Kelly Williams

Principal Member of the Technical Staff

(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

Steven Branda, Nicole Collette, Nicole Aiosa, Neha Garg, Catherine Mageeney, Kelly Williams, Ashlee Phillips, Kelsey Hern, Adam Arkin, James Ricken, Delaney Wilde, Sahiba Dogra, Brittany Humphrey, Kunal Poorey, Colleen Courtney, (2022). Reconfiguration of the Respiratory Tract Microbiome to Prevent and Treat Burkholderia Infection https://doi.org/10.2172/1898252 Publication ID: 80404

Stephen Verzi, Raga Krishnakumar, Drew Levin, Daniel Krofcheck, Kelly Williams, (2022). Data Science and Machine Learning for Genome Security https://doi.org/10.2172/1855003 Publication ID: 75932

Catherine Mageeney, Kelly Williams, (2021). Applications of Precise Prophage Mapping https://www.osti.gov/servlets/purl/1895264 Publication ID: 76509

Kelly Williams, (2021). Discovery Through Precise Prophage Mapping https://doi.org/10.2172/1889352 Publication ID: 75897

Catherine Mageeney, Joseph Schoeniger, Kelly Williams, (2021). Computational Front End for Creating a Universal Phage Engineering Platform https://doi.org/10.2172/1888459 Publication ID: 79668

Stephen Verzi, Raga Krishnakumar, Drew Levin, Daniel Krofcheck, Callie Boskin, Kelly Williams, (2021). Data Science for Detection of Genome Editing https://www.osti.gov/servlets/purl/1889012 Publication ID: 79387

Stephen Verzi, Raga Krishnakumar, Drew Levin, Daniel Krofcheck, Callie Boskin, Kelly Williams, (2021). Data Science for Characterization of Genome Noise/Mutation https://www.osti.gov/servlets/purl/1884061 Publication ID: 79291

Dario Tommasini, Catherine Mageeney, Kelly Williams, (2021). Helper-Embedded Satellites (HESs): Useful New Vectors https://doi.org/10.2172/1867558 Publication ID: 78391

Catherine Mageeney, Kelly Williams, Joseph Schoeniger, (2021). Computational Front End for Creating Universal Phage-based Vectors for Bacteria https://doi.org/10.2172/1847584 Publication ID: 77259

Catherine Mageeney, Anupama Sinha, Kelly Williams, Steven Branda, (2020). Genome Sequences of Burkholderia thailandensis Strains E421, E426, and DW503 Microbiology Resource Announcements https://doi.org/10.1128/MRA.00312-20 Publication ID: 71061

Steven Branda, Pei-Li Wang, Annette LaBauve, Anupama Sinha, Kunal Poorey, Kelly Williams, George Michailidis, Joseph Schoeniger, Catherine Mageeney, Colleen Courtney, Sahar El-Etr, Magda Franco, Victoria Lao, Patrik D’haeseleer, Jose Pena, Brent Segelke, (2019). Elucidation of Host-Pathogen Interactions via Dual RNA-Seq Analysis to Support Development of Countermeasures Against the Intracellular Bacterial Pathogen Burkholderia pseudomallei https://www.osti.gov/servlets/purl/1643632 Publication ID: 66457

Catherine Mageeney, Britney Lau, Steven Branda, Anupama Sinha, Raga Krishnakumar, Kelly Williams, (2019). Computational front end to diverse therapeutic phage cocktails https://www.osti.gov/servlets/purl/1643273 Publication ID: 66274

Raga Krishnakumar, Callie Boskin, Drew Levin, Daniel Carmody, Patrick Finley, Stephen Verzi, Kelly Williams, James Carney, (2019). Data Science for Detection of Genome Editi https://www.osti.gov/servlets/purl/1645734 Publication ID: 70337

Catherine Mageeney, Alecia Rokes, Britney Lau, Steven Branda, Anupama Sinha, Raga Krishnakumar, Kelly Williams, (2019). Computational front end to diverse therapeutic phage cocktails https://www.osti.gov/servlets/purl/1641506 Publication ID: 70235

