Rasmus Nielsen

Rasmus Nielsen

Professor

ORCID: 0000-0003-0513-6591

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  1. The lengths of admixture tracts

    Liang, M. & Nielsen, Rasmus, 2014, In: Genetics. 197, 3, p. 953-967 15 p.

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

  2. Published

    Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium

    Liang, M., Shishkin, M., Mikhailova, A., Shchur, V. & Nielsen, Rasmus, 2022, In: PLOS Genetics. 18, 7, 17 p., e1010281.

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

  3. Q A: Who is H. sapiens really, and how do we know?

    Liang, M. & Nielsen, Rasmus, 31 Mar 2011, In: B M C Biology. 9

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

  4. 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

  5. Published

    Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

    Liu, S., Lorenzen, E., Fumagalli, M., Li, B., Harris, K., Xiong, Z., Zhou, L., Korneliussen, T. S., Somel, M., Babbitt, C., Wray, G., Li, J., He, W., Wang, Z., Fu, W., Xiang, X., Morgan, C. C., Doherty, A., O'Connell, M. J., McInerney, J. O. & 9 others, Born, E. W., Dalén, L., Dietz, R., Orlando, L. A. A., Sonne, C., KU, thw266, Nielsen, Rasmus, Willerslev, Eske & Wang, J., 2014, In: Cell. 157, 4, p. 785-794 10 p.

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

  6. 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, Yang, M. A., Fu, Q., Wang, J., Zhou, L., Krogh, Anders, Zhang, H., Wang, W., Chen, Z., Cai, Z., Yin, Y., Yang, H., Mao, M., Shendure, J., Wang, J., Albrechtsen, Anders, Jin, X., Nielsen, Rasmus & Xu, X., 2018, In: Cell. 175, 2, p. 347-359, e1-e7

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

  7. Published

    Predicting Egg Passage Adaptations to Design Better Vaccines for the H3N2 Influenza Virus

    Liu, Y., Chen, H., Duan, W., Zhang, X., He, X., Nielsen, Rasmus, Ma, L. & Zhai, W., 2022, In: Viruses. 14, 9, 16 p., 2065.

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

  8. Published

    Proportionally more deleterious genetic variation in European than in African populations

    Lohmueller, K. E., Indap, A. R., Schmidt, S., Boyko, A. R., Hernandez, R. D., Hubisz, M. J., Sninsky, J. J., White, T. J., Sunyaev, S. R., Nielsen, Rasmus, Clark, A. G. & Bustamante, C. D., 2008, In: Nature. 451, 7181, p. 994-7 3 p.

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

  9. Published

    Natural selection affects multiple aspects of genetic variation at putatively peutral sites across the human genome

    Lohmueller, K. E., Albrechtsen, Anders, Li, Y., Kim, S. Y., Korneliussen, Thorfinn Sand, Vinckenbosch, N., Tian, G., Huerta-Sanchez, E., Feder, A. F., Grarup, Niels, Jørgensen, T., Jiang, T., Witte, D. R., Sandbæk, A., Hellmann, I., Lauritzen, T., Hansen, Torben, Pedersen, Oluf Borbye, Wang, J. & Nielsen, Rasmus, 2011, In: P L o S Genetics. 7, 10, 15 p.

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

  10. Published

    Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes

    Lohmueller, K. E., Sparsø, T. H., Li, Q., Galijatovic, E. A. A., Korneliussen, T. S., Albrechtsen, A., Banasik, K., Grarup, N., Hallgrimsdottir, I., Kiil, K., Oskari Kilpeläinen, T., Krarup, N. T., Pers, T. H., Sanchez, G., Hu, Y., DeGiorgio, M., Jørgensen, T., Sandbæk, A., Lauritzen, T., Brunak, S. & 6 others, Kristiansen, Karsten, Li, Y., Hansen, Torben, Wang, J., Nielsen, Rasmus & Pedersen, Oluf Borbye, 5 Dec 2013, In: American Journal of Human Genetics. 93, 6, p. 1072-1086 15 p.

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

  11. Published

    Species-specific responses of Late Quaternary megafauna to climate and humans

    Lorenzen, E., Nogues, D. B., Orlando, L. A. A., Weinstock Arenovitz, J., Binladen, J. K. M. A., Marske, K. A., Ugan, A., Borregaard, M. K., Gilbert, M. T. P., Nielsen, R., Ho, S. Y. W., Goebel, T., Graf, K. E., Byers, D., Stenderup, J., Rasmussen, M., Campos, P., Leonard, J. A., Koepfli, K-P., Froese, D. & 35 others, Zazula, G., Stafford jr., T., Aaris-Sørensen, Kim, Batra, P., Haywood, A. M., Singarayer, J. S., Valdes, P. J., Boeskorov, G., Burns, J. A., Davydov, S. P., Haile, James Seymour, Jenkins, D. L., Kosintsev, P., Kuznetsova, T., Lai, X., Martin, L. D., McDonald, H. G., Mol, D., Meldgaard, Morten, Munch, K., Stephan, E., Sablin, M., Sommer, R. S., Sipko, T., Scott, E., Suchard, M. A., Tikhonov, A., Willerslev, R., Wayne, R. K., Cooper, A., Hofreiter, M., Sher, A., Shapiro, B., Rahbek, Carsten & Willerslev, Eske, 2011, In: Nature. 479, 7373, p. 359-364 6 p.

