Papers
2024 #
Sikora, M, Canteri, E, Fernandez-Guerra, A, Oskolkov, N, Agren, R, Hansson, L, Irving-Pease, EK, Muehlemann, B, Holtsmark Nielsen, S, Scorrano, G, Allentoft, ME. Valeur Seersholm,F, Schroeder, H, Gaunitz, C, Stenderup, J, Vinner, L, Jones, TC, Nystedt, B, Parkhill, J, Fugger, L, Racimo, F, Kristiansen, K, Iversen, AKN, Willerslev, E. The landscape of ancient human pathogens in Eurasia from the Stone Age to historical times. bioRxiv. https://doi.org/10.1101/2023.10.06.561165
2023 #
Meadows, JR, Kidd, JM, Wang, GD, Parker, HG, Schall, PZ, Bianchi, M, Christmas, MJ, Bougiouri, K, Buckley, RM, Hitte C, Nguyen, AK, Wang, C, Jagannathan, V, Niskanen, JE, Frantz, LAF, Arumilli, A, Hundi, S, Lindblad-Toh, K, Ginja, C, Karang, KA, André, C, Boyko, AR, Davis, BW, Drögemüller, M, Feng, X-Y, Gkagkavouzis, K, Iliopoulos, G, Harris, AC, Hytönen, MK, Kaltkhoff, DC, Liu, Y-H, Lymberakis, P, Poulakakis, N, Pires, AE, Racimo, F, Ramos-Almodovar, F, Savolainen, P, Venetsani, S, Tammen, I, Triantafyllidis, A, vonHoldt, B, Wayne, RK, Larson, G, Nicholas, FW, Lohi, H, Leeb, T, Zhang, Y-P, Ostrander, EA. (2023) Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome biology 15;24(1):187.
Louis M, Korlević, P, Nykänen, M, Archer, F, Berrow S, Brownlow,, A, Lorenzen ED, O’Brien J, Post K, Racimo. F, Rogan E, Rosel, PE, Sinding M-HS, van der Es, H, Wales, Fontaine, MC, Gaggiotti, OE, Foote, AD (2023) Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nature Communications 14(1):4020.
Ravn, K, Cobuccio, L, Muktupavela, RA, Meisner, J, Benros, ME, Korneliussen, TS, Sikora, M, Willerslev, E, Allentoft, ME, Irving-Pease, EK, Racimo, F, Rasmussen, S. (2023) Tracing the evolutionary path of the CCR5delta32 deletion via ancient and modern genomes. medRxiv. https://doi.org/10.1101/2023.06.15.23290026
Racimo, F. An unusual suspect: the mutation landscape as a determinant of local variation in nucleotide diversity. (2023) Peer Community in Evolutionary Biology. 1:100636.
Madupe, PP, Koenig, C, Patramanis, I, Rüther, PL, Hlazo, N, Mackie, M, Tawane, M, Krueger, J, Taurozzi, AJ, Troché, GB, Kibii, J, Pickering, R, Dickinson, M, Sahle, Y, Kgotleng, D, Musiba, C, Manthi, F, Bell, L, DuPlessis, M, Gilbert, C, Zipfel, B, Kuderna, LFK, Lizano, E, Welker, F, Kyriakidou, P, Cox, J, Mollereau, C, TOkarski, C, Blackburn, J, Ramos-Madrigal, J, Marques-Bonet, T, Penkman, K, Zanolli, C, Schroeder, L, Racimo, F, Olsen, JV, Ackermann, RR, Cappellini, E. (2023) Enamel proteins reveal biological sex and genetic variability within southern African Paranthropus. bioRxiv. https://doi.org/10.1101/2023.07.03.547326
Patramanis, I, Madrigal, JR, Cappellini, E, Racimo, F. PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins. (2023) bioRxiv. https://doi.org/10.1101/2022.12.12.519721
Gower, G, Iáñez Picazo, P, Lindgren, F, Racimo, F. Inference of population genetics parameters using discriminator neural networks: an adversarial Monte Carlo approach. 2023. bioRxiv. https://doi.org/10.1101/2023.04.27.538386
Ianni-Ravn, MD, Petr, M, Racimo, F. Exploring the effects of ecological parameters on the spatial structure of genetic tree sequences. bioRxiv (2023). doi: https://doi.org/10.1101/2023.03.27.534388
Feldner-Busztin, D, Firbas Nisantzis P, Edmunds SJ, Boza G, Racimo F, Gopalakrishnan S, Tønsberg Limborg M, Lahti L, de Polavieja, GG. “Dealing with dimensionality: the application of machine learning to multi-omics data.” Bioinformatics 39, no. 2 (2023): btad021.
