hmmIBD: software to infer pairwise identity by descent between haploid genotypes by Stephen F. Schaffner, Aimee R. Taylor, Wesley Wong, Dyann F. Wirth, Daniel E. Neafsey

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Development of a SNP barcode to genotype Babesia microti infections. by Mary Lynn Baniecki, Jade Moon, Kian Sani, Jacob E Lemieux, Stephen F Schaffner, Pardis C Sabeti

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Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent. by Aimee R Taylor, Stephen F Schaffner, Gustavo C Cerqueira, Standwell C Nkhoma, Timothy J C Anderson, Kanlaya Sriprawat, Aung Pyae Phyo, François Nosten, Daniel E Neafsey, Caroline O Buckee

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High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection by Erica Normandin, Melissa Rudy, Nikolaos Barkas, Stephen F. Schaffner, Zoe Levine, Robert F. Padera, Mehrtash Babadi, Shibani S. Mukerji, Daniel J. Park, Bronwyn L. MacInnis, Katherine J. Siddle, Pardis C. Sabeti, Isaac H. Solomon

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Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111 by Aaron E. Lin, William E. Diehl, Yingyun Cai, Courtney L. Finch, Chidiebere Akusobi, Robert N. Kirchdoerfer, Laura Bollinger, Stephen F. Schaffner, Elizabeth A. Brown, Erica Ollmann Saphire, Kristian G. Andersen, Jens H. Kuhn, Jeremy Luban, Pardis C. Sabeti

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Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal. by Rachel Daniels, Hsiao-Han Chang, Papa Diogoye Séne, Danny C Park, Daniel E Neafsey, Stephen F Schaffner, Elizabeth J Hamilton, Amanda K Lukens, Daria Van Tyne, Souleymane Mboup, Pardis C Sabeti, Daouda Ndiaye, Dyann F Wirth, Daniel L Hartl, Sarah K Volkman

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Plasmepsin II–III copy number accounts for bimodal piperaquine resistance among Cambodian Plasmodium falciparum by Selina Bopp, Pamela Magistrado, Wesley Wong, Stephen F. Schaffner, Angana Mukherjee, Pharath Lim, Mehul Dhorda, Chanaki Amaratunga, Charles J. Woodrow, Elizabeth A. Ashley, Nicholas J. White, Arjen M. Dondorp, Rick M. Fairhurst, Frederic Ariey, Didier Menard, Dyann F. Wirth, Sarah K. Volkman

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Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing by Zoë C. Levine, Aita Sene, Winnie Mkandawire, Awa B. Deme, Tolla Ndiaye, Mouhamad Sy, Amy Gaye, Younouss Diedhiou, Amadou M. Mbaye, Ibrahima M. Ndiaye, Jules Gomis, Médoune Ndiop, Doudou Sene, Marietou Faye Paye, Bronwyn L. MacInnis, Stephen F. Schaffner, Daniel J. Park, Aida S. Badiane, Andres Colubri, Mouhamadou Ndiaye, Ngayo Sy, Pardis C. Sabeti, Daouda Ndiaye, Katherine J. Siddle

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Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal by Rachel F. Daniels, Stephen F. Schaffner, Yakou Dieye, Gnagna Dieng, Michael Hainsworth, Fatou B. Fall, Coumba Ndoffene Diouf, Medoune Ndiop, Moustapha Cisse, Alioune Badara Gueye, Oumar Sarr, Philippe Guinot, Awa B. Deme, Amy K. Bei, Mouhamad Sy, Julie Thwing, Bronwyn MacInnis, Duncan Earle, Caterina Guinovart, Doudou Sene, Daniel L. Hartl, Daouda Ndiaye, Richard W. Steketee, Dyann F. Wirth, Sarah K. Volkman

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Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal by Wesley Wong, Stephen F. Schaffner, Julie Thwing, Mame Cheikh Seck, Jules Gomis, Younouss Diedhiou, Ngayo Sy, Medoune Ndiop, Fatou Ba, Ibrahima Diallo, Doudou Sene, Mamadou Alpha Diallo, Yaye Die Ndiaye, Mouhamad Sy, Aita Sene, Djiby Sow, Baba Dieye, Abdoulaye Tine, Jessica Ribado, Joshua Suresh, Albert Lee, Katherine E. Battle, Joshua L. Proctor, Caitlin A. Bever, Bronwyn MacInnis, Daouda Ndiaye, Daniel L. Hartl, Dyann F. Wirth, Sarah K. Volkman

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Discovery of novel rhabdoviruses in the blood of healthy individuals from West Africa. by Matthew H Stremlau, Kristian G Andersen, Onikepe A Folarin, Jessica N Grove, Ikponmwonsa Odia, Philomena E Ehiane, Omowunmi Omoniwa, Omigie Omoregie, Pan-Pan Jiang, Nathan L Yozwiak, Christian B Matranga, Xiao Yang, Stephen K Gire, Sarah Winnicki, Ridhi Tariyal, Stephen F Schaffner, Peter O Okokhere, Sylvanus Okogbenin, George O Akpede, Danny A Asogun, Dennis E Agbonlahor, Peter J Walker, Robert B Tesh, Joshua Z Levin, Robert F Garry, Pardis C Sabeti, Christian T Happi

