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Microbial genetics

Phylogeography and phylogeny of Rhinoviruses collected from Severe Acute Respiratory Infection (SARI) cases over successive epidemic periods in Tunisia

Sondes Haddad-Boubaker, Cherif Ben Hamda, Kais Ghedira, Khaoula Mefteh, Aida Bouafsoun, Ilhem Boutiba-Ben Boubaker, Amin Slim, Khaled Menif, Henda Triki, Mohamed Ali Ben Hadj Kacem, Hanen Smaoui

published 22 Nov 2021

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A machine learning-based typing scheme refinement for Listeria monocytogenes core genome multilocus sequence typing with high discriminatory power for common source outbreak tracking

Yen-Yi Liu, Chih-Chieh Chen

published 19 Nov 2021

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High-quality whole-genome sequence analysis of Lactobacillus paragasseri UBLG-36 reveals oxalate-degrading potential of the strain

Yogita Mehra, Pragasam Viswanathan

published 19 Nov 2021

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Charting host-microbe co-metabolism in skin aging and application to metagenomics data

Wynand Alkema, Jos Boekhorst, Robyn T. Eijlander, Steve Schnittger, Fini De Gruyter, Sabina Lukovac, Kurt Schilling, Guus A. M. Kortman

published 10 Nov 2021

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LuNER: Multiplexed SARS-CoV-2 detection in clinical swab and wastewater samples

Elizabeth C. Stahl, Allan R. Gopez, Connor A. Tsuchida, Vinson B. Fan, Erica A. Moehle, Lea B. Witkowsky, Jennifer R. Hamilton, Enrique Lin-Shiao, Matthew McElroy, Shana L. McDevitt, Alison Ciling, C. Kimberly Tsui, Kathleen Pestal, Holly K. Gildea, Amanda Keller, Iman A. Sylvain, Clara Williams, Ariana Hirsh, Alexander J. Ehrenberg, Rose Kantor, Matthew Metzger, Kara L. Nelson, Fyodor D. Urnov, Bradley R. Ringeisen, Petros Giannikopoulos, Jennifer A. Doudna, IGI Testing Consortium

published 10 Nov 2021

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Profiling of Bacillus cereus on Canadian grain

Niradha Withana Gamage, Janice Bamforth, Tehreem Ashfaq, Kathryn Bernard, Tom Gräfenhan, Sean Walkowiak

published 04 Nov 2021

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Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols

Broňa Brejová, Kristína Boršová, Viktória Hodorová, Viktória Čabanová, Askar Gafurov, Dominika Fričová, Martina Neboháčová, Tomáš Vinař, Boris Klempa, Jozef Nosek

published 29 Oct 2021

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A bioinformatics pipeline for Mycobacterium tuberculosis sequencing that cleans contaminant reads from sputum samples

Betzaida Cuevas-Córdoba, Cristóbal Fresno, Joshua I. Haase-Hernández, Martín Barbosa-Amezcua, Minerva Mata-Rocha, Marcela Muñoz-Torrico, Miguel A. Salazar-Lezama, José A. Martínez-Orozco, Luis A. Narváez-Díaz, Jorge Salas-Hernández, Vanessa González-Covarrubias, Xavier Soberón

published 26 Oct 2021

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Sequencing DNA with nanopores: Troubles and biases

Clara Delahaye, Jacques Nicolas

published 01 Oct 2021

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Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere

Alexa K. Hoke, Guadalupe Reynoso, Morgan R. Smith, Malia I. Gardner, Dominique J. Lockwood, Naomi E. Gilbert, Steven W. Wilhelm, Isabella R. Becker, Grant J. Brennan, Katherine E. Crider, Shannon R. Farnan, Victoria Mendoza, Alison C. Poole, Zachary P. Zimmerman, Lucy K. Utz, Louie L. Wurch, Morgan M. Steffen

published 22 Sep 2021

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Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak

Efrat Bucris, Victoria Indenbaum, Roberto Azar, Oran Erster, Eric Haas, Ella Mendelson, Neta S. Zuckerman

published 10 Sep 2021

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Novel Drexlerviridae bacteriophage KMI8 with specific lytic activity against Klebsiella michiganensis and its biofilms

Heng Ku, Mwila Kabwe, Hiu Tat Chan, Cassandra Stanton, Steve Petrovski, Steven Batinovic, Joseph Tucci

published 07 Sep 2021

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Inconsistent PCR detection of Shiga toxin-producing Escherichia coli: Insights from whole genome sequence analyses

Vinicius Silva Castro, Rodrigo Ortega Polo, Eduardo Eustáquio de Souza Figueiredo, Emmanuel Wihkochombom Bumunange, Tim McAllister, Robin King, Carlos Adam Conte-Junior, Kim Stanford

published 03 Sep 2021

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