Discovery of a small molecule inhibitor through interference with the gp120–CD4 interaction von Williams, David H., Adam, Fiona, Fenwick, David R., Fok-Seang, Juin, Gardner, Iain, Hay, Duncan, Jaiessh, Rawal, Middleton, Donald S., Mowbray, Charles E., Parkinson, Tanya, Perros, Manos, Pickford, Christopher, Platts, Michelle, Randall, Amy, Siddle, Daniel, Stephenson, Peter T., Tran, Thien-Duc, Vuong, Hannah

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Benchmarking Metagenomics Tools for Taxonomic Classification von Ye, Simon H., Siddle, Katherine J., Park, Daniel J., Sabeti, Pardis C.

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Negative Selection by Spiral Inertial Microfluidics Improves Viral Recovery and Sequencing from Blood von Choi, Kyungyong, Ryu, Hyunryul, Siddle, Katherine J, Piantadosi, Anne, Freimark, Lisa, Park, Daniel J, Sabeti, Pardis, Han, Jongyoon

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

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The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils von Stammnitz, Maximilian R., Coorens, Tim H.H., Gori, Kevin C., Hayes, Dane, Fu, Beiyuan, Wang, Jinhong, Martin-Herranz, Daniel E., Alexandrov, Ludmil B., Baez-Ortega, Adrian, Barthorpe, Syd, Beck, Alexandra, Giordano, Francesca, Knowles, Graeme W., Kwon, Young Mi, Hall, George, Price, Stacey, Pye, Ruth J., Tubio, Jose M.C., Siddle, Hannah V.T., Sohal, Sukhwinder Singh, Woods, Gregory M., McDermott, Ultan, Yang, Fengtang, Garnett, Mathew J., Ning, Zemin, Murchison, Elizabeth P.

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Viral Lineages in the 2022 RSV Surge in the United States von Adams, Gordon, Moreno, Gage K., Petros, Brittany A., Uddin, Rockib, Levine, Zoe, Kotzen, Ben, Messer, Katelyn S., Dobbins, Sabrina T., DeRuff, Katherine C., Loreth, Christine M., Brock-Fisher, Taylor, Schaffner, Stephen F., Chaluvadi, Sushma, Kanjilal, Sanjat, Luban, Jeremy, Ozonoff, Al, Park, Daniel J., Turbett, Sarah E., Siddle, Katherine J., MacInnis, Bronwyn L., Sabeti, Pardis C., Lemieux, Jacob E.

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

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

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Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018 von Gaye, Amy, Ndiaye, Tolla, Sy, Mouhamad, Deme, Awa B., Thiaw, Alphonse B., Sene, Aita, Ndiaye, Cheikh, Diedhiou, Younouss, Mbaye, Amadou M., Ndiaye, Ibrahima, Tomkins-Tinch, Christopher, Gomis, Jules F., Badiane, Aida S., MacInnis, Bronwyn, Park, Daniel J., Ndiaye, Mouhamadou, Sy, Ngayo, Sabeti, Pardis C., Siddle, Katherine J., Ndiaye, Daouda

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

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

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“Waiting for the best day of your life”. A qualitative interview study of patients’ and clinicians’ experiences of Perthes’ disease von Galloway, Adam M., Pini, Simon, Holton, Colin, Perry, Daniel C., Redmond, Anthony, Siddle, Heidi J., Richards, Suzanne

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Amplicon deep sequencing of kelch13 in Plasmodium falciparum isolates from Senegal von Gaye, Amy, Sy, Mouhamad, Ndiaye, Tolla, Siddle, Katherine J, Park, Daniel J, Deme, Awa B, Mbaye, Aminata, Dieye, Baba, Ndiaye, Yaye Die, Neafsey, Daniel E, Early, Angela, Farrell, Timothy, Yade, Mamadou Samb, Diallo, Mamadou Alpha, Diongue, Khadim, Bei, Amy, Ndiaye, Ibrahima Mbaye, Volkman, Sarah K, Badiane, Aida Sadikh, Ndiaye, Daouda

