Rasmus Nielsen
Professor
Section for Geogenetics
Øster Voldgade 5-7, 1350 København K
Section for Geogenetics
Øster Voldgade 5-7
1350 København K
- 2019
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
Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees
Zaidi, A. A., Wilton, P. R., Su, M. S., Paul, I. M., Arbeithuber, B., Anthony, K., Nekrutenko, A., Nielsen, Rasmus & Makova, K. D., 2019, In: Proceedings of the National Academy of Sciences of the United States of America. 116, 50, p. 25172-25178 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline
Rascovan, N., Sjogren, K., Kristiansen, K., Nielsen, Rasmus, Willerslev, Eske, Desnues, C. & Rasmussen, Simon, 2019, In: Cell. 176, 1-2, p. 295-305.e10Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Human Disease Variation in the Light of Population Genomics
Prohaska, Ana, Racimo, Fernando, Schork, A. J., Sikora, Martin, Stern, A. J., Ilardo, M., Allentoft, Morten Erik, Folkersen, L., Buil, A., Moreno Mayar, J. Víctor, Korneliussen, Thorfinn Sand, Geschwind, D., Ingason, A., Werge, Thomas, Nielsen, Rasmus & Willerslev, Eske, 2019, In: Cell. 177, 1, p. 115-131 17 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Joint Estimation of Pedigrees and Effective Population Size Using Markov Chain Monte Carlo
Ko, A. & Nielsen, Rasmus, 2019, In: Genetics. 212, 3, p. 855-868Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Natural selection on the Arabidopsis thaliana genome in present and future climates
Exposito-Alonso, M., Burbano, H. A., Bossdorf, O., Nielsen, R., Weigel, D., Exposito-Alonso, M., Gomez Rodriguez, R., Barragan, C., Capovilla, G., Chae, E., Devos, J., Dogan, E. S., Friedemann, C., Gross, C., Lang, P., Lundberg, D., Middendorf, V., Kageyama, J., Karasov, T., Kersten, S. & 23 others, , 2019, In: Nature. 573, 7772, p. 126-129Research output: Contribution to journal › Letter › Research › peer-review
- Published
Parallel adaptation of rabbit populations to myxoma virus
Alves, J. M., Carneiro, M., Cheng, J. Y., Matos, A. L. D., Rahman, M. M., Loog, L., Campos, P. F., Wales, N., Eriksson, A., Manica, A., Strive, T., Graham, S. C., Afonso, S., Bell, D. J., Belmont, L., Day, J. P., Fuller, S. J., Marchandeau, S., Palmer, W. J., Queney, G. & 8 others, , 2019, In: Science. 363, 6433Research output: Contribution to journal › Journal article › Research › peer-review
Passage Adaptation Correlates With the Reduced Efficacy of the Influenza Vaccine
Chen, H., Alvarez, J. J. S., Ng, S. H., Nielsen, Rasmus & Zhai, W., 2019, In: Clinical Infectious Diseases. 69, 7, p. 1198-1204 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change
Bi, K., Linderoth, T., Singhal, S., Vanderpool, D., Patton, J. L., Nielsen, Rasmus, Moritz, C. & Good, J. M., 2019, In: PLOS Genetics. 15, 5, 22 p., e1008119.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The population history of northeastern Siberia since the Pleistocene
Sikora, M., Pitulko, V. V., Sousa, V. C., Allentoft, M. E., Vinner, L., Rasmussen, S., Margaryan, A., Damgaard, P. D. B., de la Fuente Castro, C., Renaud, G., Yang, M. A., Fu, Q., Dupanloup, I., Giampoudakis, K., Nogues, D. B., Rahbek, C., Kroonen, G., Peyrot, M., McColl, H., Vasilyev, S. V. & 27 others, , 2019, In: Nature. 570, p. 182–188Research output: Contribution to journal › Journal article › Research › peer-review
- 2018
- Published
Early human dispersals within the Americas
Moreno-Mayar, J. V., Vinner, L., de Barros Damgaard, P., de la Fuente, C., Allentoft, M. E., Vimala, T., Racimo, F., Rasmussen, S., Margaryan, A., Iraeta Orbegozo, M., Mylopotamitaki, D., Alexandersen, V., Primeau, C., Gregersen, K., Hansen, K. L., Lynnerup, N., Kjær, K., Schroeder, H., Malaspinas, A. S., Sikora, M. & 2 others, , 7 Dec 2018, In: Science (New York, N.Y.). 362, 6419, p. 1, 1-11 12 p., eaav2621.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Human adaptation to extreme environmental conditions
Ilardo, M. & Nielsen, Rasmus, 1 Dec 2018, In: Current Opinion in Genetics and Development. 53, p. 77-82 6 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
On the number of siblings and p-th cousins in a large population sample
