A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
Naccache, Samia N, Federman, Scot, Veeraraghavan, Narayanan, Zaharia, Matei, Lee, Deanna, Samayoa, Erik, Bouquet, Jerome, Greninger, Alexander L, Luk, Ka-Cheung, Enge, Barryett, Wadford, Debra A, Messenger, Sharon L, Genrich, Gillian L, Pellegrino, Kristen, Grard, Gilda, Leroy, Eric, Schneider, Bradley S, Fair, Joseph N, Martínez, Miguel A, Isa, Pavel, Crump, John A, DeRisi, Joseph L, Sittler, Taylor, Hackett, Jr, John, Miller, Steve, Chiu, Charles Y
Published in Genome research (01.07.2014)
Published in Genome research (01.07.2014)
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A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012–14): a retrospective cohort study
Greninger, Alexander L, MD, Naccache, Samia N, PhD, Messacar, Kevin, MD, Clayton, Anna, BSc, Yu, Guixia, BSc, Somasekar, Sneha, BSc, Federman, Scot, BA, Stryke, Doug, BSc, Anderson, Christopher, BSc, Yagi, Shigeo, PhD, Messenger, Sharon, PhD, Wadford, Debra, PhD, Xia, Dongxiang, MD, Watt, James P, MD, Van Haren, Keith, MD, Dominguez, Samuel R, MD, Glaser, Carol, MD, Aldrovandi, Grace, Prof, Chiu, Charles Y, Dr
Published in The Lancet infectious diseases (01.06.2015)
Published in The Lancet infectious diseases (01.06.2015)
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Case Definitions, Diagnostic Algorithms, and Priorities in Encephalitis: Consensus Statement of the International Encephalitis Consortium
Venkatesan, A., Tunkel, A. R., Bloch, K. C., Lauring, A. S., Sejvar, J., Bitnun, A., Stahl, J-P., Mailles, A., Drebot, M., Rupprecht, C. E., Yoder, J., Cope, J. R., Wilson, M. R., Whitley, R. J., Sullivan, J., Granerod, J., Jones, C., Eastwood, K., Ward, K. N., Durrheim, D. N., Solbrig, M. V., Guo-Dong, L., Glaser, C. A.
Published in Clinical infectious diseases (15.10.2013)
Published in Clinical infectious diseases (15.10.2013)
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A forty-year review of Rocky Mountain spotted fever cases in California shows clinical and epidemiologic changes
Kjemtrup, Anne M, Padgett, Kerry, Paddock, Christopher D, Messenger, Sharon, Hacker, Jill K, Feiszli, Tina, Melgar, Michael, Metzger, Marco E, Hu, Renjie, Kramer, Vicki L
Published in PLoS neglected tropical diseases (01.09.2022)
Published in PLoS neglected tropical diseases (01.09.2022)
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Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016
Chiu, Charles Y, Coffey, Lark L, Murkey, Jamie, Symmes, Kelly, Sample, Hannah A, Wilson, Michael R, Naccache, Samia N, Arevalo, Shaun, Somasekar, Sneha, Federman, Scot, Stryke, Doug, Vespa, Paul, Schiller, Gary, Messenger, Sharon, Humphries, Romney, Miller, Steve, Klausner, Jeffrey D
Published in Emerging infectious diseases (01.10.2017)
Published in Emerging infectious diseases (01.10.2017)
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Journal Article
Evaluation of co-circulating pathogens and microbiome from COVID-19 infections
Thissen, James B, Morrison, Michael D, Mulakken, Nisha, Nelson, William C, Daum, Chris, Messenger, Sharon, Wadford, Debra A, Jaing, Crystal
Published in PloS one (01.12.2022)
Published in PloS one (01.12.2022)
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Journal Article
Evaluation of co-circulating pathogens and microbiome from COVID-19 infections
Thissen, James B., Morrison, Michael D., Mulakken, Nisha, Nelson, William C., Daum, Chris, Messenger, Sharon, Wadford, Debra A., Jaing, Crystal, Onwuamah, ed., Chika Kingsley
Published in PloS one (01.12.2022)
Published in PloS one (01.12.2022)
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Epidemiologic and environmental characterization of the Re-emergence of St. Louis Encephalitis Virus in California, 2015-2020
Danforth, Mary E, Snyder, Robert E, Feiszli, Tina, Bullick, Teal, Messenger, Sharon, Hanson, Carl, Padgett, Kerry, Coffey, Lark L, Barker, Christopher M, Reisen, William K, Kramer, Vicki L
Published in PLoS neglected tropical diseases (01.08.2022)
Published in PLoS neglected tropical diseases (01.08.2022)
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West Nile virus in California, 2003-2018: A persistent threat
Snyder, Robert E, Feiszli, Tina, Foss, Leslie, Messenger, Sharon, Fang, Ying, Barker, Christopher M, Reisen, William K, Vugia, Duc J, Padgett, Kerry A, Kramer, Vicki L
Published in PLoS neglected tropical diseases (01.11.2020)
Published in PLoS neglected tropical diseases (01.11.2020)
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Long-Term Rodent Surveillance after Outbreak of Hantavirus Infection, Yosemite National Park, California, USA, 2012
Danforth, Mary E, Messenger, Sharon, Buttke, Danielle, Weinburke, Matthew, Carroll, George, Hacker, Gregory, Niemela, Michael, Andrews, Elizabeth S, Jackson, Bryan T, Kramer, Vicki, Novak, Mark
Published in Emerging infectious diseases (01.03.2020)
Published in Emerging infectious diseases (01.03.2020)
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Emerging Epidemiology of Bat-Associated Cryptic Cases of Rabies in Humans in the United States
Messenger, Sharon L., Smith, Jean S., Rupprecht, Charles E.
