Paul Keim - Scholarly Works - Northern Arizona University

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Research activity per year

416 Article
26 Chapter
18 Review article
16 Comment/debate
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1 - 50 out of 496 results

2024
A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditions
NIH Researching COVID to Enhance Recovery (RECOVER) Consortium, 2024, In: Frontiers in Systems Biology. 4, 1422384.
Research output: Contribution to journal › Review article › peer-review

Open Access
ColiSeq: a multiplex amplicon assay that provides strain level resolution of Escherichia coli directly from clinical specimens
Williamson, C. H. D., Vazquez, A. J., Nunnally, A. E., Kyger, K., Fofanov, V. Y., Furstenau, T. N., Hornstra, H. M., Terriquez, J., Keim, P. & Sahl, J. W., Jun 2024, In: Microbiology spectrum. 12, 6
Research output: Contribution to journal › Article › peer-review

Open Access
Developing a Coccidioides posadasii and SARS-CoV-2 Co-infection Model in the K18-hACE2 Transgenic Mouse
Kollath, D. R., Grill, F. J., Itogawa, A. N., Fabio-Braga, A., Morales, M. M., Shepardson, K. M., Bryant, M. L., Yi, J., Ramsey, M. L., Luberto, E. T., Celona, K. R., Keim, P. S., Settles, E. W., Lake, D. & Barker, B. M., Dec 2024, In: Communications Medicine. 4, 1, 186.
Research output: Contribution to journal › Article › peer-review

Open Access
Epistasis, core-genome disharmony, and adaptation in recombining bacteria
Taylor, A. J., Yahara, K., Pascoe, B., Ko, S., Mageiros, L., Mourkas, E., Calland, J. K., Puranen, S., Hitchings, M. D., Jolley, K. A., Kobras, C. M., Bayliss, S., Williams, N. J., van Vliet, A. H. M., Parkhill, J., Maiden, M. C. J., Corander, J., Hurst, L. D., Falush, D. & Keim, P. & 3 others, Didelot, X., Kelly, D. J. & Sheppard, S. K., Jun 2024, In: mBio. 15, 6
Research output: Contribution to journal › Article › peer-review

Open Access
In vitro small molecule screening to inform novel candidates for use in fluconazole combination therapy in vivo against Coccidioides
Mead, H. L., Valentine, M., Yin, H., Thompson, G. R., Keim, P., Engelthaler, D. M. & Barker, B. M., Oct 2024, In: Microbiology spectrum. 12, 10, 01008-24.
Research output: Contribution to journal › Article › peer-review

Open Access
Melioidosis in goats at a single Australian farm was caused by multiple diverse lineages of Burkholderia pseudomallei present in soil
Busch, J. D., Kaestli, M., Mayo, M., Roe, C. C., Vazquez, A. J., Choy, J. L., Harrington, G., Benedict, S., Stone, N. E., Allender, C. J., Bowen, R. A., Keim, P., Currie, B. J., Sahl, J. W., Tuanyok, A. & Wagner, D. M., 2024, In: PLoS neglected tropical diseases. 18, 12, e0012683.
Research output: Contribution to journal › Article › peer-review

Open Access
Multiple Introductions of Yersinia pestis during Urban Pneumonic Plague Epidemic, Madagascar, 2017
Andrianaivoarimanana, V., Savin, C., Birdsell, D. N., Vogler, A. J., Guern, A. S. L., Rahajandraibe, S., Brémont, S., Rahelinirina, S., Sahl, J. W., Ramasindrazana, B., Rakotonanahary, R. J. L., Rakotomanana, F., Randremanana, R., Maheriniaina, V., Razafimbia, V., Kwasiborski, A., Balière, C., Ratsitorahina, M., Baril, L. & Keim, P. & 6 others, Caro, V., Rasolofo, V., Spiegel, A., Pizarro-Cerda, J., Wagner, D. M. & Rajerison, M., Feb 2024, In: Emerging infectious diseases. 30, 2, p. 289-298 10 p.
Research output: Contribution to journal › Article › peer-review

