Kelly Williams, Ph.D.

Kelly Williams

Principal Member of the Technical Staff

Systems Biology Department

(925) 294-4730

Research Summary

Understanding how microbes evolve is crucial for the fields of human health, biofuels, and biosecurity. Genomic/pathogenicity islands 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. 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.

Image of pangenome — The chromosomally-ordered pan-genome.

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

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)

Publications

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.

2012 – 2014

Hudson CM, B Lau, KP Williams. (2014). Ends of the line for the tmRNA-SmpB partnership. Frontiers in Microbiology 5:421.
Hudson CM, KP Williams, DP Kelly. (2014). Assignment of the gammaproteobacterial genus Thermithiobacillus to the class Acidithiobacillia. Pol J Microbiol 63:245.
Hudson CM, ZW Bent, R Meagher, KP Williams. (2014). Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain. PLOS ONE 9:e99209.
Carney LT, SS Reinsch, PD Lane, OD Solberg, LS Jansen, KP Williams, JD Trent, TW Lane. (2014). Microbiome analysis of a microalgal mass culture growing in municipal wastewater in a prototype OMEGA photobioreactor. Algal Research 4:52.
Wattam AR, JT Foster, SP Mane, SM Beckstrom-Sternberg, JM Beckstrom-Sternberg, A Dickerman, P Keim, T Pearson, M Shukla, D Ward, KP Williams, BW Sobral, RM Tsolis, AM Whatmore, D O’Callaghan. (2014). Comparative phylogenomics and evolution of the brucellae reveal a path to virulence. Journal of Bacteriology 196:920.
Kim H, MJ Jebrail, A Sinha, Z Bent, OD Solberg, KP Williams, SA Langevin, RF Renzi, JL Van De Vreugde, R Meagher, JS Schoeniger, TW Lane, SS Branda, MS Bartsch, KD Patel. (2013). A microfluidic DNA library preparation platform for next-generation sequencing. PLoS ONE 8:e68988
Langevin SA, ZW Bent, OD Solberg, DJ Curtis, PD Lane, KP Williams, JS Schoeniger, A Sinha, TW Lane, SS Branda. (2013). Peregrine: a rapid and unbiased method to produce strand-specific RNA-seq libraries from small quantities of starting material. RNA Biology 10:502
Williams KP, DP Kelly. (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. International Journal of Systematic and Evolutionary Microbiology 63:2901
Verhoef, L, KP Williams, A Kroneman, B Sobral, H Vennema, W van Pelt, M Koopmans. (2011). Data-driven selection of the informative genomic region for linking outbreaks with norovirus as an example. Virus Genes 44:8.
Wattam AR, TJ Inzana, KP Williams, S Mane, M Shukla, NF Almeida, AW Dickerman, S Mason, I Moriyon, D O’Callaghan, AM Whatmore, BW Sobral, RV Tiller, A Hoffmaster, M Frace, C De Castro, A Molinaro, SM Boyle, B De, JC Setubal. (2012). Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. MBio 3:e00246.

2010 – 2011

Gillespie, JJ, V Joardar, KP Williams, T Driscoll, JB Hostetler, E Nordberg, M Shukla, B Wallenz, CA Hill, VM Nene, AF Azad, BW Sobral, E Caler. (2011). A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of obligate intracellular lifestyle. Journal of Bacteriology 194:376.
Gillespie, JJ, et al. (25 authors). (2011). PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun 79:4286
Bateman, A, et al. (30 authors). (2011). RNA central: a vision for an international database of RNA sequences. RNA 17:1941.
Shulaev, V, et al. (71 authors). (2011). The genome of woodland strawberry (Fragaria vesca). Nature Genetics 43:109.
Dalloul, R, et al. (74 authors). (2010). Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biology 8:e1000475.
Mane, SP, MG Dominguez-Bello, MJ Blaser, BW Sobral, R Hontecillas, J Skoneczka, SK Mohapatra, OR Crasta, C Evans, T Modise, S Shallom, M Shukla, C Varon, F Megraud, AL Maldonado-Contreras, KP Williams, J Bassaganya-Riera. (2010). Host-interactive genes in amerindian Helicobacter pylori diverge from their old world homologs and mediate inflammatory responses. Journal of Bacteriology 192:3078.
Williams, KP, JJ Gillespie, EK Nordberg, EE Snyder EE, JM Shallom, BWS Sobral, AW Dickerman. (2010). Phylogeny of Gammaproteobacteria. Journal of Bacteriology 192:2305.
Gillespie, JJ, KA Brayton, MA Quevedo Diaz, KP Williams, WC Brown, AF Azad, BW Sobral. (2010). Phylogenomics reveals a diverse Rickettsiales type IV secretion system. Infection and Immunity 78:1809.

