Kelly Williams

Principal Member of the Technical Staff

Author profile picture

Principal Member of the Technical Staff

kpwilli@sandia.gov

(925) 294-4730

Sandia National Laboratories, California
 P.O. Box 969
 Livermore, CA 94551-0969

Biography

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.

Education

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)

Memberships

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.

Publications

  • Humphrey, B., MacKenzie, M., Lobitz, M., Schambach, J.Y., Lasley, G., Kolker, S., Ricken, B., Bennett, H., Williams, K.P., Smallwood, C.R., Cahill, J., & Cahill, J. (2023). Biotic countermeasures that rescue Nannochloropsis gaditana from a Bacillus safensis infection. Frontiers in Microbiology, 14(1271836). https://doi.org/10.3389/fmicb.2023.1271836 Publication ID: 123056
  • Cahill, J., Humphrey, B., Schambach, J.Y., Lasley, G., Kolker, S., Ricken, B., Bennett, H., Williams, K.P., Smallwood, C.R., & Smallwood, C.R. (2023). Phage Therapy for Algae: Biotic Countermeasures that Rescue Algae from a Bacterial Infection [Poster]. https://doi.org/10.2172/2430502 Publication ID: 125704
  • Branda, S., Collette, N., Aiosa, N., Garg, N., Mageeney, C.M., Williams, K.P., Phillips, A., Hern, K., Arkin, A., Ricken, B., Wilde, D., Dogra, S., Humphrey, B., Poorey, K., Courtney, C., & Courtney, C. (2022). Reconfiguration of the Respiratory Tract Microbiome to Prevent and Treat Burkholderia Infection. https://doi.org/10.2172/1898252 Publication ID: 80404
  • Shen, C., Liu, B., Park, M., Warnow, T., Williams, K.P., & Williams, K.P. (2022). Scalable Alignment and Tree Estimation on Large Protein Datasets [Conference Presenation]. https://doi.org/10.2172/2004673 Publication ID: 117524
  • Williams, K.P. (2022). Precise prophage mapping [Conference Poster]. https://doi.org/10.2172/2003938 Publication ID: 115028
  • Verzi, S.J., Krishnakumar, R., Levin, D., Krofcheck, D.J., Williams, K.P., & Williams, K.P. (2022). Data Science and Machine Learning for Genome Security. https://doi.org/10.2172/1855003 Publication ID: 75932
  • Williams, K.P., Schoeniger, J.S., Mageeney, C.M., Cahill, J., Clark, L., Rybnicky, G., Shormin, F., Ghaffari, N., Jewett, M., & Jewett, M. (2022). Expanding the Utility of Integrases for Genome Editing and Stabilizing Gene Modules in Target Bacteria [Conference Poster]. https://doi.org/10.2172/2002415 Publication ID: 110592
  • Mageeney, C.M., G, R., M, J., Williams, K.P., Schoeniger, J.S., & Schoeniger, J.S. (2022). Phage Factory: Creating a phage for any bacterial species [Conference Poster]. https://doi.org/10.2172/2001647 Publication ID: 107680
  • Mageeney, C.M., Trubl, G., Williams, K.P., & Williams, K.P. (2022). Improved Mobilome Delineation in Fragmented Genomes. Frontiers in Bioinformatics, 2. https://doi.org/10.3389/fbinf.2022.866850 Publication ID: 106460
  • Mageeney, C.M., Williams, K.P., & Williams, K.P. (2021). Applications of Precise Prophage Mapping [Presentation]. https://www.osti.gov/biblio/1895264 Publication ID: 76509
  • Williams, K.P. (2021). Discovery Through Precise Prophage Mapping [Conference Presenation]. https://doi.org/10.2172/1889352 Publication ID: 75897
  • Mageeney, C.M., Schoeniger, J.S., Williams, K.P., & Williams, K.P. (2021). Computational Front End for Creating a Universal Phage Engineering Platform [Conference Presenation]. https://doi.org/10.2172/1888459 Publication ID: 79668