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COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets von Ziegler, Carly G. K., Heimberg, Graham, Normand, Rachelly, Yang, Yiming, Segerstolpe, Åsa, Abbondanza, Domenic, Fleming, Stephen J., Montoro, Daniel T., Jagadeesh, Karthik A., Dey, Kushal K., Sen, Pritha, Slyper, Michal, Pita-Juárez, Yered H., Phillips, Devan, Biermann, Jana, Bloom-Ackermann, Zohar, Barkas, Nikolaos, Ganna, Andrea, Gomez, James, Melms, Johannes C., Katsyv, Igor, Normandin, Erica, Naderi, Pourya, Popov, Yury V., Raju, Siddharth S., Niezen, Sebastian, Tsai, Linus T.-Y., Siddle, Katherine J., Sud, Malika, Tran, Victoria M., Vellarikkal, Shamsudheen K., Wang, Yiping, Amir-Zilberstein, Liat, Atri, Deepak S., Beechem, Joseph, Brook, Olga R., Chen, Jonathan, Divakar, Prajan, Engreitz, Jesse M., Essene, Adam, Fitzgerald, Donna M., Fropf, Robin, Gazal, Steven, Gould, Joshua, Grzyb, John, Harvey, Tyler, Hether, Tyler, Jané-Valbuena, Judit, Leney-Greene, Michael, Ma, Hui, McCabe, Cristin, McLoughlin, Daniel E., Miller, Eric M., Muus, Christoph, Niemi, Mari, Padera, Robert, Pan, Liuliu, Pant, Deepti, Pe’er, Carmel, Pfiffner-Borges, Jenna, Pinto, Christopher J., Plaisted, Jacob, Reeves, Jason, Ross, Marty, Rudy, Melissa, Rueckert, Erroll H., Siciliano, Michelle, Sturm, Alexander, Waghray, Avinash, Warren, Sarah, Zhang, Shuting, Zollinger, Daniel R., Cosimi, Lisa, Gupta, Rajat M., Hacohen, Nir, Hibshoosh, Hanina, Hide, Winston, Price, Alkes L., Rajagopal, Jayaraj, Tata, Purushothama Rao, Riedel, Stefan, Szabo, Gyongyi, Tickle, Timothy L., Hung, Deborah, Sabeti, Pardis C., Novak, Richard, Rogers, Robert, Ingber, Donald E., Jiang, Z. Gordon, Juric, Dejan, Izar, Benjamin, Stone, James R., Vlachos, Ioannis S., Solomon, Isaac H., Ashenberg, Orr, Porter, Caroline B. M., Li, Bo, Shalek, Alex K., Villani, Alexandra-Chloé, Regev, Aviv

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Polyphonia: detecting inter-sample contamination in viral genomic sequencing data von Krasilnikova, Lydia A, Tomkins-Tinch, Christopher H, Gayton, Alton C, Schaffner, Stephen F, Dobbins, Sabrina T, Gladden-Young, Adrianne, Siddle, Katherine J, Park, Daniel J, Sabeti, Pardis C

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Outbreak of SARS-CoV-2 Infections, Including COVID-19 Vaccine Breakthrough Infections, Associated with Large Public Gatherings — Barnstable County, Massachusetts, July 2021 von Brown, Catherine M., Vostok, Johanna, Johnson, Hillary, Burns, Meagan, Gharpure, Radhika, Sami, Samira, Sabo, Rebecca T., Hall, Noemi, Foreman, Anne, Schubert, Petra L., Gallagher, Glen R., Fink, Timelia, Madoff, Lawrence C., Gabriel, Stacey B., MacInnis, Bronwyn, Park, Daniel J., Siddle, Katherine J., Harik, Vaira, Arvidson, Deirdre, Brock-Fisher, Taylor, Dunn, Molly, Kearns, Amanda, Laney, A. Scott

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Molecular epidemiology of Plasmodium falciparum by multiplexed amplicon deep sequencing in Senegal von Ndiaye, Tolla, Sy, Mouhamad, Gaye, Amy, Siddle, Katherine J, Park, Daniel J, Bei, Amy K, Deme, Awa B, Mbaye, Aminata, Dieye, Baba, Ndiaye, Yaye Die, Ndiaye, Ibrahima Mbaye, Diallo, Mamadou Alpha, Diongue, Khadim, Volkman, Sarah K, Badiane, Aida Sadikh, Ndiaye, Daouda

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A systematic review of the non-surgical treatment of Perthes' disease von Galloway, Adam M, van-Hille, Thomas, Perry, Daniel C, Holton, Colin, Mason, Laura, Richards, Suzanne, Siddle, Heidi J, Comer, Christine

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Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants von Welch, Nicole L., Zhu, Meilin, Hua, Catherine, Weller, Juliane, Mirhashemi, Marzieh Ezzaty, Nguyen, Tien G., Mantena, Sreekar, Bauer, Matthew R., Shaw, Bennett M., Ackerman, Cheri M., Thakku, Sri Gowtham, Tse, Megan W., Kehe, Jared, Uwera, Marie-Martine, Eversley, Jacqueline S., Bielwaski, Derek A., McGrath, Graham, Braidt, Joseph, Johnson, Jeremy, Cerrato, Felecia, Moreno, Gage K., Krasilnikova, Lydia A., Petros, Brittany A., Gionet, Gabrielle L., King, Ewa, Huard, Richard C., Jalbert, Samantha K., Cleary, Michael L., Fitzgerald, Nicholas A., Gabriel, Stacey B., Gallagher, Glen R., Smole, Sandra C., Madoff, Lawrence C., Brown, Catherine M., Keller, Matthew W., Wilson, Malania M., Kirby, Marie K., Barnes, John R., Park, Daniel J., Siddle, Katherine J., Happi, Christian T., Hung, Deborah T., Springer, Michael, MacInnis, Bronwyn L., Lemieux, Jacob E., Rosenberg, Eric, Branda, John A., Blainey, Paul C., Sabeti, Pardis C., Myhrvold, Cameron

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Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery von Barnes, Kayla G., Kindrachuk, Jason, Lin, Aaron E., Wohl, Shirlee, Qu, James, Tostenson, Samantha D., Dorman, William R., Busby, Michele, Siddle, Katherine J., Luo, Cynthia Y., Matranga, Christian B., Davey, Richard T., Sabeti, Pardis C., Chertow, Daniel S.

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