Rasmus Nielsen
Professor
Section for Geogenetics
Øster Voldgade 5-7, 1350 København K
Section for Geogenetics
Øster Voldgade 5-7
1350 København K
- 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
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Fast phylogenetic DNA barcoding
Terkelsen, K. M., Boomsma, Wouter, Willerslev, Eske & Nielsen, Rasmus, 2008, In: Philosophical Transactions of the Royal Society of London. Biological Sciences. 363, 1512, p. 3997-4002 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models
Wong, W. S. W. & Nielsen, Rasmus, 2007, In: Bioinformatics. 23, 16, p. 2031-7 6 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
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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
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Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells
Li, H., Bartke, R., Zhao, Lei, Verma, Y., Horacek, A., Rechav Ben-Natan, A., Pangilinan, G. R., Krishnappa, N., Nielsen, Rasmus & Hockemeyer, D., 2024, In: Nature Biomedical Engineering. 8, 2, p. 165-176Research output: Contribution to journal › Journal article › Research › peer-review
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Genes under positive selection in Escherichia coli
Petersen, L., Bollback, J. P., Dimmic, M., Hubisz, M. & Nielsen, Rasmus, 2007, In: Genome Research. 17, 9, p. 1336-43 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets
Grarup, N., Sulem, P., Sandholt, C. H., Thorleifsson, G., Ahluwalia, T. V. S., Steinthorsdottir, V., Bjarnason, H., Gudbjartsson, D. F., Magnusson, O. T., Sparsø, T., Albrechtsen, A., Kong, A., Masson, G., Tian, G., Cao, H., Nie, C., Kristiansen, K., Husemoen, L. L., Thuesen, B., Li, Y. & 10 others, , 2013, In: P L o S Genetics. 9, 6, 12 p., e1003530.Research output: Contribution to journal › Journal article › Research › peer-review
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Genetic rescue and the maintenance of native ancestry
Harris, K., Zhang, Y. & Nielsen, Rasmus, Feb 2019, In: Conservation Genetics. 20, 1, p. 59-64Research output: Contribution to journal › Journal article › Research › peer-review
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Genetic risk for Multiple Sclerosis originated in Pastoralist Steppe populations
Barrie, W., Yang, Y., Attfield, K. E., Irving-Pease, E., Scorrano, G., Jensen, L. T., Armen, A. P., Dimopoulos, E. A., Stern, A., Refoyo-Martínez, A., Ramsøe, A., Gaunitz, C., Demeter, F., Jørkov, M. L. S., Møller, S. B., Springborg, B., Klassen, L., Hyldgård, I. M., Wickmann, N., Vinner, L. & 9 others, , 2022, bioRxiv, 55 p.Research output: Working paper › Preprint › Research
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Genetic signatures reveal high-altitude adaptation in a set of Ethiopian populations
Huerta-Sánchez, E., DeGiorgio, M., Pagani, L., Tarekegn, A., Ekong, R., Antao, T., Cardona, A., Montgomery, H. E., Cavalleri, G. L., Robbins, P. A., Weale, M. E., Bradman, N., Bekele, E., Kivisild, T., Tyler-Smith, C. & Nielsen, Rasmus, 2013, In: Molecular Biology and Evolution. 30, 8, p. 1877-1888 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques
Yan, G., Zhang, G., Fang, X., Zhang, Y., Li, C., Ling, F., Cooper, D. N., Li, Q., Li, Y., van Gool, A. J., Du, H., Chen, J., Chen, R., Zhang, P., Huang, Z., Thompson, J. R., Meng, Y., Bai, Y., Wang, J., Zhuo, M. & 26 others, , 2011, In: Nature Biotechnology. 29, 11, p. 1019-1023 5 p.Research output: Contribution to journal › Letter › Research › peer-review
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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. 2518-2525Research output: Contribution to journal › Journal article › Research › peer-review
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Genome-wide patterns of nucleotide polymorphism in domesticated rice
Caicedo, A. L., Williamson, S. H., Hernandez, R. D., Boyko, A., Fledel-Alon, A., York, T. L., Polato, N. R., Olsen, K. M., Nielsen, Rasmus, McCouch, S. R., Bustamante, C. D. & Purugganan, M. D., 2007, In: PLoS Genetics. 3, 9, p. 1745-56 11 p.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
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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
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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