Open Access
4 Scopus citations
2023
A conserved active site PenA β-lactamase Ambler motif specific for Burkholderia pseudomallei/B. mallei is likely responsible for intrinsic amoxicillin-clavulanic acid sensitivity and facilitates a simple diagnostic PCR assay for melioidosis
Somprasong, N., Hagen, J. P., Sahl, J. W., Webb, J. R., Hall, C. M., Currie, B. J., Wagner, D. M., Keim, P. & Schweizer, H. P., Mar 2023, In: International Journal of Antimicrobial Agents. 61, 3, 106714.
Research output: Contribution to journal › Article › peer-review

Open Access
4 Scopus citations
A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment
Williamson, C. H. D., Roe, C. C., Terriquez, J., Hornstra, H., Lucero, S., Nunnally, A. E., Vazquez, A. J., Vinocur, J., Plude, C., Nienstadt, L., Stone, N. E., Celona, K. R., Wagner, D. M., Keim, P. & Sahl, J. W., 2023, In: Microbial Genomics. 9, 6, 001046.
Research output: Contribution to journal › Article › peer-review

Open Access
5 Scopus citations
Antibody responses to the host microbiome in chronic rhinosinusitis
Lal, D., Song, L., Brar, T., Cope, E. K., Keim, P., Williams, S., Chung, Y., Murugan, V., LaBaer, J. & Magee, D. M., Aug 2023, In: International Forum of Allergy and Rhinology. 13, 8, p. 1503-1510 8 p.
Research output: Contribution to journal › Article › peer-review
5 Scopus citations
Burkholderia thailandensis Isolated from the Environment, United States
Hall, C. M., Stone, N. E., Martz, M., Hutton, S. M., Santana-Propper, E., Versluis, L., Guidry, K., Ortiz, M., Busch, J. D., Maness, T., Stewart, J., Sidwa, T., Gee, J. E., Elrod, M. G., Petras, J. K., Ty, M. C., Gulvik, C., Weiner, Z. P., Salzer, J. S. & Hoffmaster, A. R. & 6 others, Rivera-Garcia, S., Keim, P., Kieffer, A., Sahl, J. W., Soltero, F. & Wagner, D. M., Mar 2023, In: Emerging infectious diseases. 29, 3, p. 618-621 4 p.
Research output: Contribution to journal › Article › peer-review

Open Access
5 Scopus citations
Development and evaluation of a multiplex serodiagnostic bead assay (BurkPx) for accurate melioidosis diagnosis
Settles, E. W., Sonderegger, D., Shannon, A. B., Celona, K. R., Lederer, R., Yi, J., Seavey, C., Headley, K., Mbegbu, M., Harvey, M., Keener, M., Allender, C., Hornstra, H., Monroy, F. P., Woerle, C., Theobald, V., Mayo, M., Currie, B. J. & Keim, P., Feb 8 2023, In: PLoS neglected tropical diseases. 17, 2, e0011072.
Research output: Contribution to journal › Article › peer-review

Open Access
2 Scopus citations
Exploring Cefiderocol Resistance Mechanisms in Burkholderia pseudomallei
Hall, C. M., Somprasong, N., Hagen, J. P., Nottingham, R., Sahl, J. W., Webb, J. R., Mayo, M., Currie, B. J., Podin, Y., Wagner, D. M., Keim, P. & Schweizer, H. P., Jun 2023, In: Antimicrobial Agents and Chemotherapy. 67, 6
Research output: Contribution to journal › Article › peer-review

Open Access
6 Scopus citations
Factor Xa cleaves SARS-CoV-2 spike protein to block viral entry and infection
Dong, W., Wang, J., Tian, L., Zhang, J., Settles, E. W., Qin, C., Steinken-Kollath, D. R., Itogawa, A. N., Celona, K. R., Yi, J., Bryant, M., Mead, H., Jaramillo, S. A., Lu, H., Li, A., Zumwalt, R. E., Dadwal, S., Feng, P., Yuan, W. & Whelan, S. P. J. & 4 others, Keim, P. S., Barker, B. M., Caligiuri, M. A. & Yu, J., Dec 2023, In: Nature Communications. 14, 1, 1936.
Research output: Contribution to journal › Article › peer-review

