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Humphrey, B., MacKenzie, M., Lobitz, M., Schambach, J.Y., Lasley, G., Kolker, S., Ricken, B., Bennett, H.L., 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). 10.3389/fmicb.2023.1271836

Cahill, J., Humphrey, B., Schambach, J.Y., Lasley, G., Kolker, S., Ricken, B., Bennett, H.L., Williams, K.P., Smallwood, C.R., & Smallwood, C.R. (2023). Phage Therapy for Algae: Biotic Countermeasures that Rescue Algae from a Bacterial Infection [Poster]. 10.2172/2430502

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. 10.2172/1898252

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 Presentation]. 10.2172/2004673

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. 10.2172/1855003

Williams, K.P., Schoeniger, J.S., Mageeney, C.M., Cahill, J., Clark, L., Rybnicky, G., Shormin, F., Ghaffari, N., Jewett, M., & Jewett, M. (2021). Expanding the Utility of Integrases for Genome Editing and Stabilizing Gene Modules in Target Bacteria [Conference Poster]. 10.2172/2002415

Mageeney, C.M., G, R., M, J., Williams, K.P., Schoeniger, J.S., & Schoeniger, J.S. (2021). Phage Factory: Creating a phage for any bacterial species [Conference Poster]. 10.2172/2001647

Mageeney, C.M., Schoeniger, J.S., Williams, K.P., & Williams, K.P. (2021). Computational Front End for Creating a Universal Phage Engineering Platform [Conference Presentation]. 10.2172/1888459

Tommasini, D., Mageeney, C.M., Williams, K.P., & Williams, K.P. (2021). Helper-Embedded Satellites (HESs): Useful New Vectors [Conference Presentation]. 10.2172/1867558

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]. 10.2172/1847584

Treece, A., Corbin, W., Caskey, S., 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. 10.2172/1617440

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., Haeseleer, J., 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

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

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

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

Peterson, K.J., 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

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

Ruffing, A.M., Bachand, G.D., Timlin, J.A., Manginell, R., Hudson, C.M., Williams, K.P., Rempe, S., 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

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

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. 10.1093/nar/gkw601

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. 10.1016/j.algal.2016.05.011

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

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

Ray, D., Schoeniger, J.S., Williams, K.P., Hudson, C.M., & Hudson, C.M. (2015). Genomic Prediction & comparative analysis of Pathogenicity of the new ?super bug?: Clostridium difficile [Presentation]. https://www.osti.gov/biblio/1342460

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

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

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

Hudson, C.M., Lau, B.Y., Williams, K.P., & Williams, K.P. (2015). Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes. Nucleic Acids Research, 43(D1), pp. D48-D53. 10.1093/nar/gku1072

Williams, K.P., Hudson, C.M., Otherauthors, A., & Otherauthors, A. (2014). RNAcentral: an international database of ncRNA sequences. Nucleic Acids Research, 43(D1). 10.1093/nar/gku991

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.T., & Jones, H.T. (2014). A Novel Approach to Unknown Virus Identification in Clinical Samples [Presentation]. https://www.osti.gov/biblio/1496684

Turner, K., Hudson, C.M., Tran-Gyamfi, M., Powell, A.J., Williams, K.P., & Williams, K.P. (2013). Understanding and regulation of microbial lignolysis for renewable platform chemicals. 10.2172/1322272

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

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

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

la Bauve, E., Jones, H.D.T., Sinclair, M.B., Williams, K.P., Solberg, O.D., Timlin, J.A., Hatch, A., Carson, B., & Carson, B. (2013). A novel approach to unknown pathogen detection in clinical samples [Presentation]. https://www.osti.gov/biblio/1299038

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). 10.2144/000113937

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

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

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

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

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

94 Results
94 Results