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Genomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera Morales, C. E., Avila Arcos, M. D. 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. L., Rasmussen, M. & 81 others, , 2015, In: Science (New York, N.Y.). 349, 6250, 6250.Research output: Contribution to journal › Journal article › Research › peer-review
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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. 1566-1575Research output: Contribution to journal › Journal article › Research › peer-review
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Genotype and SNP calling from next-generation sequencing data
Nielsen, Rasmus, Paul, J. S., Albrechtsen, Anders & Song, Y. S., 2011, In: Nature Reviews. Genetics. 12, 6, p. 443-451 9 p.Research output: Contribution to journal › Review › Research › peer-review
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Greenlandic Inuit show genetic signatures of diet and climate adaptation
Fumagalli, M., Moltke, Ida, Grarup, Niels, Racimo, F., Bjerregaard, P., Jørgensen, M. E., Korneliussen, Thorfinn Sand, Gerbault, P., Skotte, L., Linneberg, Allan René, Christensen, C., Brandslund, I., Jørgensen, T., Huerta-Sánchez, E., Schmidt, E. B., Pedersen, Oluf Borbye, Hansen, T., Albrechtsen, Anders & Nielsen, Rasmus, 2015, In: Science (New York, N.Y.). 349, 6254, p. 1343-1347 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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
Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes
Ai, H., Zhang, M., Yang, B., Goldberg, A., Li, W., Ma, J., Brandt, D., Zhang, Z., Nielsen, Rasmus & Huang, L., 2021, In: Molecular Biology and Evolution. 38, 11, p. 5051-5065 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Identification of physicochemical selective pressure on protein encoding nucleotide sequences
Wong, W. S. W., Sainudiin, R. & Nielsen, Rasmus, 2006, In: BMC Bioinformatics. 7, 10 p., 148.Research output: Contribution to journal › Journal article › Research › peer-review
In defence of model-based inference in phylogeography
Beaumont, M. A., Nielsen, R., Robert, C., Hey, J., Gaggiotti, O., Knowles, L., Estoup, A., Panchal, M., Corander, J., Hickerson, M., Sisson, S. A., Fagundes, N., Chikhi, L., Beerli, P., Vitalis, R., Cornuet, J. M., Huelsenbeck, J., Foll, M., Yang, Z., Rousset, F. & 2 others, , 2010, In: Molecular Ecology. 19, 3, p. 436-446 11 p.Research output: Contribution to journal › Review › Research › peer-review
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In defense of statistical methods for detecting positive selection
Yang, Z., Nielsen, Rasmus & Goldman, N., 2009, In: Proceedings of the National Academy of Science of the United States of America. 106, 36, p. E95Research output: Contribution to journal › Journal article › Research › peer-review
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Inference of historical changes in migration rate from the lengths of migrant tracts
Pool, J. E. & Nielsen, Rasmus, 2009, In: Genetics. 181, 2, p. 711-9 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Inferring Adaptive Introgression Using Hidden Markov Models
Svedberg, J., Shchur, V., Reinman, S., Nielsen, Rasmus & Corbett-Detig, R., 2021, In: Molecular Biology and Evolution. 38, 5, p. 2152-2165 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Inferring demographic history from a spectrum of shared haplotype lengths
Harris, K. & Nielsen, Rasmus, 2013, In: P L o S Genetics. 9, 6, 20 p., e1003521.Research output: Contribution to journal › Journal article › Research › peer-review
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Inferring the ancestry of parents and grandparents from genetic data
Pei, J., Zhang, Y., Nielsen, Rasmus & Wu, Y., 2020, In: PLOS Computational Biology. 16, 8, 22 p., 1008065.Research output: Contribution to journal › Journal article › Research › peer-review
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Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
Hey, J. & Nielsen, Rasmus, 2007, In: Proceedings of the National Academy of Science of the United States of America. 104, 8, p. 2785-90 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Intracellular calcium modulates basolateral K(+)-permeability in frog skin epithelium
Larsen, Birger Brodin, Rytved, K. A. & Nielsen, Rasmus, 1994, In: Pflügers Archiv - European Journal of Physiology. 426, 1-2, p. 171-3 3 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
Investigate the origins of COVID-19
Bloom, J. D., Chan, Y. A., Baric, R. S., Bjorkman, P. J., Cobey, S., Deverman, B. E., Fisman, D. N., Gupta, R., Iwasaki, A., Lipsitch, M., Medzhitov, R., Neher, R. A., Nielsen, Rasmus, Patterson, N., Stearns, T., van Nimwegen, E., Worobey, M. & Relman, D. A., 2021, In: Science. 372, 6543, p. 694 1 p.Research output: Contribution to journal › Letter › Research › peer-review