  • Verzi, S.J., Krishnakumar, R., Levin, D., Krofcheck, D.J., Boskin, C., Williams, K.P., & Williams, K.P. (2021). Data Science for Detection of Genome Editing [Presentation]. https://www.osti.gov/biblio/1889012 Publication ID: 79387
  • Verzi, S.J., Krishnakumar, R., Levin, D., Krofcheck, D.J., Boskin, C., Williams, K.P., & Williams, K.P. (2021). Data Science for Characterization of Genome Noise/Mutation [Presentation]. https://www.osti.gov/biblio/1884061 Publication ID: 79291
  • Tommasini, D., Mageeney, C.M., Williams, K.P., & Williams, K.P. (2021). Helper-Embedded Satellites (HESs): Useful New Vectors [Conference Presenation]. https://doi.org/10.2172/1867558 Publication ID: 78391
  • Mageeney, C.M., Williams, K.P., Schoeniger, J.S., & Schoeniger, J.S. (2021). Computational Front End for Creating Universal Phage-based Vectors for Bacteria [Conference Poster]. https://doi.org/10.2172/1847584 Publication ID: 77259
  • Williams, K.P. (2020). Diversified Therapeutic Phage Cocktails from Close Relatives of the Target Bacterium. https://doi.org/10.2172/1669211 Publication ID: 99932
  • Mageeney, C.M., Sinha, A., Williams, K.P., Branda, S., & Branda, S. (2020). Genome Sequences of Burkholderia thailandensis Strains E421, E426, and DW503. Microbiology Resource Announcements, 9(21). https://doi.org/10.1128/mra.00312-20 Publication ID: 71061
  • Treece, A., Corbin, W.C., Caskey, S.A., Krishnakumar, R., Williams, K.P., Branch, D.W., Harmon, B.N., Polsky, R., Bauer, T.L., Finley, P.D., Jeffers, R., Safta, C., Makvandi, M., Laird, C., Domino, S.P., Ho, C.K., Grillet, A.M., Pacheco, J.L., Nemer, M., … Thelen, P.M. (2020). COVID-19 LDRD Project Summaries. https://doi.org/10.2172/1617440 Publication ID: 105920
  • Williams, K.P. (2020). Precise mapping of new group I introns in tRNA genes. https://doi.org/10.1101/2020.01.27.920355 Publication ID: 105396
  • Mageeney, C.M., Lau, B.Y., Branda, S., Sinha, A., Krishnakumar, R., Williams, K.P., & Williams, K.P. (2019). Computational front end to diverse therapeutic phage cocktails [Conference Poster]. https://www.osti.gov/biblio/1643273 Publication ID: 66274
  • Branda, S., Wang, P., Labauve, A., Sinha, A., Poorey, K., Williams, K.P., Michailidis, G., Schoeniger, J.S., Mageeney, C.M., Courtney, C.M., el-Etr, S., Franco, M., Lao, V., D’Haeseleer, P., Pena, J., Segelke, B., & Segelke, B. (2019). Elucidation of Host-Pathogen Interactions via Dual RNA-Seq Analysis to Support Development of Countermeasures Against the Intracellular Bacterial Pathogen Burkholderia pseudomallei [Conference Poster]. https://www.osti.gov/biblio/1643632 Publication ID: 66457
  • Krishnakumar, R., Boskin, C., Levin, D., Carmody, D., Finley, P.D., Verzi, S.J., Williams, K.P., Carney, J., & Carney, J. (2019). Data Science for Detection of Genome Editi [Presentation]. https://www.osti.gov/biblio/1645734 Publication ID: 70337
  • Mageeney, C.M., Rokes, A.B., Lau, B.Y., Branda, S., Sinha, A., Krishnakumar, R., Williams, K.P., & Williams, K.P. (2019). Computational front end to diverse therapeutic phage cocktails [Conference Poster]. https://www.osti.gov/biblio/1641506 Publication ID: 70235
  • Swecker, E., Williams, K.P., & Williams, K.P. (2019). Streamlining Genome Database Updates [Conference Poster]. https://www.osti.gov/biblio/1641300 Publication ID: 69993
  • Mageeney, C.M., Rokes, A.B., Lau, B.Y., Branda, S., Krishnakumar, R., Williams, K.P., & Williams, K.P. (2019). Computational front end to diverse therapeutic phage cocktails [Conference Poster]. https://www.osti.gov/biblio/1640900 Publication ID: 69317
