1. Early Neolithic genomes from the eastern Fertile Crescent.

    Science 353(6298):499 (2016) PMID 27417496

    We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially...
  2. Early farmers from across Europe directly descended from Neolithic Aegeans.

    PNAS 113(25):6886 (2016) PMID 27274049 PMCID PMC4922144

    Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local for...
  3. The Kalash Genetic Isolate? The Evidence for Recent Admixture.

    The American Journal of Human Genetics 98(2):396 (2016) PMID 26849116 PMCID PMC4746362

  4. The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape

    Current Biology 25(21):2878 (2015)

  5. The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape.

    Current Biology 25(19):2518 (2015) PMID 26387712 PMCID PMC4714572

    Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-...
  6. Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference.

    PLoS Genetics 11(8):e1005397 (2015) PMID 26291793 PMCID PMC4546361

    The Ari peoples of Ethiopia are comprised of different occupational groups that can be distinguished genetically, with Ari Cultivators and the socially marginalised Ari Blacksmiths recently shown to have a similar level of genetic differentiation between them (FST ≈ 0.023 - 0.04) as that observe...
  7. Evidence for negative selection of gene variants that increase dependence on dietary choline in a Gambian cohort.

    FASEB Journal 29(8):3426 (2015) PMID 25921832 PMCID PMC4511208

    Choline is an essential nutrient, and the amount needed in the diet is modulated by several factors. Given geographical differences in dietary choline intake and disparate frequencies of single-nucleotide polymorphisms (SNPs) in choline metabolism genes between ethnic groups, we tested the hypot...
  8. The fine-scale genetic structure of the British population.

    Nature 519(7543):309 (2015) PMID 25788095 PMCID PMC4632200

    Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide single nucleotide polymorphism (SNP) data from a c...
  9. The genomic and phenotypic diversity of Schizosaccharomyces pombe.

    Nature Genetics 47(3):235 (2015) PMID 25665008 PMCID PMC4645456

    Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To extend the usefulness of this model, we surveyed the genom...
  10. Human Dispersal Out of Africa: A Lasting Debate.

    Evolutionary Bioinformatics 11(Suppl 2):57 (2015) PMID 27127403 PMCID PMC4844272

    Unraveling the first migrations of anatomically modern humans out of Africa has invoked great interest among researchers from a wide range of disciplines. Available fossil, archeological, and climatic data offer many hypotheses, and as such genetics, with the advent of genome-wide genotyping and...
  11. Unravelling the hidden ancestry of American admixed populations.

    Nature Communications 6:6596 (2015) PMID 25803618 PMCID PMC4374169

    The movement of people into the Americas has brought different populations into contact, and contemporary American genomes are the product of a range of complex admixture events. Here we apply a haplotype-based ancestry identification approach to a large set of genome-wide SNP data from a variet...
  12. A genetic atlas of human admixture history.

