{"id":2,"date":"2017-07-14T06:41:39","date_gmt":"2017-07-14T06:41:39","guid":{"rendered":"http:\/\/wp.unil.ch\/egg\/?page_id=2"},"modified":"2018-03-17T14:52:05","modified_gmt":"2018-03-17T13:52:05","slug":"sample-page","status":"publish","type":"page","link":"https:\/\/wp.unil.ch\/egg\/sample-page\/","title":{"rendered":"Publications"},"content":{"rendered":"

2018<\/strong><\/p>\n

Moreno-Mayar, J.V., Potter, B.A., Vinner, L., Steinr\u00fccken, M., Rasmussen, S., Terhorst, J., Kamm, J.A., Albrechtsen, A., Malaspinas, A.-S., Sikora, M., Reuther, J.D., Irish, J.D., Malhi, R.S., Orlando, L., Song, Y.S., Nielsen, R., Meltzer, D.J., Willerslev, E., 2018. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature <\/strong>553, 203. https:\/\/doi.org\/10.1038\/nature25173<\/p>\n

D\u00e1valos, D.I.C., Nieves-Col\u00f3n, M.A., Sockell, A., Poznik, D.G., Schroeder, H., Stone, A.C., Bustamante, C.D., Malaspinas, A.-S., \u00c1vila-Arcos, M.C., 2017. In-solution Y-chromosome capture-enrichment on ancient DNA libraries. bioRxiv <\/strong>223214. https:\/\/doi.org\/10.1101\/223214<\/p>\n

2017<\/strong><\/p>\n

Dortch, J., Malaspinas, A.-S., 2017. Madjedbebe and genomic histories of Aboriginal Australia. Australian Archaeology<\/strong> 83, 174\u2013177. https:\/\/doi.org\/10.1080\/03122417.2017.1408546<\/p>\n

2016<\/strong><\/p>\n

Malaspinas, A.-S., Westaway, M.C., Muller, C., Sousa, V.C., Lao, O., Alves, I., Bergstr\u00f6m, A., Athanasiadis, G., Cheng, J.Y., Crawford, J.E., Heupink, T.H., Macholdt, E., Peischl, S., Rasmussen, S., Schiffels, S., Subramanian, S., Wright, J.L., Albrechtsen, A., Barbieri, C., Dupanloup, I., Eriksson, A., Margaryan, A., Moltke, I., Pugach, I., Korneliussen, T.S., Levkivskyi, I.P., Moreno-Mayar, J.V., Ni, S., Racimo, F., Sikora, M., Xue, Y., Aghakhanian, F.A., Brucato, N., Brunak, S., Campos, P.F., Clark, W., Ellingv\u00e5g, S., Fourmile, G., Gerbault, P., Injie, D., Koki, G., Leavesley, M., Logan, B., Lynch, A., Matisoo-Smith, E.A., McAllister, P.J., Mentzer, A.J., Metspalu, M., Migliano, A.B., Murgha, L., Phipps, M.E., Pomat, W., Reynolds, D., Ricaut, F.-X., Siba, P., Thomas, M.G., Wales, T., Wall, C.M., Oppenheimer, S.J., Tyler-Smith, C., Durbin, R., Dortch, J., Manica, A., Schierup, M.H., Foley, R.A., Lahr, M.M., Bowern, C., Wall, J.D., Mailund, T., Stoneking, M., Nielsen, R., Sandhu, M.S., Excoffier, L., Lambert, D.M., Willerslev, E., 2016. A genomic history of Aboriginal Australia. Nature <\/strong>538, 207\u2013214. https:\/\/doi.org\/10.1038\/nature18299<\/p>\n

Malaspinas, A.-S., 2016. Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective. Mol Ecol<\/strong> 25, 24\u201341. https:\/\/doi.org\/10.1111\/mec.13492<\/p>\n