Open Access
6 Scopus citations
Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition
Highlander, S. K., Wood, J. M., Gillece, J. D., Folkerts, M., Fofanov, V., Furstenau, T., Singh, N. K., Guan, L., Seuylemezian, A., Benardini, J. N., Engelthaler, D. M., Venkateswaran, K. & Keim, P. S., Mar 2023, In: PLoS ONE. 18, 3 March, e0282428.
Research output: Contribution to journal › Article › peer-review

Open Access
4 Scopus citations
NHP BurkPx: A multiplex serodiagnostic bead assay to monitor Burkholderia pseudomallei exposures in non-human primates
Celona, K. R., Shannon, A. B., Sonderegger, D., Yi, J., Monroy, F. P., Allender, C., Hornstra, H., Barnes, M. B., Didier, E. S., Bohm, R. P., Phillippi-Falkenstein, K., Sanford, D., Keim, P. & Settles, E. W., Feb 8 2023, In: PLoS neglected tropical diseases. 17, 2, e0011067.
Research output: Contribution to journal › Article › peer-review

Open Access
Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections
Liu, C. M., Aziz, M., Park, D. E., Wu, Z., Stegger, M., Li, M., Wang, Y., Schmidlin, K., Johnson, T. J., Koch, B. J., Hungate, B. A., Nordstrom, L., Gauld, L., Weaver, B., Rolland, D., Statham, S., Hall, B., Sariya, S., Davis, G. S. & Keim, P. S. & 2 others, Johnson, J. R. & Price, L. B., Jun 2023, In: One Health. 16, 100518.
Research output: Contribution to journal › Article › peer-review

Open Access
21 Scopus citations
2022
A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain "Silveira"
De Melo Teixeira, M., Stajich, J. E., Sahl, J. W., Thompson, G. R., Brem, R. B., Dubin, C. A., Blackmon, A. V., Mead, H. L., Keim, P. & Barker, B. M., Apr 2022, In: G3: Genes, Genomes, Genetics. 12, 4, jkac031.
Research output: Contribution to journal › Article › peer-review

Open Access
11 Scopus citations
Coccidioidomycosis in Northern Arizona: an Investigation of the Host, Pathogen, and Environment Using a Disease Triangle Approach
Mead, H. L., Kollath, D. R., de Melo Teixeira, M., Roe, C. C., Plude, C., Nandurkar, N., Donohoo, C., O'Connor, B. L. W., Terriquez, J., Keim, P. & Barker, B. M., Sep 2022, In: mSphere. 7, 5
Research output: Contribution to journal › Article › peer-review

Open Access
4 Scopus citations
COVID-19 vaccination elicits an evolving, cross-reactive antibody response to epitopes conserved with endemic coronavirus spike proteins
Elko, E. A., Nelson, G. A., Mead, H. L., Kelley, E. J., Carvalho, S. T., Sarbo, N. G., Harms, C. E., Le Verche, V., Cardoso, A. A., Ely, J. L., Boyle, A. S., Piña, A., Henson, S. N., Rahee, F., Keim, P. S., Celona, K. R., Yi, J., Settles, E. W., Bota, D. A. & Yu, G. C. & 4 others, Morris, S. R., Zaia, J. A., Ladner, J. T. & Altin, J. A., Jul 5 2022, In: Cell Reports. 40, 1, 111022.
Research output: Contribution to journal › Article › peer-review

Open Access
12 Scopus citations
Expanding the Burkholderia pseudomallei Complex with the Addition of Two Novel Species: Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov.
Hall, C. M., Baker, A. L., Sahl, J. W., Mayo, M., Scholz, H. C., Kaestli, M., Schupp, J., Martz, M., Settles, E. W., Busch, J. D., Sidak-Loftis, L., Thomas, A., Kreutzer, L., Georgi, E., Schweizer, H. P., Warner, J. M., Keim, P., Currie, B. J. & Wagner, D. M., Jan 2022, In: Applied and Environmental Microbiology. 88, 1, e01583-21.
Research output: Contribution to journal › Article › peer-review