Reeve, AH, Gower, G, Pujolar, JM, Smith, BT, Petersen, B, Olsson, U, Haryoko, T, Koane, B, Maiah, G Blom, MP, Ericson, PG, Irestedt, M, Racimo F, Jønsson KA (2023) Population genomics of the island thrush elucidates one of earth’s great archipelagic radiations. Evolution Letters 7 (1), 24-36.
2022 #
Racimo, F. A match made in the Anthropocene: human-mediated adaptive introgression across a speciation continuum. (2022) Peer Community in Evolutionary Biology. 1:100149.
Wang, Y, Prohaska, A, Dong, H, Alberti, A, Alsos, IG, Beilman, DW, Bjørk, AA, Cao, J, Cherezova, AA, Coissac, E, De Sanctis, B, Denoeud, F, Dockter, C, Durbin, R, Edwards, ME, Edwards, NR, Esdale, J, Fedorov, GB, Fernandez-Guerra, A, Froese, DG, Gusarova, G, Haile, James, Holden, PB, Kjeldsen, KK, Kjær, KH, Korneliussen, TS, Lammers, Y, Krog Larsen, N, Macleod, Ruairidh, Mangerud, J, McColl, H, Føreid Merkel, MK, Money, D, Möller, P, Nogués-Bravo, D, Orlando, L, Owens, HL, Pedersen, MW, Racimo, F, Rahbek, C, Rasic, JT, Rouillard, A, Ruter, AH, Skadhauge, B, Svendsen, JI, Tikhonov, A, Vinner, L, Wincker, P, Xing, Y, Zhang, Y, Meltzer, DJ, Willerslev, E (2022) Reply to: When did mammoths go extinct? Nature 1;612(7938):E4-6.
Racimo, F, Valentini, E, Rijo De León, G, Santos, TL, Norberg, A, Atmore, LM, Murray, M, Hakala, S, Appel Olsen, F, Gardner, CJ, Halder, JB (2022). The Biospheric Emergency Calls for Scientists to Change Tactics. eLife 11:e83292.
Muktupavela, RA, Petr, M, Ségurel, L, Korneliussen, TS, Novembre, J, Racimo, F. (2022). Modelling the spatiotemporal spread of beneficial alleles using ancient genomes. eLife 11, e73767. DOI: https://doi.org/10.7554/eLife.73767
Allentoft, ME*, Sikora, M*, Refoyo-Martínez, A*, Irving-Pease, EK*, Fischer, A*, Barrie, W*, Ingason, A*, Stenderup, J, Sjögren, K-G, Pearson, A, Mota, B, Schulz Paulsson, B, Halgren, A, Macleod, R, Schjellerup Jørkov, ML, Demeter, F, Novosolov, M, Sørensen, L, Nielsen, P-O, Henriksen, RHA, Vimala, T, McColl, H, Margaryan, A, Ilardo, M, Vaughn, A, Fischer Mortensen, M, Nielsen AB, Ulfeldt Hede, M, Rasmussen P, Vinner, L, Renaud, G, Stern, A, Trolle Jensen, TZ, Nørkjær Johannsen, N, Scorrano, G, Schroeder, H, Lysdahl, P, Ramsøe, AD, Skorobogatov, A, Schork, AJ, Rosengren, A, Ruter, A, Outram, A, Timoshenko, AA, Buzhilova, A, Coppa, A, Zubova, A, Silva, AM, Hansen, AJ, Gromov, A, Logvin, A, Gotfredsen, AB, Nielsen, BH, González-Rabanal, B, Lalueza-Fox, C, McKenzie, CJ, Gaunitz, C, Blasco, C, Liesau, C, Martinez-Labarga, C, Pozdnyakov, DV, Cuenca-Solana, D, Lordkipanidze, DO, En’shin, D, Salazar-García, DC, Price, TD, Borić, D, Kostyleva, E, Veselovskaya, EV, Usmanova, ER, Cappellini, E, Petersen, EB, Kannegaard, E, Radina, F, Yediay, FE, Duday, H, Gutiérrez-Zugasti, I, Potekhina, I, Shevnina, I, Altinkaya, I, Guilaine, J, Hansen, J, Tortosa, JEA, Zilhão, J, Vega, J, Pedersen, KB, Tunia, K, Zhao, L, Mylnikova, LN, Larsson, L, Metz, L, Yeppiskoposyan, L, Pedersen, L, Sarti, L, Orlando, L, Slimak, L, Klassen, L, Blank, M, González-Morales, M, Silvestrini, M, Vretemark, M, Nesterova, MS, Rykun, M, Rolfo, MF, Szmyt, M, Przybyła, M, Calattini, M, Sablin, M, Dobisíková, M, Meldgaard, M, Johansen, M, Berezina, N, Card, N, Saveliev, NA, Poshekhonova, O, Rickards, O, Lozovskaya, OV, Uldum, OC, Aurino, P, Kosintsev, P, Courtaud, P, Ríos, P, Mortensen, P, Lotz, P, Persson, PA, Bangsgaard, P, de Barros Damgaard, P, Petersen, PV, Prieto Martinez, P, Włodarczak, P, Smolyaninov, RV, Maring, R, Meduiña, R, Badalvan, R, Iversen, R, Turin, R, Vasilyev, S, Wåhlin, S, Borutskaya, S, Skochina, S, Sørensen, SA, Andersen, SH, Jørgensen, T, Serikov, YB, Molodin, VI, Smrcka, V, Merz, V, Appadurai, V, Moiseyev, V, Magnusson, Y, Kjær, KH, Lynnerup, N, Lawson, DJ, Sudman, PH, Rasmussen, S, Korneliussen, T, Durbin, R, Nielsen, R, Delaneau, O, Werge, T, Racimo, F, Kristiansen, K, Willerselv, E. Population Genomics of Stone Age Eurasia. Nature 625(7994), 301-311 (2022) doi: https://doi.org/10.1101/2022.05.04.490594
Irving-Pease, EK, Refoyo-Martínez, A, Ingason, A, Pearson, A, Fischer, A, Barrie, W, Sjögren, KG, Halgren, AS, Macleod, R, Demeter, F, Henriksen, RA, Vimala, T, McColl, H, Vaughn, A, Stern AJ, Speidel, L, Scorrano, G, Ramsøe, A, Schork, AJ, Rosengren, A, Zhao, L, Kristiansen, K, Sudmant, PH, Lawson, DJ, Durbin, R, Korneliussen, T, Werge, T, Allentoft, ME, Sikora, M, Nielsen, R, Racimo, F, Willerslev, E. (2022) The Selection Landscape and Genetic Legacy of Ancient Eurasians. Nature 625(7994), 312-320 bioRxiv. doi: https://doi.org/10.1101/2022.09.22.509027
Petr, M, Haller, BC, Ralph, PL, Racimo, F. (2022). slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes. PCI EvolBiol https://evolbiol.peercommunityin.org/articles/rec?id=630
Racimo, F, Galtier, N, De Herde, V, Aubert Bonn, N, Phillips, B, Guillemaud, T, Bourguet, D. (2022). Ethical publishing: how do we get there?. Philosophy, Theory, and Practice in Biology 14: 15. doi: https://doi.org/10.3998/ptpbio.3363