2015 <\/strong><\/p>\n

Raghavan, M., Steinr\u00fccken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera, C., \u00c1vila-Arcos, M.C., Malaspinas, A.-S., Eriksson, A., Moltke, I., Metspalu, M., Homburger, J.R., Wall, J., Cornejo, O.E., Moreno-Mayar, J.V., Korneliussen, T.S., Pierre, T., Rasmussen, M., Campos, P.F., Damgaard, P. de B., Allentoft, M.E., Lindo, J., Metspalu, E., Rodr\u00edguez-Varela, R., Mansilla, J., Henrickson, C., Seguin-Orlando, A., Malmstr\u00f6m, H., Stafford, T., Shringarpure, S.S., Moreno-Estrada, A., Karmin, M., Tambets, K., Bergstr\u00f6m, A., Xue, Y., Warmuth, V., Friend, A.D., Singarayer, J., Valdes, P., Balloux, F., Leboreiro, I., Vera, J.L., Rangel-Villalobos, H., Pettener, D., Luiselli, D., Davis, L.G., Heyer, E., Zollikofer, C.P.E., Le\u00f3n, M.S.P. de, Smith, C.I., Grimes, V., Pike, K.-A., Deal, M., Fuller, B.T., Arriaza, B., Standen, V., Luz, M.F., Ricaut, F., Guidon, N., Osipova, L., Voevoda, M.I., Posukh, O.L., Balanovsky, O., Lavryashina, M., Bogunov, Y., Khusnutdinova, E., Gubina, M., Balanovska, E., Fedorova, S., Litvinov, S., Malyarchuk, B., Derenko, M., Mosher, M.J., Archer, D., Cybulski, J., Petzelt, B., Mitchell, J., Worl, R., Norman, P.J., Parham, P., Kemp, B.M., Kivisild, T., Tyler-Smith, C., Sandhu, M.S., Crawford, M., Villems, R., Smith, D.G., Waters, M.R., Goebel, T., Johnson, J.R., Malhi, R.S., Jakobsson, M., Meltzer, D.J., Manica, A., Durbin, R., Bustamante, C.D., Song, Y.S., Nielsen, R., Willerslev, E., 2015. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science<\/strong> 349, aab3884. https:\/\/doi.org\/10.1126\/science.aab3884<\/p>\n

Allentoft, M.E., Sikora, M., Sj\u00f6gren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P.B., Schroeder, H., Ahlstr\u00f6m, T., Vinner, L., Malaspinas, A.-S., Margaryan, A., Higham, T., Chivall, D., Lynnerup, N., Harvig, L., Baron, J., Casa, P.D., D?browski, P., Duffy, P.R., Ebel, A.V., Epimakhov, A., Frei, K., Furmanek, M., Gralak, T., Gromov, A., Gronkiewicz, S., Grupe, G., Hajdu, T., Jarysz, R., Khartanovich, V., Khokhlov, A., Kiss, V., Kol\u00e1?, J., Kriiska, A., Lasak, I., Longhi, C., McGlynn, G., Merkevicius, A., Merkyte, I., Metspalu, M., Mkrtchyan, R., Moiseyev, V., Paja, L., P\u00e1lfi, G., Pokutta, D., Pospieszny, ?., Price, T.D., Saag, L., Sablin, M., Shishlina, N., Smr?ka, V., Soenov, V.I., Szever\u00e9nyi, V., T\u00f3th, G., Trifanova, S.V., Varul, L., Vicze, M., Yepiskoposyan, L., Zhitenev, V., Orlando, L., Sicheritz-Pont\u00e9n, T., Brunak, S., Nielsen, R., Kristiansen, K., Willerslev, E., 2015. Population genomics of Bronze Age Eurasia. Nature <\/strong>522, 167\u2013172. https:\/\/doi.org\/10.1038\/nature14507<\/p>\n

\u00c1vila-Arcos, M.C., Sandoval-Velasco, M., Schroeder, H., Carpenter, M.L., Malaspinas, A.-S., Wales, N., Pe\u00f1aloza, F., Bustamante, C.D., Gilbert, M.T.P., 2015. Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries. Methods Ecol Evol<\/strong> 6, 725\u2013734. https:\/\/doi.org\/10.1111\/2041-210X.12353<\/p>\n

Schroeder, H., \u00c1vila-Arcos, M.C., Malaspinas, A.-S., Poznik, G.D., Sandoval-Velasco, M., Carpenter, M.L., Moreno-Mayar, J.V., Sikora, M., Johnson, P.L.F., Allentoft, M.E., Samaniego, J.A., Haviser, J.B., Dee, M.W., Stafford, T.W., Salas, A., Orlando, L., Willerslev, E., Bustamante, C.D., Gilbert, M.T.P., 2015. Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean. PNAS <\/strong>112, 3669\u20133673. https:\/\/doi.org\/10.1073\/pnas.1421784112<\/p>\n