    Science 343(6172):747 (2014) PMID 24531965 PMCID PMC4209567

    Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at f...
  13. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
    Ashley H Beecham, Nikolaos A Patsopoulos, Dionysia K Xifara, Mary F Davis, Anu Kemppinen, Chris Cotsapas, Tejas Shah, Chris Spencer, David Booth, An Goris, Annette Oturai, Janna Saarela, Bertrand Fontaine, Bernhard Hemmer, Claes Martin, Frauke Zipp, Sandra D'Alfonso, Filippo Martinelli-Boneschi, Bruce Taylor, Hanne F Harbo, Ingrid Kockum, Jan Hillert, Tomas Olsson, Maria Ban, Jorge R Oksenberg, Rogier Hintzen, Lisa F Barcellos, Cristina Agliardi, Lars Alfredsson, Mehdi Alizadeh, Carl Anderson, Robert Andrews, Helle Bach Søndergaard, Amie Baker, Gavin Band, Sergio E Baranzini, Nadia Barizzone, Jeffrey Barrett, Céline Bellenguez, Laura Bergamaschi, Luisa Bernardinelli, Achim Berthele, Viola Biberacher, Thomas M C Binder, Hannah Blackburn, Izaura L Bomfim, Paola Brambilla, Simon Broadley, Bruno Brochet, Lou Brundin, Dorothea Buck, Helmut Butzkueven, Stacy J Caillier, William Camu, Wassila Carpentier, Paola Cavalla, Elisabeth G Celius, Irène Coman, Giancarlo Comi, Lucia Corrado, Leentje Cosemans, Isabelle Cournu-Rebeix, Bruce A Cree, Daniele Cusi, Vincent Damotte, Gilles Defer, Silvia R Delgado, Panos Deloukas, Alessia di Sapio, Alexander T Dilthey, Peter Donnelly, Bénédicte Dubois, Martin Duddy, Sarah Edkins, Irina Elovaara, Federica Esposito, Nikos Evangelou, Barnaby Fiddes, Judith Field, Andre Franke, Colin Freeman, Irene Y Frohlich, Daniela Galimberti, Christian Gieger, Pierre-Antoine Gourraud, Christiane Graetz, Andrew Graham, Verena Grummel, Clara Guaschino, Athena Hadjixenofontos, Hakon Hakonarson, Christopher Halfpenny, Gillian Hall, Per Hall, Anders Hamsten, James Harley, Timothy Harrower, Clive Hawkins, Garrett Hellenthal, Charles Hillier, Jeremy Hobart, Muni Hoshi, Sarah E Hunt, Maja Jagodic, Ilijas Jelčić, Angela Jochim, Brian Kendall, Allan Kermode, Trevor Kilpatrick, Keijo Koivisto, Ioanna Konidari, Thomas Korn, Helena Kronsbein, Cordelia Langford, Malin Larsson, Mark Lathrop, Christine Lebrun-Frenay, Jeannette Lechner-Scott, Michelle H Lee, Maurizio A Leone, Virpi Leppä, Giuseppe Liberatore, Benedicte A Lie, Christina M Lill, Magdalena Lindén, Jenny Link, Felix Luessi, Jan Lycke, Fabio Macciardi, Satu Männistö, Clara P Manrique, Roland Martin, Vittorio Martinelli, Deborah Mason, Gordon Mazibrada, Cristin McCabe, Inger-Lise Mero, Julia Mescheriakova, Loukas Moutsianas, Kjell-Morten Myhr, Guy Nagels, Richard Nicholas, Petra Nilsson, Fredrik Piehl, Matti Pirinen, Siân E Price, Hong Quach, Mauri Reunanen, Wim Robberecht, Neil P Robertson, Mariaemma Rodegher, David Rog, Marco Salvetti, Nathalie C Schnetz-Boutaud, Finn Sellebjerg, Rebecca C Selter, Catherine Schaefer, Sandip Shaunak, Ling Shen, Simon Shields, Volker Siffrin, Mark Slee, Per Soelberg Sorensen, Melissa Sorosina, Mireia Sospedra, Anne Spurkland, Amy Strange, Emilie Sundqvist, Vincent Thijs, John Thorpe, Anna Ticca, Pentti Tienari, Cornelia van Duijn, Elizabeth M Visser, Steve Vucic, Helga Westerlind, James S Wiley, Alastair Wilkins, James F Wilson, Juliane Winkelmann, John Zajicek, Eva Zindler, Jonathan L Haines, Margaret A Pericak-Vance, Adrian J Ivinson, Graeme Stewart, David Hafler, Stephen L Hauser, Alastair Compston, Gil McVean, Philip De Jager, Stephen J Sawcer, and Jacob L McCauley