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Combining genomics and epidemiology to track mumps virus transmission in the United States. by Shirlee Wohl, Hayden C Metsky, Stephen F Schaffner, Anne Piantadosi, Meagan Burns, Joseph A Lewnard, Bridget Chak, Lydia A Krasilnikova, Katherine J Siddle, Christian B Matranga, Bettina Bankamp, Scott Hennigan, Brandon Sabina, Elizabeth H Byrne, Rebecca J McNall, Rickey R Shah, James Qu, Daniel J Park, Soheyla Gharib, Susan Fitzgerald, Paul Barreira, Stephen Fleming, Susan Lett, Paul A Rota, Lawrence C Madoff, Nathan L Yozwiak, Bronwyn L MacInnis, Sandra Smole, Yonatan H Grad, Pardis C Sabeti

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Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum. by Daria Van Tyne, Daniel J Park, Stephen F Schaffner, Daniel E Neafsey, Elaine Angelino, Joseph F Cortese, Kayla G Barnes, David M Rosen, Amanda K Lukens, Rachel F Daniels, Danny A Milner, Charles A Johnson, Ilya Shlyakhter, Sharon R Grossman, Justin S Becker, Daniel Yamins, Elinor K Karlsson, Daouda Ndiaye, Ousmane Sarr, Souleymane Mboup, Christian Happi, Nicholas A Furlotte, Eleazar Eskin, Hyun Min Kang, Daniel L Hartl, Bruce W Birren, Roger C Wiegand, Eric S Lander, Dyann F Wirth, Sarah K Volkman, Pardis C Sabeti

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Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal by Stephen F. Schaffner, Aida Badiane, Akanksha Khorgade, Medoune Ndiop, Jules Gomis, Wesley Wong, Yaye Die Ndiaye, Younouss Diedhiou, Julie Thwing, Mame Cheikh Seck, Angela Early, Mouhamad Sy, Awa Deme, Mamadou Alpha Diallo, Ngayo Sy, Aita Sene, Tolla Ndiaye, Djiby Sow, Baba Dieye, Ibrahima Mbaye Ndiaye, Amy Gaye, Aliou Ndiaye, Katherine E. Battle, Joshua L. Proctor, Caitlin Bever, Fatou Ba Fall, Ibrahima Diallo, Seynabou Gaye, Doudou Sene, Daniel L. Hartl, Dyann F. Wirth, Bronwyn MacInnis, Daouda Ndiaye, Sarah K. Volkman

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Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time by Kayla G. Barnes, Anna E. Lachenauer, Adam Nitido, Sameed Siddiqui, Robin Gross, Brett Beitzel, Katherine J. Siddle, Catherine A. Freije, Bonnie Dighero-Kemp, Samar B. Mehta, Amber Carter, Jessica Uwanibe, Fehintola Ajogbasile, Testimony Olumade, Ikponmwosa Odia, John Demby Sandi, Mambu Momoh, Hayden C. Metsky, Chloe K. Boehm, Aaron E. Lin, Molly Kemball, Daniel J. Park, Luis Branco, Matt Boisen, Brian Sullivan, Mihret F. Amare, Abdulwasiu B. Tiamiyu, Zahra F. Parker, Michael Iroezindu, Donald S. Grant, Kayvon Modjarrad, Cameron Myhrvold, Robert F. Garry, Gustavo Palacios, Lisa E. Hensley, Stephen F. Schaffner, Christian T. Happi, Andres Colubri, Pardis C. Sabeti

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Two decades of molecular surveillance in Senegal reveal rapid changes in known drug resistance mutations over time by Yaye D. Ndiaye, Wesley Wong, Julie Thwing, Stephen F. Schaffner, Katelyn Vendrely Brenneman, Abdoulaye Tine, Mamadou A. Diallo, Awa B. Deme, Mouhamad Sy, Amy K. Bei, Alphonse B. Thiaw, Rachel Daniels, Tolla Ndiaye, Amy Gaye, Ibrahima M. Ndiaye, Mariama Toure, Nogaye Gadiaga, Aita Sene, Djiby Sow, Mamane N. Garba, Mamadou S. Yade, Baba Dieye, Khadim Diongue, Daba Zoumarou, Aliou Ndiaye, Jules F. Gomis, Fatou B. Fall, Medoune Ndiop, Ibrahima Diallo, Doudou Sene, Bronwyn Macinnis, Mame C. Seck, Mouhamadou Ndiaye, Bassirou Ngom, Younouss Diedhiou, Amadou M. Mbaye, Lamine Ndiaye, Ngayo Sy, Aida S. Badiane, Daniel L. Hartl, Dyann F. Wirth, Sarah K. Volkman, Daouda Ndiaye