Seguin-Orlando, A., Korneliussen, T.S., Sikora, M., Malaspinas, A.-S., Manica, A., Moltke, I., Albrechtsen, A., Ko, A., Margaryan, A., Moiseyev, V., Goebel, T., Westaway, M., Lambert, D., Khartanovich, V., Wall, J.D., Nigst, P.R., Foley, R.A., Lahr, M.M., Nielsen, R., Orlando, L., Willerslev, E., 2014. Genomic structure in Europeans dating back at least 36,200 years. Science <\/strong>346, 1113\u20131118. https:\/\/doi.org\/10.1126\/science.aaa0114<\/p>\n

2014<\/strong><\/p>\n

Moreno-Mayar, J.V., Rasmussen, S., Seguin-Orlando, A., Rasmussen, M., Liang, M., Fl\u00e5m, S.T., Lie, B.A., Gilfillan, G.D., Nielsen, R., Thorsby, E., Willerslev, E., Malaspinas, A.-S., 2014. Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans. Current Biology<\/strong> 24, 2518\u20132525. https:\/\/doi.org\/10.1016\/j.cub.2014.09.057<\/p>\n

Malaspinas, A.-S., Lao, O., Schroeder, H., Rasmussen, M., Raghavan, M., Moltke, I., Campos, P.F., Sagredo, F.S., Rasmussen, S., Gon\u00e7alves, V.F., Albrechtsen, A., Allentoft, M.E., Johnson, P.L.F., Li, M., Reis, S., Bernardo, D.V., DeGiorgio, M., Duggan, A.T., Bastos, M., Wang, Y., Stenderup, J., Moreno-Mayar, J.V., Brunak, S., Sicheritz-Ponten, T., Hodges, E., Hannon, G.J., Orlando, L., Price, T.D., Jensen, J.D., Nielsen, R., Heinemeier, J., Olsen, J., Rodrigues-Carvalho, C., Lahr, M.M., Neves, W.A., Kayser, M., Higham, T., Stoneking, M., Pena, S.D.J., Willerslev, E., 2014. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Current Biology <\/strong>24, R1035\u2013R1037. https:\/\/doi.org\/10.1016\/j.cub.2014.09.078<\/p>\n

Malaspinas, A.-S., Tange, O., Moreno-Mayar, J.V., Rasmussen, M., DeGiorgio, M., Wang, Y., Valdiosera, C.E., Politis, G., Willerslev, E., Nielsen, R., 2014. bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). Bioinformatics <\/strong>30, 2962\u20132964. https:\/\/doi.org\/10.1093\/bioinformatics\/btu410<\/p>\n

Raghavan, M., DeGiorgio, M., Albrechtsen, A., Moltke, I., Skoglund, P., Korneliussen, T.S., Gr\u00f8nnow, B., Appelt, M., Gull\u00f8v, H.C., Friesen, T.M., Fitzhugh, W., Malmstr\u00f6m, H., Rasmussen, S., Olsen, J., Melchior, L., Fuller, B.T., Fahrni, S.M., Stafford, T., Grimes, V., Renouf, M.A.P., Cybulski, J., Lynnerup, N., Lahr, M.M., Britton, K., Knecht, R., Arneborg, J., Metspalu, M., Cornejo, O.E., Malaspinas, A.-S., Wang, Y., Rasmussen, M., Raghavan, V., Hansen, T.V.O., Khusnutdinova, E., Pierre, T., Dneprovsky, K., Andreasen, C., Lange, H., Hayes, M.G., Coltrain, J., Spitsyn, V.A., G\u00f6therstr\u00f6m, A., Orlando, L., Kivisild, T., Villems, R., Crawford, M.H., Nielsen, F.C., Dissing, J., Heinemeier, J., Meldgaard, M., Bustamante, C., O\u2019Rourke, D.H., Jakobsson, M., Gilbert, M.T.P., Nielsen, R., Willerslev, E., 2014. The genetic prehistory of the New World Arctic. Science 345, 1255832. https:\/\/doi.org\/10.1126\/science.1255832<\/p>\n

Foll, M., Poh, Y.-P., Renzette, N., Ferrer-Admetlla, A., Bank, C., Shim, H., Malaspinas, A.-S., Ewing, G., Liu, P., Wegmann, D., Caffrey, D.R., Zeldovich, K.B., Bolon, D.N., Wang, J.P., Kowalik, T.F., Schiffer, C.A., Finberg, R.W., Jensen, J.D., 2014. Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective. PLoS Genet<\/strong> 10, e1004185. https:\/\/doi.org\/10.1371\/journal.pgen.1004185<\/p>\n

