Study systems include
- Bacterial Genomics
- Paleogenomics and Metagenomics
- Population Genomics
Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010 Feb 18;463(7283):943-7.
Qi J, Zhao F, Buboltz A, Schuster SC. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics. 2010 Jan 1;26(1):127-9. Epub 2009 Oct 30.2010.
Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander ES, Knight JR, Irzyk GP, Fredrikson KM, Harkins TT, Sheridan S, Pringle T, Schuster SC. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 2008 Nov 20;456(7220):387-90.
Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007 Mar;17(3):377-86. Epub 2007 Jan 25.
Eppinger M, Baar C, Linz B, Raddatz G, Lanz C, Keller H, Morelli G, Gressmann H, Achtman M, Schuster SC. Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet. 2006 Jul;2(7):e120. Epub 2006 Jun 15.
My group uses genomics to examine topics in the fields of evolutionary microbiology, gene regulation, population ecology and conservation biology. Our group has two main areas of CIDD-related research:
Evolutionary and comparative bacterial genomics
We generate and analyze bacterial genomes to determine the molecular mechanisms that have driven the speciation process from free-living last common ancestors to the obligatory pathogenic species that we see today.
Population genetics and conservation biology
We examine how the level of genetic diversity in a host population relates to the extinction or endangerment of species, which are often threatened by disease, and use this data to aid species conservation efforts.