Elena Swecker, Kelly Williams, (2019). Streamlining Genome Database Updates https://www.osti.gov/servlets/purl/1641300 Publication ID: 69993

Catherine Mageeney, Kelly Williams, Steven Branda, Raga Krishnakumar, (2019). Diverse therapeutic phage cocktails through a computational front end https://www.osti.gov/servlets/purl/1640653 Publication ID: 68942

Catherine Mageeney, Alecia Rokes, Britney Lau, Steven Branda, Raga Krishnakumar, Kelly Williams, (2019). Computational front end to diverse therapeutic phage cocktails https://www.osti.gov/servlets/purl/1640900 Publication ID: 69317

Corey Hudson, Joshua Podlevsky, Kelly Williams, (2019). Targeted Assembly of cas Gene Clusters from High Throughput Sequencing Data https://www.osti.gov/servlets/purl/1639517 Publication ID: 67675

Catherine Mageeney, Alecia Rokes, Briney Lau, Steven Branda, Raga Krishnakumar, Kelly Williams, (2019). Diverse therapeutic phage cocktails through a computational front end https://www.osti.gov/servlets/purl/1639435 Publication ID: 67521

Steven Branda, Colleen Courtney, Anupama Sinha, Kunal Poorey, Joseph Schoeniger, Annette LaBauve, Kelly Williams, (2018). Elucidation & manipulation of host-pathogen interactions for development of countermeasures against intracellular bacterial pathogen Burkholderiapseudomallei https://www.osti.gov/servlets/purl/1594641 Publication ID: 59351

Kara Peterson, Mauro Perego, Jennifer Frederick, Lauren Wheeler, Peter Bosler, Anne Ruffing, Ryan Davis, Leanne Whitmore, Kunal Poorey, Kelly Williams, Erika Roesler, Paul Bryan, Andrew Salinger, Jasper Hardesty, Vincent Tidwell, Anup Singh, (2018). SNL/BER Review 2018 https://www.osti.gov/servlets/purl/1594318 Publication ID: 59367

Britney Lau, Catherine Mageeney, Steven Branda, Kelly Williams, (2018). Phage Therapy against Pseudomonas aeruginosa in a Galleria mellonella infection model https://www.osti.gov/servlets/purl/1806628 Publication ID: 63262

Alecia Rokes, Danielle Dufek, Catherine Mageeney, Anupama Sinha, Kelly Williams, (2018). Engineering Phages for Therapeutic Use https://www.osti.gov/servlets/purl/1806666 Publication ID: 63274

Corey Hudson, Kelly Williams, Jerilyn Timlin, (2018). CasAnn: Targeted Identification of CRISPR Associated Gene Operons from Next Generation Sequences https://www.osti.gov/servlets/purl/1529773 Publication ID: 62727

Corey Hudson, Jerilyn Timlin, Kelly Williams, (2018). CasANN: Targeted Identification of CRISPR Associated Gene Operons from Next Generation Sequences https://www.osti.gov/servlets/purl/1513657 Publication ID: 58783

Kelly Williams, (2017). The tmRNA Website: Curating Too Many Sequences https://www.osti.gov/servlets/purl/1481717 Publication ID: 54053

Britney Lau, Raga Krishnakumar, Julian Wagner, Anupama Sinha, Corey Hudson, Joseph Schoeniger, Steven Branda, Kelly Williams, (2017). Discovering and converting temperate phages for therapy https://www.osti.gov/servlets/purl/1483224 Publication ID: 54346

Julian Wagner, Kelly Williams, (2017). Comparator: Scaling up Genomic Island Finding with a Comparative Genomic Approach https://www.osti.gov/servlets/purl/1508230 Publication ID: 57546

Sankalp Sinha, Raga Krishnakumar, Kelly Williams, Joseph Schoeniger, (2017). Comparative Analysis between Genomic Islands and Host Species https://www.osti.gov/servlets/purl/1508231 Publication ID: 57547

Kelly Williams, Britney Lau, Raga Krishnakumar, Julian Wagner, Corey Hudson, Joseph Schoeniger, (2017). Reconsidering temperate phages for therapy https://www.osti.gov/servlets/purl/1458119 Publication ID: 56671