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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
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Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation
Rocha, J. L., Godinho, R., Brito, J. C. & Nielsen, Rasmus, 2021, In: Trends in Ecology & Evolution. 36, 7, p. 637-650Research output: Contribution to journal › Review › Research › peer-review
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
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Localizing recent adaptive evolution in the human genome
Williamson, S. H., Hubisz, M. J., Clark, A. G., Payseur, B. A., Bustamante, C. D. & Nielsen, Rasmus, 2007, In: PLoS Genetics. 3, 6, p. e90Research output: Contribution to journal › Journal article › Research › peer-review
Looking for Darwin in Genomic Sequences-Validity and Success of Statistical Methods
Zhai, W., Nielsen, Rasmus, Goldman, N. & Yang, Z., 2012, In: Molecular Biology and Evolution. 29, 10, p. 2889-2893 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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.). WileyResearch output: Chapter in Book/Report/Conference proceeding › Book chapter › Research
Massive haplotypes underlie ecotypic differentiation in sunflowers
Todesco, M., Owens, G. L., Bercovich, N., Légaré, J. S., Soudi, S., Burge, D. O., Huang, K., Ostevik, K. L., Drummond, E. B. M., Imerovski, I., Lande, K., Pascual-Robles, M. A., Nanavati, M., Jahani, M., Cheung, W., Staton, S. E., Muños, S., Nielsen, R., Donovan, L. A., Burke, J. M. & 2 others, , 2020, In: Nature. 584, 7822, p. 602-607 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA
Rebolledo-Jaramillo, B., Su, M. S., Stoler, N., McElhoe, J. A., Dickins, B., Blankenberg, D., Korneliussen, Thorfinn Sand, Chiaromonte, F., Nielsen, Rasmus, Holland, M. M., Paul, I. M., Nekrutenko, A. & Makova, K. D., 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 43, p. 15474-15479 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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
Modeling gene expression evolution with an extended ornstein-uhlenbeck process accounting for within-species variation
Rohlfs, R. V., Harrigan, P. & Nielsen, Rasmus, 2014, In: Molecular Biology and Evolution. 31, 1, p. 201-211 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Modern population genetics and race
Nielsen, Rasmus, 2022, Remapping Race in a Global Context. Lorusso, L. & Winther, R. G. (eds.). Routledge, p. 157-163 7 p. (History and Philosophy of Biology).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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Molecular Signatures of Natural Selection
Nielsen, Rasmus, 2005, In: Annual Review of Genetics. 39, p. 197-218Research 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
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Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing
Li, Y., Zhao, S., Ma, J., Li, D., Yan, L., Li, J., Qi, X., Guo, X., Zhang, L., He, W., Chang, R., Liang, Q., Guo, Y., Ye, C., Wang, X., Tao, Y., Guan, R., Wang, J., Liu, Y., Jin, L. & 15 others, , 2013, In: BMC Genomics. 14, 12 p., 579.Research output: Contribution to journal › Journal article › Research › peer-review
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Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
Yang, Z. & Nielsen, Rasmus, 2008, In: Molecular Biology and Evolution. 25, 3, p. 568-79 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
Natural Selection Reduced Diversity on Human Y Chromosomes
Wilson Sayres, M. A., Lohmueller, K. E. & Nielsen, Rasmus, 2014, In: PLOS Genetics. 10, 1, 12 p., e1004064.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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Natural selection and the distribution of identity-by-descent in the human genome
Albrechtsen, Anders, Moltke, Ida & Nielsen, Rasmus, 2010, In: Genetics. 186, 1, p. 295-308 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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Natural selection on protein-coding genes in the human genome
Bustamente, C. D., Fledel-Alon, A., Williamson, S., Nielsen, Rasmus, Hubisz, M., Glanowski, S., Tanenbaum, D. M., White, T. J., Sninsky, J. J., Hernandez, R. D., Civello, D., Adams, M. D., Cargill, M. & Clark, A. G., 2005, In: Nature. 437, 7062, p. 1153-1157Research output: Contribution to journal › Letter › Research
