Now showing items 1-20 of 57

    • The adaptive variant EDARV370A is associated with straight hair in East Asians 

      Tan, Jingze; Yang, Yajun; Tang, Kun; Sabeti, Pardis Christine; Jin, Li; Wang, Sijia (Springer Science + Business Media, 2013)
      Hair straightness/curliness is a highly heritable trait amongst human populations. Previous studies have reported European specific genetic variants influencing hair straightness, but those in East Asians remain unknown. ...
    • Ancient and Recent Adaptive Evolution of Primate Non-Homologous End Joining Genes 

      Demogines, Ann; East, Alysia M.; Lee, Ji-Hoon; Grossman, Sharon Rachel; Sabeti, Pardis Christine; Paull, Tanya T.; Sawyer, Sara L. (Public Library of Science, 2010)
      In human cells, DNA double-strand breaks are repaired primarily by the non-homologous end joining (NHEJ) pathway. Given their critical nature, we expected NHEJ proteins to be evolutionarily conserved, with relatively little ...
    • The Case for Selection at CCR5-Δ32 

      Walsh, Emily; Schaffner, Steve F; Varilly, Patrick; Fry, Ben; Hutcheson, Holli B; Cullen, Mike; Mikkelsen, Tarjei S; Roy, Jessica; Patterson, Nick; Sabeti, Pardis Christine; Cooper, Richard; Reich, David Emil; Altshuler, David Matthew; O'Brien, Stephen James; Lander, Eric Steven (Public Library of Science, 2005)
      The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Δ32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Δ32 arose within the past 1,000 y and rose to ...
    • Cleaning up the record on the maximal information coefficient and equitability 

      Reshef, David N.; Reshef, Yakir Abraham; Mitzenmacher, Michael D.; Sabeti, Pardis Christine (Proceedings of the National Academy of Sciences, 2014)
    • Clinical Illness and Outcomes in Patients with Ebola in Sierra Leone 

      Schieffelin, John S.; Shaffer, Jeffrey G.; Goba, Augustine; Gbakie, Michael; Gire, Stephen; Colubri, Andres; SEALFON, RACHEL; Kanneh, Lansana; Moigboi, Alex; Momoh, Mambu; Fullah, Mohammed; Moses, Lina M.; Brown, Bethany L.; Andersen, Kristian G; Winnicki, Sarah M.; Schaffner, Stephen; Park, Daniel John; Yozwiak, Nathan; Jiang, Pan-Pan Xueke; Kargbo, David; Jalloh, Simbirie; Fonnie, Mbalu; Sinnah, Vandi; French, Issa; Kovoma, Alice; Kamara, Fatima K.; Tucker, Veronica; Konuwa, Edwin; Sellu, Josephine; Mustapha, Ibrahim; Foday, Momoh; Yillah, Mohamed; Kanneh, Franklyn; Saffa, Sidiki; Massally, James L.B.; Boisen, Matt L.; Branco, Luis M.; Vandi, Mohamed A.; Grant, Donald S.; Happi, Christian Tientcha; Gevao, Sahr M.; Fletcher, Thomas E.; Fowler, Robert A.; Bausch, Daniel G.; Sabeti, Pardis Christine; Khan, S. Humarr; Garry, Robert F. (New England Journal of Medicine (NEJM/MMS), 2014)
      Background;Limited clinical and laboratory data are available on patients with Ebola virus disease (EVD). The Kenema Government Hospital in Sierra Leone, which had an existing infrastructure for research regarding viral ...
    • Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus 

      Sabeti, Pardis Christine (Elsevier BV, 2015)
      The 2013-2015 West African epidemic of Ebola virus disease (EVD) reminds us how little is known about biosafety level-4 viruses. Like Ebola virus, Lassa virus (LASV) can cause hemorrhagic fever with high case fatality ...
    • A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection 

      Shylakhter, Ilya; Karlsson, Elinor Kathryn; Byrne, Elizabeth Hockfield; Morales, Shannon; Frieden, Gabriel; Hostetter, Elizabeth; Angelino, Elaine Lee; Garber, Manuel; Zuk, Or; Lander, Eric Steven; Schaffner, Stephen; Sabeti, Pardis Christine; Grossman, Sharon Rachel (American Association for Advancement of Science, 2010)
      The human genome contains hundreds of regions whose patterns of genetic variation indicate recent positive natural selection, yet for most the underlying gene and the advantageous mutation remain unknown. We developed a ...
    • Detecting Natural Selection in Genomic Data 