Rasmussen, M., Anzick, S.L., Waters, M.R., Skoglund, P., DeGiorgio, M., Stafford Jr, T.W., Rasmussen, S., Moltke, I., Albrechtsen, A., Doyle, S.M., Poznik, G.D., Gudmundsdottir, V., Yadav, R., Malaspinas, A.-S., V, S.S.W., Allentoft, M.E., Cornejo, O.E., Tambets, K., Eriksson, A., Heintzman, P.D., Karmin, M., Korneliussen, T.S., Meltzer, D.J., Pierre, T.L., Stenderup, J., Saag, L., Warmuth, V.M., Lopes, M.C., Malhi, R.S., Brunak, S., Sicheritz-Ponten, T., Barnes, I., Collins, M., Orlando, L., Balloux, F., Manica, A., Gupta, R., Metspalu, M., Bustamante, C.D., Jakobsson, M., Nielsen, R., Willerslev, E., 2014. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature <\/strong> 506, 225\u2013229. https:\/\/doi.org\/10.1038\/nature13025<\/p>\n

2013<\/strong><\/p>\n

Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., Johnson, P.L.F., Fumagalli, M., Vilstrup, J.T., Raghavan, M., Korneliussen, T., Malaspinas, A.-S., Vogt, J., Szklarczyk, D., Kelstrup, C.D., Vinther, J., Dolocan, A., Stenderup, J., Velazquez, A.M.V., Cahill, J., Rasmussen, M., Wang, X., Min, J., Zazula, G.D., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J.F., Weinstock, J., Gregersen, K., R\u00f8ed, K.H., Eisenmann, V., Rubin, C.J., Miller, D.C., Antczak, D.F., Bertelsen, M.F., Brunak, S., Al-Rasheid, K.A.S., Ryder, O., Andersson, L., Mundy, J., Krogh, A., Gilbert, M.T.P., Kj\u00e6r, K., Sicheritz-Ponten, T., Jensen, L.J., Olsen, J.V., Hofreiter, M., Nielsen, R., Shapiro, B., Wang, J., Willerslev, E., 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74\u201378. https:\/\/doi.org\/10.1038\/nature12323<\/p>\n

Gon\u00e7alves, V.F., Stenderup, J., Rodrigues-Carvalho, C., Silva, H.P., Gon\u00e7alves-Dornelas, H., L\u00edryo, A., Kivisild, T., Malaspinas, A.-S., Campos, P.F., Rasmussen, M., Willerslev, E., Pena, S.D.J., 2013. Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil. PNAS <\/strong>110, 6465\u20136469. https:\/\/doi.org\/10.1073\/pnas.1217905110<\/p>\n

2012 <\/strong><\/p>\n

Yang, M.A., Malaspinas, A.-S., Durand, E.Y., Slatkin, M., 2012. Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity. Mol Biol Evol<\/strong> 29, 2987\u20132995. https:\/\/doi.org\/10.1093\/molbev\/mss117<\/p>\n

Malaspinas, A.-S., Malaspinas, O., Evans, S.N., Slatkin, M., 2012. Estimating Allele Age and Selection Coefficient from Time-Serial Data. Genetics <\/strong>192, 599\u2013607. https:\/\/doi.org\/10.1534\/genetics.112.140939<\/p>\n

2011 <\/strong><\/p>\n

Malaspinas, A.-S., Slatkin, M., Song, Y.S., 2011. Match probabilities in a finite, subdivided population. Theoretical Population Biology<\/strong> 79, 55\u201363. https:\/\/doi.org\/10.1016\/j.tpb.2011.01.003<\/p>\n

Malaspinas, A.-S., Uhler, C., 2011. Detecting epistasis via Markov bases. Journal of Algebraic Statistics<\/strong> 2, 36\u201353. https:\/\/doi.org\/10.18409\/jas.v2i1.27<\/p>\n

Malaspinas, A.-S., Eriksson, N., Huggins, P., 2011. Parametric Analysis of Alignment and Phylogenetic Uncertainty. Bull Math Biol<\/strong> 73, 795. https:\/\/doi.org\/10.1007\/s11538-010-9610-8<\/p>\n

