Browsing by Author "Sankararaman, Sriram"

Now showing items 1-8 of 8

    • Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes 

      Lipson, Mark; Loh, Po-Ru; Sankararaman, Sriram; Patterson, Nick; Berger, Bonnie; Reich, David (Public Library of Science, 2015)
      The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease. Nevertheless, our current estimates ...

    • The Date of Interbreeding between Neandertals and Modern Humans 

      Sankararaman, Sriram; Patterson, Nick; Li, Heng; Pääbo, Svante; Reich, David Emil (Public Library of Science, 2012)
      Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals ...

    • Evidence of Widespread Selection on Standing Variation in Europe at Height-Associated SNPs 

      Turchin, Michael C.; Chiang, Charleston W. K.; Palmer, Cameron Douglas; Sankararaman, Sriram; Reich, David Emil; Hirschhorn, Joel Naom; GIANT Consortium (Nature Publishing Group, 2012)
      Strong signatures of positive selection at newly arising genetic variants are well-documented in humans, but this form of selection may not be widespread in recent human evolution. Because many human traits are highly ...

    • Inferring parental genomic ancestries using pooled semi-Markov processes 

      Zou, James Y.; Halperin, Eran; Burchard, Esteban; Sankararaman, Sriram (Oxford University Press, 2015)
      Motivation: A basic problem of broad public and scientific interest is to use the DNA of an individual to infer the genomic ancestries of the parents. In particular, we are often interested in the fraction of each parent’s ...

    • The landscape of Neandertal ancestry in present-day humans 

      Sankararaman, Sriram; Mallick, Swapan; Dannemann, Michael; Prüfer, Kay; Kelso, Janet; Pääbo, Svante; Patterson, Nick; Reich, David (2014)
      Analyses of Neandertal genomes have revealed that Neandertals have contributed genetic variants to modern humans1–2. The antiquity of Neandertal gene flow into modern humans means that regions that derive from Neandertals ...

    • Leveraging population admixture to explain missing heritability of complex traits 

      Zaitlen, Noah; Pasaniuc, Bogdan; Sankararaman, Sriram; Bhatia, Gaurav; Zhang, Jianqi; Gusev, Alexander; Young, Taylor; Tandon, Arti; Pollack, Samuela; Vilhjálmsson, Bjarni J.; Assimes, Themistocles L.; Berndt, Sonja I.; Blot, William J.; Chanock, Stephen; Franceschini, Nora; Goodman, Phyllis G.; He, Jing; Hennis, Anselm JM; Hsing, Ann; Ingles, Sue A.; Isaacs, William; Kittles, Rick A.; Klein, Eric A.; Lange, Leslie A.; Nemesure, Barbara; Patterson, Nick; Reich, David; Rybicki, Benjamin A.; Stanford, Janet L.; Stevens, Victoria L; Strom, Sara S.; Whitsel, Eric A; Witte, John S.; Xu, Jianfeng; Haiman, Christopher; Wilson, James G.; Kooperberg, Charles; Stram, Daniel; Reiner, Alex P.; Tang, Hua; Price, Alkes L. (2014)
      Despite recent progress on estimating the heritability explained by genotyped SNPs (hg2), a large gap between hg2 and estimates of total narrow-sense heritability (h2) remains. Explanations for this gap include rare variants, ...

    • Phylogenetic Inference via Sequential Monte Carlo 

      Bouchard-Côté, Alexandre; Sankararaman, Sriram; Jordan, Michael I. (Oxford University Press, 2012)
      Bayesian inference provides an appealing general framework for phylogenetic analysis, able to incorporate a wide variety of modeling assumptions and to provide a coherent treatment of uncertainty. Existing computational ...

    • The Simons Genome Diversity Project: 300 genomes from 142 diverse populations 

      Mallick, Swapan; Li, Heng; Lipson, Mark Israel; Mathieson, Iain; Gymrek, Melissa Ann; Racimo, Fernando; Zhao, Mengyao; Chennagiri, Niru; Nordenfelt, Susanne; Tandon, Arti; Skoglund, Pontus R; Lazaridis, Iosif; Sankararaman, Sriram; Fu, Qiaomei; Rohland-Pinello, Nadin; Renaud, Gabriel; Erlich, Yaniv; Willems, Thomas; Gallo, Carla; Spence, Jeffrey P.; Song, Yun; Poletti, Giovanni; Balloux, Francois; van Driem, George; de Knijff, Peter; Romero, Irene Gallego; Jha, Aashish R.; Behar, Doron M.; Bravi, Claudio M.; Capelli, Cristian; Hervig, Tor; Moreno-Estrada, Andres; Posukh, Olga L.; Balanovska, Elena; Balanovsky, Oleg; Karachanak-Yankova, Sena; Sahakyan, Hovhannes; Toncheva, Draga; Yepiskoposyan, Levon; Tyler-Smith, Chris; Xue, Yali; Abdullah, M. Syafiq; Ruiz-Linares, Andres; Beall, Cynthia M.; Di Rienzo, Anna; Jeong, Choongwon; Starikovskaya, Elena B.; Metspalu, Ene; Parik, Jüri; Villems, Richard; Henn, Brenna M.; Hodoglugil, Ugur; Mahley, Robert; Sajantila, Antti; Stamatoyannopoulos, George; Wee, Joseph T. S.; Khusainova, Rita; Khusnutdinova, Elza; Litvinov, Sergey; Ayodo, George; Comas, David; Hammer, Michael F.; Kivisild, Toomas; Klitz, William; Winkler, Cheryl A.; Labuda, Damian; Bamshad, Michael; Jorde, Lynn B.; Tishkoff, Sarah A.; Watkins, W. Scott; Metspalu, Mait; Dryomov, Stanislav; Sukernik, Rem; Singh, Lalji; Thangaraj, Kumarasamy; Pääbo, Svante; Kelso, Janet; Patterson, Nick; Reich, David Emil (Springer Nature, 2016)
      We report the Simons Genome Diversity Project (SGDP) dataset: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human ...