Publications by authors named "Ruth Timme"

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Harnessing methods, data analysis, and near-real-time wastewater monitoring for enhanced public health response using high throughput sequencing.
Padmini Ramachandran, Tunc Kayikcioglu, Tamara Walsky, Kathryn Judy, Jasmine Amirzadegan, Ruth Timme

Environ Res· August 2025

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Genomic Surveillance of Foodborne Pathogens: Advances and Obstacles.
Kathleen Gensheimer, Marc W Allard, Ruth E Timme, Eric Brown, Leslie Hintz

J Public Health Manag Pract· April 2025

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serotypes in the genomic era: simplified serotype interpretation from DNA sequence data.
Xiangyu Deng, Shaoting Li, Tongzhou Xu, Zhemin Zhou, Michelle M Moore, Ruth Timme

Appl Environ Microbiol· March 2025

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A Comprehensive Guide to Quality Assessment and Data Submission for Genomic Surveillance of Enteric Pathogens.
Ruth E Timme, Tina Pfefer, C Hope Bias, Marc W Allard, Xinyang Huang

Methods Mol Biol· September 2024

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SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA's GenomeTrakr network.
Ruth E Timme, Jacquelina Woods, Jessica L Jones, Kevin R Calci, Rachel Rodriguez

mSystems· June 2024

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PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.
Emma J Griffiths, Inês Mendes, Finlay Maguire, Jennifer L Guthrie, Bryan A Wee, Ruth E Timme

Microb Genom· June 2024

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A One Health Perspective on Salmonella enterica Serovar Infantis, an Emerging Human Multidrug-Resistant Pathogen.
Jennifer Mattock, Marie Anne Chattaway, Hassan Hartman, Timothy J Dallman, Anthony M Smith, Ruth Timme

Emerg Infect Dis· April 2024

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Editorial: Integration of NGS in clinical and public health microbiology workflows: applications, compliance, quality considerations.
Shangxin Yang, Varvara K Kozyreva, Ruth E Timme, Peera Hemarajata

Front Public Health· February 2024

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Application of quasimetagenomics methods to define microbial diversity and subtype in dairy and seafood production facilities.
Brandon Kocurek, Padmini Ramachandran, Christopher J Grim, Paul Morin, Laura Howard, Ruth Timme

Microbiol Spectr· December 2023

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Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications.
Ruth E Timme, Ilene Karsch-Mizrachi, Zahra Waheed, Masanori Arita, Duncan MacCannell

Microb Genom· December 2023

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draft genome sequences: 15 historical (1998-2004) and 30 contemporary (2015-2016) clinical isolates from Pakistan.
Matthew A Crawford, Christine Lascols, Sara Lomonaco, Ruth E Timme, Debra J Fisher

Microbiol Resour Announc· September 2023

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A Schema for Digitized Surface Swab Site Metadata in Open-Source DNA Sequence Databases.
Jingzhang Feng, Devin Daeschel, Damion Dooley, Emma Griffiths, Marc Allard, Ruth Timme

mSystems· April 2023

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Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.
Tunc Kayikcioglu, Jasmine Amirzadegan, Hugh Rand, Bereket Tesfaldet, Ruth E Timme

PeerJ· February 2023

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Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States.
Eric L Stevens, Heather A Carleton, Jennifer Beal, Glenn E Tillman, Rebecca L Lindsey, Ruth E Timme

J Food Prot· May 2022

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Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of , and .
Patrick K Mitchell, Leyi Wang, Bryce J Stanhope, Brittany D Cronk, Renee Anderson, Ruth Timme

Microb Genom· February 2022

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Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Emma J Griffiths, Ruth E Timme, Catarina Inês Mendes, Andrew J Page, Nabil-Fareed Alikhan

Gigascience· February 2022

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Salmonella Genomics in Public Health and Food Safety.
Eric W Brown, Rebecca Bell, Guodong Zhang, Ruth Timme, Jie Zheng

EcoSal Plus· December 2021

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Antimicrobial and Genomic Characterization of Salmonella Nigeria from Pigs and Poultry in Ilorin, North-central, Nigeria.
Ibrahim A Raufu, Olayiwola A Ahmed, Abdulfatai Aremu, James A Ameh, Ruth E Timme

J Infect Dev Ctries· December 2021

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Investigating the Distribution of Strains of and Streptomycin Resistance in Apple Orchards in New York Using Clustered Regularly Interspaced Short Palindromic Repeat Profiles: A 6-Year Follow-Up.
Anna Wallis, Isabella M Yannuzzi, Mei-Wah Choi, John Spafford, Matthew Fenn, Ruth Timme

Plant Dis· November 2021

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Interpretative Labor and the Bane of Nonstandardized Metadata in Public Health Surveillance and Food Safety.
James B Pettengill, Jennifer Beal, Maria Balkey, Marc Allard, Hugh Rand, Ruth Timme

Clin Infect Dis· October 2021

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Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".
Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L Beck, Daniel C Berrios, Ruth E Timme

mSystems· May 2021

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Erratum for Miller et al., "Phylogenetic and Biogeographic Patterns of Vibrio parahaemolyticus Strains from North America Inferred from Whole-Genome Sequence Data".
John J Miller, Bart C Weimer, Ruth Timme, Catharina H M Lüdeke, James B Pettengill

Appl Environ Microbiol· May 2021

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Phylogeny of subspecies by whole-genome sequencing reveals high incidence of polyphyly and low phase 1 H antigen variability.
Nikki W Shariat, Ruth E Timme, Abigail T Walters

Microb Genom· February 2021

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Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.
Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L Beck, Daniel C Berrios, Ruth E Timme

mSystems· February 2021

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Gen-FS coordinated proficiency test data for genomic foodborne pathogen surveillance, 2017 and 2018 exercises.
Ruth E Timme, Patricia C Lafon, Maria Balkey, Jennifer K Adams, Darlene Wagner

Sci Data· November 2020

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