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Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria by Judith U. Oguzie, Brittany A. Petros, Paul E. Oluniyi, Samar B. Mehta, Philomena E. Eromon, Parvathy Nair, Opeoluwa Adewale-Fasoro, Peace Damilola Ifoga, Ikponmwosa Odia, Andrzej Pastusiak, Otitoola Shobi Gbemisola, John Oke Aiyepada, Eghosasere Anthonia Uyigue, Akhilomen Patience Edamhande, Osiemi Blessing, Michael Airende, Christopher Tomkins-Tinch, James Qu, Liam Stenson, Stephen F. Schaffner, Nicholas Oyejide, Nnenna A. Ajayi, Kingsley Ojide, Onwe Ogah, Chukwuyem Abejegah, Nelson Adedosu, Oluwafemi Ayodeji, Ahmed A. Liasu, Sylvanus Okogbenin, Peter O. Okokhere, Daniel J. Park, Onikepe A. Folarin, Isaac Komolafe, Chikwe Ihekweazu, Simon D. W. Frost, Ethan K. Jackson, Katherine J. Siddle, Pardis C. Sabeti, Christian T. Happi

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Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria by Idowu B. Olawoye, Paul E. Oluniyi, Judith U. Oguzie, Jessica N. Uwanibe, Tolulope A. Kayode, Testimony J. Olumade, Fehintola V. Ajogbasile, Edyth Parker, Philomena E. Eromon, Priscilla Abechi, Tope A. Sobajo, Chinedu A. Ugwu, Uwem E. George, Femi Ayoade, Kazeem Akano, Nicholas E. Oyejide, Iguosadolo Nosamiefan, Iyanuoluwa Fred-Akintunwa, Kemi Adedotun-Sulaiman, Farida B. Brimmo, Babatunde B. Adegboyega, Courage Philip, Richard A. Adeleke, Grace C. Chukwu, Muhammad I. Ahmed, Oludayo O. Ope-Ewe, Shobi G. Otitoola, Olusola A. Ogunsanya, Mudasiru F. Saibu, Ayotunde E. Sijuwola, Grace O. Ezekiel, Oluwagboadurami G. John, Julie O. Akin-John, Oluwasemilogo O. Akinlo, Olanrewaju O. Fayemi, Testimony O. Ipaye, Deborah C. Nwodo, Abolade E. Omoniyi, Iyobosa B. Omwanghe, Christabel A. Terkuma, Johnson Okolie, Olubukola Ayo-Ale, Odia Ikponmwosa, Ebo Benevolence, Grace O. Naregose, Akhilomen E. Patience, Osiemi Blessing, Airende Micheal, Agbukor Jacqueline, John O. Aiyepada, Paulson Ebhodaghe, Omiunu Racheal, Esumeh Rita, Giwa E. Rosemary, Ehikhametalor Solomon, Ekanem Anieno, Yerumoh Edna, Aire O. Chris, Adomeh I. Donatus, Ephraim Ogbaini-Emovon, Mirabeau Y. Tatfeng, Hannah E. Omunakwe, Mienye Bob-Manuel, Rahaman A. Ahmed, Chika K. Onwuamah, Joseph O. Shaibu, Azuka Okwuraiwe, Anthony E. Ataga, Andrew Bock-Oruma, Funmi Daramola, Ibrahim F. Yusuf, Akinwumi Fajola, Nsikak-Abasi Ntia, Julie J. Ekpo, Anietie E. Moses, Beatrice W. Moore-Igwe, Oluwatosin E. Fakayode, Monilade Akinola, Ibrahim M. Kida, Bamidele S. Oderinde, Zara W. Wudiri, Oluwapelumi O. Adeyemi, Olusola A. Akanbi, Anthony Ahumibe, Afolabi Akinpelu, Oyeronke Ayansola, Olajumoke Babatunde, Adesuyi A. Omoare, Chimaobi Chukwu, Nwando G. Mba, Ewean C. Omoruyi, Olasunkanmi Olisa, Olatunji K. Akande, Ifeanyi E. Nwafor, Matthew A. Ekeh, Erim Ndoma, Richard L. Ewah, Rosemary O. Duruihuoma, Augustine Abu, Elizabeth Odeh, Venatius Onyia, Chiedozie K. Ojide, Sylvanus Okoro, Daniel Igwe, Emeka O. Ogah, Kamran Khan, Nnennaya A. Ajayi, Collins N. Ugwu, Kingsley N. Ukwaja, Ngozi I. Ugwu, Chukwuyem Abejegah, Nelson Adedosu, Olufemi Ayodeji, Ahmed A. Liasu, Rafiu O. Isamotu, Galadima Gadzama, Brittany A. Petros, Katherine J. Siddle, Stephen F. Schaffner, George Akpede, Cyril Oshomah Erameh, Marycelin M. Baba, Femi Oladiji, Rosemary Audu, Nnaemeka Ndodo, Adeola Fowotade, Sylvanus Okogbenin, Peter O. Okokhere, Danny J. Park, Bronwyn L. Mcannis, Ifedayo M. Adetifa, Chikwe Ihekweazu, Babatunde L. Salako, Oyewale Tomori, Anise N. Happi, Onikepe A. Folarin, Kristian G. Andersen, Pardis C. Sabeti, Christian T. Happi

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