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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
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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
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North African fox genomes show signatures of repeated introgression and adaptation to life in deserts
L. Rocha, J., Silva, P., Santos, N., Nakamura, M., Afonso, S., Qninba, A., Boratynski, Z., Sudmant, P. H., Brito, J. C., Nielsen, Rasmus & Godinho, R., 2023, In: Nature Ecology and Evolution. 7, 8, p. 1267-1286Research output: Contribution to journal › Journal article › Research › peer-review
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Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences
Nightingale, K. K., Lyles, K., Ayodele, M., Jalan, P., Nielsen, Rasmus & Wiedmann, M., 2006, In: Journal of Clinical Microbiology. 44, 10, p. 3742-3751Research 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
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On detecting incomplete soft or hard selective sweeps using haplotype structure
Ferrer-Admetlla, A., Liang, M., Korneliussen, Thorfinn Sand & Nielsen, Rasmus, 2014, In: Molecular Biology and Evolution. 31, 5, p. 1275-1291 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
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On the Distribution of Tract Lengths During Adaptive Introgression
Shchur, V., Svedberg, J., Medina, P., Corbett-Detig, R. & Nielsen, Rasmus, 2020, In: G3: Genes, Genomes, Genetics (Bethesda). 10, 10, p. 3663-3673 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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
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Patterns of mutation and selection at synonymous sites in Drosophila
Singh, N. D., Bauer DuMont, V. L., Hubisz, M. J., Nielsen, Rasmus & Aquadro, C. F., 2007, In: Molecular Biology and Evolution. 24, 12, p. 2687-97 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Patterns of positive selection in six Mammalian genomes
Kosiol, C., Vinar, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, Rasmus & Siepel, A., 2008, In: PLoS Genetics. 4, 8, p. e1000144Research output: Contribution to journal › Journal article › Research › peer-review
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Peopling the Americas
Nielsen, Rasmus, 2005, In: European Journal of Human Genetics. 13, 10, p. 1100-1101Research output: Contribution to journal › Comment/debate › Research
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
Phenotypic Convergence Is Not Mirrored at the Protein Level in a Lizard Adaptive Radiation
Corbett-Detig, R. B., Russell, S. L., Nielsen, Rasmus & Losos, J., 2020, In: MOLECULAR BIOLOGY AND EVOLUTION . 37, 6, p. 1604-1614 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Phylogenetic ANOVA: the expression variance and evolution model for quantitative trait evolution
Rohlfs, R. V. & Nielsen, Rasmus, 2015, In: Systematic Biology. 64, 5, p. 695-708 14 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 Variegated Toad-Headed Lizard Phrynocephalus versicolor and Its Adaptation to the Colorful Sand of the Gobi Desert
Jin, Y., Aguilar-Gómez, D., Brandt, D. Y. C., Square, T. A., Li, J., Liu, Z., Wang, T., Sudmant, P. H., Miller, C. T. & Nielsen, Rasmus, 2022, In: Genome Biology and Evolution. 14, 7, 14 p., evac076.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
Hellmann, I., Mang, Y., Gu, Z., Li, P., de la Vega, F. M., Clark, A. G. & Nielsen, Rasmus, 2008, In: Genome Research. 18, 7, p. 1020-9 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Population genomics of bronze age Eurasia
Allentoft, M. E., Sikora, M., Sjogren, K-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. D. B., Schroeder, H., Ahlstrom, T., Vinner, L., Malaspinas, A. S., Margaryan, A., Higham, T., Chivall, D., Lynnerup, N., Harvig, L. L., Baron, J., Della Casa, P., Dabrowski, P., Duffy, P. R. & 46 others, , 2015, In: Nature Genetics. 522, 7555, p. 167-172 6 p.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
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Population genomics of post-glacial western Eurasia
Allentoft, M. E., Sikora, M., Refoyo-Martínez, A., Irving-Pease, E. K., Fischer, A., Barrie, W., Ingason, A., Stenderup, J., Sjögren, K-G., Pearson, A., da Mota, B. S., Paulsson, B. S., Halgren, A., Macleod, R., Jørkov, M. L. S., Demeter, F., Sørensen, L., Nielsen, P. O., Henriksen, R. A., Vimala, T. & 144 others, , 2024, In: Nature. 625, 7994, p. 301-311Research output: Contribution to journal › Journal article › Research › peer-review
