Insights from genomics into bacterial pathogen populations. by Daniel J Wilson

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Practical Approaches for Detecting Selection in Microbial Genomes. by Jessica Hedge, Daniel J Wilson

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ClonalFrameML: efficient inference of recombination in whole bacterial genomes. by Xavier Didelot, Daniel J Wilson

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Machine learning to predict the source of campylobacteriosis using whole genome data. by Nicolas Arning, Samuel K Sheppard, Sion Bayliss, David A Clifton, Daniel J Wilson

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Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission. by David W Eyre, Madeleine L Cule, David Griffiths, Derrick W Crook, Tim E A Peto, A Sarah Walker, Daniel J Wilson

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Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differenc... by David W Eyre, Mirjam Laager, A Sarah Walker, Ben S Cooper, Daniel J Wilson, CDC Modeling Infectious Diseases in Healthcare Program (MInD-Healthcare)

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Evolution of an agriculture-associated disease causing Campylobacter coli clade: evidence from national surveillance data in Scotland. by Samuel K Sheppard, John F Dallas, Daniel J Wilson, Norval J C Strachan, Noel D McCarthy, Keith A Jolley, Frances M Colles, Ovidiu Rotariu, Iain D Ogden, Ken J Forbes, Martin C J Maiden

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Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis. by Sarah G Earle, Mariya Lobanovska, Hayley Lavender, Changyan Tang, Rachel M Exley, Elisa Ramos-Sevillano, Douglas F Browning, Vasiliki Kostiou, Odile B Harrison, Holly B Bratcher, Gabriele Varani, Christoph M Tang, Daniel J Wilson, Martin C J Maiden

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A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. by Elizabeth M Batty, T H Nicholas Wong, Amy Trebes, Karène Argoud, Moustafa Attar, David Buck, Camilla L C Ip, Tanya Golubchik, Madeleine Cule, Rory Bowden, Charis Manganis, Paul Klenerman, Eleanor Barnes, A Sarah Walker, David H Wyllie, Daniel J Wilson, Kate E Dingle, Tim E A Peto, Derrick W Crook, Paolo Piazza

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Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus. by Maisem Laabei, Anne-Catrin Uhlemann, Franklin D Lowy, Eloise D Austin, Maho Yokoyama, Khadija Ouadi, Edward Feil, Harry A Thorpe, Barnabas Williams, Mark Perkins, Sharon J Peacock, Stephen R Clarke, Janina Dordel, Matthew Holden, Antonina A Votintseva, Rory Bowden, Derrick W Crook, Bernadette C Young, Daniel J Wilson, Mario Recker, Ruth C Massey

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Challenges of COVID-19 Case Forecasting in the US, 2020-2021. by Velma K Lopez, Estee Y Cramer, Robert Pagano, John M Drake, Eamon B O'Dea, Madeline Adee, Turgay Ayer, Jagpreet Chhatwal, Ozden O Dalgic, Mary A Ladd, Benjamin P Linas, Peter P Mueller, Jade Xiao, Johannes Bracher, Alvaro J Castro Rivadeneira, Aaron Gerding, Tilmann Gneiting, Yuxin Huang, Dasuni Jayawardena, Abdul H Kanji, Khoa Le, Anja Mühlemann, Jarad Niemi, Evan L Ray, Ariane Stark, Yijin Wang, Nutcha Wattanachit, Martha W Zorn, Sen Pei, Jeffrey Shaman, Teresa K Yamana, Samuel R Tarasewicz, Daniel J Wilson, Sid Baccam, Heidi Gurung, Steve Stage, Brad Suchoski, Lei Gao, Zhiling Gu, Myungjin Kim, Xinyi Li, Guannan Wang, Lily Wang, Yueying Wang, Shan Yu, Lauren Gardner, Sonia Jindal, Maximilian Marshall, Kristen Nixon, Juan Dent, Alison L Hill, Joshua Kaminsky, Elizabeth C Lee, Joseph C Lemaitre, Justin Lessler, Claire P Smith, Shaun Truelove, Matt Kinsey, Luke C Mullany, Kaitlin Rainwater-Lovett, Lauren Shin, Katharine Tallaksen, Shelby Wilson, Dean Karlen, Lauren Castro, Geoffrey Fairchild, Isaac Michaud, Dave Osthus, Jiang Bian, Wei Cao, Zhifeng Gao, Juan Lavista Ferres, Chaozhuo Li, Tie-Yan Liu, Xing Xie, Shun Zhang, Shun Zheng, Matteo Chinazzi, Jessica T Davis, Kunpeng Mu, Ana Pastore Y Piontti, Alessandro Vespignani, Xinyue Xiong, Robert Walraven, Jinghui Chen, Quanquan Gu, Lingxiao Wang, Pan Xu, Weitong Zhang, Difan Zou, Graham Casey Gibson, Daniel Sheldon, Ajitesh Srivastava, Aniruddha Adiga, Benjamin Hurt, Gursharn Kaur, Bryan Lewis, Madhav Marathe, Akhil Sai Peddireddy, Przemyslaw Porebski, Srinivasan Venkatramanan, Lijing Wang, Pragati V Prasad, Jo W Walker, Alexander E Webber, Rachel B Slayton, Matthew Biggerstaff, Nicholas G Reich, Michael A Johansson

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