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

  12. Published

    Evidence for a Na+/Ca2+ exchange mechanism in frog skin epithelium

    Madsen, K. H., Larsen, Birger Brodin & Nielsen, Rasmus, 1999, In: Pflügers Archiv - European Journal of Physiology. 437, 2, p. 175-81 7 p.

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

  13. Published

    No statistical evidence for an effect of CCR5-∆32 on lifespan in the UK Biobank cohort

    Maier, R., Akbari, A., Wei, X., Patterson, N., Nielsen, Rasmus & Reich, D., 2020, In: Nature Medicine. 26, 2, p. 178-180 3 p.

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

  14. 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

  15. 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

  16. Published

    Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Malaspinas, A. S., Lao, O., Schroeder, H., Rasmussen, M., Raghavan, M., Moltke, I., Campos, P., 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. & 20 others, Stenderup, Jesper Tandberg, Moreno Mayar, J. Víctor, Brunak, S., Sicheritz-Ponten, T., Hodges, E., Hannon, G. J., Orlando, L. A. A., Price, T. D., Jensen, J. D., Nielsen, Rasmus, Heinemeier, J., Olsen, J., Rodrigues-Carvalho, C., Lahr, M. M., Neves, W. A., Kayser, M., Higham, T., Stoneking, M., Pena, S. D. J. & Willerslev, Eske, 2014, In: Current biology : CB. 24, 21, p. R1035-R1037 3 p.

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

  17. Published

    Population genomics of the Viking world: [incl. correction]

    Margaryan, A., Lawson, D. J., Sikora, M., Racimo, F., Rasmussen, S., Moltke, I., Cassidy, L. M., Jørsboe, E., Ingason, A., Pedersen, M. W., Korneliussen, T., Wilhelmson, H., Buś, M. M., de Barros Damgaard, P., Martiniano, R., Renaud, G., Bhérer, C., Moreno-Mayar, J. V., Fotakis, A. K., Allen, M. & 30 others, Allmäe, R., Molak, M., Cappellini, Enrico, Scorrano, Gabriele, McColl, Hugh, Buzhilova, A., Fox, A., Albrechtsen, Anders, Schütz, B., Skar, B., Arcini, C., Lundstrøm, I., Cheng, J., Stenderup, Jesper Tandberg, Iversen, K. H., Arge, S. V., Ellingvåg, S., Orlando, L., Pentz, P., Jessen, M. D., Pedersen, A., Jørkov, M L S, Lynnerup, Niels, Gilbert, M Thomas P, Allentoft, Morten Erik, Sindbæk, S. M., Kristiansen, K., Nielsen, Rasmus, Werge, Thomas & Willerslev, Eske, 2020, In: Nature. 585, 7825, p. 390-396 7 p.

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

  18. 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

  19. 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

  20. The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity

    Meyer, R. S., Ramos, M. M., Lin, M., Schweizer, T. M., Gold, Z., Ramos, D. R., Shirazi, S., Kandlikar, G., Kwan, W. Y., Curd, E. E., Freise, A., Parker, J. M., Sexton, J. P., Wetzer, R., Pentcheff, N. D., Wall, A. R., Pipes, L., Garcia- Vedrenne, A., Mejia, M. P., Moore, T. & 12 others, Orland, C., Ballare, K. M., Worth, A., Beraut, E., Aronson, E. L., Nielsen, Rasmus, Lewin, H. A., Barber, P. H., Wall, J., Kraft, N., Shapiro, B. & Wayne, R. K., 2021, In: California Agriculture. 75, 1, p. 20-32 13 p.

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

  21. Published

    Uncovering the genetic history of the present-day greenlandic population

    Moltke, Ida, Fumagalli, M., Korneliussen, Thorfinn Sand, Crawford, J. E., Bjerregaard, P., Jørgensen, M. E., Grarup, Niels, Gulløv, H. C., Linneberg, Allan René, Pedersen, Oluf Borbye, Hansen, Torben, Nielsen, Rasmus & Albrechtsen, Anders, 2015, In: American Journal of Human Genetics. 96, 1, p. 54-69 16 p.