Alves, I, Giemza, J, Blum, M, Bernhardsson, C, Chatel, S, Karakachoff, M, Saint Pierre, A, Herzig, AF, Olaso, R, Monteil, M, Gallien, V, Cabot, E, Svensson, E, Bacq-Daian, D, Baron, E, Berthellier, C, Besse, C, Blaché, H, Bocher, O, Boland, A, Bonnaud, S, Charpentier, E, Dandine-Roulland, C, Férec, C, Fruchet, C, Lecointe, S, Le Floch, E, Ludwig, T, Marenne, G, Meyer, V, Quellery E, Racimo, F, Rouault, K, Sandron, F, Schott, J-J, Suarez, LV, Violleau, J, Willerslev, E, Coativy, Y, Jézéquel, M, Le-Bris, D, Nicola, C, Pailler, Y, Goldberg, M, Zins, M, Le-Marec, H, Jakobsson, M, Darlu, P, Génin, E, Deleuze, J-F, Redon, R, Dina, C. (2022) Genetic population structure across Brittany and the downstream Loire basin provides new insights on the demographic history of Western Europe. bioRxiv. DOI: 10.1101/2022.02.03.478491
Cheng, JY, Stern, A, Racimo F, Nielsen, R. (2022). Ohana: detecting selection in multiple populations by modeling ancestral admixture components. Molecular Biology and Evolution 39(1). DOI: 10.1093/molbev/mst012
Jagoda, E, Xue, JR, Reilly, SK, Dannemann, M, Racimo, F, Huerta-Sanchez, E, Sankararaman, S, Kelso, J, Pagani, L, Sabeti, PC, Capellini, TD. Detection of Neanderthal Adaptively Introgressed Genetic Variants that Modulate Reporter Gene Expression in Human Immune Cells. Molecular Biology and Evolution (2022). DOI: 10.1093/molbev/msab304
2021 #
Wang Y, Pedersen MW, Alsos IG, De Sanctis B, Racimo F, Prohaska A, Coissac E, Owens HL, Merkel MK, Fernandez-Guerra A, Rouillard A, Lammers, Y, Alberti, A, Denoeud, F, Money, D, Ruter, AH, McColl, H, Krog Larsen, N, Cherezova, AA, Edwards, ME, Fedorov, GB, Haile, J, Orlando, L, Vinner, L, Korneliussen, TS, Beilman DW, Bjørk AA, Cao, J, Dockter, C, Esdale, J, Gusarova, G, Kjeldsen, KK, Mangerud, J, Rasic, JT, Skadhauge, B, Svendsen, JI, Tikhonov, A, Wincker, P, Xing, Y, Zhang, Y, Froese, DG, Rahbek, C, Nogués-Bravo, D, Holden, PB, Edwards, NR, Durbin, R, Meltzer, DJ, Kjær, KH, Möller, P, Willerslev, E. (2021) Late Quaternary dynamics of Arctic biota from ancient environmental genomics. Nature 600(7887):86-92.
Gower, GR, Iáñez Picazo, P, Fumagalli, M, & Racimo, F. (2021) Detecting adaptive introgression in human evolution using convolutional neural networks. eLife 10: e64669. DOI: 10.7554/eLife.64669
Irving-Pease, EK, Muktupavela, R, Dannemann, M, Racimo, F. (2021). Quantitative Human Paleogenetics: what can ancient DNA tell us about complex trait evolution?. Frontiers in Genetics. 12: 703541
Refoyo-Martínez, A., Liu, S., Jørgensen, A. M., Jin, X., Albrechtsen, A., Martin, A. R., & Racimo, F. How robust are cross-population signatures of polygenic adaptation in humans?. Peer Community Journal 1, e22. DOI: 10.1101/2020.07.13.200030 Peer Community Journal: 10.24072/pci.evolbiol.100125
2020 #
Racimo F, Woodbridge J, Fyfe R, Sikora M, Sjogren KG, Kristiansen K, Vander Linden M. The spatiotemporal spread of human migrations during the European Holocene. PNAS 117 (16), 8989-9000 (2020).