Kelly Williams, Raga Krishnakumar, Julian Wagner, Corey Hudson, Joseph Schoeniger, Kelly Williams, (2017). The Bacterial and Archaeal Pan-Mobilome https://www.osti.gov/servlets/purl/1456320 Publication ID: 55476

Anton Petrov, Simon Kay, Ioanna Kalvari, Kevin Howe, Kristian Gray, Elspeth Bruford, Paul Kersey, Guy Cochrane, Robert Finn, Alex Bateman, Ana Kozomara, Sam Griffiths-Jones, Adam Frankish, Christian Zwieb, Britney Lau, Kelly Williams, Patricia Chan, Todd Lowe, Jamie Cannone, Robin Gutell, Magdalena Machnicka, Janusz Bujnicki, Maki Yoshihama, Naoya Kenmochi, Benli Chai, James Cole, Maciej Szymanski, Wojciech Karlowski, Valerie Wood, Eva Huala, Tanya Berardini, Yi Zhao, Runsheng Chen, Weimin Zhu, Maria Paraskevopoulou, Ioannis Vlachos, Artemis Hatzigeorgiou, Lina Ma, Zhang Zhang, Joern Puetz, Peter Stadler, Daniel McDonald, Siddhartha Basu, Petra Fey, Stacia Engel, J. Cherry, Pieter Volders, Pieter Mestdagh, Jacek Wower, Michael Clark, Xiu Quek, Marcel Dinger, (2017). RNAcentral: A comprehensive database of non-coding RNA sequences Nucleic Acids Research https://doi.org/10.1093/nar/gkw1008 Publication ID: 52970

Zachary Bent, Kunal Poorey, Annette LaBauve, Rachelle Hamblin, Kelly Williams, Robert Meagher, (2016). A rapid spin column-based method to enrich pathogen transcripts from eukaryotic host cells prior to sequencing PLoS ONE https://doi.org/10.1371/journal.pone.0168788 Publication ID: 49972

Anne Ruffing, George Bachand, Jerilyn Timlin, Ronald Manginell, Corey Hudson, Kelly Williams, Susan Rempe, C. Brinker, Maryla Olszewska-Wasiolek, Don Hanson, Victoria VanderNoot, (2016). SNL Capabilities for IV&V – DARPA BTO https://www.osti.gov/servlets/purl/1428154 Publication ID: 47973

Joseph Schoeniger, Debjit Ray, Steven Branda, Kelly Williams, Corey Hudson, Christopher Polage, (2016). Cheap and Fast Multiplexed Bacterial Genomic Sequencing: Enabling Comparative Genomic Analysis of Antibiotic Resistance in BWA and Hospital Acquired Infections https://www.osti.gov/servlets/purl/1505457 Publication ID: 52119

Joseph Schoeniger, Corey Hudson, Zachary Bent, Anupama Sinha, Kelly Williams, (2016). Experimental single-strain mobilomics reveals events that shape pathogen emergence Nucleic Acids Research https://doi.org/10.1093/nar/gkw601 Publication ID: 50979

Laura Carney, Joshua Wilkenfeld, Pamela Lane, Owen Solberg, Zachary Fuqua, Nina Cornelius, Shaunette Gillespie, Kelly Williams, Tzachi Samocha, Todd Lane, (2016). Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina Algal Research https://doi.org/10.1016/j.algal.2016.05.011 Publication ID: 44389

Debjit Ray, Joseph Schoeniger, Kelly Williams, Rachelle Hamblin, Anupama Sinha, Corey Hudson, Steven Branda, (2016). Genome-Based Prediction pathogenic potential of the new ?super bug?: Clostridium difficile https://www.osti.gov/servlets/purl/1365235 Publication ID: 49554

Debjit Ray, Joseph Schoeniger, Kelly Williams, Corey Hudson, (2016). Genomic Prediction & comparative analysis of Pathogenicity of the new ?super bug?: Clostridium difficile https://www.osti.gov/servlets/purl/1342460 Publication ID: 46896

