Rasmus Nielsen

Rasmus Nielsen

Professor

ORCID: 0000-0003-0513-6591

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  1. Published

    100 ancient genomes show repeated population turnovers in Neolithic Denmark

    Allentoft, M. E., Sikora, M., Fischer, A., Sjögren, K-G., Ingason, A., Macleod, R., Rosengren, A., Schulz Paulsson, B., Jørkov, M. L. S., Novosolov, M., Stenderup, J., Price, T. D., Mortensen, M. F., Nielsen, A. B., Hede, M. U., Sørensen, L., Nielsen, P. O., Rasmussen, P., Jensen, T. Z. T., Refoyo-Martínez, A. & 48 others, Irving-Pease, Evan, Barrie, William, Pearson, A., Sousa da Mota, B., Demeter, Fabrice, Henriksen, Rasmus Henrik Amund, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew Howland, Vinner, Lasse, Renaud, Gabriel, Stern, A., Johannsen, N. N., Ramsøe, Abigail Daisy, Schork, A. J., Ruter, Anthony Henry, Gotfredsen, Anne Birgitte, Nielsen, B. H., Petersen, Erik Brinch, Kannegaard, E., Hansen, J., Pedersen, K. B., Pedersen, L., Klassen, L., Meldgaard, Morten, Johansen, M., Uldum, O. C., Lotz, P., Lysdahl, P., Bangsgaard, Pernille, Petersen, P. V., Maring, R., Iversen, Rune, Wåhlin, S., Sørensen, S. A., Andersen, S. H., Jørgensen, T., Lynnerup, Niels, Lawson, D. J., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Kjær, Kurt H., Durbin, R., Nielsen, Rasmus, Delaneau, O., Werge, Thomas, Kristiansen, Kristian & Willerslev, Eske, 2024, In: Nature. 625, 7994, p. 329-337 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  2. Published

    137 ancient human genomes from across the Eurasian steppes

    Damgaard, P. D. B., Marchi, N., Rasmussen, S., Peyrot, M., Renaud, G., Korneliussen, T. S., Moreno-Mayar, J. V., Pedersen, M. W., Goldberg, A., Usmanova, E., Baimukhanov, N., Loman, V., Hedeager, L., Pedersen, A. G., Nielsen, K., Afanasievl, G., Akmatov, K., Aldashev, A., Alpaslan, A., Baimbetov, G. & 55 others, Bazaliiskii, V. I., Beisenov, A., Boldbaatar, B., Boldgiv, B., Dorzhu, C., Ellingvag, S., Erdenebaatar, D., Dajani, R., Dmitriev, E., Evdokimov, V., Frei, K. M., Gromov, A., Goryachev, A., Hakonarson, H., Hegay, T., Khachatryan, Z., Khaskhanov, R., Kitov', E., Kolbina, A., Kubatbek, T., Kukushkin, A., Kukushkin, I., Lau, N., Margaryan, Ashot, Merkyte, Inga, Mertz, I. V., Mertz, V. K., Mijiddorj, E., Moiyesev, V., Mukhtarova, G., Nurmukhanbetov, B., Orozbekova, Z., Panyushkina, I., Pieta, K., Smrčka, V., Shevnina, I., Logvin, A., Sjögren, K., Štolcová, T., Tashbaeva, K., Tkachev, A., Tulegenov, T., Voyakin, D., Yepiskoposyan, L., Undrakhbold, S., Varfolomeev, V., Weber, A., Kradin, N., Allentoft, Morten Erik, Orlando, L. A. A., Nielsen, Rasmus, Sikora, Martin, Heyer, E., Kristiansen, K. & Willerslev, Eske, 2018, In: Nature. 557, 7705, p. 369-374 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

    Malaspinas, A. S., Tange, O., Moreno Mayar, J. Víctor, Rasmussen, M., DiGiorgio, M., Wang, Y., Valdiosera Morales, C. E., Politis, G., Willerslev, Eske & Nielsen, Rasmus, 2014, In: Bioinformatics. 30, 20, p. 2962-2964 3 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    ngsTools : methods for population genetics analyses from next-generation sequencing data

    Fumagalli, M., Vieira, Filipe Garrett, Linderoth, T. & Nielsen, Rasmus, 2014, In: Bioinformatics. 30, 10, p. 1486-1487 2 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. A Bayesian Framework for Inferring the Influence of Sequence Context on Point Mutations

    Ling, G., Miller, D., Nielsen, Rasmus & Stern, A., 2020, In: Molecular Biology and Evolution. 37, 3, p. 893-903 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. Published

    A Bayesian multilocus association method: allowing for higher-order interaction in association studies

    Albrechtsen, Anders, Castella, S., Andersen, G., Hansen, T., Pedersen, O. & Nielsen, Rasmus, 2007, In: Genetics. 176, 2, p. 1197-208 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees

    Nielsen, Rasmus, Bustamente, C., Clark, A. G., Glanowski, S., Sackton, T. B., Hubisz, M. J., Fledel-Alon, A., Tanenbaum, D. M., Civello, D., White, T. J., Sninsky, J. J., Adams, M. D. & Cargill, M., 2005, In: PLoS - Biology. 3, 6, p. e170

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    A draft genome sequence of the elusive giant squid, Architeuthis dux

    da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, Â. M., Barrio-Hernandez, I., Hoving, H-J., Tafur-Jimenez, R., Chu, C., Frazão, B., Petersen, B., Peñaloza, F., Musacchia, F., Alexander, G. C. & 24 others, Osório, H., Winkelmann, I., Simakov, O., Rasmussen, Simon, Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., KU, thw266, Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Pontén, Thomas, Nielsen, Rasmus & Gilbert, M Thomas P, 2020, In: GigaScience. 9, 1, 12 p., giz152.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. A draft sequence of the neandertal genome

    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. & 36 others, 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., De La Rasilla, M., Fortea, J., Rosas, A., Schmitz, R. W., Johnson, P. L. F., Eichler, E. E., Falush, D., Birney, E., Mullikin, J. C., Slatkin, M., Nielsen, Rasmus, Kelso, J., Lachmann, M., Reich, D. & Pääbo, S., 2010, In: Science. 328, 5979, p. 710-722 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  10. A genome-wide scan for signatures of directional selection in domesticated pigs

    Moon, S., Kim, T. H., Lee, K. T., Kwak, W., Lee, T., Lee, S. W., Kim, M. J., Cho, K., Kim, N., Chung, W. H., Sung, S., Park, T., Cho, S., Groenen, M. A. M., Nielsen, Rasmus, Kim, Y. & Kim, H., 25 Feb 2015, In: BMC Genomics. 16, 1, 130.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Published

    A genomic history of aboriginal Australia

    Malaspinas, A. S., Westaway, M. C., Muller, C. E., 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. & 55 others, Eriksson, A., Margaryan, Ashot, Moltke, Ida, Pugach, I., Korneliussen, Thorfinn Sand, Levkivskyi, I. P., Moreno Mayar, J. Víctor, Ni, S., Racimo, F., Sikora, Martin, Xue, Y., Aghakhanian, F. A., Brucato, N., Brunak, Søren, Campos, P., 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., 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, Rasmus, Sandhu, M. S., Excoffier, L., Lambert, D. M. & Willerslev, Eske, 2016, In: Nature. 538, 7624, p. 207-214 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy

    Corbett-Detig, R. & Nielsen, Rasmus, 3 Jan 2017, In: PLoS Genetics. 13, 1, 40 p., e1006529.

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Published

    A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data

    Moreno-Mayar, J. V., Korneliussen, Thorfinn Sand, Dalal, J., Renaud, Gabriel, Albrechtsen, Anders, Nielsen, Rasmus & Malaspinas, A., 2020, In: Bioinformatics. 36, 3, p. 828-841 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    A likelihood ratio test for species membership based on DNA sequence data

    Matz, M. V. & Nielsen, Rasmus, 2005, In: Philosophical Transactions of the Royal Society of London. Biological Sciences. 360, 1462, p. 1969-1974

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

    A method for detecting IBD regions simultaneously in multiple individuals--with applications to disease genetics

    Moltke, Ida, Albrechtsen, Anders, Hansen, Thomas van Overeem, Nielsen, Finn Cilius & Nielsen, Rasmus, 2011, In: Genome Research. 21, 7, p. 1168-80 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. A population phylogenetic view of mitochondrial heteroplasmy

    Wilton, P. R., Zaidi, A., Makova, K. & Nielsen, Rasmus, 2018, In: Genetics. 208, 3, p. 1261-1274 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Published

    A recent bottleneck of Y chromosome diversity coincides with a global change in culture

    Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M. A., Järve, M., Talas, U. G., Rootsi, S., Ilumäe, A-M., Mägi, R., Mitt, M., Pagani, L., Puurand, T., Faltyskova, Z., Clemente, F., Cardona, A., Metspalu, E., Sahakyan, H., Yunusbayev, B., Hudjashov, G., DeGiorgio, M. & 80 others, Loogväli, E., Eichstaedt, C., Eelmets, M., Chaubey, G., Tambets, K., Litvinov, S., Mormina, M., Xue, Y., Ayub, Q., Zoraqi, G., Korneliussen, Thorfinn Sand, Akhatova, F., Lachance, J., Tishkoff, S., Momynaliev, K., Ricaut, F., Kusuma, P., Razafindrazaka, H., Pierron, D., Cox, M. P., Sultana, G. N. N., Willerslev, R., Muller, C., Westaway, M., Lambert, D., Skaro, V., Kovačevic, L., Turdikulova, S., Dalimova, D., Khusainova, R., Trofimova, N., Akhmetova, V., Khidiyatova, I., Lichman, D. V., Isakova, J., Pocheshkhova, E., Sabitov, Z., Barashkov, N. A., Nymadawa, P., Mihailov, E., Seng, J. W. T., Evseeva, I., Migliano, A. B., Abdullah, S., Andriadze, G., Primorac, D., Atramentova, L., Utevska, O., Yepiskoposyan, L., Marjanovic, D., Kushniarevich, A., Behar, D. M., Gilissen, C., Vissers, L., Veltman, J. A., Balanovska, E., Derenko, M., Malyarchuk, B., Metspalu, A., Fedorova, S., Eriksson, A., Manica, A., Mendez, F. L., Karafet, T. M., Veeramah, K. R., Bradman, N., Hammer, M. F., Osipova, L. P., Balanovsky, O., Khusnutdinova, E. K., Johnsen, K., Remm, M., Thomas, M. G., Tyler-Smith, C., Underhill, P. A., Willerslev, Eske, Nielsen, Rasmus, Metspalu, M., Villems, R. & Kivisild, T., 2015, In: Genome Research. 25, 4, p. 459-466 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. A scan for human-specific relaxation of negative selection reveals unexpected Polymorphism in Proteasome Genes

    Somel, M., Sayres, M. A. W., Jordan, G., Huerta-Sanchez, E., Fumagalli, M., Ferrer-Admetlla, A. & Nielsen, Rasmus, 2013, In: Molecular Biology and Evolution. 30, 8, p. 1808-1815 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  19. Published

    ANGSD: analysis of next generation sequencing data

    Korneliussen, Thorfinn Sand, Albrechtsen, Anders & Nielsen, Rasmus, 2014, In: B M C Bioinformatics. 15, 13 p., 356.

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    Adaptionism-30 years after Gould and Lewontin

    Nielsen, Rasmus, 2009, In: Evolution. 63, 10, p. 2487-90 3 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation

    Jobson, R. W., Nielsen, Rasmus, Laakkonen, L., Wikström, M. & Albert, V. A., 2004, In: Proceedings of the National Academy of Sciences of the United States of America. 101, 52, p. 18064-18068 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Adaptive genic evolution in the Drosophila genomes

    Shapiro, J. A., Huang, W., Zhang, C., Hubisz, M. J., Lu, J., Turissini, D. A., Fang, S., Wang, H., Hudson, R. R., Nielsen, Rasmus, Chen, Z. & Wu, C., 2007, In: Proceedings of the National Academy of Science of the United States of America. 104, 7, p. 2271-6 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Published

    Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

    Huerta-Sanchez, E., Jin, X., Asan, Bianba, Z., Peter, B. M., Vinckenbosch, N., Liang, Y., Yi, X., He, M., Somel, M., Ni, P., Wang, B., Ou, X., Huasang, Luosang, J., Cuo, Z. X. P., Li, K., Gao, G., Yin, Y., Wang, W. & 7 others, Zhang, X., Xu, X., Yang, H., Li, Y., Wang, J., Wang, J. & Nielsen, Rasmus, 2014, In: Nature. 512, 7513, p. 194-197 4 p.

    Research output: Contribution to journal › Letter › Research › peer-review

  24. Published

    An Aboriginal Australian genome reveals separate human dispersals into Asia

    Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., Kivisild, T., Zhai, W., Eriksson, A., Manica, A., Orlando, L., De La Vega, F. M., Tridico, S., Metspalu, E., Nielsen, K., Avila Arcos, M. D. C. & 38 others, Moreno Mayar, J. Víctor, Muller, C., Dortch, J., Gilbert, M Thomas P, Lund, O., Wesolowska, A., Karmin, M., Weinert, L. A., Wang, B., Li, J., Tai, S., Xiao, F., Hanihara, T., van Driem, G., Jha, A. R., Ricaut, F., de Knijff, P., Migliano, A. B., Gallego Romero, I., Kristiansen, Karsten, Lambert, D. M., Brunak, Søren, Forster, P., Brinkmann, B., Nehlich, O., Bunce, M., Richards, M., Gupta, R., Bustamante, C. D., Krogh, Anders, Foley, R. A., Lahr, M. M., Balloux, F., Sicheritz-Pontén, T., Villems, R., Nielsen, Rasmus, Wang, J. & Willerslev, Eske, 2011, In: Science. 334, 6052, p. 94-98 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data

    Stern, A. J., Wilton, P. R. & Nielsen, Rasmus, 2019, In: PLOS Genetics. 15, 9, 32 p., e1008384.

    Research output: Contribution to journal › Journal article › Research › peer-review

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