2008 – 2009

Mao, C, K Bhardwaj, SM Sharkady, RI Fish, T Driscoll, J Wower, C Zwieb, BW Sobral, KP Williams KP. (2009). Variations on the tmRNA gene. RNA Biology 6:351. (Cover Article).
Duan, Y, L Zhou, DG Hall, L Wenbin, H Doddapaneni, H Lin, L Liu, DW Gabriel, CM Vahling, KP Williams, A Dickerman, T Gottwald. (2009). Complete genome sequence of citrus huanglongbing bacterium, Candidatus Liberibacter asiaticus obtained through metagenomics. Molecular Plant-Microbe Interactions 22:1011.
Wattam, AR, KP Williams, EE Snyder, NF Almeida Jr, M Shukla, AW Dickerman, OR Crasta, R Kenyon, J Lu, JM Shallom, H Yoo, TA Ficht, RM Tsolis, C Munk, R Tapia, CS Han, JC Detter, D Bruce, TS Brettin, BW Sobral, SM Boyle, JC Setubal. (2009). Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. Journal of Bacteriology 191:3569.
Beare, PA, N Unsworth, M Andoh, DE Voth, A Omsland, SD Gilk, KP Williams, BW Sobral, JJ Kupko III, SF Porcella, JE Samuel, RA Heinzen. (2009). Comparative genomics reveal extensive transposon-mediated genomic plasticity and diversity among potential effector proteins within the genus Coxiella. Infection and Immunity 77:642.
Sriranganathan, N, MN Seleem, SC Olsen, LE Samartino, AM Whatmore, B Bricker, D O’Callaghan, SM Halling, OR Crasta, RA Wattam, A Purkayastha, BW Sobral, EE Snyder, KP Williams, GX Yu, TA Ficht, CM Roop Jr, P de Figueiredo, SM Boyle, O He, RM Tsolis. (2009). Brucella. In Genome Mapping and Genomics in Animal-Associated Microbes. V. Nene & C. Kole, eds. (Berlin, Springer), pp. 1-64.
Williams, KP. (2008). Strong mimicry of an rRNA binding site for two proteins by the mRNA encoding both proteins. RNA Biology 5:145.
Gillespie, JJ, KP Williams, M Shukla, EE Snyder, EK Nordberg, SM Ceraul, C Dharmanolla, D Rainey, J Soneja, JM Shallom, ND Vishnubhat, R Wattam, A Purkayastha, M Czar, O Crasta, JC Setubal, AF Azad, BS Sobral. (2008). Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. PLoS ONE 3:e2018.