Patrik D’haeseleer, Shannon Johnson, Karen Davenport, Patrick Chain, Joseph Schoeniger, Debjit Ray, Anupama Sinha, Kelly Williams, José Peña, Steven Branda, Sahar El-Etr, (2016). Genome sequence of the historical clinical isolate Burkholderia pseudomallei PHLS 6 Genome Announcements https://doi.org/10.1128/genomeA.00649-16 Publication ID: 50052

Corey Hudson, Joseph Schoeniger, Kunal Poorey, Debjit Ray, Kelly Williams, (2015). Sandia?s Web-Based Bioinformatics Tools https://www.osti.gov/servlets/purl/1331543 Publication ID: 44564

Julian Wagner, Kelly Williams, Corey Hudson, (2015). Genomic Island Discovery Via Integration Site Identification https://www.osti.gov/servlets/purl/1339233 Publication ID: 44671

Corey Hudson, Kelly Williams, (2015). Hyper-finishing: Catching DNA mobilization in the act https://www.osti.gov/servlets/purl/1530952 Publication ID: 44157

Bryan Carson, Jerilyn Timlin, Michael Sinclair, Stephen Anthony, Matthew Moorman, Jaclyn Murton, Kelly Williams, Kunal Poorey, Elisa La Bauve, (2015). Unknown Pathogen Detection in Clinical Samples: A Novel Hyperspectral Imaging and Single Cell Sequencing Approach https://www.osti.gov/servlets/purl/1258188 Publication ID: 43536

Bryan Carson, Jerilyn Timlin, Michael Sinclair, Stephen Anthony, Matthew Moorman, Elisa La Bauve, Jaclyn Murton, Kelly Williams, Kunal Poorey, Howland Jones, (2015). Identification of Unknown Viral Infections by Hyperspectral Cell Sorting and Deep Sequencing https://www.osti.gov/servlets/purl/1258189 Publication ID: 43537

Corey Hudson, Kelly Williams, (2015). Tools for detecting evidence of bioengineering in bacteria https://www.osti.gov/servlets/purl/1252949 Publication ID: 43387

Kunal Poorey, Anupama Sinha, Deanna Curtis, Kelly Williams, Steven Branda, Robert Meagher, (2015). A transcriptomic analysis of Yersinia enterocolitica biovar 1B infecting murine macrophages reveals new mechanisms of intracellular survival Infection and Immunity https://doi.org/10.1128/IAI.02922-14 Publication ID: 40615

Corey Hudson, Kelly Williams, (2015). Juxtaposer: A tool for assembling mobilized genomic elements in high-throughput sequences https://www.osti.gov/servlets/purl/1331667 Publication ID: 42729

Corey Hudson, Kelly Williams, (2015). Islander: A tool for precisely mapping genomic islands in tRNA and tmRNA genes https://www.osti.gov/servlets/purl/1531266 Publication ID: 41541

Corey Hudson, Kelly Williams, (2015). The tmRNA website Nucleic Acids Research https://doi.org/10.1093/nar/gku1109 Publication ID: 38313

Kelly Williams, Corey Hudson, 34 authors, (2014). RNAcentral: an international database of ncRNA sequences Nucleic Acids Research https://doi.org/10.1093/nar/gku991 Publication ID: 38312

Corey Hudson, Kelly Williams, (2014). LearnedPhyloblocks: Novel Genomic Islands through Phylogenetic Profiling https://www.osti.gov/servlets/purl/1567815 Publication ID: 39201

Corey Hudson, Kelly Williams, (2014). Ends of the line for tmRNA-SmpB Frontiers in Microbiology https://doi.org/10.3389/fmicb.2014.00421 Publication ID: 41174

Lucy Cui, Kelly Williams, Todd Lane, Kunal Poorey, (2014). Metagenomics Analysis on Arizona Algae Cultivation System https://www.osti.gov/servlets/purl/1494259 Publication ID: 37773