    Nature Genetics 45(11):1353 (2013) PMID 24076602 PMCID PMC3832895

    Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-w...
  14. Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    Stephan Ripke, Colm O'Dushlaine, Kimberly Chambert, Jennifer L Moran, Anna Kähler, Susanne Akterin, Sarah E Bergen, Ann L Collins, James Crowley, Menachem Fromer, Yunjung Kim, Sang Hong Lee, Patrik K E Magnusson, Nick Sanchez, Eli A Stahl, Stephanie Williams, Naomi R Wray, Kai Xia, Francesco Bettella, Anders D Borglum, Brendan K Bulik-Sullivan, Paul Cormican, Nick Craddock, Christiaan de Leeuw, Naser Durmishi, Michael Gill, Vera Golimbet, Marian L Hamshere, Peter Holmans, David M Hougaard, Kenneth S Kendler, Kuang Lin, Derek W Morris, Ole Mors, Preben B Mortensen, Benjamin M Neale, Francis A O'Neill, Michael J Owen, Milica Pejovic Milovancevic, Danielle Posthuma, John Powell, Alexander L Richards, Brien P Riley, Douglas Ruderfer, Dan Rujescu, Engilbert Sigurdsson, Teimuraz Silagadze, August B Smit, Hreinn Stefansson, Stacy Steinberg, Jaana Suvisaari, Sarah Tosato, Matthijs Verhage, James T Walters, Douglas F Levinson, Pablo V Gejman, Kenneth S Kendler, Claudine Laurent, Bryan J Mowry, Michael C O'Donovan, Michael J Owen, Ann E Pulver, Brien P Riley, Sibylle G Schwab, Dieter B Wildenauer, Frank Dudbridge, Peter Holmans, Jianxin Shi, Margot Albus, Madeline Alexander, Dominique Campion, David Cohen, Dimitris Dikeos, Jubao Duan, Peter Eichhammer, Stephanie Godard, Mark Hansen, F Bernard Lerer, Kung-Yee Liang, Wolfgang Maier, Jacques Mallet, Deborah A Nertney, Gerald Nestadt, Nadine Norton, Francis A O'Neill, George N Papadimitriou, Robert Ribble, Alan R Sanders, Jeremy M Silverman, Dermot Walsh, Nigel M Williams, Brandon Wormley, Maria J Arranz, Steven Bakker, Stephan Bender, Elvira Bramon, David Collier, Benedicto Crespo-Facorro, Jeremy Hall, Conrad Iyegbe, Assen Jablensky, Rene S Kahn, Luba Kalaydjieva, Stephen Lawrie, Cathryn M Lewis, Kuang Lin, Don H Linszen, Ignacio Mata, Andrew McIntosh, Robin Murray, Roel A Ophoff, John Powell, Dan Rujescu, Jim Van Os, Muriel Walshe, Matthias Weisbrod, Durk Wiersma, Peter Donnelly, Ines Barroso, Jenefer M Blackwell, Elvira Bramon, Matthew A Brown, Juan P Casas, Aiden P Corvin, Panos Deloukas, Audrey Duncanson, Janusz Jankowski, Hugh S Markus, Christopher G Mathew, Colin N A Palmer, Robert Plomin, Anna Rautanen, Stephen J Sawcer, Richard C Trembath, Ananth C Viswanathan, Nicholas Wood, Chris A Spencer, Gavin Band, Céline Bellenguez, Colin Freeman, Garrett Hellenthal, Eleni Giannoulatou, Matti Pirinen, Richard D Pearson, Amy Strange, Zhan Su, Damjan Vukcevic, Peter Donnelly, Cordelia Langford, Sarah E Hunt, Sarah Edkins, Rhian Gwilliam, Hannah Blackburn, Suzannah J Bumpstead, Serge Dronov, Matthew Gillman, Emma Gray, Naomi Hammond, Alagurevathi Jayakumar, Owen T McCann, Jennifer Liddle, Simon C Potter, Radhi Ravindrarajah, Michelle Ricketts, Avazeh Tashakkori-Ghanbaria, Matthew J Waller, Paul Weston, Sara Widaa, Pamela Whittaker, Ines Barroso, Panos Deloukas, Christopher G Mathew, Jenefer M Blackwell, Matthew A Brown, Aiden P Corvin, Mark I McCarthy, Chris A Spencer, Elvira Bramon, Aiden P Corvin, Michael C O'Donovan, Kari Stefansson, Edward Scolnick, Shaun Purcell, Steven A McCarroll, Pamela Sklar, Christina M Hultman, and Patrick F Sullivan