  • Mageeney, C.M., Williams, K.P., Branda, S., Krishnakumar, R., & Krishnakumar, R. (2019). Diverse therapeutic phage cocktails through a computational front end [Conference Poster]. https://www.osti.gov/biblio/1640653 Publication ID: 68942
  • Mageeney, C.M., Rokes, A.B., Lau, B.Y., Branda, S., Krishnakumar, R., Williams, K.P., & Williams, K.P. (2019). Diverse therapeutic phage cocktails through a computational front end [Conference Poster]. https://www.osti.gov/biblio/1639435 Publication ID: 67521
  • Hudson, C.M., Podlevsky, J., Williams, K.P., & Williams, K.P. (2019). Targeted Assembly of cas Gene Clusters from High Throughput Sequencing Data [Conference Poster]. https://www.osti.gov/biblio/1639517 Publication ID: 67675
  • Peterson, K., Perego, M., Frederick, J.M., Wheeler, L.B., Bosler, P.A., Ruffing, A.M., Davis, R.W., Whitmore, L.S., Poorey, K., Williams, K.P., Roesler, E.L., Bryan, P.F., Salinger, A.G., Hardesty, J., Tidwell, V.C., Singh, A.K., & Singh, A.K. (2018). SNL/BER Review 2018 [Presentation]. https://www.osti.gov/biblio/1594318 Publication ID: 59367
  • Branda, S., Courtney, C.M., Sinha, A., Poorey, K., Schoeniger, J.S., Labauve, A.E., Williams, K.P., & Williams, K.P. (2018). Elucidation & manipulation of host-pathogen interactions for development of countermeasures against intracellular bacterial pathogen Burkholderiapseudomallei [Presentation]. https://www.osti.gov/biblio/1594641 Publication ID: 59351
  • Rokes, A., Dufek, D., Mageeney, C.M., Sinha, A., Williams, K.P., & Williams, K.P. (2018). Engineering Phages for Therapeutic Use [Presentation]. https://www.osti.gov/biblio/1806666 Publication ID: 63274
  • Lau, B.Y., Mageeney, C.M., Branda, S., Williams, K.P., & Williams, K.P. (2018). Phage Therapy against Pseudomonas aeruginosa in a Galleria mellonella infection model [Conference Poster]. https://www.osti.gov/biblio/1806628 Publication ID: 63262
  • Hudson, C.M., Williams, K.P., Timlin, J.A., & Timlin, J.A. (2018). CasAnn: Targeted Identification of CRISPR Associated Gene Operons from Next Generation Sequences [Conference Poster]. https://www.osti.gov/biblio/1529773 Publication ID: 62727
  • Hudson, C.M., Timlin, J.A., Williams, K.P., & Williams, K.P. (2018). CasANN: Targeted Identification of CRISPR Associated Gene Operons from Next Generation Sequences [Conference Poster]. https://www.osti.gov/biblio/1513657 Publication ID: 58783
  • Williams, K.P. (2017). The tmRNA Website: Curating Too Many Sequences [Conference Poster]. https://www.osti.gov/biblio/1481717 Publication ID: 54053
  • Lau, B., Krishnakumar, R., Wagner, J., Sinha, A., Hudson, C.M., Schoeniger, J.S., Branda, S., Williams, K.P., & Williams, K.P. (2017). Discovering and converting temperate phages for therapy [Conference Poster]. https://www.osti.gov/biblio/1483224 Publication ID: 54346
  • Wagner, J., Williams, K.P., & Williams, K.P. (2017). Comparator: Scaling up Genomic Island Finding with a Comparative Genomic Approach [Presentation]. https://www.osti.gov/biblio/1508230 Publication ID: 57546
  • Sinha, S., Krishnakumar, R., Williams, K.P., Schoeniger, J.S., & Schoeniger, J.S. (2017). Comparative Analysis between Genomic Islands and Host Species [Presentation]. https://www.osti.gov/biblio/1508231 Publication ID: 57547
  • Williams, K.P., Lau, B.Y., Krishnakumar, R., Wagner, J.M., Hudson, C.M., Schoeniger, J.S., & Schoeniger, J.S. (2017). Reconsidering temperate phages for therapy [Conference Poster]. https://www.osti.gov/biblio/1458119 Publication ID: 56671