      Vitti, Joseph J.; Grossman, Sharon R.; Sabeti, Pardis Christine (Annual Reviews, 2013)
      The past fifty years have seen the development and application of numerous statistical methods to identify genomic regions that appear to be shaped by natural selection. These methods have been used to investigate the ...
    • Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections 

      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. (Public Library of Science, 2015)
      Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25–40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective ...
    • Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa 

      Stremlau, Matthew H.; Andersen, Kristian G.; Folarin, Onikepe A.; Grove, Jessica N.; Odia, Ikponmwonsa; Ehiane, Philomena E.; Omoniwa, Omowunmi; Omoregie, Omigie; Jiang, Pan-Pan; Yozwiak, Nathan L.; Matranga, Christian B.; Yang, Xiao; Gire, Stephen K.; Winnicki, Sarah; Tariyal, Ridhi; Schaffner, Stephen F.; Okokhere, Peter O.; Okogbenin, Sylvanus; Akpede, George O.; Asogun, Danny A.; Agbonlahor, Dennis E.; Walker, Peter J.; Tesh, Robert B.; Levin, Joshua Z.; Garry, Robert F.; Sabeti, Pardis C.; Happi, Christian T. (Public Library of Science, 2015)
      Next-generation sequencing (NGS) has the potential to transform the discovery of viruses causing unexplained acute febrile illness (UAFI) because it does not depend on culturing the pathogen or a priori knowledge of the ...
    • Ebola Virus Epidemiology and Evolution in Nigeria 

      Folarin, Onikepe A.; Ehichioya, Deborah; Schaffner, Stephen F.; Winnicki, Sarah M.; Wohl, Shirlee; Eromon, Philomena; West, Kendra L.; Gladden-Young, Adrianne; Oyejide, Nicholas E.; Matranga, Christian B.; Deme, Awa Bineta; James, Ayorinde; Tomkins-Tinch, Christopher; Onyewurunwa, Kenneth; Ladner, Jason T.; Palacios, Gustavo; Nosamiefan, Iguosadolo; Andersen, Kristian G.; Omilabu, Sunday; Park, Daniel J.; Yozwiak, Nathan L.; Nasidi, Abdusallam; Garry, Robert F.; Tomori, Oyewale; Sabeti, Pardis C.; Happi, Christian T. (Oxford University Press, 2016)
      Containment limited the 2014 Nigerian Ebola virus (EBOV) disease outbreak to 20 reported cases and 8 fatalities. We present here clinical data and contact information for at least 19 case patients, and full-length EBOV ...
    • Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples 

      Matranga, Christian B; Andersen, Kristian G; Winnicki, Sarah; Busby, Michele; Gladden, Adrianne D; Tewhey, Ryan; Stremlau, Matthew; Berlin, Aaron; Gire, Stephen K; England, Eleina; Moses, Lina M; Mikkelsen, Tarjei S; Odia, Ikponmwonsa; Ehiane, Philomena E; Folarin, Onikepe; Goba, Augustine; Kahn, S Humarr; Grant, Donald S; Honko, Anna; Hensley, Lisa; Happi, Christian; Garry, Robert F; Malboeuf, Christine M; Birren, Bruce W; Gnirke, Andreas; Levin, Joshua Z; Sabeti, Pardis C (BioMed Central, 2014)
      We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase ...
    • Evaluation of the Potential Impact of Ebola Virus Genomic Drift on the Efficacy of Sequence-Based Candidate Therapeutics 

      Kugelman, Jeffrey R.; Sanchez-Lockhart, Mariano; Andersen, Kristian G.; Gire, Stephen; Park, Daniel J.; Sealfon, Rachel; Lin, Aaron E.; Wohl, Shirlee; Sabeti, Pardis C.; Kuhn, Jens H.; Palacios, Gustavo F. (American Society of Microbiology, 2015)
      ABSTRACT Until recently, Ebola virus (EBOV) was a rarely encountered human pathogen that caused disease among small populations with extraordinarily high lethality. At the end of 2013, EBOV initiated an unprecedented disease ...
    • Evolution and Spread of Ebola Virus in Liberia, 2014–2015 