2004 – 2007

Williams, KP, BS Sobral, AW Dickerman. (2007). A robust species tree for the alphaproteobacteria. Journal of Bacteriology 189:4578.
Wang, C, BS Sobral, KP Williams. (2007). Loss in a bacterial group of a universal tRNA feature. Journal of Bacteriology 189:1954.
Zhao, J, T Xue, B Yang, KP Williams, AR Wattam, R Will, B Sharp, R Kenyon, O Crasta, B Sobral. (2006). Genome Annotation and Comparison System. In Proceedings of the 2006 International Conference on Bioinformatics & Computational Biology. HR Arabnia and H Valafar, eds. (CSREA Press, USA), pp. 1-7.
Jacob, Y, SM Sharkady, K Bhardwaj, A Sanda, KP Williams. (2005). Function of the SmpB tail in tmRNA translation revealed by a nucleus-encoded form. Journal of Biological Chemistry 280:5503.
Sharkady, SM, KP Williams. (2004). A third lineage with two-piece tmRNA. Nucleic Acids Research 32:4531.
Trimble, MJ, A Minnicus, KP Williams. (2004). tRNA slippage at the tmRNA resume codon. RNA 10:805.
Williams, KP. (2004). Evolutionary resealing of a split RNA: reversal of gene permutation. RNA 10:555.
Gueneau de Novoa, P, KP Williams. (2004). The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts. Nucleic Acids Research 32:D104.
Mantri, Y, KP Williams. (2004). Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site-specificities. Nucleic Acids Research 32:D55.

2000 – 2003

Williams, KP (2003). Traffic at the tmRNA gene. Journal of Bacteriology 185:1059.
Williams, KP (2002). Descent of a split RNA. Nucleic Acids Research 30:2025.
Gaudin, C, X Zhou, KP Williams, B Felden. (2002). Two-piece tmRNA in cyanobacteria and its structural analysis. Nucleic Acids Research 30:2018.
Williams, KP. (2002). Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Research 30:866.
Williams, KP. (2002). The tmRNA website: invasion by an intron. Nucleic Acids Research 30:179.
Zhao, S, KP Williams. (2002). Integrative genetic element that reverses the usual target gene orientation. Journal of Bacteriology 184:859.
Keiler, KC, L Shapiro, KP Williams. (2000). tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter. Proceedings of the National Academy of Sciences USA 97:7778.
Williams, KP. (2000). The tmRNA website. Nucleic Acids Research 28:168.

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.

1993 – 1995

Williams, KP, S Ciafre, GP Tocchini-Valentini. (1995). Selection of novel Mg2+-dependent self-cleaving ribozymes. EMBO Journal 14:4551.
Williams, KP, DP Bartel. (1995). PCR product with strands of unequal length. Nucleic Acids Research 23:4220.
Williams, KP. (1994). L’approccio selezione-amplificazione per l’esplorazione delle funzioni dell’RNA. Biologi Italiani 24:12.
Williams, KP, H Imahori, DN Fujimoto, T Inoue. (1994). Selection of novel forms of a functional domain within the Tetrahymena ribozyme. Nucleic Acids Research 22:2003.
Williams, KP, DN Fujimoto, T Inoue. (1994). Two universally conserved adenosines of the group I intron that are important for self-splicing but not for core catalytic activity. Journal of Biochemistry (Tokyo) 115:126.
Tinker, RL, KP Williams, GA Kassavetis, EP Geiduschek. (1994). Transcriptional activation by a DNA-tracking protein: structural consequences of enhancement at the T4 late promoter. Cell 77:225.
Williams, KP, DR Herendeen, GA Kassavetis, EP Geiduschek. (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.
Williams, KP. (1993). Simplifications of a self-replication model. Science 261:925.

1987 – 1992

Williams, KP, DN Fujimoto, T Inoue. (1992). A region of group I introns that contains universally conserved residues but is not essential for self-splicing. Proceedings of the National Academy of Sciences USA 89:10400.
Herendeen, DR, KP Williams, GA Kassavetis, EP Geiduschek. (1990). An RNA polymerase-binding protein that is required for communication between an enhancer and a promoter. Science 248:573.
Williams, KP, R Muller, W Ruger, EP Geiduschek. (1989). Overproduced gene 33 protein of bacteriophage T4 is an RNA polymerase-binding protein. Journal of Bacteriology 171:3579.
Williams, KP, GA Kassavetis, FS Esch, EP Geiduschek. (1987). Identification of the gene encoding an RNA polymerase-binding protein of bacteriophage T4. Journal of Virology 61:597.
Williams, KP, GA Kassavetis, EP Geiduschek. (1987). Interactions of the T4 gene 55 product with Escherichia coli RNA polymerase. Journal of Biological Chemistry 262:12365.