Published in Clinical infectious diseases (15.09.2002)
Published in Clinical infectious diseases (15.09.2002)
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The Eco-epidemiology of Pacific Coast Tick Fever in California
Padgett, Kerry A, Bonilla, Denise, Eremeeva, Marina E, Glaser, Carol, Lane, Robert S, Porse, Charsey Cole, Castro, Martin B, Messenger, Sharon, Espinosa, Alex, Hacker, Jill, Kjemtrup, Anne, Ryan, Bonnie, Scott, Jamesina J, Hu, Renjie, Yoshimizu, Melissa Hardstone, Dasch, Gregory A, Kramer, Vicki
Published in PLoS neglected tropical diseases (05.10.2016)
Published in PLoS neglected tropical diseases (05.10.2016)
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Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples
Kimbrel, Jeffrey, Moon, Joseph, Avila-Herrera, Aram, Martí, Jose Manuel, Thissen, James, Mulakken, Nisha, Sandholtz, Sarah H, Ferrell, Tyshawn, Daum, Chris, Hall, Sara, Segelke, Brent, Arrildt, Kathryn T, Messenger, Sharon, Wadford, Debra A, Jaing, Crystal, Allen, Jonathan E, Borucki, Monica K
Published in Viruses (13.12.2022)
Published in Viruses (13.12.2022)
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Journal Article
Novel Focus of Sin Nombre Virus in Peromyscus eremicus Mice, Death Valley National Park, California, USA
Burns, Joseph E, Metzger, Marco E, Messenger, Sharon, Fritz, Curtis L, Vilcins, Inger-Marie E, Enge, Barryett, Bronson, Lawrence R, Kramer, Vicki L, Hu, Renjie
Published in Emerging infectious diseases (01.06.2018)
Published in Emerging infectious diseases (01.06.2018)
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Journal Article
Hantavirus infections among overnight visitors to Yosemite National Park, California, USA, 2012
Núñez, Jonathan J, Fritz, Curtis L, Knust, Barbara, Buttke, Danielle, Enge, Barryett, Novak, Mark G, Kramer, Vicki, Osadebe, Lynda, Messenger, Sharon, Albariño, César G, Ströher, Ute, Niemela, Michael, Amman, Brian R, Wong, David, Manning, Craig R, Nichol, Stuart T, Rollin, Pierre E, Xia, Dongxiang, Watt, James P, Vugia, Duc J
Published in Emerging infectious diseases (01.03.2014)
Published in Emerging infectious diseases (01.03.2014)
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Journal Article
Bat-associated rabies virus in Skunks
Leslie, Mira J, Messenger, Sharon, Rohde, Rodney E, Smith, Jean, Cheshier, Ronald, Hanlon, Cathleen, Rupprecht, Charles E
Published in Emerging infectious diseases (01.08.2006)
Published in Emerging infectious diseases (01.08.2006)
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Journal Article
Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission
Borucki, Monica K, Chen-Harris, Haiyin, Lao, Victoria, Vanier, Gilda, Wadford, Debra A, Messenger, Sharon, Allen, Jonathan E
Published in PLoS neglected tropical diseases (01.11.2013)
Published in PLoS neglected tropical diseases (01.11.2013)
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Journal Article
Rickettsia spp. 364D causing a cluster of eschar-associated illness, California
Johnston, Samantha H, Glaser, Carol A, Padgett, Kerry, Wadford, Debra A, Espinosa, Alex, Espinosa, Natasha, Eremeeva, Marina E, Tait, Karen, Hobson, Barbara, Shtivelman, Sarit, Hsieh, Charlotte, Messenger, Sharon L
Published in The Pediatric infectious disease journal (01.09.2013)
Published in The Pediatric infectious disease journal (01.09.2013)
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