Open Access
14 Scopus citations
Genomic characterization of Francisella tularensis and other diverse Francisella species from complex samples
Wagner, D. M., Birdsell, D. N., McDonough, R. F., Nottingham, R., Kocos, K., Celona, K., Özsürekci, Y., Öhrman, C., Karlsson, L., Myrtennäs, K., Sjödin, A., Johansson, A., Keim, P. S., Forsman, M. & Sahl, J. W., Oct 2022, In: PLoS ONE. 17, 10 October, e0273273.
Research output: Contribution to journal › Article › peer-review

Open Access
7 Scopus citations
Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations
Williamson, C. H. D., Stone, N. E., Nunnally, A. E., Roe, C. C., Vazquez, A. J., Lucero, S. A., Hornstra, H., Wagner, D. M., Keim, P., Rupnik, M., Janezic, S. & Sahl, J. W., 2022, In: Microbial Genomics. 8, 2, 000742.
Research output: Contribution to journal › Article › peer-review

Open Access
17 Scopus citations
Multiple phylogenetically-diverse, differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand
Roe, C., Vazquez, A. J., Phillips, P. D., Allender, C. J., Bowen, R. A., Nottingham, R. D., Doyle, A., Wongsuwan, G., Wuthiekanun, V., Limmathurotsakul, D., Peacock, S., Keim, P., Tuanyok, A., Wagner, D. M. & Sahl, J. W., Feb 2022, In: PLoS neglected tropical diseases. 16, 2, e0010172.
Research output: Contribution to journal › Article › peer-review

Open Access
8 Scopus citations
Off-the-shelf CAR natural killer cells secreting IL-15 target spike in treating COVID-19
Lu, T., Ma, R., Dong, W., Teng, K. Y., Kollath, D. S., Li, Z., Yi, J., Bustillos, C., Ma, S., Tian, L., Mansour, A. G., Li, Z., Settles, E. W., Zhang, J., Keim, P. S., Barker, B. M., Caligiuri, M. A. & Yu, J., Dec 2022, In: Nature Communications. 13, 1, 2576.
Research output: Contribution to journal › Article › peer-review

Open Access
35 Scopus citations
Stenoparib, an inhibitor of cellular poly (ADP-ribose) polymerases (PARPs), blocks in vitro replication of SARS-CoV-2 variants
Zarn, K. E., Jaramillo, S. A., Zapata, A. R., Stone, N. E., Jones, A. N., Nunnally, H. E., Settles, E. W., Ng, K., Keim, P. S., Knudsen, S., Nuijten, P. M., Tijsma, A. S. L. & French, C. T., Sep 2022, In: PLoS ONE. 17, 9 September, e0272916.
Research output: Contribution to journal › Article › peer-review

Open Access
6 Scopus citations
The K18-Human ACE2 Transgenic Mouse Model Recapitulates Non-severe and Severe COVID-19 in Response to an Infectious Dose of the SARS-CoV-2 Virus
Dong, W., Mead, H., Tian, L., Park, J. G., Garcia, J. I., Jaramillo, S., Barr, T., Kollath, D. S., Coyne, V. K., Stone, N. E., Jones, A., Zhang, J., Li, A., Wang, L. S., Milanes-Yearsley, M., Torrelles, J. B., Martinez-Sobrido, L., Keim, P. S., Marie Barker, B. & Caligiuri, M. A. & 1 others, Yu, J., Jan 2022, In: Journal of Virology. 96, 1, e00964-21.
Research output: Contribution to journal › Article › peer-review

Open Access
105 Scopus citations
2021
Burkholderia pseudomallei OMVs derived from infection mimicking conditions elicit similar protection to a live-attenuated vaccine
Baker, S. M., Settles, E. W., Davitt, C., Gellings, P., Kikendall, N., Hoffmann, J., Wang, Y., Bitoun, J., Lodrigue, K. R., Sahl, J. W., Keim, P., Roy, C., McLachlan, J. & Morici, L. A., Dec 2021, In: npj Vaccines. 6, 1, 18.
Research output: Contribution to journal › Article › peer-review

Open Access
29 Scopus citations
Burkholderia ubonensis high-level tetracycline resistance is due to efflux pump synergy involving a novel teta(64) resistance determinant
Somprasong, N., Hall, C. M., Webb, J. R., Sahl, J. W., Wagner, D. M., Keim, P., Currie, B. J. & Schweizer, H. P., Mar 2021, In: Antimicrobial Agents and Chemotherapy. 65, 3, e01767-20.
Research output: Contribution to journal › Article › peer-review

