Craig Lowe – Publications

Assistant Professor

Publications

Lowe*, N. Sanchez-Luege*, T. R. Howes, S. D. Brady, R. R. Richardson, F. C. Jones, M. A. Bell, D. M. Kingsley. Detecting Copy Number Variation Associated With Phenotypic Classes. Genome Res., 2016.  In revision.

Lowe, J. A. Clarke, A. J. Baker, D. Haussler, S. V. Edwards. Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol Biol Evol. 2015 Jan;32(1):23-8.

Lowe and D. Haussler. 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS ONE, 7(8):e43128, 2012. 29 mammals sequencing and analysis consortium.

(co-2nd author)A high-resolution map of human evolutionary constraint using 29 mammals. Nature, 478(7370):476–482, Oct 2011.

Anolis genome sequencing consortium.  (8th author) The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature, 477(7366):587–591, Sep 2011.

Lowe, M. Kellis, A. Siepel, B. J. Raney, M. Clamp, S. R. Salama, D. M. Kingsley, Lindblad-Toh, and D. Haussler. Three periods of regulatory innovation during vertebrate evolution. Science, 333:1019–1024, Aug 2011.

McLean, D. Bristor, M. Hiller, S. L. Clarke, B. T. Schaar, C. B. Lowe, A. M. Wenger, and G. Bejerano. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol., 28:495–501, May 2010.

Lowe, G. Bejerano, S. R. Salama, and D. Haussler. Endangered species hold clues to human evolution. Hered., 101:437–447, 2010.

Zhu, J. Z. Sanborn, M. Diekhans, C. B. Lowe, T. H. Pringle, and D. Haussler. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput. Biol., 3:e247, Dec 2007.

Wang, J. Zeng, C. B. Lowe, R. G. Sellers, S. R. Salama, M. Yang, S. M. Burgess, R. K. Brachmann, and D. Haussler.

Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc. Natl. Acad. Sci. U.S.A., 104:18613–18618, Nov 2007.

Lowe, G. Bejerano, and D. Haussler. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes.

Proc. Natl. Acad. Sci. U.S.A., 104:8005–8010, May 2007. Bejerano, C. B. Lowe, N. Ahituv, B. King, A. Siepel, S. R. Salama, E. M. Rubin, W. J. Kent, and D. Haussler.

A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature, 441:87–90, May 2006.