Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant von Yurkovetskiy, Leonid, Wang, Xue, Pascal, Kristen E., Tomkins-Tinch, Christopher, Nyalile, Thomas P., Wang, Yetao, Baum, Alina, Diehl, William E., Dauphin, Ann, Carbone, Claudia, Veinotte, Kristen, Egri, Shawn B., Schaffner, Stephen F., Lemieux, Jacob E., Munro, James B., Rafique, Ashique, Barve, Abhi, Sabeti, Pardis C., Kyratsous, Christos A., Dudkina, Natalya V., Shen, Kuang, Luban, Jeremy

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Searching for missing heritability: Designing rare variant association studies von Zuk, Or, Schaffner, Stephen F, Samocha, Kaitlin, Do, Ron, Hechter, Eliana, Kathiresan, Sekar, Daly, Mark J, Neale, Benjamin M, Sunyaev, Shamil R, Lander, Eric S

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Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay von Tewhey, Ryan, Kotliar, Dylan, Park, Daniel S., Liu, Brandon, Winnicki, Sarah, Reilly, Steven K., Andersen, Kristian G., Mikkelsen, Tarjei S., Lander, Eric S., Schaffner, Stephen F., Sabeti, Pardis C.

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

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Identifying Recent Adaptations in Large-Scale Genomic Data von Grossman, Sharon R., Andersen, Kristian G., Shlyakhter, Ilya, Tabrizi, Shervin, Winnicki, Sarah, Yen, Angela, Park, Daniel J., Griesemer, Dustin, Karlsson, Elinor K., Wong, Sunny H., Cabili, Moran, Adegbola, Richard A., Bamezai, Rameshwar N.K., Hill, Adrian V.S., Vannberg, Fredrik O., Rinn, John L., Lander, Eric S., Schaffner, Stephen F., Sabeti, Pardis C.

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

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

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Clinical and laboratory predictors of Lassa fever outcome in a dedicated treatment facility in Nigeria: a retrospective, observational cohort study von Okokhere, Peter, Colubri, Andres, Azubike, Chukwuemeka, Iruolagbe, Christopher, Osazuwa, Omoregie, Tabrizi, Shervin, Chin, Elizabeth, Asad, Sara, Ediale, Ehi, Rafiu, Mojeed, Adomeh, Donatus, Odia, Ikponmwosa, Atafo, Rebecca, Aire, Chris, Okogbenin, Sylvanus, Pahlman, Meike, Becker-Ziaja, Beate, Asogun, Danny, Fradet, Terrence, Fry, Ben, Schaffner, Stephen F, Happi, Christian, Akpede, George, Günther, Stephan, Sabeti, Pardis C

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Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution von Aldea, Daniel, Atsuta, Yuji, Kokalari, Blerina, Schaffner, Stephen F., Prasasya, Rexxi D., Aharoni, Adam, Dingwall, Heather L., Warder, Bailey, Kamberov, Yana G.

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Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics von Kotliar, Dylan, Lin, Aaron E., Logue, James, Hughes, Travis K., Khoury, Nadine M., Raju, Siddharth S., Wadsworth, Marc H., Chen, Han, Kurtz, Jonathan R., Dighero-Kemp, Bonnie, Bjornson, Zach B., Mukherjee, Nilanjan, Sellers, Brian A., Tran, Nancy, Bauer, Matthew R., Adams, Gordon C., Adams, Ricky, Rinn, John L., Melé, Marta, Schaffner, Stephen F., Nolan, Garry P., Barnes, Kayla G., Hensley, Lisa E., McIlwain, David R., Shalek, Alex K., Sabeti, Pardis C., Bennett, Richard S.

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Modeling malaria genomics reveals transmission decline and rebound in Senegal von Daniels, Rachel F., Schaffner, Stephen F., Wenger, Edward A., Proctor, Joshua L., Chang, Hsiao-Han, Wong, Wesley, Baro, Nicholas, Ndiaye, Daouda, Fall, Fatou Ba, Ndiop, Medoune, Ba, Mady, Milner, Danny A., Taylor, Terrie E., Neafsey, Daniel E., Volkman, Sarah K., Eckhoff, Philip A., Hartl, Daniel L., Wirth, Dyann F.

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Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection von Grossman, Sharon R, Shylakhter, Ilya, Karlsson, Elinor K, Byrne, Elizabeth H, Morales, Shannon, Frieden, Gabriel, Hostetter, Elizabeth, Angelino, Elaine, Garber, Manuel, Zuk, Or, Lander, Eric S, Schaffner, Stephen F, Sabeti, Pardis C

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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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Calibrating a coalescent simulation of human genome sequence variation von Schaffner, Stephen F, Foo, Catherine, Gabriel, Stacey, Reich, David, Daly, Mark J, Altshuler, David

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

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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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Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections von Baniecki, Mary Lynn, Faust, Aubrey L, Schaffner, Stephen F, Park, Daniel J, Galinsky, Kevin, Daniels, Rachel F, Hamilton, Elizabeth, Ferreira, Marcelo U, Karunaweera, Nadira D, Serre, David, Zimmerman, Peter A, Sá, Juliana M, Wellems, Thomas E, Musset, Lise, Legrand, Eric, Melnikov, Alexandre, Neafsey, Daniel E, Volkman, Sarah K, Wirth, Dyann F, Sabeti, Pardis C

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High-resolution haplotype structure in the human genome von Daly, Mark J., Rioux, John D., Schaffner, Stephen F., Hudson, Thomas J., Lander, Eric S.

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

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The Structure of Haplotype Blocks in the Human Genome von Gabriel, Stacey B., Schaffner, Stephen F., Nguyen, Huy, Moore, Jamie M., Roy, Jessica, Blumenstiel, Brendan, Higgins, John, DeFelice, Matthew, Lochner, Amy, Faggart, Maura, Liu-Cordero, Shau Neen, Rotimi, Charles, Adeyemo, Adebowale, Cooper, Richard, Ward, Ryk, Lander, Eric S., Daly, Mark J., Altshuler, David

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