Bryan Carson, Michael Sinclair, Jerilyn Timlin, Kelly Williams, Kunal Poorey, Anson Hatch, Conrad James, Ryan Davis, Elisa La Bauve, Howland, Jones, (2014). A Novel Approach to Unknown Virus Identification in Clinical Samples https://www.osti.gov/servlets/purl/1496684 Publication ID: 37598

Michael Sinclair, Jerilyn Timlin, Kelly Williams, Anson Hatch, Bryan Carson, Ryan Davis, (2014). A Novel Approach to Unknown Virus Identification in Clinical Samples https://www.osti.gov/servlets/purl/1140493 Publication ID: 37206

Michael Sinclair, Jerilyn Timlin, Kelly Williams, Anson Hatch, Ryan Davis, Bryan Carson, (2014). A Novel Approach to Unknown Virus Detection in Clinical Samples https://www.osti.gov/servlets/purl/1140514 Publication ID: 37207

Kevin Turner, Corey Hudson, Mary Tran-Gyamfi, Amy Powell, Kelly Williams, (2014). Understanding and regulation of microbial lignolysis for renewable platform chemicals https://doi.org/10.2172/1322272 Publication ID: 36881

Todd Lane, Pamela Lane, Kelly Williams, (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

Kelly Williams, (2013). Pathogenicity island mobility and gene content https://doi.org/10.2172/1104780 Publication ID: 36235

Kelly Williams, Corey Hudson, (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

Todd Lane, Pamela Lane, Kelly Williams, (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

Elisa La Bauve, Bryan Carson, Anson Hatch, Jerilyn Timlin, Michael Sinclair, Kelly Williams, (2013). A Novel Approach to Unknown Virus Identification in Clinical Samples https://www.osti.gov/servlets/purl/1110696 Publication ID: 35697

Hanyoup Kim, Mais Jebrail, Anupama Sinha, Zachary Bent, Owen Solberg, Kelly Williams, Stanley Langevin, Ronald Renzi, James Van De Vreugde, Robert Meagher, Joseph Schoeniger, Todd Lane, Steven Branda, Michael Bartsch, Kamlesh Patel, (2013). A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing PLoS ONE https://www.osti.gov/biblio/1072475 Publication ID: 32780

Corey Hudson, Zachary Bent, Robert Meagher, Kelly Williams, (2013). Mobilome of an NDM-1-encoding Klebsiella pneumoniae strain Antimicrobial Agents and Chemotherapy https://www.osti.gov/biblio/1113066 Publication ID: 34365

Jerilyn Timlin, Michael Sinclair, Bryan Carson, Kelly Williams, Anson Hatch, (2013). A Novel Approach to Unknown Virus Detection in Clinical Samples https://www.osti.gov/servlets/purl/1106843 Publication ID: 34643

Britney Lau, Corey Hudson, Kelly Williams, (2013). Genomic Islands PPT https://www.osti.gov/servlets/purl/1666214 Publication ID: 34745

Todd Lane, Pamela Lane, Kelly Williams, (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

Stanley Langevin, Zachary Bent, Owen Solberg, Deanna Curtis, Pamela Lane, Kelly Williams, Joseph Schoeniger, Todd Lane, Anupama Sinha, (2013). Peregrine: A rapid and unbiased method to produce strand-specific RNA-seq libraries from small quantities of starting material RNA Biology https://www.osti.gov/biblio/1145385 Publication ID: 32058

Todd Lane, Pamela Lane, Kelly Williams, Owen Solberg, (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

Elisa La Bauve, Bryan Carson, Howland Jones, Michael Sinclair, Kelly Williams, Anson Hatch, Jerilyn Timlin, Owen Solberg, (2013). A novel approach to unknown pathogen detection in clinical samples https://www.osti.gov/servlets/purl/1299038 Publication ID: 32148

Stanley Langevin, Todd Lane, Pamela Lane, Zachary Bent, Owen Solberg, Deanna Curtis, Kelly Williams, Steven Branda, Kamlesh Patel, Joseph Schoeniger, (2012). cDNA normalization by hydroxyapatite chromatography to enhance transcriptome diversity in RNA-Seq Applications Biotechniques https://doi.org/10.2144/000113937 Publication ID: 30653

