Kelly Williams

Principal Member of the Technical Staff

Portrait of Kelly Williams

genomes evolve. A particular focus is on the mobile DNAs that can fine-tune pathogenicity mechanisms. One of his software tools examines the numerous DNA mobility events that can occur in different subpopulations of a single overnight culture. Other software precisely maps mobile genomic islands and transposons; he has applied this to all available genomes. Since many genomic islands are prophages, the resulting database serves as a bioinformatic front end that he employs in his phage therapy program. He isolates phages for treatment of antibiotic-resistant bacterial infections.


Bachelor’s Degree: Physiology and Cell Biology; Environmental Biology, University of California-Santa Barbara (1983)

Doctoral Degree: Biology, University of California-San Diego (1991)

Postdoctoral Fellowships:

  • Whitehead Institute for Biomedical Research (1995-1998)
  • CNR Institute of Cell Biology – Rome, Italy (1992-1995)
  • Salk Institute (1991-1992)

Relevant Prior Positions

Assistant Professor, Biology Department, Indiana University (1998-2005)

Research Investigator, Virginia Bioinformatics Institute, Virginia Tech (2005-2010)


American Cancer Society Postdoctoral Fellow (1991-1993)

Selected Book Chapters

Williams KP, Bartel DP. 1996. In vitro selection of catalytic RNA. In Nucleic Acids and Molecular Biology, vol. 10, Lilley DM, Eckstein F, eds. (Berlin: Springer-Verlag), pp.367-381.

Williams KP, Herendeen DR, Kassavetis GA, Geiduschek EP. 1994. Regulation of late gene expression. In Molecular Biology of Bacteriophage T4, Karam JD, ed. (Washington, D.C.: American Society for Microbiology), pp. 161-175.

Selected Publications

  • Schoeniger JS, Hudson CM, Bent ZW, Sinha A, Williams KP. 2016. Experimental single-strain mobilomics reveals events that shape pathogen emergence. Nucleic Acids Res 44:6830-6839.
  • Hudson CM, Lau BY, Williams KP. 2015. Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes. Nucleic Acids Res 43: D48-D53. Hudson CM, Lau BY, Williams KP. 2014. Ends of the line for tmRNA-SmpB. Front Microbiol 5:421. [25165464]
  • Hudson CM, Bent ZW, Meagher RJ, Williams KP. 2014. Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain. PLoS One 9: e99209.
  • Williams KP, Kelly DP. 2013. Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. Int J Syst Evol Microbiol 63: 2901-2906.
  • Mane SP, Dominguez-Bello MG, Blaser MJ, Sobral BW, Hontecillas R, Skoneczka J, Mohapatra SK, Crasta OR, Evans C, Modise T, Shallom S, Shukla M, Varon C, Mégraud F, Maldonado-Contreras AL, Williams KP, Bassaganya-Riera J. 2010. Host-interactive genes in amerindian Helicobacter pylori diverge from their old world homologs and mediate inflammatory responses. J Bacteriol 192:3078-3092.
  • Williams KP, Gillespie JJ, Nordberg EK, Snyder EE, Shallom JM, Sobral BWS, Dickerman AW. 2010. Phylogeny of Gammaproteobacteria. J Bacteriol 192:2305-2314.
  • Williams KP. 2008. Strong mimicry of an rRNA binding site for two proteins by the mRNA encoding both proteins. RNA Biol 5:145-148.
  • Williams KP, Sobral BS, Dickerman AW. 2007. A robust species tree for the alphaproteobacteria. J Bacteriol 189:4578-4586.
  • Jacob Y, Sharkady SM, Bhardwaj K, Sanda A, Williams KP. 2005. Function of the SmpB tail in tmRNA translation revealed by a nucleus-encoded form. J Biol Chem 280:5503-5509.
  • Trimble MJ, Minnicus A, Williams KP. 2004. tRNA slippage at the tmRNA resume codon. RNA 10:805-812.
  • Williams KP. 2004. Evolutionary resealing of a split RNA: reversal of gene permutation. RNA 10:555-557.
  • Williams KP. 2003. Traffic at the tmRNA gene. J Bacteriol 185:1059-1070.
  • Williams KP. 2002. Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res 30:866-875.
  • Scarabino D, Crisari A, Lorenzini S, Williams KP, Tocchini-Valentini GP. 1999. tRNA prefers to kiss. EMBO J 18:4571-4578.
  • Williams KP, Martindale KA, Bartel DP. 1999. Resuming translation on tmRNA: a unique mode of determining a reading frame. EMBO J 18:5423-5433.
  • Williams KP, Liu XH, Schumacher TNM, Lin HY, Ausiello DA, Kim PS, Bartel DP. 1997. Bioactive and nuclease-resistant mirror-image L-DNA ligand of vasopressin. Proc Natl Acad Sci USA 94:11285-11290.
  • Williams KP, Ciafré S, Tocchini-Valentini GP. 1995. Selection of novel Mg2+-dependent self-cleaving ribozymes. EMBO J 14:4551-4557.
  • Williams KP, Imahori H, Fujimoto DN, Inoue T. 1994. Selection of novel forms of a functional domain within the Tetrahymena ribozyme. Nucleic Acids Res 22: 2003-2009.
  • Williams KP. 1993. Simplifications of a self-replication model. Science 261:925.
  • Tinker RL, Williams KP, Kassavetis GA, Geiduschek EP. 1994. Transcriptional activation by a DNA-tracking protein: structural consequences of enhancement at the T4 late promoter. Cell 77:225-237.
  • Herendeen DR, Williams KP, Kassavetis GA, Geiduschek EP. 1990. An RNA polymerase-binding protein that is required for communication between an enhancer and a promoter. Science 248:573-578.