Adrion JR, Cole CB, Dukler N, Galloway JG, Gladstein AL, Gower G, Kyriazis CC, Ragsdale AP, Tsambos G, Baumdicker F, Carlson J, Cartwright RA, Durvasula A, Gronau I, Kim BY, McKenzie P, Messer PW, Noskova E, Ortega Del Vecchyo D, Racimo F, Struck TJ, Gravel S, Gutenkunst R, Lohmueller KE, Ralph PL, Schrider DR, Siepel A, Kelleher J, Kern AD. A community-maintained standard library of population genetic models. eLife 9: e54967 (2020)
Welker F, Ramos-Madrigal J, Gutenbrunner P, Mackie M, Tiwary S, Jersie-Christensen RR, Chiva C, Dickinson MR, Kuhlwilm M, de Manuel M, Gelabert P, Martinón-Torres M, Margvelashvili A, Arsuaga JL, Carbonell E, Marques-Bonet T, Penkman K, Sabidó E, Cox J, Olsen JV, Lordkipanidze D, Racimo F, Lalueza-Fox C, Bermúdez de Castro JM, Willerslev E, Cappellini E. The dental proteome of Homo antecessor. Nature. Apr 1:1-4 (2020).
Racimo F, Sikora M, Vander Linden, M. Schroeder H, Lalueza-Fox C. Beyond broad strokes: sociocultural insights from the study of ancient genomes. Nature Reviews Genetics (2020): https://doi.org/10.1038/s41576-020-0218-z
Margaryan A*, Lawson D*, Sikora M*, Racimo F*, Rasmussen S, Moltke I, Cassidy L, Jørsboe E, Ingason A, Pedersen M, Korneliussen T, Wilhelmson H, Bu M, de Barros Damgaard P, Martiniano R, Renaud G, Bhérer C, Moreno-Mayar JV, Fotakis A, Allen M, Molak M, Cappellini E, Scorrano G, Buzhilova A, Fox A, Albrechtsen A, Schütz B, Skar B, Arcini C, Falys C, Jonson CH, Baszczyk D, Pezhemsky D, Turner-Walker G, Gestsdóttir H, Lundstrøm I, Gustin I, Mainland I, Potekhina I, Muntoni I, Cheng J, Stenderup J, Ma J, Gibson J, Peets J, Gustafsson J, Iversen K, Simpson L, Strand L, Loe L, Sikora M, Florek M, Vretemark M, Redknap M, Bajka M, Pushkina T, Søvsø M, Grigoreva N, Christensen T, Kastholm O, Uldum O, Favia P, Holck P, Allmäe R, Sten S, Arge S, Ellingvåg S, Moiseyev V, Bogdanowicz W, Magnusson Y, Orlando L, Bradley D, Jørkov ML, Arneborg J, Lynnerup N, Price N, Gilbert MT, Allentoft M, Bill J, Sindbæk S, Hedeager L, Kristiansen K, Nielsen R, Werge T, Willerslev E. Population genomics of the Viking world. Nature 585: 7825 (2020).
2019 #
Refoyo-Martínez, A, da Fonseca, RR, Halldórsdóttir, K, Árnason, E, Mailund, T, Racimo, F. Identifying loci under positive selection in complex population histories. Genome Research: 246777.118 (2019).
Prohaska, A*, Racimo, F*, Schork, A.J.*, Sikora, M, Stern, A, Ilardo, M, Allentoft, ME, Folkersen, L, Buil, A, Moreno-Mayar, JV, Korneliussen, T, Geschwind, D, Ingason, A, Werge, T, Nielsen, R, Willerslev, E. Human disease variation in the light of population genomics. Cell 177(1): 115-131 (2019).
Berg JJ, Harpak A, Sinnott-Armstrong N, Jørgensen AM, Mostafavi H, Field Y, Boyle EA, Zhang X, Racimo F, Pritchard JK, Coop G. Reduced signal for polygenic adaptation of height in UK Biobank. eLife 8: e39725 (2019).
