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Publications

2018

Moreno-Mayar, J.V., Potter, B.A., Vinner, L., Steinrücken, 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 553, 203. https://doi.org/10.1038/nature25173

Dávalos, D.I.C., Nieves-Colón, M.A., Sockell, A., Poznik, D.G., Schroeder, H., Stone, A.C., Bustamante, C.D., Malaspinas, A.-S., Ávila-Arcos, M.C., 2017. In-solution Y-chromosome capture-enrichment on ancient DNA libraries. bioRxiv 223214. https://doi.org/10.1101/223214

2017

Dortch, J., Malaspinas, A.-S., 2017. Madjedbebe and genomic histories of Aboriginal Australia. Australian Archaeology 83, 174–177. https://doi.org/10.1080/03122417.2017.1408546

2016

Malaspinas, A.-S., Westaway, M.C., Muller, C., Sousa, V.C., Lao, O., Alves, I., Bergström, 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., Ellingvåg, 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 538, 207–214. https://doi.org/10.1038/nature18299

Malaspinas, A.-S., 2016. Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective. Mol Ecol 25, 24–41. https://doi.org/10.1111/mec.13492

2015

Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera, C., Ávila-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., Rodríguez-Varela, R., Mansilla, J., Henrickson, C., Seguin-Orlando, A., Malmström, H., Stafford, T., Shringarpure, S.S., Moreno-Estrada, A., Karmin, M., Tambets, K., Bergström, 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., León, 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 349, aab3884. https://doi.org/10.1126/science.aab3884

Allentoft, M.E., Sikora, M., Sjögren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P.B., Schroeder, H., Ahlström, T., Vinner, L., Malaspinas, A.-S., Margaryan, A., Higham, T., Chivall, D., Lynnerup, N., Harvig, L., Baron, J., Casa, P.D., Dąbrowski, 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., Kolář, J., Kriiska, A., Lasak, I., Longhi, C., McGlynn, G., Merkevicius, A., Merkyte, I., Metspalu, M., Mkrtchyan, R., Moiseyev, V., Paja, L., Pálfi, G., Pokutta, D., Pospieszny, Ł., Price, T.D., Saag, L., Sablin, M., Shishlina, N., Smrčka, V., Soenov, V.I., Szeverényi, V., Tóth, G., Trifanova, S.V., Varul, L., Vicze, M., Yepiskoposyan, L., Zhitenev, V., Orlando, L., Sicheritz-Pontén, T., Brunak, S., Nielsen, R., Kristiansen, K., Willerslev, E., 2015. Population genomics of Bronze Age Eurasia. Nature 522, 167–172. https://doi.org/10.1038/nature14507

Ávila-Arcos, M.C., Sandoval-Velasco, M., Schroeder, H., Carpenter, M.L., Malaspinas, A.-S., Wales, N., Peñaloza, 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 6, 725–734. https://doi.org/10.1111/2041-210X.12353

Schroeder, H., Ávila-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 112, 3669–3673. https://doi.org/10.1073/pnas.1421784112

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 346, 1113–1118. https://doi.org/10.1126/science.aaa0114

2014

Moreno-Mayar, J.V., Rasmussen, S., Seguin-Orlando, A., Rasmussen, M., Liang, M., Flåm, 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 24, 2518–2525. https://doi.org/10.1016/j.cub.2014.09.057

Malaspinas, A.-S., Lao, O., Schroeder, H., Rasmussen, M., Raghavan, M., Moltke, I., Campos, P.F., Sagredo, F.S., Rasmussen, S., Gonçalves, 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 24, R1035–R1037. https://doi.org/10.1016/j.cub.2014.09.078

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 30, 2962–2964. https://doi.org/10.1093/bioinformatics/btu410

Raghavan, M., DeGiorgio, M., Albrechtsen, A., Moltke, I., Skoglund, P., Korneliussen, T.S., Grønnow, B., Appelt, M., Gulløv, H.C., Friesen, T.M., Fitzhugh, W., Malmström, 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., Götherström, A., Orlando, L., Kivisild, T., Villems, R., Crawford, M.H., Nielsen, F.C., Dissing, J., Heinemeier, J., Meldgaard, M., Bustamante, C., O’Rourke, 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

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 10, e1004185. https://doi.org/10.1371/journal.pgen.1004185

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 506, 225–229. https://doi.org/10.1038/nature13025

2013

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., Røed, 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., Kjær, 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, 74–78. https://doi.org/10.1038/nature12323

Gonçalves, V.F., Stenderup, J., Rodrigues-Carvalho, C., Silva, H.P., Gonçalves-Dornelas, H., Líryo, 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 110, 6465–6469. https://doi.org/10.1073/pnas.1217905110

2012

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 29, 2987–2995. https://doi.org/10.1093/molbev/mss117

Malaspinas, A.-S., Malaspinas, O., Evans, S.N., Slatkin, M., 2012. Estimating Allele Age and Selection Coefficient from Time-Serial Data. Genetics 192, 599–607. https://doi.org/10.1534/genetics.112.140939

2011

Malaspinas, A.-S., Slatkin, M., Song, Y.S., 2011. Match probabilities in a finite, subdivided population. Theoretical Population Biology 79, 55–63. https://doi.org/10.1016/j.tpb.2011.01.003

Malaspinas, A.-S., Uhler, C., 2011. Detecting epistasis via Markov bases. Journal of Algebraic Statistics 2, 36–53. https://doi.org/10.18409/jas.v2i1.27

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

2010

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., Prüfer, K., Meyer, M., Burbano, H.A., Good, J.M., Schultz, R., Aximu-Petri, A., Butthof, A., Höber, B., Höffner, 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, Ž., Gušic, 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 328, 710–722. https://doi.org/10.1126/science.1188021

2009

Ludwig, A., Pruvost, M., Reissmann, M., Benecke, N., Brockmann, G.A., Castaños, 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 324, 485–485. https://doi.org/10.1126/science.1172750

2008

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 134, 416–426. https://doi.org/10.1016/j.cell.2008.06.021

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’Brien, 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 8, 220. https://doi.org/10.1186/1471-2148-8-220

2007

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 5, e207. https://doi.org/10.1371/journal.pbio.0050207