Browsing by Author "Sabeti, Pardis"

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    • Lassa Hemorrhagic Fever in a Late Term Pregnancy from Northern Sierra Leone with a Positive Maternal Outcome: Case Report 

      Branco, Luis M.; Boisen, Matt L.; Andersen, Kristian G; Grove, Jessica N.; Moses, Lina M.; Muncy, Ivana J.; Henderson, Lee A.; Schieffellin, John S.; Robinson, James E.; Bangura, James J.; Grant, Donald S.; Raabe, Vanessa N.; Fonnie, Mbalu; Sabeti, Pardis Christine; Garry, Robert F. (BioMed Central, 2011)
      Lassa fever (LF) is a devastating viral disease prevalent in West Africa. Efforts to take on this public health crisis have been hindered by lack of infrastructure and rapid field deployable diagnosis in areas where the ...

    • A Malaria Fingerprint in the Human Genome? 

      Daily, Johanna P.; Sabeti, Pardis Christine (Massachusetts Medical Society, 2008)

    • Malaria Life Cycle Intensifies Both Natural Selection and Random Genetic Drift 

      Chang, Hsiao-Han; Moss, Eli L.; Park, Daniel John; Ndiaye, Daouda; Mboup, Souleymane; Cooke, Sarah K.; Sabeti, Pardis Christine; Wirth, Dyann F.; Neafsey, Daniel Edward; Hartl, Daniel L. (Proceedings of the National Academy of Sciences, 2013)
      Analysis of genome sequences of 159 isolates of Plasmodium falciparum from Senegal yields an extraordinarily high proportion (26.85%) of protein-coding genes with the ratio of nonsynonymous to synonymous polymorphism greater ...

    • Many ways to die, one way to arrive: how selection acts through pregnancy 

      Brown, Elizabeth Anne; Ruvolo, Maryellen; Sabeti, Pardis Christine (Elsevier BV, 2013)
      When considering selective forces shaping human evolution, the importance of pregnancy to fitness should not be underestimated. Although specific mortality factors may only impact upon a fraction of the population, birth ...

    • A Map of Human Genome Variation from Population Scale Sequencing 

      Altshuler, David Matthew; Lander, Eric Steven; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Lee, Charles; Mills, Ryan Edward; Shi, Xinghua; Daly, Mark Joseph; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon Rachel; Handsaker, Robert E; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; Nemesh, James C.; McKenna, Aaron; Philippakis, Anthony Andrew; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis Christine; Schaffner, Stephen; Shlyakhter, Ilya (Nature Publishing Group, 2010)
      The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot ...

    • Mapping Copy Number Variation by Population Scale Genome Sequencing 

      Mills, Ryan Edward; Handsaker, Robert E; Korn, Joshua; Nemesh, James; Shi, Xinghua; Lee, Charles; McCarroll, Steven A.; Altshuler, David Matthew; Gabriel, Stacey B.; Lander, Eric Steven; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Daly, Mark Joseph; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon Rachel; Handsaker, Robert E; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Li, Heng; Maguire, Jared R.; McKenna, Aaron; Philippakis, Anthony Andrew; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis Christine; Schaffner, Stephen; Shlyakhter, Ilya; DePristo, Mark A.; Wilkinson, Jane (Nature Publishing Group, 2011)
      Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of ...

    • Metabolic Adaptations in Modern Human Populations: Evidence, Theory, and Investigation 

      Brown, Elizabeth Anne (2015-05-15)
      Diverse climates, infectious agents, and subsistence patterns drove humans to adapt metabolically to different environments since the migration out of Africa 100,000 years ago. In this dissertation, I review current ...

    • Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant 

      Kamberov, Yana George; Wang, Sijia; Tan, Jingze; Gerbault, Pascale; Wark, Abigail; Tan, Longzhi; Yang, Yajun; Li, Shilin; Tang, Kun; Chen, Hua; Powell, Adam; Itan, Yuval; Fuller, Dorian; Lohmueller, Jason; Mao, Junhao; Schachar, Asa; Paymer, Madeline; Hostetter, Elizabeth; Byrne, Elizabeth; Burnett, Melissa; McMahon, Andrew P.; Thomas, Mark G.; Lieberman, Daniel E.; Jin, Li; Tabin, Clifford James; Morgan, Bruce Allan; Sabeti, Pardis Christine (Elsevier BV, 2013)
      An adaptive variant of the human Ectodysplasin receptor, EDARV370A, is one of the strongest candidates of recent positive selection from genome-wide scans. We have modeled EDAR370A in mice and characterized its phenotype ...

    • Molecular Diagnostics for Lassa Fever at Irrua Specialist Teaching Hospital, Nigeria: Lessons Learnt from Two Years of Laboratory Operation 

      Asogun, Danny A.; Adomeh, Donatus I.; Ehimuan, Jacqueline; Odia, Ikponmwonsa; Hass, Meike; Gabriel, Martin; Ölschläger, Stephan; Becker-Ziaja, Beate; Folarin, Onikepe; Phelan, Eric; Ehiane, Philomena E.; Ifeh, Veritas E.; Uyigue, Eghosasere A.; Oladapo, Yemisi T.; Muoebonam, Ekene B.; Osunde, Osagie; Dongo, Andrew; Okokhere, Peter O.; Okogbenin, Sylvanus A.; Momoh, Mojeed; Alikah, Sylvester O.; Akhuemokhan, Odigie C.; Imomeh, Peter; Odike, Maxy A. C.; Gire, Stephen; Andersen, Kristian G; Sabeti, Pardis Christine; Happi, Christian Tientcha; Akpede, George O.; Günther, Stephan (Public Library of Science, 2012)
      Background: Lassa fever is a viral hemorrhagic fever endemic in West Africa. However, none of the hospitals in the endemic areas of Nigeria has the capacity to perform Lassa virus diagnostics. Case identification and ...

    • Most neutralizing human monoclonal antibodies target novel epitopes requiring both Lassa virus glycoprotein subunits 

      Robinson, James E.; Hastie, Kathryn M.; Cross, Robert W.; Yenni, Rachael E.; Elliott, Deborah H.; Rouelle, Julie A.; Kannadka, Chandrika B.; Smira, Ashley A.; Garry, Courtney E.; Bradley, Benjamin T.; Yu, Haini; Shaffer, Jeffrey G.; Boisen, Matt L.; Hartnett, Jessica N.; Zandonatti, Michelle A.; Rowland, Megan M.; Heinrich, Megan L.; Martínez-Sobrido, Luis; Cheng, Benson; de la Torre, Juan C.; Andersen, Kristian G.; Goba, Augustine; Momoh, Mambu; Fullah, Mohamed; Gbakie, Michael; Kanneh, Lansana; Koroma, Veronica J.; Fonnie, Richard; Jalloh, Simbirie C.; Kargbo, Brima; Vandi, Mohamed A.; Gbetuwa, Momoh; Ikponmwosa, Odia; Asogun, Danny A.; Okokhere, Peter O.; Follarin, Onikepe A.; Schieffelin, John S.; Pitts, Kelly R.; Geisbert, Joan B.; Kulakoski, Peter C.; Wilson, Russell B.; Happi, Christian T.; Sabeti, Pardis C.; Gevao, Sahr M.; Khan, S. Humarr; Grant, Donald S.; Geisbert, Thomas W.; Saphire, Erica Ollmann; Branco, Luis M.; Garry, Robert F. (Nature Publishing Group, 2016)
      Lassa fever is a severe multisystem disease that often has haemorrhagic manifestations. The epitopes of the Lassa virus (LASV) surface glycoproteins recognized by naturally infected human hosts have not been identified or ...