Open Access
7 Scopus citations
Conservation of resistance-nodulation-cell division efflux pump-mediated antibiotic resistance in burkholderia cepacia complex and burkholderia pseudomallei complex species
Somprasong, N., Yi, J., Hall, C. M., Webb, J. R., Sahl, J. W., Wagner, D. M., Keim, P., Currie, B. J. & Schweizer, H. P., Sep 2021, In: Antimicrobial Agents and Chemotherapy. 65, 9, e00920-21.
Research output: Contribution to journal › Article › peer-review

Open Access
8 Scopus citations
Detection of SARS-CoV-2 and its S and N proteins using surface enhanced Raman spectroscopy
Sanchez, J. E., Jaramillo, S. A., Settles, E., Velazquez Salazar, J. J., Lehr, A., Gonzalez, J., Rodríguez Aranda, C., Navarro-Contreras, H. R., Raniere, M. O., Harvey, M., Wagner, D. M., Koppisch, A., Kellar, R., Keim, P. & Jose Yacaman, M., Jul 2 2021, In: RSC Advances. 11, 41, p. 25788-25794 7 p.
Research output: Contribution to journal › Article › peer-review

Open Access
61 Scopus citations
Leptospira in river and soil in a highly endemic area of Ecuador
Miller, E., Barragan, V., Chiriboga, J., Weddell, C., Luna, L., Jiménez, D. J., Aleman, J., Mihaljevic, J. R., Olivas, S., Marks, J., Izurieta, R., Nieto, N., Keim, P., Trueba, G., Caporaso, J. G. & Pearson, T., Dec 2021, In: BMC microbiology. 21, 1, 17.
Research output: Contribution to journal › Article › peer-review

Open Access
19 Scopus citations
No evidence for enzootic plague within black-tailed prairie dog (Cynomys ludovicianus) populations
Colman, R. E., Brinkerhoff, R. J., Busch, J. D., Ray, C., Doyle, A., Sahl, J. W., Keim, P., Collinge, S. K. & Wagner, D. M., Nov 2021, In: Integrative Zoology. 16, 6, p. 834-851 18 p.
Research output: Contribution to journal › Article › peer-review

Open Access
10 Scopus citations
Plasma metagenomic sequencing to detect and quantify bacterial DNA in ICU patients suspected of sepsis: A proof-of-principle study
Kisat, M. T., Odenheimer-Bergman, A., Markus, H., Joseph, B., Srivatsan, S. N., Contente-Cuomo, T., Khalpey, Z., Keim, P., O'Keeffe, T., Askari, R., Salim, A., Rhee, P. & Murtaza, M., Dec 2021, In: Journal of Trauma and Acute Care Surgery. 91, 6, p. 988-994 7 p.
Research output: Contribution to journal › Article › peer-review
3 Scopus citations
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics
Martínez Arbas, S., Narayanasamy, S., Herold, M., Lebrun, L. A., Hoopmann, M. R., Li, S., Lam, T. J., Kunath, B. J., Hicks, N. D., Liu, C. M., Price, L. B., Laczny, C. C., Gillece, J. D., Schupp, J. M., Keim, P. S., Moritz, R. L., Faust, K., Tang, H., Ye, Y. & Skupin, A. & 3 others, May, P., Muller, E. E. L. & Wilmes, P., Jan 2021, In: Nature Microbiology. 6, 1, p. 123-135 13 p.
Research output: Contribution to journal › Article › peer-review

Open Access
44 Scopus citations
St. Louis Encephalitis Virus in the Southwestern United States: A Phylogeographic Case for a Multi-Variant Introduction Event
Ridenour, C. L., Cocking, J., Poidmore, S., Erickson, D., Brock, B., Valentine, M., Roe, C. C., Young, S. J., Henke, J. A., Hung, K. Y., Wittie, J., Stefanakos, E., Sumner, C., Ruedas, M., Raman, V., Seaton, N., Bendik, W., Hornstra O’Neill, H. M., Sheridan, K. & Centner, H. & 9 others, Lemmer, D., Fofanov, V., Smith, K., Will, J., Townsend, J., Foster, J. T., Keim, P. S., Engelthaler, D. M. & Hepp, C. M., Jun 8 2021, In: Frontiers in Genetics. 12, 667895.
Research output: Contribution to journal › Article › peer-review