- 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, , 2020, In: Nature. 585, 7825, p. 390-396 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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, , 2014, In: Cell. 157, 4, p. 785-794 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Population size changes reshape genomic patterns of diversity
Pool, J. E. & Nielsen, Rasmus, 2007, In: Evolution. 61, 12, p. 3001-6 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
Positive Selection in the Human Genome Inferred from Human-Chimp-Mouse Orthologous Gene Alignments
Clark, A. G., Glanowski, S., Nielsen, Rasmus, Thomas, P., Kejariwal, A., Todd, M. J., Tanenbaum, D. M., Civello, D., Lu, F., Murphy, B., Ferriera, S., Wang, G., Zheng, X., White, T. J., Sninsky, J. J., Adams, M. D. & Cargill, M., 2003, In: Cold Spring Harbor Symposia on Quantitative Biology. 68, 1, p. 479-486 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Positive selection on apoptosis related genes
Rodrigues da Fonseca, Rute Andreia, Kosiol, C., Vinař, T., Siepel, A. & Nielsen, Rasmus, 2010, In: FEBS Letters. 584, 3, p. 469-476 8 p.Research output: Contribution to journal › Review › Research › peer-review
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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
- 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
Pronounced somatic bottleneck in mitochondrial DNA of human hair
Barrett, A., Arbeithuber, B., Zaidi, A., Wilton, P., Paul, I. M., Nielsen, Rasmus & Makova, K. D., 2020, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 375, 1790, 11 p., 20190175.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
Q A: Who is H. sapiens really, and how do we know?
Liang, M. & Nielsen, Rasmus, 31 Mar 2011, In: B M C Biology. 9Research 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
Quantifying population genetic differentiation from next-generation sequencing data
Fumagalli, M., Vieira, Filipe Garrett, Korneliussen, Thorfinn Sand, Linderoth, T., Huerta-Sánchez, E., Albrechtsen, Anders & Nielsen, Rasmus, Nov 2013, In: Genetics. 195, 3, p. 979-992 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
REDUCING AN INTELLECTUAL DEFICIT: COALESCENT THEORY FOR (ALMOST) EVERYONE
Nielsen, Rasmus, 2006, In: Evolution. 60, 1, p. 208-209Research output: Contribution to journal › Review › Research
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
- Published
Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata
Pastene, L. A., Goto, M., Kanda, N., Zerbini, A. N., Kerem, D., Watanabe, K., Bessho, Y., Hasegawa, M., Nielsen, Rasmus, Larsen, F. & Palsbøll, P. J., 2007, In: Molecular Ecology. 16, 7, p. 1481-1495 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Radiation of extant Cetaceans Driven by Restructuring of the Oceans
Steeman, M. E., Hebsgaard, M. B., Fordyce, J., Syw, H., Rabovsky, D., Nielsen, Rasmus, Rahbek, Carsten, Glenner, Henrik, Sørensen, Martin Vinther & Willerslev, Eske, 2009, In: Systematic Biology. 58, p. 573-585 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Recent and ongoing selection in the human genome
Nielsen, Rasmus, Hellmann, I., Hubisz, M., Bustamante, C. & Clark, A. G., 2007, In: Nature Reviews. Genetics. 8, 11, p. 857-68 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium
Albrechtsen, Anders, Korneliussen, Thorfinn Sand, Moltke, Ida, van Overseem Hansen, T., Nielsen, Finn Cilius & Nielsen, Rasmus, 2009, In: Genetic Epidemiology. 33, 3, p. 266-274Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
Xu, X., Liu, X., Ge, S., Jensen, J. D., Hu, F., Li, X., Dong, Y., Gutenkunst, R. N., Fang, L., Huang, L., Li, J., He, W., Zhang, G., Zheng, X., Zhang, F., Li, Y., Yu, C., Kristiansen, K., Zhang, X., Wang, J. & 5 others, , 2012, In: Nature Biotechnology. 30, 1, p. 105-111 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants
Li, Y., Vinckenbosch, N., Tian, G., Huerta-Sanchez, E., Jiang, T., Jiang, H., Albrechtsen, A., Andersen, G., Cao, H., Korneliussen, T. S., Grarup, N., Guo, Y., Hellman, I., Jin, X., Li, Q., Liu, J., Liu, X., Sparsø, T., Tang, M., Wu, H. & 18 others, , 2010, In: Nature Genetics. 42, 11, p. 969-72 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
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
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
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
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