Moreno-Mayar, V, Vinner, L, de Barros Damgaard, P, de la Fuente, C, Chan, J, Spence, JP, Allentoft, ME, Vimala, T, Racimo, F, Pinotti, T, Rasmussen, S, Margaryan, A, Iraeta Orbegozo, M, Milopotamitaki, D, Wooller, M, Bataille, C, Becerra-Valdivia, L, Chivall, D, Comeskey, D, Devièse, T, Grayson, DK, George, L, Harry H, Alexandersen, V, Primeau, C, Erlandson, J, Rodrigues-Carvalho, C, Reis, S, Bastos, MQR, Cybulski, J, Vullo, C, Morello, F, Vilar, M, Wells, S, Gregersen, K, Hansen, KL, Lynnerup, N, Mirazón Lahr, M, Kjær, K, Strauss, A, Alfonso-Durruty, M, Salas, A, Schroeder, H, Higham, T, Malhi, RS, Rasic, JT, Souza, L, Santos, FR, Malaspinas A-S, Sikora, M, Nielsen, R, Song, YS, Meltzer, DJ, Willerslev, E. Early human dispersals within the Americas. Science 362(6419): eaav2621 (2019).
2018 #
Dannemann, M, Racimo, F. Something old, something borrowed: Admixture and adaptation in human evolution. Current Opinions in Genetics and Development (2018). doi: 10.1016/j.gde.2018.05.009
Cappellini, E, Prohaska, A, Racimo, F, Welker, F, Winther Pedersen, M, Allentoft, ME, de Barros Damgaard, P, Gutenbrunner P, Dunne, J, Hammann, S, Roffet-Salque, M, Ilardo, M, Moreno-Mayar, JV, Wang, Y, Sikora, M, Vinner, L, Cox, J, Evershed, RP, Willerslev, E. Ancient biomolecules and evolutionary inference. Annual Review of Biochemistry 87:36.1–36.32 (2018).
Ilardo, MA, Moltke I, Korneliussen TS, Cheng J, Stern AJ, Racimo F, de Barros Damgaard P, Sikora M, Seguin-Orlando A, Rasmussen S, van den Munckhof ICL, ter Horst R, A.B. Joosten L, Netea MG, Salingkat S, Nielsen R, Willerslev E. Physiological and Genetic Adaptations to Diving in Sea Nomads. Cell (2018). doi: https://doi.org/10.1016/j.cell.2018.03.054
McColl H*, Racimo F*, Vinner L*, Demeter F*, Gakuhari T, Moreno-Mayar JV, Van Driem G, Wilken UG, Seguin-Orlando A, De la Fuente Castro C, Wasef S, Shoocongdej R, Souksavatdy V, Sayavongkhamdy T, Saidin MM, Allentoft ME, Sato T, Malaspinas A-S, Aghakhanian FA, Korneliussen T, Prohaska A, Margaryan A, de Barros Damgaard P, Kaewsutthi S, Lertrit P, Nguyen TMH, Hung H-C, Tran TM, Truong HN, Nguyen GH, Shahidan S, Wiradnyana K, Matsumae H, Shigehara N, Yoneda M, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Hanihara T, Nakagome S, Deviese T, Bacon A-M, Duringer P, Ponche J-L, Shackelford L, Patole-Edoumba E, Nguyen AN, Bellina-Pryce B, Galipaud J-C, Kinaston R, Buckley H, Pottier C, Rasmussen S, Higham T, Foley RA, Mirazón Lahr M, Orlando L, Sikora M, Phipps ME, Oota H, Higham C, Lambert DM, Willerslev, E. The prehistoric peopling of Southeast Asia. Science 361(6397): 88-92 (2018). doi: 10.1101/278374
Racimo F, Berg JJ, Pickrell JK. Detecting polygenic adaptation in admixture graphs. Genetics (2018): genetics-300489.