Open Access
7 Scopus citations
Stenoparib, an inhibitor of cellular poly(Adp-ribose) polymerase, blocks replication of the sars-cov-2 and hcov-nl63 human coronaviruses in vitro
Stone, N. E., Jaramillo, S. A., Jones, A. N., Vazquez, A. J., Martz, M., Versluis, L. M., Raniere, M. O., Nunnally, H. E., Zarn, K. E., Nottingham, R., Ng, K. R., Sahl, J. W., Wagner, D. M., Knudsen, S., Settles, E. W., Keim, P. & French, C. T., 2021, In: mBio. 12, 1, p. 1-12 12 p., e03495-20.
Research output: Contribution to journal › Article › peer-review

Open Access
16 Scopus citations
The Distinctive Evolution of orfX Clostridium parabotulinum Strains and Their Botulinum Neurotoxin Type A and F Gene Clusters Is Influenced by Environmental Factors and Gene Interactions via Mobile Genetic Elements
Smith, T. J., Williamson, C. H. D., Hill, K. K., Johnson, S. L., Xie, G., Anniballi, F., Auricchio, B., Fernández, R. A., Caballero, P. A., Keim, P. & Sahl, J. W., Feb 26 2021, In: Frontiers in Microbiology. 12, 566908.
Research output: Contribution to journal › Article › peer-review

Open Access
13 Scopus citations
2020
An early pandemic analysis of sars-cov-2 population structure and dynamics in arizona
Ladner, J. T., Larsen, B. B., Bowers, J. R., Hepp, C. M., Bolyen, E., Folkerts, M., Sheridan, K., Pfeiffer, A., Yaglom, H., Lemmer, D., Sahl, J. W., Kaelin, E. A., Maqsood, R., Bokulich, N. A., Quirk, G., Watts, T. D., Komatsu, K. K., Waddell, V., Lim, E. S. & Caporaso, J. G. & 3 others, Engelthaler, D. M., Worobey, M. & Keim, P., Sep 1 2020, In: mBio. 11, 5, p. 1-13 13 p., e02107-20.
Research output: Contribution to journal › Article › peer-review

Open Access
20 Scopus citations
Burkholderia ubonensis meropenem resistance: insights into distinct properties of class a β-lactamases in burkholderia cepacia complex and burkholderia pseudomallei complex bacteria
Somprasong, N., Hall, C. M., Webb, J. R., Sahl, J. W., Wagner, D. M., Keim, P., Currie, B. J. & Schweizer, H. P., Mar 1 2020, In: mBio. 11, 2, e00592-20.
Research output: Contribution to journal › Article › peer-review

Open Access
8 Scopus citations
Differential thermotolerance adaptation between species of coccidioides
Mead, H. L., Hamm, P. S., Shaffer, I. N., Teixeira, M. D. M., Wendel, C. S., Wiederhold, N. P., Thompson, G. R., Muñiz-Salazar, R., Castañón-Olivares, L. R., Keim, P., Plude, C., Terriquez, J., Galgiani, J. N., Orbach, M. J. & Barker, B. M., Dec 2020, In: Journal of Fungi. 6, 4, p. 1-14 14 p., 366.
Research output: Contribution to journal › Article › peer-review

Open Access
20 Scopus citations
Draft whole-genome sequences of ciprofloxacin-resistant derivatives of a bacillus anthracis ΔANR strain lacking pXO1 and pXO2 plasmids
Biggs, T. D., Karavis, M. A., Harris, J. V., Hill, J. M., Bernhards, R. C., Price, L. B., Keim, P., Goodwin, B. G. & Sozhamannan, S., Apr 9 2020, In: Microbiology Resource Announcements. 9, 15, e00056-20.
Research output: Contribution to journal › Article › peer-review