      Ladner, Jason T.; Wiley, Michael R.; Mate, Suzanne; Dudas, Gytis; Prieto, Karla; Lovett, Sean; Nagle, Elyse R.; Beitzel, Brett; Gilbert, Merle L.; Fakoli, Lawrence; Diclaro, Joseph W.; Schoepp, Randal J.; Fair, Joseph; Kuhn, Jens H.; Hensley, Lisa E.; Park, Daniel J.; Sabeti, Pardis Christine; Rambaut, Andrew; Sanchez-Lockhart, Mariano; Bolay, Fatorma K.; Kugelman, Jeffrey R.; Palacios, Gustavo (Elsevier BV, 2015)
      The 2013–present Western African Ebola virus disease (EVD) outbreak is the largest ever recorded with >28,000 reported cases. Ebola virus (EBOV) genome sequencing has played an important role throughout this outbreak; ...
    • Evolutionary Adaptation and Antimalarial Resistance in Plasmodium falciparum 

      Park, Daniel John (2013-10-14)
      The malaria parasite, Plasmodium falciparum, has a demonstrated history of adaptation to antimalarials and host immune pressure. This ability unraveled global eradication programs fifty years ago and seriously threatens ...
    • FRESCo: finding regions of excess synonymous constraint in diverse viruses 

      Sealfon, Rachel S; Lin, Michael F; Jungreis, Irwin; Wolf, Maxim Y; Kellis, Manolis; Sabeti, Pardis C (BioMed Central, 2015)
      Background: The increasing availability of sequence data for many viruses provides power to detect regions under unusual evolutionary constraint at a high resolution. One approach leverages the synonymous substitution rate ...
    • A General SNP-Based Molecular Barcode for Plasmodium Falciparum Identification and Tracking 

      Mahesh, Nira; Rosen, David; Daniels, Rachel; Volkman, Sarah K.; Milner, Danny Arnold; Neafsey, Daniel Edward; Park, Daniel John; Angelino, Elaine; Sabeti, Pardis Christine; Wirth, Dyann Fergus; Wiegand, Roger C. (BioMed Central, 2008)
      Background: Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. ...
    • A genetic basis of variation in eccrine sweat gland and hair follicle density 

      Kamberov, Yana George; Karlsson, Elinor; Kamberova, Gerda L.; Lieberman, Daniel E.; Sabeti, Pardis Christine; Morgan, Bruce Allan; Tabin, Clifford James (Proceedings of the National Academy of Sciences, 2015)
      Among the unique features of humans, one of the most salient is the ability to effectively cool the body during extreme prolonged activity through the evapotranspiration of water on the skin's surface. The evolution of ...
    • Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal 

      Daniels, Rachel Fath; Chang, Hsiao-Han; Séne, Papa Diogoye; Park, Danny C.; Neafsey, Daniel Edward; Schaffner, Stephen; Hamilton, Elizabeth Julia; Lukens, Amanda Kathleen; Van Tyne, Daria Natalie; Mboup, Souleymane; Sabeti, Pardis Christine; Ndiaye, Daouda; Wirth, Dyann Fergus; Hartl, Daniel L.; Cooke, Sarah Volkman (Public Library of Science, 2013)
      Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically ...
    • Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis 

      Wagschal, Alexandre; Najafi-Shoushtari, S Hani; Wang, Lifeng; Goedeke, Leigh; Sinha, Sumita; deLemos, Andrew S; Black, Josh C; Ramírez, Cristina M; Li, Yingxia; Tewhey, Ryan; Hatoum, Ida; Shah, Naisha; Lu, Yong; Kristo, Fjoralba; Psychogios, Nikolaos; Vrbanac, Vladimir; Lu, Yi-Chien; Hla, Timothy T; de Cabo, Rafael; Tsang, John S; Schadt, Eric; Sabeti, Pardis Christine; Kathiresan, Sekar; Cohen, David E; Whetstine, Johnathan; Chung, Raymond Taeyong; Fernández-Hernando, Carlos; Kaplan, Lee Michael; Bernards, Andre; Gerszten, Robert Edgardo; Naar, Anders Michael (Springer Nature, 2015)
      Genome-wide association studies (GWASs) have linked genes to various pathological traits. However, the potential contribution of regulatory noncoding RNAs, such as microRNAs (miRNAs), to a genetic predisposition to ...