Crawford J, Amaru R, Song J, Julian CG, Racimo F, Cheng JY, Guo X, Yao J, Ambale-Venkatesh B, Lima JA, Rotter JI, Stehlik J, Moore LG, Prchal JT, Nielsen R. Natural selection on genes related to cardiovascular health in high-altitude adapted Andeans. American Journal of Human Genetics 101(5): 757-767 (2018). doi: 10.1016/j.ajhg.2017.09.023
2017 #
Posth C, Wiing C, Kitagawa K, Pagani L, von Holstein L, Racimo F, Wehrberger K, Conard NJ, Kind CJ, Bocherens H, Krause J. Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals. Nature Communications 8: 16046 (2017). doi: 10.1038/ncomms16046
Theunert C, Racimo F, Slatkin M. Joint estimation of relatedness coefficients and allele frequencies from ancient samples. Genetics 117 (2017). doi: 10.1534/genetics.117.200600
Buckley MT, Racimo F, Allentoft ME, Karoline MK, Jonsson A, Huang H, Hormozdiari F, Sikora M, Marnetto D, Eskin E, Jørgensen ME, Grarup N, Pedersen O, Hansen T, Kraft P, Willerslev, E, Nielsen, R. Selection in Europeans on fatty acid desaturases associated with dietary changes. Molecular Biology and Evolution 34(6): 1307-1318. doi: 10.1093/molbev/msx103
Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, Moltke I, Albrechtsen A, Carmel L, Huerta-Sánchez E, Nielsen R. Archaic adaptive introgression in TBX15/WARS2. Molecular Biology and Evolution 34, 3: 509-524 (2017). doi: 10.1093/molbev/msw283
2016 #
Racimo F, Marnetto D, Huerta-Sánchez E. Signatures of adaptive introgression in modern human populations. Molecular Biology and Evolution 34, 2: 296-317 (2016). doi: 10.1093/molbev/msw216
Mallick S, Li H, Lipson M, Mathieson I, Gymrek, M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de Knijff P, Gallego Romero I, Jha AR, Behar DM, Bravi CM, Capelli C, Hervig T, Moreno-Estrada A, Posukh OL, Balanovska E, Balanovsky O, Karachanak-Yankova S, Sahakyan H, Toncheva D, Yepiskoposyan L, Tyler-Smith C, Xue Y, Abdullah MS, Ruiz-Linares A, Beall CM, Di Rienzo A, Jeong C, Starikovskaya EB, Metspalu E, Parik J, Villems R, Henna BM, Hodoglugil U, Mahley R, Sajantila A, Stamatoyannopoulos G, Wee JTS, Khusainova R, Khusnutdinova E, Litvinov S, Ayodo G, Comas D, Hammer MF, Kivisild T, Klitz W, Winkler CA, Labuda D, Bamshad M, Jorde LB, Tishkoff SA, Watkins WS, Metspalu M, Dryomov S, Sukernik R, Singh L, Thangaraj K, Pääbo S, Kelso J, Patterson N, Reich D. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538: 201-206 (2016). doi: 10.1038/nature18964
Malaspinas A-S, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis G, Cheng JY, Crawford JE, Heupink TH, Macholdt E, Peischl S, Rasmussen S, Schiffels S, Subramanian S, Wright JL, Albrechsten A, Barbieri C, Dupanloup I, Eriksson A, Margaryan A, Moltke I, Pugach I, Korneliussen TS, Levkivskyi IP, Moreno-Mayar JV, Ni S, Racimo F, Sikora M, Xue Y, Aghakhanian FA, Brucato N, Brunak S, Campos PF, Clark W, Ellingvåg S, Fourmile G, Gerbault P, Injie D, Koki G, Leavesley M, Logan B, Lynch A, Matisoo-Smith EA, McAllister PJ, Mentzer AJ, Metspalu M, Migliano AB, Murgha L, Phipps ME, Pomat W, Reynolds D, Ricaut FX, Siba P, Thomas MG, Wales T, Wall CM, Oppenheimer SJ, Tyler-Smith C, Durbin R, Dortch J, Manica A, Schierup MH, Foley RA, Lahr MM, Bowern C, Wall JD, Mailund T, Stoneking M, Nielsen R, Sandhu MS, Excoffier L, Lambert DM, Willerslev E. A genomic history of aboriginal Australia. Nature 538: 207-214 (2016). doi: 10.1038/nature18299