Open Access
Genomic Characterization of Newly Completed Genomes of Botulinum Neurotoxin-Producing Species from Argentina, Australia, and Africa
Smith, T. J., Xie, G., Williamson, C. H. D., Hill, K. K., Fernández, R. A., Sahl, J. W., Keim, P., Johnson, S. L. & Delaye, L., Mar 17 2020, In: Genome Biology and Evolution. 12, 3, p. 229-242 14 p.
Research output: Contribution to journal › Article › peer-review

Open Access
13 Scopus citations
Genomic characterization of Parengyodontium americanum sp. nov
Teixeira, M. D. M., Muszewska, A., Travis, J., Moreno, L. F., Ahmed, S., Roe, C., Mead, H., Steczkiewicz, K., Lemmer, D., de Hoog, S., Keim, P., Wiederhold, N. & Barker, B. M., May 2020, In: Fungal Genetics and Biology. 138, 103351.
Research output: Contribution to journal › Article › peer-review

Open Access
4 Scopus citations
Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance
Herold, M., Martínez Arbas, S., Narayanasamy, S., Sheik, A. R., Kleine-Borgmann, L. A. K., Lebrun, L. A., Kunath, B. J., Roume, H., Bessarab, I., Williams, R. B. H., Gillece, J. D., Schupp, J. M., Keim, P. S., Jäger, C., Hoopmann, M. R., Moritz, R. L., Ye, Y., Li, S., Tang, H. & Heintz-Buschart, A. & 4 others, May, P., Muller, E. E. L., Laczny, C. C. & Wilmes, P., Dec 1 2020, In: Nature Communications. 11, 1, 5281.
Research output: Contribution to journal › Article › peer-review

Open Access
59 Scopus citations
Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection
Pearson, T., Sahl, J. W., Hepp, C. M., Handady, K., Hornstra, H., Vazquez, A. J., Settles, E., Mayo, M., Kaestli, M., Williamson, C. H. D., Price, E. P., Sarovich, D. S., Cook, J. M., Wolken, S. R., Bowen, R. A., Tuanyok, A., Foster, J. T., Drees, K. P., Kidd, T. J. & Bell, S. C. & 2 others, Currie, B. J. & Keim, P., 2020, In: PLoS Pathogens. 16, 3, e1008298.
Research output: Contribution to journal › Article › peer-review

Open Access
16 Scopus citations
Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity
Caporaso, J. G., Bolyen, E., Dillon, M. R., Bokulich, N. A., Ladner, J. T., Larsen, B. B., Hepp, C. M., Lemmer, D., Sahl, J. W., Sanchez, A., Holdgraf, C., Sewell, C., Choudhury, A. G., Stachurski, J., McKay, M., Simard, A., Engelthaler, D. M., Worobey, M. & Keim, P., 2020, In: F1000Research. 9, 657.
Research output: Contribution to journal › Article › peer-review

Open Access
14 Scopus citations
2019
A global to local genomics analysis of clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network
Williamson, C. H. D., Stone, N. E., Nunnally, A. E., Hornstra, H. M., Wagner, D. M., Roe, C. C., Vazquez, A. J., Nandurkar, N., Vinocur, J., Terriquez, J., Gillece, J., Travis, J., Lemmer, D., Keim, P. & Sahl, J. W., Jul 2019, In: Microbial Genomics. 5, 7, 000271.
Research output: Contribution to journal › Article › peer-review

Open Access
6 Scopus citations
A single introduction of Yersinia pestis to Brazil during the 3^rd plague pandemic
Vogler, A. J., Sahl, J. W., Leal, N. C., Sobreira, M., Williamson, C. H. D., Bollig, M. C., Birdsell, D. N., Rivera, A., Thompson, B., Nottingham, R., Rezende, A. M., Keim, P., Almeida, A. M. P. & Wagner, D. M., Jan 2019, In: PLoS ONE. 14, 1, e0209478.
Research output: Contribution to journal › Article › peer-review

Open Access
9 Scopus citations
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (Nature Biotechnology, (2019), 37, 8, (852-857), 10.1038/s41587-019-0209-9)
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J. & Cope, E. K. & 92 others, Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R. & Caporaso, J. G., Sep 1 2019, In: Nature Biotechnology. 37, 9, p. 1091 1 p.
Research output: Contribution to journal › Comment/debate › peer-review

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455 Scopus citations