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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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, Nielsen, Rasmus & Willerslev, Eske, 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

  27. Published

    Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans

    Moreno Mayar, J. Víctor, Rasmussen, Simon, Seguin-Orlando, A., Rasmussen, M., Liang, M., Flåm, S. T., Lie, B. A., Gilfillan, G. D., Nielsen, Rasmus, Thorsby, E., Willerslev, Eske & Malaspinas, A., 2014, In: Current Biology. 24, 21, p. 2518-2525

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

  28. Published

    Divergence, gene flow, and the origin of leapfrog geographic distributions: The history of colour pattern variation in Phyllobates poison-dart frogs

    Márquez, R., Linderoth, T. P., Mejia-Vargas, D., Nielsen, Rasmus, Amezquita, A. & Kronforst, M. R., 2020, In: Molecular Ecology. 29, 19, p. 3702-3719 18 p.

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

  29. Published

    REDUCING AN INTELLECTUAL DEFICIT: COALESCENT THEORY FOR (ALMOST) EVERYONE

    Nielsen, Rasmus, 2006, In: Evolution. 60, 1, p. 208-209

    Research output: Contribution to journal › Review › Research

  30. Published

    Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila

    Nielsen, Rasmus, Bauer DuMont, V. L., Hubisz, M. J. & Aquadro, C. F., 2007, In: Molecular Biology and Evolution. 24, 1, p. 228-35 7 p.

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

  31. Published

    Molecular Signatures of Natural Selection

    Nielsen, Rasmus, 2005, In: Annual Review of Genetics. 39, p. 197-218

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

  32. Published

    Statistical Methods in Molecular Evolution

    Nielsen, Rasmus (ed.), 2005, New York: Springer. 508 p. (Statistics for Biology and Health).

    Research output: Book/Report › Book › Research › peer-review

  33. Published

    Disclosure of variation

    Nielsen, Rasmus, 2005, In: Nature. 434, 7031, p. 288-289

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

  34. 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

  35. Published

    Statistical inferences in phylogeography

    Nielsen, Rasmus & Beaumont, M. A., 2009, In: Molecular Ecology. 18, 6, p. 1034-47 13 p.

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

  36. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

    Nielsen, Rasmus & Yang, Z., 1 Mar 1998, In: Genetics. 148, 3, p. 929-936 8 p.

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

  37. Published

    Mapping Mutations on Phylogenies

    Nielsen, Rasmus, 2005, Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Dunn, M. J., Jorde, L. B., Little, P. F. R. & Subramaniam, S. (eds.). Wiley

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research

  38. Robustness of the Estimator of the Index of Dispersion for DNA Sequences

    Nielsen, Rasmus, 1 Jun 1997, In: Molecular Phylogenetics and Evolution. 7, 3, p. 346-351 6 p.

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

  39. Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation

    Nielsen, Rasmus, Mountain, J. L., Huelsenbeck, J. P. & Slatkin, M., 1 Jan 1998, In: Evolution. 52, 3, p. 669-677 9 p.

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

  40. Published

    Why Sex?

    Nielsen, Rasmus, 2006, In: Science. 311, 5763, p. 960-961

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

  41. 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

  42. Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA

    Nielsen, Rasmus, 1 Jan 1997, In: Systematic Biology. 46, 2, p. 346-353 8 p.

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

  43. Published

    Peopling the Americas

    Nielsen, Rasmus, 2005, In: European Journal of Human Genetics. 13, 10, p. 1100-1101

    Research output: Contribution to journal › Comment/debate › Research

  44. 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

  45. Published

    SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data

    Nielsen, Rasmus, Korneliussen, Thorfinn Sand, Albrechtsen, Anders, Li, Y. & Wang, J., 2012, In: PLoS ONE. 7, 7, 11 p., e37558.

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

  46. Distinguishing Migration From Isolation: A Markov Chain Monte Carlo Approach

    Nielsen, Rasmus & Wakeley, J., 2001, In: Genetics. 158, 2, p. 885-896 12 p.

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

  47. Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium

    Nielsen, Rasmus & Signorovitch, J., 2003, In: Theoretical Population Biology. 63, 3, p. 245-255 11 p.

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

  48. Published

    Single-Locus Tests of Microsatellite Evolution: Multi-Step Mutations and Constraints on Allele Size

    Nielsen, Rasmus & Palsbøll, P. J., 1999, In: Molecular Phylogenetics and Evolution. 11, 3, p. 477-484 8 p.

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

  49. The molecular clock is gone but not forgotten: What about Molecular Clocks? Symposium at the Annual Meeting of the Society for the Study of Evolution (SSE), Madison, Wisconsin, USA, 22-26 June 1999

    Nielsen, Rasmus, 1999, In: Trends in Genetics. 15, 11, p. 442-443 2 p.

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

  50. Published

    Genomic scans for selective sweeps using SNP data

    Nielsen, Rasmus, Williamson, S., Kim, Y., Hubisz, M. J., Clark, A. G. & Bustamente, C., 2005, In: Genome Research. 15, 11, p. 1566-1575

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

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