Not logged in Salmonella serotypes in the genomic era: simplified Salmonella serotype interpretation from DNA sequence data Deng, Xiangyu; Li, Shaoting; Xu, Tongzhou; Zhou, Zhemin; Moore, Michelle M.; Timme, Ruth; Zhao, Shaohua; Lane, Charlotte; Dinsmore, Blake A.; Weill, Francois-Xavier; Fields, Patricia I. Share Save
SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA's GenomeTrakr network Timme, Ruth E.; Woods, Jacquelina; Jones, Jessica L.; Calci, Kevin R.; Rodriguez, Rachel; Barnes, Candace; Leard, Elizabeth; Craven, Mark; Chen, Haifeng; Boerner, Cameron; Grim, Christopher; Windsor, Amanda M.; Ramachandran, Padmini; Muruvanda, Tim; Rand, Hugh; Tesfaldet, Bereket; Amirzadegan, Jasmine; Kayikcioglu, Tunc; Walsky, Tamara; Allard, Marc; Balkey, Maria; Bias, C. Hope; Brown, Eric; Judy, Kathryn; Pfefer, Tina; Tallent, Sandra M.; Hoffmann, Maria; Pettengill, James Share Save
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training Griffiths, Emma J.; Mendes, Ines; Maguire, Finlay; Guthrie, Jennifer L.; Wee, Bryan A.; Schmedes, Sarah; Holt, Kathryn; Yadav, Chanchal; Cameron, Rhiannon; Barclay, Charlotte; Dooley, Damion; Maccannell, Duncan; Chindelevitch, Leonid; Mizrachi, Ilene Karsch-; Waheed, Zahra; Katz, Lee; Petit, Robert, III; Dave, Mugdha; Oluniyi, Paul; Nasar, Muhammad Ibtisam; Raphenya, Amogelang; Hsiao, William W. L.; Timme, Ruth E. Share Save
A One Health Perspective on Salmonella enterica Serovar Infantis, an Emerging Human Multidrug-Resistant Pathogen Mattock, Jennifer; Chattaway, Marie Anne; Hartman, Hassan; Dallman, Timothy J.; Smith, Anthony M.; Keddy, Karen; Petrovska, Liljana; Manners, Emma J.; Duze, Sanelisiwe T.; Smouse, Shannon; Tau, Nomsa; Timme, Ruth; Baker, Dave J.; Mather, Alison E.; Wain, John; Langridge, Gemma C. Share Save
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Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities Kocurek, Brandon; Ramachandran, Padmini; Grim, Christopher J.; Morin, Paul; Howard, Laura; Ottesen, Andrea; Timme, Ruth; Leonard, Susan R.; Rand, Hugh; Strain, Errol; Tadesse, Daniel; Pettengill, James B.; Lacher, David W.; Mammel, Mark; Jarvis, Karen G.; Wang, Luxin Share Save
Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications Timme, Ruth E.; Karsch-Mizrachi, Ilene; Waheed, Zahra; Arita, Masanori; Maccannell, Duncan; Maguire, Finlay; Petit III, Robert; Page, Andrew J.; Mendes, Catarina Ines; Nasar, Muhammad Ibtisam; Oluniyi, Paul; Tyler, Andrea D.; Raphenya, Amogelang R.; Guthrie, Jennifer L.; Olawoye, Idowu; Rinck, Gabriele; O'Cathail, Colman; Lees, John; Cochrane, Guy; Cummins, Carla; Brister, J. Rodney; Klimke, William; Feldgarden, Michael; Griffiths, Emma Share Save
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Multi- laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria Mitchell, Patrick K.; Wang, Leyi; Stanhope, Bryce J.; Cronk, Brittany D.; Anderson, Renee; Mohan, Shipra; Zhou, Lijuan; Sanchez, Susan; Bartlett, Paula; Maddox, Carol; DeShambo, Vanessa; Mani, Rinosh; Hengesbach, Lindsy M.; Gresch, Sarah; Wright, Katie; Mor, Sunil; Zhang, Shuping; Shen, Zhenyu; Yan, Lifang; Mackey, Rebecca; Franklin-Guild, Rebecca; Zhang, Yan; Prarat, Melanie; Shiplett, Katherine; Ramachandran, Akhilesh; Narayanan, Sai; Sanders, Justin; Hunkapiller, Andree A.; Lahmers, Kevin; Carbonello, Amanda A.; Aulik, Nicole; Lim, Ailam; Cooper, Jennifer; Jones, Angelica; Guag, Jake; Nemser, Sarah M.; Tyson, Gregory H.; Timme, Ruth; Strain, Errol; Reimschuessel, Renate; Ceric, Olgica; Goodman, Laura B. Share Save