  • Williams, K.P., Krishnakumar, R., Wagner, J., Hudson, C.M., Schoeniger, J.S., & Schoeniger, J.S. (2017). The Bacterial and Archaeal Pan-Mobilome [Conference Poster]. https://www.osti.gov/biblio/1456320 Publication ID: 55476
  • Meagher, R.J., Poorey, K., Labauve, A.E., Hamblin, R., Williams, K.P., Bent, Z.W., & Bent, Z.W. (2016). A rapid spin column-based method to enrich pathogen transcripts from eukaryotic host cells prior to sequencing. PLoS ONE, 11(12). https://doi.org/10.1371/journal.pone.0168788 Publication ID: 49972
  • Ruffing, A.M., Bachand, G.D., Timlin, J.A., Manginell, R., Hudson, C.M., Williams, K.P., Rempe, S.B., Brinker, C.J., Olszewska-Wasiolek, M.A., Hanson, D.J., Vandernoot, V.A., & Vandernoot, V.A. (2016). SNL Capabilities for IV&V – DARPA BTO [Presentation]. https://www.osti.gov/biblio/1428154 Publication ID: 47973
  • Williams, K.P., Lau, B.Y., & Lau, B.Y. (2016). RNAcentral: A comprehensive database of non-coding RNA sequences. Nucleic Acids Research, 45(D1). https://doi.org/10.1093/nar/gkw1008 Publication ID: 52970
  • Schoeniger, J.S., Ray, D., Branda, S., Williams, K.P., Hudson, C.M., Polage, C., & Polage, C. (2016). Cheap and Fast Multiplexed Bacterial Genomic Sequencing: Enabling Comparative Genomic Analysis of Antibiotic Resistance in BWA and Hospital Acquired Infections [Conference Poster]. https://www.osti.gov/biblio/1505457 Publication ID: 52119
  • Schoeniger, J.S., Hudson, C.M., Bent, Z.W., Sinha, A., Williams, K.P., & Williams, K.P. (2016). Experimental single-strain mobilomics reveals events that shape pathogen emergence. Nucleic Acids Research, 44(14), pp. 6830-6839. https://doi.org/10.1093/nar/gkw601 Publication ID: 50979
  • Lane, T., Lane, P., Williams, K.P., Wilkenfeld, J.S., Solberg, O.D., Fuqua, Z.B., Cornelius, N.G., Gillespie, S., Samocha, T.M., Carney, L.T., & Carney, L.T. (2016). Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina. Algal Research, 17, pp. 341-347. https://doi.org/10.1016/j.algal.2016.05.011 Publication ID: 44389
  • Ray, D., Schoeniger, J.S., Williams, K.P., Hamblin, R., Sinha, A., Hudson, C.M., Branda, S., & Branda, S. (2016). Genome-Based Prediction pathogenic potential of the new ?super bug?: Clostridium difficile [Conference Poster]. https://www.osti.gov/biblio/1365235 Publication ID: 49554
  • D’Haeseleer, P., Johnson, S.L., Davenport, K.W., Chain, P.S., Schoeniger, J.S., Ray, D., Sinha, A., Williams, K.P., Pena, J., Branda, S., el-Etr, S., & el-Etr, S. (2016). Genome sequence of the historical clinical isolate Burkholderia pseudomallei PHLS 6. Genome Announcements, 4(3). https://doi.org/10.1128/genomeA.00649-16 Publication ID: 50052
  • Ray, D., Schoeniger, J.S., Williams, K.P., Hudson, C.M., & Hudson, C.M. (2016). Genomic Prediction & comparative analysis of Pathogenicity of the new ?super bug?: Clostridium difficile [Presentation]. https://www.osti.gov/biblio/1342460 Publication ID: 46896
  • Wagner, J., Williams, K.P., Hudson, C.M., & Hudson, C.M. (2015). Genomic Island Discovery Via Integration Site Identification [Presentation]. https://www.osti.gov/biblio/1339233 Publication ID: 44671
  • Hudson, C.M., Schoeniger, J.S., Poorey, K., Ray, D., Williams, K.P., & Williams, K.P. (2015). Sandia?s Web-Based Bioinformatics Tools [Conference Poster]. https://www.osti.gov/biblio/1331543 Publication ID: 44564
  • Hudson, C.M., Williams, K.P., & Williams, K.P. (2015). Hyper-finishing: Catching DNA mobilization in the act [Conference Poster]. https://www.osti.gov/biblio/1530952 Publication ID: 44157