Slatkin, M, Racimo F. Ancient DNA and human history. PNAS 113, 23: 6380-6387 (2016). doi: 10.1073/pnas.1524306113
Racimo F, Renaud G, Slatkin M. Joint estimation of error, contamination and demography for nuclear DNA from ancient humans. PLoS Genetics 12, 4: e1005972 (2016). doi: 10.1371/journal.pgen.1005972
Racimo F. Testing for ancient selection using cross-population allele frequency differentiation. Genetics 116, 2: 733-750 (2016). doi: 10.1534/genetics.115.178095
2015 #
Fumagalli M, Moltke I, Grarup N, Racimo F, Bjerregard P, Jørgensen ME, Korneliussen TS, Gerbault P, Skotte L, Linneberg A, Christensen C, Brandslund I, Jørgensen T, Huerta-Sánchez E, Schmidt EB, Pedersen O, Hansen T, Albrechtsen A, Nielsen R. Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science 349, 6254: 1343-1347 (2015). doi: 10.1126/science.aab2319
Racimo F, Sankararaman S, Nielsen R, Huerta-Sánchez E. Evidence for archaic adaptive introgression in humans. Nature Reviews Genetics 16, 6: 359-371 (2015). doi: 10.1038/nrg3936
Teixeira JC, de Filippo C, Weihmann A, Meneu JR, Racimo F, Dannemann M, Nickel B, Meyer M, Parra G, Pääbo S, Andrés AM. Long-term balancing selection in LAD1 maintains a missense trans-species polymorphism in humans, chimpanzees and bonobos. Molecular biology and evolution 32, 5: 1186-1196 (2015). doi: 10.1093/molbev/msv007
2014 #
Racimo F, Schraiber J. Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms. PLoS Genetics 10, 11: e1004697 (2014). doi: 10.1371/journal.pgen.1004697
Racimo F, Kuhlwilm M, Slatkin M. A test for ancient selective sweeps and an application to candidate sites in modern humans. Molecular Biology and Evolution 31, 12: 3344-3358 (2014). doi: 10.1093/molbev/msu255
Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Saywer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Dornoichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neandertal from the Altai Mountains. Nature 505, 7481: 43-49 (2014). doi: 10.1038/nature12886
Castellano S, Parra G*, Sánchez-Quinto F*, Racimo F*, Kuhlwilm M*, Kircher M, Swayer S, Fu Q, Heinze A, Nickel B, Dabney J, Siebauer M, White L, Burbano H, Renaud G, Stenzel U, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajković D, Kucani Z, Gušicj I, Shunkov MV, Derevianko AP, Viola B, Meyer M, Kelso J, Andrés AM, Pääbo S. Patterns of coding variation in the complete exomes of three Neandertals. Proceedings of the National Academy of Sciences 111, 18: 6666-6671 (2014). doi: 10.1073/pnas.1405138111
Kim W, Racimo F, Levy S, Foster KR. Importance of positioning for microbial evolution. Proceedings of the National Academy of Sciences 111, 16: E1639-E1647 (2014). doi: 10.1073/pnas.1323632111
2012 #
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudman PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés A, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A high coverage genome sequence from an archaic Denisovan individual. Science 338, 6104: 222-226 (2012). doi: 10.1126/science.1224344
Bhullar BAS, Marugán-Lobón J, Racimo F, Bever GS, Norell MA, Rowe TB, Abzhanov A. Birds have paedomorphic dinosaur skulls: Ontogeny and phylogeny in avian cranial evolution. Nature 487: 223-226 (2012) doi: 10.1038/nature11146