Shchur, V. & Nielsen, Rasmus, 1 Nov 2018, In: Journal of Mathematical Biology. 77, 5, p. 1279-1298Research output: Contribution to journal › Journal article › Research › peer-review
- 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, , 2018, In: Nature. 557, 7705, p. 369-374 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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
- Published
Estimating the timing of multiple admixture pulses during local ancestry inference
Medina, P., Thornlow, B., Nielsen, Rasmus & Corbett-Detig, R., 2018, In: Genetics. 210, 3, p. 1089-1107 19 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History
Liu, S., Huang, S., Chen, F., Zhao, L., Yuan, Y., Francis, S. S., Fang, L., Li, Z., Lin, L., Liu, R., Zhang, Y., Xu, H., Li, S., Zhou, Y., Davies, R. W., Liu, Q., Walters, R. G., Lin, K., Ju, J., Komeliussen, T. & 18 others, , 2018, In: Cell. 175, 2, p. 347-359, e1-e7Research output: Contribution to journal › Journal article › Research › peer-review
Molecular footprints of aquatic adaptation including bone mass changes in cetaceans
Zhou, X., Sun, D., Guang, X., Ma, S., Fang, X., Mariotti, M., Nielsen, Rasmus, Gladyshev, V. N. & Yang, G., 2018, In: Genome Biology and Evolution. 10, 3, p. 967-975 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
Pervasive introgression facilitated domestication and adaptation in the Bos species complex
Wu, D., Ding, X. D., Wang, S., Wójcik, J. M., Zhang, Y., Tokarska, M., Li, Y., Wang, M. S., Faruque, O., Nielsen, Rasmus, Zhang, Q. & Zhang, Y., 2018, In: Nature Ecology and Evolution. 2, 7, p. 1139-1145 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Physiological and Genetic Adaptations to Diving in Sea Nomads
Ilardo, M. A., Moltke, Ida, Korneliussen, Thorfinn Sand, Cheng, J., Stern, A. J., Racimo, Fernando, Damgaard, P. D. B., Sikora, Martin, Seguin-Orlando, A., Rasmussen, Simon, van den Munckhof, I. C. L., ter Horst, R., Joosten, L. A. B., Netea, M. G., Salingkat, S., Nielsen, Rasmus & Willerslev, Eske, 2018, In: Cell. 173, 3, p. 569-580 12 p., e15.Research output: Contribution to journal › Journal article › Research › peer-review
Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater
Zhou, X., Guang, X., Sun, D., Xu, S., Li, M., Seim, I., Jie, W., Yang, L., Zhu, Q., Xu, J., Gao, Q., Kaya, A., Dou, Q., Chen, B., Ren, W., Li, S., Zhou, K., Gladyshev, V. N., Nielsen, R., Fang, X. & 1 others, , 2018, In: Nature Communications. 9, 8 p., 1276.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans
Moreno Mayar, J. Víctor, Potter, B. A., Vinner, Lasse, Steinrucken, M., Rasmussen, Simon, Terhorst, J., Kamm, J. A., Albrechtsen, Anders, Malaspinas, A., Sikora, Martin, Reuther, J. D., Irish, J. D., Malhi, R. S., Orlando, L. A. A., Song, Y. S., Nielsen, Rasmus, Meltzer, D. J. & Willerslev, Eske, 2018, In: Nature Genetics. 553, 7687, p. 203-207 5 p.Research output: Contribution to journal › Letter › Research › peer-review
The Genetic Basis of Adaptation following Plastic Changes in Coloration in a Novel Environment
Corl, A., Bi, K., Luke, C., Challa, A. S., Stern, A. J., Sinervo, B. & Nielsen, Rasmus, 2018, In: Current Biology. 28, 18, p. 2970-2977, e1-e7Research output: Contribution to journal › Journal article › Research › peer-review
- 2017
- Published
Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers
Sikora, M., Seguin-Orlando, A., Sousa, V. C., Albrechtsen, A., Korneliussen, T. S., Ko, A., Rasmussen, S., Dupanloup, I., Nigst, P. R., Bosch, M. D., Renaud, G., Allentoft, M. E., Margaryan, A., Vasilyev, S. V., Veselovskaya, E. V., Borutskaya, S. B., Deviese, T., Comeskey, D., Higham, T., Manica, A. & 7 others, , 3 Nov 2017, In: Science. 358, 6363, p. 659-662 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Natural selection on genes related to cardiovascular health in high-altitude adapted Andeans
Crawford, J. E., Amaru, R., Song, J., Julian, C. G., Racimo, Fernando, Cheng, J. Y., Guo, X., Yao, J., Ambale-Venkatesh, B., Lima, J. A., Rotter, J. I., Stehlik, J., Moore, L. G., Prchal, J. T. & Nielsen, Rasmus, 2 Nov 2017, In: American Journal of Human Genetics. 101, 5, p. 752-767 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Q&A: where did the Neanderthals go?
