprocal translocation dissects functions of Pax6 alternative promoters and regulatory elements in development of pancreas, brain and eye. Genesis 51:630-646, 2013.

Nowick, K. Fields, C., Gernat, T., Caetano-Anolles, D., Kholina, N., and Stubbs, L. Gain, loss and divergence in primate zinc-finger genes: a rich resource for the evolution of regulatory differences between species. PLoS One 6:e21553, 2011

Nowick K., Hamilton A.T., Zhang H., and Stubbs L. Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes. Mol Biol Evol 27:2606-2617, 2010.

Nowick K., Gernat T., Almaas E., and Stubbs L. Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proc Natl Acad Sci USA 106:22358-22363, 2009.

Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, and Stubbs L. 2006. A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Research 16:669-677.

Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W and Stubbs L. Evolution and functional classification of vertebrate gene deserts. Genome Res, 15, 137-145, 2005.

Dehal, P., Predki, P., Olsen, A.S., Kobayashi, A., Folta, P., Lucas, S., Land, M., Terry, A., Zhou, C.L.E, Rash, S., Zhang, Q., Gordon, L., Kim, J., Elkin, C., Pollard, M., Richardson, P., Rokhsar, D., Uberbacher, E., Hawkins, T., Branscomb, E., Stubbs, L. Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. Science 293: 104-111, 2001.

Complete Publications List (PubMed)