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

Volltext

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

Volltext

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.

Volltext

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

Volltext

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.

Volltext

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

Volltext

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.

Volltext

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

Volltext

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.

Volltext

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.

Volltext

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.

Volltext

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

Volltext

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

Volltext

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.

Volltext

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.

Volltext

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

Volltext

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.

Volltext

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

Volltext

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

Volltext

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

Volltext