  • Carson, B., Timlin, J.A., Sinclair, M.B., Anthony, S.M., Moorman, M.W., la Bauve, E., Murton, J.K., Williams, K.P., Poorey, K., Jones, H.D., & Jones, H.D. (2015). Identification of Unknown Viral Infections by Hyperspectral Cell Sorting and Deep Sequencing [Conference Poster]. https://www.osti.gov/biblio/1258189 Publication ID: 43537
  • Carson, B., Timlin, J.A., Sinclair, M.B., Anthony, S.M., Moorman, M.W., Murton, J.K., Williams, K.P., Poorey, K., la Bauve, E., & la Bauve, E. (2015). Unknown Pathogen Detection in Clinical Samples: A Novel Hyperspectral Imaging and Single Cell Sequencing Approach [Conference Poster]. https://www.osti.gov/biblio/1258188 Publication ID: 43536
  • Hudson, C.M., Williams, K.P., & Williams, K.P. (2015). Tools for detecting evidence of bioengineering in bacteria [Conference Poster]. https://www.osti.gov/biblio/1252949 Publication ID: 43387
  • Poorey, K., Sinha, A., Curtis, D.J., Williams, K.P., Branda, S., Meagher, R.J., & Meagher, R.J. (2015). A transcriptomic analysis of Yersinia enterocolitica biovar 1B infecting murine macrophages reveals new mechanisms of intracellular survival. Infection and Immunity, 83(7), pp. 2672-2685. https://doi.org/10.1128/IAI.02922-14 Publication ID: 40615
  • Hudson, C.M., Williams, K.P., & Williams, K.P. (2015). Juxtaposer: A tool for assembling mobilized genomic elements in high-throughput sequences [Conference Poster]. https://www.osti.gov/biblio/1331667 Publication ID: 42729
  • Hudson, C.M., Williams, K.P., & Williams, K.P. (2015). Islander: A tool for precisely mapping genomic islands in tRNA and tmRNA genes [Presentation]. https://www.osti.gov/biblio/1531266 Publication ID: 41541
  • Hudson, C.M., Williams, K.P., & Williams, K.P. (2015). The tmRNA website. Nucleic Acids Research, 43(D1), pp. D138-D140. https://doi.org/10.1093/nar/gku1109 Publication ID: 38313
  • Williams, K.P., Hudson, C.M., Otherauthors, A., & Otherauthors, A. (2014). RNAcentral: an international database of ncRNA sequences. Nucleic Acids Research, 43(D1). https://doi.org/10.1093/nar/gku991 Publication ID: 38312
  • Hudson, C.M., Williams, K.P., & Williams, K.P. (2014). LearnedPhyloblocks: Novel Genomic Islands through Phylogenetic Profiling [Conference Poster]. https://www.osti.gov/biblio/1567815 Publication ID: 39201
  • Hudson, C.M., Williams, K.P., & Williams, K.P. (2014). Ends of the line for tmRNA-SmpB. Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00421 Publication ID: 41174
  • Cui, L., Williams, K.P., Lane, T., Poorey, K., & Poorey, K. (2014). Metagenomics Analysis on Arizona Algae Cultivation System [Presentation]. https://www.osti.gov/biblio/1494259 Publication ID: 37773
  • Carson, B., Sinclair, M.B., Timlin, J.A., Williams, K.P., Poorey, K., Hatch, A., James, C.D., Davis, R.W., la Bauve, E., Jones, H., & Jones, H. (2014). A Novel Approach to Unknown Virus Identification in Clinical Samples [Presentation]. https://www.osti.gov/biblio/1496684 Publication ID: 37598
  • Sinclair, M.B., Timlin, J.A., Williams, K.P., Hatch, A., Davis, R.W., Carson, B., & Carson, B. (2014). A Novel Approach to Unknown Virus Detection in Clinical Samples [Conference]. https://www.osti.gov/biblio/1140514 Publication ID: 37207
  • Sinclair, M.B., Timlin, J.A., Williams, K.P., Hatch, A., Carson, B., Davis, R.W., & Davis, R.W. (2014). A Novel Approach to Unknown Virus Identification in Clinical Samples [Conference]. https://www.osti.gov/biblio/1140493 Publication ID: 37206
  • Turner, K., Hudson, C.M., Tran-Gyamfi, M., Powell, A.J., Williams, K.P., & Williams, K.P. (2014). Understanding and regulation of microbial lignolysis for renewable platform chemicals. https://doi.org/10.2172/1322272 Publication ID: 36881