    • Multiple introductions of Zika virus into the United States revealed through genomic epidemiology 

      Grubaugh, Nathan D; Ladner, Jason T; Kraemer, Moritz UG; Dudas, Gytis; Tan, Amanda L; Gangavarapu, Karthik; Wiley, Michael R; White, Stephen; Thézé, Julien; Magnani, Diogo M; Prieto, Karla; Reyes, Daniel; Bingham, Andrea; Paul, Lauren M; Robles-Sikisaka, Refugio; Oliveira, Glenn; Pronty, Darryl; Metsky, Hayden C; Baniecki, Mary Lynn; Barnes, Kayla G; Chak, Bridget; Freije, Catherine A; Gladden-Young, Adrianne; Gnirke, Andreas; Luo, Cynthia; MacInnis, Bronwyn; Matranga, Christian B; Park, Daniel J; Qu, James; Schaffner, Stephen F; Tomkins-Tinch, Christopher; West, Kendra L; Winnicki, Sarah M; Wohl, Shirlee; Yozwiak, Nathan L; Quick, Joshua; Fauver, Joseph R; Khan, Kamran; Brent, Shannon E; Reiner, Robert C; Lichtenberger, Paola N; Ricciardi, Michael; Bailey, Varian K; Watkins, David I; Cone, Marshall R; Kopp, Edgar W; Hogan, Kelly N; Cannons, Andrew C; Jean, Reynald; Garry, Robert F; Loman, Nicholas J; Faria, Nuno R; Porcelli, Mario C; Vasquez, Chalmers; Nagle, Elyse R; Cummings, Derek AT; Stanek, Danielle; Rambaut, Andrew; Sanchez-Lockhart, Mariano; Sabeti, Pardis Christine; Gillis, Leah D; Michael, Scott F; Bedford, Trevor; Pybus, Oliver G; Isern, Sharon; Palacios, Gustavo; Andersen, Kristian G (2017)
      Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital syndromes1,2. In July 2016, mosquito-borne ZIKV transmission was first reported in the continental United States and since then, hundreds ...

    • Natural selection and infectious disease in human populations 

      Karlsson, Elinor Kathryn; Kwiatkowski, Dominic P.; Sabeti, Pardis Christine (Springer Nature, 2014)
      The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important implications for the growing field of medical genomics. As humans migrated ...

    • Natural Selection in a Bangladeshi Population from the Cholera-Endemic Ganges River Delta 

      Karlsson, Elinor Kathryn; Harris, J. B.; Tabrizi, Shervin; Rahman, A.; Shlyakhter, Ilya; Patterson, N.; O, C.; Schaffner, Stephen; Gupta, S.; Chowdhury, F.; Sheikh, A.; Shin, O. S.; Ellis, C.; Becker, C. E.; Stuart, L. M.; Calderwood, Stephen Beaven; Ryan, Edward Thomas; Qadri, F.; Sabeti, Pardis Christine; Larocque, Regina Celes (American Association for the Advancement of Science (AAAS), 2013)
      As an ancient disease with high fatality, cholera has likely exerted strong selective pressure on affected human populations. We performed a genome-wide study of natural selection in a population from the Ganges River ...

    • Polymorphisms in the Gene That Encodes the Iron Transport Protein Ferroportin 1 Influence Susceptibility to Tuberculosis 

      Baker, Meghan Ann; Wilson, Douglas; Wallengren, Kristina; Sandgren, Andreas; Iartchouk, Oleg; Broodie, Nisha Monique; Goonesekera, Sunali D.; Sabeti, Pardis Christine; Murray, Megan Blanche (Oxford University Press, 2012)
      Background: We studied the association between iron intake and polymorphisms in the iron transporter gene, SLC40A1, and the risk of tuberculosis. Methods: We compared iron intake, the frequency of SLC40A1 mutations, and ...

    • Population Genetic Study of the Brain-Derived Neurotrophic Factor (BDNF) Gene 

      Petryshen, Tracey Lynn; Sabeti, Pardis Christine; Aldinger, Kimberly A.; Fry, Ben; Fan, Jinbo B.; Schaffner, Stephen; Waggoner, Skye G.; Tahl, Anthony R.; Sklar, Pamela (Nature Publishing Group, 2010)
      Genetic variants in the brain-derived neurotrophic factor (BDNF) gene, predominantly the functional Val66Met polymorphism, have been associated with risk of bipolar disorder and other psychiatric disorders. However, not ...