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package Griffiths, Emma J.; Timme, Ruth E.; Mendes, Catarina Ines; Page, Andrew J.; Alikhan, Nabil-Fareed; Fornika, Dan; Maguire, Finlay; Campos, Josefina; Park, Daniel; Olawoye, Idowu B.; Oluniyi, Paul E.; Anderson, Dominique; Christoffels, Alan; da Silva, Anders Goncalves; Cameron, Rhiannon; Dooley, Damion; Katz, Lee S.; Black, Allison; Karsch-Mizrachi, Ilene; Barrett, Tanya; Johnston, Anjanette; Connor, Thomas R.; Nicholls, Samuel M.; Witney, Adam A.; Tyson, Gregory H.; Tausch, Simon H.; Raphenya, Amogelang R.; Alcock, Brian; Aanensen, David M.; Hodcroft, Emma; Hsiao, William W. L.; Vasconcelos, Ana Tereza R.; MacCannell, Duncan R. Share Save
Investigating the Distribution of Strains of Erwinia amylovora and Streptomycin Resistance in Apple Orchards in New York Using Clustered Regularly Interspaced Short Palindromic Repeat Profiles: A 6-Year Follow-Up Wallis, Anna; Yannuzzi, Isabella M.; Choi, Mei-Wah; Spafford, John; Fenn, Matthew; Ramachandran, Padmini; Timme, Ruth; Pettengill, James B.; Cagle, Robin; Ottesen, Andrea; Cox, Kerik D. Share Save
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Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities (vol 6, e01194-20, 2021) Vangay, Pajau; Burgin, Josephine; Johnston, Anjanette; Beck, Kristen L.; Berrios, Daniel C.; Blumberg, Kai; Canon, Shane; Chain, Patrick; Chandonia, John-Marc; Christianson, Danielle; Costes, Sylvain V.; Damerow, Joan; Duncan, William D.; Dundore-Arias, Jose Pablo; Fagnan, Kjiersten; Galazka, Jonathan M.; Gibbons, Sean M.; Hays, David; Hervey, Judson; Hu, Bin; Hurwitz, Bonnie L.; Jaiswal, Pankaj; Joachimiak, Marcin P.; Kinkel, Linda; Ladau, Joshua; Martin, Stanton L.; McCue, Lee Ann; Miller, Kayd; Mouncey, Nigel; Mungall, Chris; Pa, Evangelos; Reddy, T. B. K.; Richardson, Lorna; Roux, Simon; Schriml, Lynn M.; Shaffer, Justin P.; Sundaramurthi, Jagadish Chandrabose; Thompson, Luke R.; Timme, Ruth E.; Zheng, Jie; Wood-Charlson, Elisha M.; Eloe-Fadrosh, Emiley A. Share Save
Phylogenetic and Biogeographic Patterns of Vibrio parahaemolyticus Strains from North America Inferred from Whole-Genome Sequence Data (vol 87, e01403-20, 2021) Miller, John J.; Weimer, Bart C.; Timme, Ruth; Ludeke, Catharina H. M.; Pettengill, James B.; Bandoy, D. J. Darwin; Weis, Allison M.; Kaufman, James; Huang, B. Carol; Payne, Justin; Strain, Errol; Jones, Jessica L. Share Save
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities Vangay, Pajau; Burgin, Josephine; Johnston, Anjanette; Beck, Kristen L.; Berrios, Daniel C.; Blumberg, Kai; Canon, Shane; Chain, Patrick; Chandonia, John-Marc; Christianson, Danielle; Costes, Sylvain V.; Damerow, Joan; Duncan, William D.; Dundore-Arias, Jose Pablo; Fagnan, Kjiersten; Galazka, Jonathan M.; Gibbons, Sean M.; Hays, David; Hervey, Judson; Hu, Bin; Hurwitz, Bonnie L.; Jaiswal, Pankaj; Joachimiak, Marcin P.; Kinkel, Linda; Ladau, Joshua; Martin, Stanton L.; McCue, Lee Ann; Miller, Kayd; Mouncey, Nigel; Mungall, Chris; Pafilis, Evangelos; Reddy, T. B. K.; Richardson, Lorna; Roux, Simon; Schriml, Lynn M.; Shaffer, Justin P.; Sundaramurthi, Jagadish Chandrabose; Thompson, Luke R.; Timme, Ruth E.; Zheng, Jie; Wood-Charlson, Elisha M.; Eloe-Fadrosh, Emiley A. Share Save
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Phylogenetic and Biogeographic Patterns of Vibrio parahaemolyticus Strains from North America Inferred from Whole-Genome Sequence Data Miller, John J.; Weimer, Bart C.; Timme, Ruth; Luedeke, Catharina H. M.; Pettengill, James B.; Bandoy, D. J. Darwin; Weis, Allison M.; Kaufman, James; Huang, B. Carol; Payne, Justin; Strain, Errol; Jones, Jessica L. Share Save
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Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance Timme, Ruth E.; Strain, Errol; Baugher, Joseph D.; Davis, Steven; Gonzalez-Escalona, Narjol; Leon, Maria Sanchez; Allard, Marc W.; Brown, Eric W.; Tallent, Sandra; Rand, Hugh Share Save
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