  • Lane, T., Lane, P., Williams, K.P., & Williams, K.P. (2013). Pond Crash Forensics: molecular diagnostics in replicate raceway mass cultures of the alga Nannochloropsis salina. Biotechnology and Bioengineering. https://www.osti.gov/biblio/1118186 Publication ID: 36586
  • Williams, K.P. (2013). Pathogenicity island mobility and gene content. https://doi.org/10.2172/1104780 Publication ID: 36235
  • la Bauve, E., Carson, B., Hatch, A., Timlin, J.A., Sinclair, M.B., Williams, K.P., & Williams, K.P. (2013). A Novel Approach to Unknown Virus Identification in Clinical Samples [Conference]. https://www.osti.gov/biblio/1110696 Publication ID: 35697
  • Lane, T., Lane, P., Williams, K.P., & Williams, K.P. (2013). Microbiome analysis of a microalgal mass culture growing in municipal wastewater in a prototype OMEGA photobioreactor. Algal Research. https://www.osti.gov/biblio/1110359 Publication ID: 35635
  • Williams, K.P., Hudson, C.M., & Hudson, C.M. (2013). Confirmation that the genus Thermithiobacillus is correctly assigned to the class Acidithiobacillia. International Journal of Systematic and Evolutionary Microbiology. https://www.osti.gov/biblio/1140623 Publication ID: 35600
  • Kim, H., Jebrail, M.J., Sinha, A., Bent, Z., Solberg, O.D., Williams, K.P., Langevin, S.A., Renzi, R.F., van de Vreugde, J.L., Meagher, R.J., Schoeniger, J.S., Lane, T., Branda, S., Bartsch, M.S., Patel, K.D., & Patel, K.D. (2013). A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing. PLoS ONE, 8(7). https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84880646994&origin=inward Publication ID: 32780
  • Lau, B.Y., Hudson, C.M., Williams, K.P., & Williams, K.P. (2013). Genomic Islands PPT [Presentation]. https://www.osti.gov/biblio/1666214 Publication ID: 34745
  • Timlin, J.A., Sinclair, M.B., Carson, B., Williams, K.P., Hatch, A., & Hatch, A. (2013). A Novel Approach to Unknown Virus Detection in Clinical Samples [Conference]. https://www.osti.gov/biblio/1106843 Publication ID: 34643
  • Hudson, C.M., Bent, Z., Meagher, R.J., Williams, K.P., & Williams, K.P. (2013). Mobilome of an NDM-1-encoding Klebsiella pneumoniae strain. Antimicrobial Agents and Chemotherapy. https://www.osti.gov/biblio/1113066 Publication ID: 34365
  • Lane, T., Lane, P., Williams, K.P., & Williams, K.P. (2013). Microbiome analysis of a microalgal mass culture growing in municipal wastewater in a prototype OMEGA photobioreactor1. Algal Research. https://www.osti.gov/biblio/1078938 Publication ID: 33340
  • la Bauve, E., Carson, B., Jones, H.D.T., Sinclair, M.B., Williams, K.P., Hatch, A., Timlin, J.A., Solberg, O.D., & Solberg, O.D. (2013). A novel approach to unknown pathogen detection in clinical samples [Conference]. https://www.osti.gov/biblio/1299038 Publication ID: 32148
  • Lane, T., Lane, P., Williams, K.P., Solberg, O.D., & Solberg, O.D. (2013). Metagenomic analysis of a microalgal mass culture growing in municipal wastewater in a prototype OMEGA photobioreactor. Proposed for publication in Biotechnology and Bioengineering.. https://www.osti.gov/biblio/1063338 Publication ID: 32137
  • Langevin, S.A., Bent, Z., Solberg, O.D., Curtis, D.J., Lane, P., Williams, K.P., Schoeniger, J.S., Lane, T., Sinha, A., & Sinha, A. (2013). Peregrine: A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material. RNA Biology, 10(4), pp. 502-515. https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84879016540&origin=inward Publication ID: 32058