2010 <\/strong><\/p>\n

Green, R.E., Krause, J., Briggs, A.W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.H.-Y., Hansen, N.F., Durand, E.Y., Malaspinas, A.-S., Jensen, J.D., Marques-Bonet, T., Alkan, C., Pr\u00fcfer, K., Meyer, M., Burbano, H.A., Good, J.M., Schultz, R., Aximu-Petri, A., Butthof, A., H\u00f6ber, B., H\u00f6ffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E.S., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, \u017d., Gu\u0161ic, I., Doronichev, V.B., Golovanova, L.V., Lalueza-Fox, C., Rasilla, M. de la, Fortea, J., Rosas, A., Schmitz, R.W., Johnson, P.L.F., Eichler, E.E., Falush, D., Birney, E., Mullikin, J.C., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., Paabo, S., 2010. A Draft Sequence of the Neandertal Genome. Science <\/strong>328, 710\u2013722. https:\/\/doi.org\/10.1126\/science.1188021<\/p>\n

2009 <\/strong><\/p>\n

Ludwig, A., Pruvost, M., Reissmann, M., Benecke, N., Brockmann, G.A., Casta\u00f1os, P., Cieslak, M., Lippold, S., Llorente, L., Malaspinas, A.-S., Slatkin, M., Hofreiter, M., 2009. Coat Color Variation at the Beginning of Horse Domestication. Science <\/strong>324, 485\u2013485. https:\/\/doi.org\/10.1126\/science.1172750<\/p>\n

2008 <\/strong><\/p>\n

Green, R.E., Malaspinas, A.-S., Krause, J., Briggs, A.W., Johnson, P.L.F., Uhler, C., Meyer, M., Good, J.M., Maricic, T., Stenzel, U., Prufer, K., Siebauer, M., Burbano, H.A., Ronan, M., Rothberg, J.M., Egholm, M., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Wikstrom, M., Laakkonen, L., Kelso, J., Slatkin, M., Paabo, S., 2008. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell <\/strong>134, 416\u2013426. https:\/\/doi.org\/10.1016\/j.cell.2008.06.021<\/p>\n

Krause, J., Unger, T., Nocon, A., Malaspinas, A.-S., Kolokotronis, S.-O., Stiller, M., Soibelzon, L., Spriggs, H., Dear, P.H., Briggs, A.W., Bray, S.C., O\u2019Brien, S.J., Rabeder, G., Matheus, P., Cooper, A., Slatkin, M., Paabo, S., Hofreiter, M., 2008. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol <\/strong>8, 220. https:\/\/doi.org\/10.1186\/1471-2148-8-220<\/p>\n

2007 <\/strong><\/p>\n

Rohland, N., Malaspinas, A.-S., Pollack, J.L., Slatkin, M., Matheus, P., Hofreiter, M., 2007. Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as Outgroup. PLoS Biol<\/strong> 5, e207. https:\/\/doi.org\/10.1371\/journal.pbio.0050207<\/p>\n","protected":false},"excerpt":{"rendered":"

2018 Moreno-Mayar, J.V., Potter, B.A., Vinner, L., Steinr\u00fccken, M., Rasmussen, S., Terhorst, J., Kamm, J.A., Albrechtsen, A., Malaspinas, A.-S., Sikora, M., Reuther, J.D., Irish, J.D., Malhi, R.S., Orlando, L., Song, Y.S., Nielsen, R., Meltzer, D.J., Willerslev, E., 2018. Terminal Pleistocene<\/p>\n","protected":false},"author":1001558,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"_seopress_robots_primary_cat":"","_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","footnotes":""},"class_list":["post-2","page","type-page","status-publish"],"_links":{"self":[{"href":"https:\/\/wp.unil.ch\/egg\/wp-json\/wp\/v2\/pages\/2","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wp.unil.ch\/egg\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wp.unil.ch\/egg\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/egg\/wp-json\/wp\/v2\/users\/1001558"}],"replies":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/egg\/wp-json\/wp\/v2\/comments?post=2"}],"version-history":[{"count":0,"href":"https:\/\/wp.unil.ch\/egg\/wp-json\/wp\/v2\/pages\/2\/revisions"}],"wp:attachment":[{"href":"https:\/\/wp.unil.ch\/egg\/wp-json\/wp\/v2\/media?parent=2"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}