Bioinformatics

Kelly Williams, Ph.D.

  • Photo of Kelly Williams
  • Kelly Williams

    Principal Member of the Technical Staff

    Systems Biology Department

    (925) 294-4730

    kpwilli@sandia.gov

Research Summary

The chromosomally-ordered pan-genome.

The chromosomally-ordered pan-genome.

Understanding how microbes evolve is crucial for the fields of human health, biofuels, and biosecurity. Genomic/pathogenicity islands (see our website Islander) are key units of bacterial evolution that are mobile, and thus able to move clusters of genes between species. Genes transferred on islands can have major effects on the phenotype of the host bacterium. For example, islands can convert non-pathogens into pathogens, or modulate pathogenicity through combinatorial effects of multiple islands. Upon entering a new host bacterium islands integrate into the host chromosome, tending to favor a limited number of chromosomal sites within tRNA and related genes (see The tmRNA Website). Major goals are to understand mechanisms of island mobility/integration, and the range of island effects on bacterial physiology. Research avenues pursued include comparative genomics, high-throughput sequencing, and phylogenetics.


Appointments

2010 – present Principal Member of Technical Staff, Sandia National Laboratories, Livermore, CA
2005 – 2010 Research Investigator, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA
1998 – 2005 Assistant Professor of Biology, Indiana University, Bloomington, IN
1995 – 1998 Postdoctoral Fellow, Whitehead Institute for Biomedical Research (RNA biology, with David Bartel), Cambridge, MA
1992 – 1995 American Cancer Society Postdoctoral Fellow, National Research Council (RNA evolution, with Glauco Tocchini-Valentini), Rome, Italy
1991 – 1992 American Cancer Society Postdoctoral Fellow, Salk Institute (catalytic RNA, with Tan Inoue), La Jolla, CA

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Education

1991 PhD, Biology, University of California, San Diego, CA (biochemistry and molecular genetics of bacterial/bacteriophage transcription, with E. Peter Geiduschek)
1983 BA, Environmental Biology, Physiology and Cell Biology, University of California, Santa Barbara, CA (Tetrahymena genetics, with Eduardo Orias)
1980 AA, Biology, Pierce College, Woodland Hills, CA (California flora, with Barbara Hopper)

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Publications (see also MyBibliography at NCBI)

2015 – present
  • 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.
  • D'haeseleer P, Johnson SL, Davenport KW, Chain PSG, Schoeniger JS, Ray D, Sinha A, Williams KP, Peña J, Branda SS, El-Etr S. (2016). Genome sequence of the historical clinical isolate Burkholderia pseudomallei PHLS 6. Genome Announc 4: e00649-16.
  • Carney LT, Wilkenfield JS, Lane PD, Solberg OD, Fuqua ZB, Cornelius NG, Gillespie S, Williams KP, Samocha TM, Lane TW. (2016). Pond crash forensics: presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina. Algal Res 17:341-347.
  • Hudson CM, Kirton E, Hutchinson MI, Redfern JL, Simmons B, Ackerman E, Singh S, Williams KP, Natvig DO, Powell AJ. (2015). Lignin-modifying processes in the rhizosphere of aridland grasses. Environ Microbiol 17:4965-4978.
  • Perez-Arriaga MO, Wilson S, Williams KP, Schoeniger J, Waymire RL, Powell AJ. (2015). Omics metadata management software (OMMS). Bioinformation 11:165-172.
  • Hudson CM, B Lau, KP Williams. (2015). Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes. Nucleic Acids Research 43: D48-53.
  • Hudson CM, KP Williams. (2015). The tmRNA Website. Nucleic Acids Research 43: D138-140.
  • Petrov AI, et al. (39 authors). (2015). RNAcentral: An international database of ncRNA sequences. Nucleic Acids Research 43: D123-129.

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2012 – 2014

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2010 – 2011

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2008 – 2009

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2004 – 2007

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2000 – 2003

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1996 – 1999
  • Scarabino, D, A Crisari, S Lorenzini, KP Williams, GP Tocchini-Valentini. (1999). tRNA prefers to kiss. EMBO Journal 18:4571.
  • Gueneau, P, S Loiseaux-De Goer, KP Williams. (1999). The GC rich region and TpsiC tRNA arm found in the petF region of the Thalassiosira weissflogii plastid genome encodes a tmRNA. European Journal of Phycology 34:533.
  • Williams, KP, KA Martindale, DP Bartel. (1999). Resuming translation on tmRNA: a unique mode of determining a reading frame. EMBO Journal 18:5423.
  • Williams, KP. (1999). The tmRNA website. Nucleic Acids Research 27:165.
  • Williams, KP, DP Bartel. (1998). The tmRNA website. Nucleic Acids Research 26:163.
  • Williams, KP, XH Liu, TNM Schumacher, HY Lin, DA Ausiello, PS Kim, DP Bartel. (1997). Bioactive and nuclease-resistant mirror-image L-DNA ligand of vasopressin. Proceedings of the National Academy of Sciences USA 94:11285.
  • Williams, KP, S Ciafre, GP Tocchini-Valentini. (1996). I ribozimi artificiali: esempio di selezione di nuovi ribozimi. In Gli Oligonucleotidi Sintetici. Cascino A, Nicolin A, eds. (Milano: UTET Periodici Scientifici), pp. 201-209.
  • Williams, KP, DP Bartel. (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, Bartel DP. (1996). Phylogenetic analysis of tmRNA secondary structure. RNA 2:1306.

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1993 – 1995

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1987 – 1992

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