  • Langevin, S.A., Lane, T., Lane, P., Bent, Z., Solberg, O.D., Curtis, D.J., Williams, K.P., Branda, S., Patel, K., Schoeniger, J.S., & Schoeniger, J.S. (2012). cDNA normalization by hydroxyapatite chromatography to enhance transcriptome diversity in RNA-Seq Applications. Biotechniques, 53(6). https://doi.org/10.2144/000113937 Publication ID: 30653
  • Williams, K.P. (2012). Pathogenicity Island Mobility and Gene Content [Presentation]. https://www.osti.gov/biblio/1648001 Publication ID: 30237
  • Williams, K.P. (2012). Bioinformatic and Molecular Suppression of Human Sequences in Clinical Samples [Conference]. https://www.osti.gov/biblio/1073463 Publication ID: 29731
  • Branda, S., Jebrail, M.J., van de Vreugde, J.L., Langevin, S.A., Bent, Z., Curtis, D.J., Lane, P., Carson, B., la Bauve, E., Patel, K., Ricken, B., Schoeniger, J.S., Solberg, O.D., Williams, K.P., Misra, M., Powell, A.J., Pattengale, N.D., May, E., Lane, T., … Meagher, R.J. (2012). Characterization of Pathogens in Clinical Specimens via Suppression of Host Background for Efficient Second Generation Sequencing Analyses [Conference]. https://www.osti.gov/biblio/1141142 Publication ID: 28871
  • Lane, T., Lane, P., Carney, L.T., Solberg, O.D., Williams, K.P., & Williams, K.P. (2012). Pond Crash Forensics: Identification and early detection of pond crash agents [Conference]. https://www.osti.gov/biblio/1064189 Publication ID: 28627
  • Lane, T., Williams, K.P., Solberg, O.D., Patel, K., Branda, S., Langevin, S.A., Lane, P., Bent, Z., Curtis, D.J., Tran-Gyamfi, M., Vandernoot, V.A., Schoeniger, J.S., & Schoeniger, J.S. (2012). Rapid Threat Organism Recognition [Conference]. https://www.osti.gov/biblio/1067717 Publication ID: 28455
  • Branda, S., Jebrail, M.J., van de Vreugde, J.L., Langevin, S.A., Bent, Z., Curtis, D.J., Lane, P., Carson, B., la Bauve, E., Patel, K., Ricken, B., Schoeniger, J.S., Solberg, O.D., Williams, K.P., Misra, M., Powell, A.J., Pattengale, N.D., May, E., Lane, T., … Meagher, R.J. (2012). Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples [Conference]. https://www.osti.gov/biblio/1067707 Publication ID: 27930
  • Branda, S., Jebrail, M.J., van de Vreugde, J.L., Langevin, S.A., Bent, Z., Curtis, D.J., Lane, P., Carson, B., la Bauve, E., Patel, K., Ricken, B., Schoeniger, J.S., Solberg, O.D., Williams, K.P., Misra, M., Powell, A.J., Pattengale, N.D., May, E., Lane, T., … Meagher, R.J. (2012). Copy of Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples [Presentation]. https://www.osti.gov/biblio/1688623 Publication ID: 27929
  • Langevin, S.A., Bent, Z., Solberg, O.D., Curtis, D.J., Lane, P., Williams, K.P., Schoeniger, J.S., Lane, T., Branda, S., & Branda, S. (2012). Peregrine : [Conference]. https://www.osti.gov/biblio/1294360 Publication ID: 27691
  • Williams, K.P. (2012). Bioinformatic and Molecular Suppression of Human Sequences in Clinical Samples [Conference]. https://www.osti.gov/biblio/1068429 Publication ID: 27475
  • Langevin, S.A., Lane, T., Lane, P., Bent, Z., Solberg, O.D., Curtis, D.J., Williams, K.P., Branda, S., Patel, K., Schoeniger, J.S., & Schoeniger, J.S. (2012). cDNA normalization by hydroxyapatite chromatography to enhance transcriptome diversity in RNA-Seq Applications. Nucleic Acid Research. https://www.osti.gov/biblio/1078779 Publication ID: 26144
  • Williams, K.P., Curtis, D.J., Lane, P., Lane, T., & Lane, T. (2011). Pond Crash Forensics [Conference]. https://www.osti.gov/biblio/1107562 Publication ID: 23246
Showing 10 of 93 publications.

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.