    Nature Genetics 45(10):1150 (2013) PMID 23974872 PMCID PMC3827979

    Schizophrenia is an idiopathic mental disorder with a heritable component and a substantial public health impact. We conducted a multi-stage genome-wide association study (GWAS) for schizophrenia beginning with a Swedish national sample (5,001 cases and 6,243 controls) followed by meta-analysis ...
  15. Inference of population structure using dense haplotype data.

    PLoS Genetics 8(1):e1002453 (2012) PMID 22291602 PMCID PMC3266881

    The advent of genome-wide dense variation data provides an opportunity to investigate ancestry in unprecedented detail, but presents new statistical challenges. We propose a novel inference framework that aims to efficiently capture information on population structure provided by patterns of hap...
  16. Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population.

    PLoS Genetics 8(3):e1002504 (2012) PMID 22396655 PMCID PMC3291532

    In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts o...
  17. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
    Stephen Sawcer, Garrett Hellenthal, Matti Pirinen, Chris A Spencer, Nikolaos A Patsopoulos, Loukas Moutsianas, Alexander Dilthey, Zhan Su, Colin Freeman, Sarah E Hunt, Sarah Edkins, Emma Gray, David R Booth, Simon C Potter, An Goris, Gavin Band, Annette Bang Oturai, Amy Strange, Janna Saarela, Céline Bellenguez, Bertrand Fontaine, Matthew Gillman, Bernhard Hemmer, Rhian Gwilliam, Frauke Zipp, Alagurevathi Jayakumar, Roland Martin, Stephen Leslie, Stanley Hawkins, Eleni Giannoulatou, Sandra D'alfonso, Hannah Blackburn, Filippo Martinelli Boneschi, Jennifer Liddle, Hanne F Harbo, Marc L Perez, Anne Spurkland, Matthew J Waller, Marcin P Mycko, Michelle Ricketts, Manuel Comabella, Naomi Hammond, Ingrid Kockum, Owen T McCann, Maria Ban, Pamela Whittaker, Anu Kemppinen, Paul Weston, Clive Hawkins, Sara Widaa, John Zajicek, Serge Dronov, Neil Robertson, Suzannah J Bumpstead, Lisa F Barcellos, Rathi Ravindrarajah, Roby Abraham, Lars Alfredsson, Kristin Ardlie, Cristin Aubin, Amie Baker, Katharine Baker, Sergio E Baranzini, Laura Bergamaschi, Roberto Bergamaschi, Allan Bernstein, Achim Berthele, Mike Boggild, Jonathan P Bradfield, David Brassat, Simon A Broadley, Dorothea Buck, Helmut Butzkueven, Ruggero Capra, William M Carroll, Paola Cavalla, Elisabeth G Celius, Sabine Cepok, Rosetta Chiavacci, Françoise Clerget-Darpoux, Katleen Clysters, Giancarlo Comi, Mark Cossburn, Isabelle Cournu-Rebeix, Mathew B Cox, Wendy Cozen, Bruce A Cree, Anne H Cross, Daniele Cusi, Mark J Daly, Emma Davis, Paul I W de Bakker, Marc Debouverie, Marie Beatrice, Katherine Dixon, Rita Dobosi, Bénédicte Dubois, David Ellinghaus, Irina Elovaara, Federica Esposito, Claire Fontenille, Simon Foote, Andre Franke, Daniela Galimberti, Angelo Ghezzi, Joseph Glessner, Refujia Gomez, Olivier Gout, Colin Graham, Struan F A Grant, Franca Rosa Guerini, Hakon Hakonarson, Per Hall, Anders Hamsten, Hans-Peter Hartung, Rob N Heard, Simon Heath, Jeremy Hobart, Muna