Harris, K. & Nielsen, Rasmus, 1 Sep 2017, In: BMC Biology. 15, 3 p., 73.Research output: Contribution to journal › Comment/debate › Research › peer-review
- Published
Composite likelihood method for inferring local pedigrees
Ko, A. & Nielsen, Rasmus, 21 Aug 2017, In: PLoS Genetics. 13, 8, 21 p., e1006963.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Fast admixture analysis and population tree estimation for SNP and NGS data
Cheng, J. Y., Mailund, T. & Nielsen, Rasmus, 15 Jul 2017, In: Bioinformatics. 33, 14, p. 2148-2155 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Selection in Europeans on fatty acid desaturases associated with dietary changes
Buckley, M. T., Racimo, Fernando, Allentoft, Morten Erik, Jensen, M. K., Jonsson, Anna Elisabet, Huang, H., Hormozdiari, F., Sikora, Martin, Marnetto, D., Eskin, E., Jørgensen, M. E., Grarup, Niels, Pedersen, Oluf Borbye, Hansen, Torben, Kraft, P., Willerslev, Eske & Nielsen, Rasmus, Jun 2017, In: Molecular Biology and Evolution. 34, 6, p. 1307-1318 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Tracing the peopling of the world through genomics
Nielsen, Rasmus, Akey, J. M., Jakobsson, M., Pritchard, J. K., Tishkoff, S. & Willerslev, Eske, 19 Jan 2017, In: Nature. 541, 7637, p. 302-310 9 p.Research output: Contribution to journal › Review › Research › peer-review
- 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
Genome-wide signatures of complex introgression and adaptive evolution in the big cats
Figueiró, H. V., Li, G., Trindade, F. J., Assis, J., Pais, F., Fernandes, G., Santos, S. H. D., Hughes, G. M., Komissarov, A., Antunes, A., Trinca, C. S., Rodrigues, M. R., Linderoth, T., Bi, K., Silveira, L., Azevedo, F. C. C., Kantek, D., Ramalho, E., Brassaloti, R. A., Villela, P. M. S. & 13 others, , 1 Jan 2017, In: Science Advances. 3, 7, 13 p., e1700299.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Archaic adaptive introgression in TBX15/WARS2
Racimo, Fernando, Gokhman, D., Fumagalli, M., Ko, A., Hansen, Torben, Moltke, Ida, Albrechtsen, Anders, Carmel, L., Huerta-Sánchez, E. & Nielsen, Rasmus, 2017, In: Molecular Biology and Evolution. 34, 3, p. 509-524 16 p., msw283.Research output: Contribution to journal › Journal article › Research › peer-review
- 2016
- Published
Genomic analyses inform on migration events during the peopling of Eurasia
Pagani, L., Lawson, D. J., Jagoda, E., Moerseburg, A., Eriksson, A., Mitt, M., Clemente, F., Hudjashov, G., DeGiorgio, M., Saag, L., Wall, J. D., Cardona, A., Maegi, R., Sayres, M. A. W., Kaewert, S., Inchley, C., Scheib, C. L., Jaerve, M., Karmin, M., Jacobs, G. S. & 78 others, , 13 Oct 2016, In: Nature. 538, 7624, p. 238-242 5 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
The power of inbreeding: NGS-based GWAS of rice reveals convergent evolution during rice domestication
Wang, H., Xu, X., Vieira, Filipe Garrett, Xiao, Y., Li, Z., Wang, J., Nielsen, Rasmus & Chu, C., 6 Jul 2016, In: Molecular Plant. 9, 7, p. 975-985 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The genetic cost of Neanderthal introgression
Harris, K. & Nielsen, Rasmus, Jun 2016, In: Genetics (Online). 203, 2, p. 881-891 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 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, , 2016, In: Nature. 538, 7624, p. 207-214 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
Detecting recent selective sweeps while controlling for mutation rate and background selection
Huber, C. D., DeGiorgio, M., Hellmann, I. & Nielsen, Rasmus, 2016, In: Molecular Ecology. 25, 1, p. 142-156 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimating IBD tracts from low coverage NGS data