Kelly Williams, (2012). Pathogenicity Island Mobility and Gene Content https://www.osti.gov/servlets/purl/1648001 Publication ID: 30237

Kelly Williams, (2012). Bioinformatic and Molecular Suppression of Human Sequences in Clinical Samples https://www.osti.gov/biblio/1073463 Publication ID: 29731

Todd Lane, Kelly Williams, Owen Solberg, Kamlesh Patel, Steven Branda, Stanley Langevin, Pamela Lane, Zachary Bent, Deanna Curtis, Mary Tran-Gyamfi, Victoria VanderNoot, Joseph Schoeniger, (2012). Rapid Threat Organism Recognition https://www.osti.gov/biblio/1067717 Publication ID: 28455

Steven Branda, Mais Jebrail, James Van De Vreugde, Stanley Langevin, Zachary Bent, Deanna Curtis, Pamela Lane, Bryan Carson, Elisa La Bauve, Kamlesh Patel, James Ricken, Joseph Schoeniger, Owen Solberg, Kelly Williams, Milind Misra, Amy Powell, Nicholas Pattengale, Elebeoba May, Todd Lane, Duane Lindner, Malin Young, Victoria VanderNoot, Numrin Thaitrong, Michael Bartsch, Ronald Renzi, Mary Tran-Gyamfi, Robert Meagher, (2012). Characterization of Pathogens in Clinical Specimens via Suppression of Host Background for Efficient Second Generation Sequencing Analyses https://www.osti.gov/servlets/purl/1141142 Publication ID: 28871

Todd Lane, Pamela Lane, Laura Carney, Owen Solberg, Kelly Williams, (2012). Pond Crash Forensics: Identification and early detection of pond crash agents https://www.osti.gov/biblio/1064189 Publication ID: 28627

Steven Branda, Mais Jebrail, James Van De Vreugde, Stanley Langevin, Zachary Bent, Deanna Curtis, Pamela Lane, Bryan Carson, Elisa La Bauve, Kamlesh Patel, James Ricken, Joseph Schoeniger, Owen Solberg, Kelly Williams, Milind Misra, Amy Powell, Nicholas Pattengale, Elebeoba May, Todd Lane, Duane Lindner, Malin Young, Victoria VanderNoot, Numrin Thaitrong, Michael Bartsch, Ronald Renzi, Mary Tran-Gyamfi, Robert Meagher, (2012). Copy of Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples https://www.osti.gov/servlets/purl/1688623 Publication ID: 27929

Steven Branda, Mais Jebrail, James Van De Vreugde, Stanley Langevin, Zachary Bent, Deanna Curtis, Pamela Lane, Bryan Carson, Elisa La Bauve, Kamlesh Patel, James Ricken, Joseph Schoeniger, Owen Solberg, Kelly Williams, Milind Misra, Amy Powell, Nicholas Pattengale, Elebeoba May, Todd Lane, Duane Lindner, Malin Young, Victoria VanderNoot, Numrin Thaitrong, Michael Bartsch, Ronald Renzi, Mary Tran-Gyamfi, Robert Meagher, (2012). Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples https://www.osti.gov/biblio/1067707 Publication ID: 27930

Stanley Langevin, Zachary Bent, Owen Solberg, Deanna Curtis, Pamela Lane, Kelly Williams, Joseph Schoeniger, Todd Lane, Steven Branda, (2012). Peregrine : https://www.osti.gov/servlets/purl/1294360 Publication ID: 27691

Kelly Williams, (2012). Bioinformatic and Molecular Suppression of Human Sequences in Clinical Samples https://www.osti.gov/biblio/1068429 Publication ID: 27475

Stanley Langevin, Todd Lane, Pamela Lane, Zachary Bent, Owen Solberg, Deanna Curtis, Kelly Williams, Steven Branda, Kamlesh Patel, Joseph Schoeniger, (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

Kelly Williams, Deanna Curtis, Pamela Lane, Todd Lane, (2011). Pond Crash Forensics https://www.osti.gov/servlets/purl/1107562 Publication ID: 23246

Showing Results. Show More 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.