Hoshi, Carmen Infante-Duarte, Gillian Ingram, Wendy Ingram, Talat Islam, Maja Jagodic, Michael Kabesch, Allan G Kermode, Trevor J Kilpatrick, Cecilia Kim, Norman Klopp, Keijo Koivisto, Malin Larsson, Mark Lathrop, Jeannette S Lechner-Scott, Maurizio A Leone, Virpi Leppä, Ulrika Liljedahl, Izaura Lima Bomfim, Robin Lincoln, Jenny Link, Jianjun Liu, Aslaug R Lorentzen, Sara Lupoli, Fabio Macciardi, Thomas Mack, Mark Marriott, Vittorio Martinelli, Deborah Mason, Jacob L McCauley, Frank Mentch, Inger-Lise Mero, Tania Mihalova, Xavier Montalban, John Mottershead, Kjell-Morten Myhr, Paola Naldi, William Ollier, Alison Page, Aarno Palotie, Jean Pelletier, Laura Piccio, Trevor Pickersgill, Fredrik Piehl, Susan Pobywajlo, Hong L Quach, Patricia Ramsay, Mauri Reunanen, Richard Reynolds, John D Rioux, Mariaemma Rodegher, Sabine Roesner, Justin P Rubio, Ina-Maria Rückert, Marco Salvetti, Erika Salvi, Adam Santaniello, Catherine A Schaefer, Stefan Schreiber, Christian Schulze, Rodney J Scott, Finn Sellebjerg, Krzysztof W Selmaj, David Sexton, Ling Shen, Brigid Simms-Acuna, Sheila Skidmore, Patrick M A Sleiman, Cathrine Smestad, Per Soelberg Sørensen, Helle Bach Søndergaard, Jim Stankovich, Richard C Strange, Anna-Maija Sulonen, Emilie Sundqvist, Ann-Christine Syvänen, Francesca Taddeo, Bruce Taylor, Jenefer M Blackwell, Pentti Tienari, Elvira Bramon, Ayman Tourbah, Matthew A Brown, Ewa Tronczynska, Juan P Casas, Niall Tubridy, Aiden Corvin, Jane Vickery, Janusz Jankowski, Pablo Villoslada, Hugh S Markus, Kai Wang, Christopher G Mathew, James Wason, Colin N A Palmer, H-Erich Wichmann, Robert Plomin, Ernest Willoughby, Anna Rautanen, Juliane Winkelmann, Michael Wittig, Richard C Trembath, Jacqueline Yaouanq, Ananth C Viswanathan, Haitao Zhang, Nicholas Wood, Rebecca Zuvich, Panos Deloukas, Cordelia Langford, Audrey Duncanson, Jorge R Oksenberg, Margaret A Pericak-Vance, Jonathan L Haines, Tomas Olsson, Jan Hillert, Adrian J Ivinson, Philip L De Jager, Leena Peltonen, Graeme J Stewart, David A Hafler, Stephen L Hauser, Gil McVean, Peter Donnelly, and Alastair Compston

    Nature 476(7359):214 (2011) PMID 21833088 PMCID PMC3182531

    Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that ...
  18. The major histocompatibility complex and multiple sclerosis: a smoking gun?

    Brain 134(Pt 3):638 (2011) PMID 21310724

  19. Inferring human colonization history using a copying model.

    PLoS Genetics 4(5):e1000078 (2008) PMID 18497854 PMCID PMC2367454

    Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach that uses Single Nucleotide Polymorphism (SNP) data to identify sharing of chromosomal segments be...
  20. msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots.

    PMID 17150995

    We have incorporated both crossover and gene conversion hotspots into an existing coalescent-based program for simulating genetic variation data for a sample of chromosomes from a population. The source code for msHOT is available at http://home.uchicago.edu/~rhudson1, along with accompanying in...