Vieira, Filipe Garrett, Albrechtsen, Anders & Nielsen, Rasmus, 2016, In: Bioinformatics. 32, 14, p. 2096-2102 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae s.l., and its impact on susceptibility to Plasmodium infection
Crawford, J. E., Riehle, M. M., Markianos, K., Bischoff, E., Guelbeogo, W. M., Gneme, A., Sagnon, N., Vernick, K. D., Nielsen, Rasmus & Lazzaro, B. P., 2016, In: Molecular Ecology. 25, 7, p. 1494-1510 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Fumio Tajima and the origin of modern population genetics
Nielsen, Rasmus, 2016, In: Genetics. 204, 2, p. 389-390 2 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Postglacial viability and colonization in North America’s ice-free corridor
Pedersen, Mikkel Winther, Ruter, Anthony Henry, Schweger, C., Friebe, H., Staff, R. A., Kjeldsen, Kristian Kjellerup, Zepeda Mendoza, M. L., Beaudoin, A. B., Zutter, C., Larsen, Nicolaj Krog, Potter, B. A., Nielsen, Rasmus, Rainville, R. A., Orlando, L. A. A., Meltzer, D. J., Kjær, Kurt H. & Willerslev, Eske, 2016, In: Nature. 537, 7618, p. 45–49 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
REPdenovo: Inferring De Novo repeat motifs from short sequence reads
Chu, C., Nielsen, Rasmus & Wu, Y., 2016, In: PLoS ONE. 11, 3, 17 p., e0150719.Research output: Contribution to journal › Journal article › Research › peer-review
- 2015
Reticulate speciation and barriers to introgression in the anopheles gambiae species complex
Crawford, J. E., Riehle, M. M., Guelbeogo, W. M., Gneme, A., Sagnon, N., Vernick, K. D., Nielsen, Rasmus & Lazzaro, B. P., 1 Nov 2015, In: Genome Biology and Evolution. 7, 11, p. 3116-3131 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
Introduction: Genomics and philosophy of race
Winther, Rasmus, Millstein, R. L. & Nielsen, Rasmus, 1 Aug 2015, In: Studies in History and Philosophy of Science Part C :Studies in History and Philosophy of Biological and Biomedical Sciences. 52, p. 1-4 4 p.Research output: Contribution to journal › Editorial › Research › peer-review
The mind, the lab, and the field: Three kinds of populations in scientific practice
Winther, Rasmus, Giordano, R., Edge, M. D. & Nielsen, Rasmus, 1 Aug 2015, In: Studies in History and Philosophy of Science Part C :Studies in History and Philosophy of Biological and Biomedical Sciences. 52, p. 12-21 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
Fitting the Balding-Nichols model to forensic databases
Rohlfs, R. V., Aguiar, V. R. C., Lohmueller, K. E., Castro, A. M., Ferreira, A. C. S., Almeida, V. C. O., Louro, I. D. & Nielsen, Rasmus, 16 Jul 2015, In: Forensic Science International: Genetics. 19, p. 86-91 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog ranitomeya imitator
Vestergaard, J. S., Twomey, E., Larsen, Rasmus Stenbak, Summers, K. & Nielsen, Rasmus, 22 May 2015, In: Proceedings of the Royal Society B: Biological Sciences. 282, 1807, 20141950.Research output: Contribution to journal › Journal article › Research › peer-review
Evidence for archaic adaptive introgression in humans
Racimo, Fernando, Sankararaman, S., Nielsen, Rasmus & Huerta-Sánchez, E., 18 May 2015, In: Nature Reviews Genetics. 16, 6, p. 359-371 13 p.Research output: Contribution to journal › Review › Research › peer-review
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
ID: 3311
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Natural selection affects multiple aspects of genetic variation at putatively peutral sites across the human genome
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Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets
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SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data
Research output: Contribution to journal › Journal article › Research › peer-review
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