    • Positive Selection of a CD36 Nonsense Variant in Sub-Saharan Africa, but No Association with Severe Malaria Phenotypes 

      Fry, Andrew E.; Ghansa, Anita; Small, Kerrin S.; Palma, Alejandro; Auburn, Sarah; Diakite, Mahamadou; Green, Angela; Campino, Susana; Teo, Yik Y.; Clark, Taane G.; Jeffreys, Anna E.; Wilson, Jonathan; Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; Griffiths, Michael J.; Peshu, Norbert; Williams, Thomas N.; Newton, Charles R.; Marsh, Kevin; Molyneux, Malcolm E.; Taylor, Terrie E.; Koram, Kwadwo A.; Oduro, Abraham R.; Rogers, William O.; Rockett, Kirk A.; Kwiatkowski, Dominic P.; Sabeti, Pardis Christine (Oxford University Press, 2009)
      The prevalence of CD36 deficiency in East Asian and African populations suggests that the causal variants are under selection by severe malaria. Previous analysis of data from the International HapMap Project indicated ...

    • Positive Selection of a Pre-Expansion CAG Repeat of the Human SCA2 Gene 

      Yu, Fuli; Hardenbol, Paul; Fu, Qing; Fry, Ben; Lu, Xiuhua; Ghose, Sy; Vega, Richard; Perez, Ag; Pasternak, Shiran; Leal, Suzanne M.; Willis, Thomas D.; Belmont, John; Gibbs, Richard A.; Sabeti, Pardis Christine; Nelson, David L. (Public Library of Science, 2005)
      A region of approximately one megabase of human Chromosome 12 shows extensive linkage disequilibrium in Utah residents with ancestry from northern and western Europe. This strikingly large linkage disequilibrium block was ...

    • Rapid, Field-Deployable Method for Genotyping and Discovery of Single-Nucleotide Polymorphisms Associated with Drug Resistance in Plasmodium falciparum 

      Daniels, Rachel Fath; Ndiaye, Daouda; Wall, Mikeal; McKinney, Jason; Séne, Papa Diogoye; Sabeti, Pardis Christine; Volkman, Sarah K.; Mboup, Souleymane; Wirth, Dyann Fergus (American Society for Microbiology, 2012)
      Despite efforts to reduce malaria morbidity and mortality, drug-resistant parasites continue to evade control strategies. Recently, emphasis has shifted away from control and toward regional elimination and global eradication ...

    • The regulatory capacity of long non-coding RNA in Plasmodium falciparum malaria 

      Broadbent, Kate Mariel (2014-10-21)
      The mechanisms underpinning gene regulation in P. falciparum malaria remain largely elusive, though mounting evidence suggests a major role for epigenetic feedback. Interestingly, long non-(protein)-coding RNAs (lncRNAs) ...

    • Sequence-Based Association and Selection Scans Identify Drug Resistance Loci in the Plasmodium Falciparum Malaria Parasite 

      Park, Daniel John; Lukens, Amanda Kathleen; Neafsey, Daniel Edward; Schaffner, Stephen; Chang, Hsiao-Han; Valim, Clarissa; Ribacke, Ulf Erik; Van Tyne, Daria Natalie; Galinsky, Kevin Joseph; Galligan, Meghan; Becker, Justin S.; Ndiaye, Daouda; Mboup, Souleymane; Wiegand, Roger C.; Hartl, Daniel L.; Sabeti, Pardis Christine; Wirth, Dyann F.; Cooke, Sarah K. (Proceedings of the National Academy of Sciences, 2012)
      Through rapid genetic adaptation and natural selection, the Plasmodium falciparum parasite—the deadliest of those that cause malaria—is able to develop resistance to antimalarial drugs, thwarting present efforts to control ...