Rasmus Nielsen
Professor
Section for Geogenetics
Øster Voldgade 5-7, 1350 København K
Section for Geogenetics
Øster Voldgade 5-7
1350 København K
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
- 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
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Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes
Albrechtsen, A., Grarup, N., Li, Y., Sparsø, T. H., Tian, G., Cao, H., Jiang, T., Kim, S. Y., Korneliussen, T. S., Li, Q., Nie, C., Wu, R., Skotte, L., Morris, A. P., Ladenvall, C., Cauchi, S., Stancáková, A., Andersen, G., Astrup, A., Banasik, K. & 86 others, , 2013, In: Diabetologia. 56, 2, p. 298-310 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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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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
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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, , 2024, In: Nature. 625, 7994, p. 329-337 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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
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Targets of balancing selection in the human genome
Andrés, A. M., Hubisz, M. J., Indap, A., Torgerson, D. G., Degenhardt, J. D., Boyko, A. R., Gutenkunst, R. N., White, T. J., Green, E. D., Bustamante, C. D., Clark, A. G. & Nielsen, Rasmus, 2009, In: Molecular Biology and Evolution. 26, 12, p. 2755-64 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
Balancing Selection Maintains a Form of ERAP2 that Undergoes Nonsense-Mediated Decay and Affects Antigen Presentation
Andrés, A. M., Dennis, M. Y., Kretzschmar, W. W., Cannons, J. L., Lee-Lin, S., Hurle, B., Schwartzberg, P. L., Williamson, S. H., Bustamante, C. D., Nielsen, Rasmus, Clark, A. G. & Green, E. D., 2010, In: PLOS Genetics. 6, 10, 13 p., e1001157.Research output: Contribution to journal › Journal article › Research › peer-review
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The effect of ancient DNA damage on inferences of demographic histories
Axelsson, E., Willerslev, Eske, Gilbert, M Thomas P & Nielsen, Rasmus, 2008, In: Molecular Biology and Evolution. 25, 10, p. 2181-7 6 p.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
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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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Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations
Barrie, W., Yang, Y., Irving-Pease, E. K., Attfield, K. E., Scorrano, G., Jensen, L. T., Armen, A. P., Dimopoulos, E. A., Stern, A., Refoyo-Martinez, A., Pearson, A., Ramsøe, A., Gaunitz, C., Demeter, F., Jørkov, M. L. S., Møller, S. B., Springborg, B., Klassen, L., Hyldgård, I. M., Wickmann, N. & 11 others, , 2024, In: Nature. 625, 7994, p. 321-328Research 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
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
Unlocking the vault: next-generation museum population genomics
Bi, K., Linderoth, T., Vanderpool, D., Good, J. M., Nielsen, Rasmus & Moritz, C., 2013, In: Molecular Ecology. 22, 24, p. 6018-6032 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.
Binladen, J., Gilbert, M Thomas P, Bollback, J. P., Panitz, F., Bendixen, C., Nielsen, Rasmus & Willerslev, Eske, 2007, In: PLoS ONE. 2, 2, p. e197Research output: Contribution to journal › Journal article › 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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Estimation of 2N(e)s from temporal allele frequency data
Bollback, J. P., York, T. L. & Nielsen, Rasmus, 2008, In: Genetics. 179, p. 497-502 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Assessing the evolutionary impact of amino acid mutations in the human genome
Boyko, A. R., Williamson, S. H., Indap, A. R., Degenhardt, J. D., Hernandez, R. D., Lohmueller, K. E., Adams, M. D., Schmidt, S., Sninsky, J. J., Sunyaev, S. R., White, T. J., Nielsen, Rasmus, Clark, A. G. & Bustamante, C. D., 2008, In: PLoS Genetics. 4, 5, p. e1000083Research output: Contribution to journal › Journal article › Research › peer-review
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The evolution of gene expression levels in mammalian organs
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csardi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., Albert, F. W., Zeller, U., Khaitovich, P., Gruetzner, F., Bergmann, S., Nielsen, Rasmus, Paeaebo, S. & Kaessmann, H., 20 Oct 2011, In: Nature. 478, 7369, p. 343-348 6 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
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An increase in [Ca2+]i activates basolateral chloride channels and inhibits apical sodium channels in frog skin epithelium
Larsen, Birger Brodin, Rytved, K. A. & Nielsen, Rasmus, 1996, In: Pflügers Archiv - European Journal of Physiology. 433, 1-2, p. 16-25 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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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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
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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Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep
Chen, Z., Xu, Y., Xie, X., Wang, D., Aguilar-Gómez, D., Liu, G., Li, X., Esmailizadeh, A., Rezaei, V., Kantanen, J., Ammosov, I., Nosrati, M., Periasamy, K., Coltman, D. W., Lenstra, J. A., Nielsen, Rasmus & Li, M., 2021, In: Communications Biology . 4, 15 p., 1307.Research output: Contribution to journal › Journal article › Research › peer-review
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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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Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components
Cheng, J. Y., Stern, A. J., Racimo, Fernando & Nielsen, Rasmus, 2022, In: Molecular Biology and Evolution. 39, 1, 14 p., msab294.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
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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Evolution of genes and genomes on the Drosophila phylogeny. Drosophila 12 Genomes Consortium
Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., Iyer, V. N., Pollard, D. A., Sackton, T. B., Larracuente, A. M., Singh, N. D., Abad, J. P., Abt, D. N., Adryan, B., Aguade, M., Akashi, H., Anderson, W. W. & 31 others, , 2007, In: Nature. 450, 7167, p. 203-18 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Ascertainment bias in studies of human genome-wide polymorphism
Clark, A. G., Hubisz, M. J., Bustamente, C. D., Williamson, S. H. & Nielsen, Rasmus, 2005, In: Genome Research. 15, 11, p. 1496-1502Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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
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
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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
Detecting adaptive trait loci in nonmodel systems: divergence or admixture mapping?
Crawford, J. E. & Nielsen, Rasmus, 2013, In: Molecular Ecology. 22, 24, p. 6131-6148 18 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
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
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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
The distribution of waiting distances in ancestral recombination graphs
Deng, Y., Song, Y. S. & Nielsen, Rasmus, 2021, In: Theoretical Population Biology. 141, p. 34-43 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Detecting coevolving amino acid sites using Bayesian mutational mapping
Dimmic, M. W., Hubisz, M. J., Bustamente, C. D. & Nielsen, Rasmus, 2005, In: Bioinformatics. 21, 1, p. i126-i135Research output: Contribution to journal › Journal article › Research › peer-review
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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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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
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
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
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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
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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
Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution
Fumagalli, M., Sironi, M., Pozzoli, U., Ferrer-Admettla, A., Pattini, L. & Nielsen, Rasmus, 1 Nov 2011, In: P L o S Genetics. 7, 11Research output: Contribution to journal › Journal article › Research › peer-review
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Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation
Vieira, Filipe Garrett, Fumagalli, M., Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: Genome Research. 23, p. 1852-1861 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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Evolutionary and biomedical insights from the rhesus macaque genome
Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., Batzer, M. A., Bustamante, C. D., Eichler, E. E., Hahn, M. W., Hardison, R. C., Makova, K. D., Miller, W., Milosavljevic, A., Palermo, R. E., Siepel, A. & 31 others, , 2007, In: Science. 316, 5822, p. 222-34 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
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The population genomic legacy of the second plague pandemic
Gopalakrishnan, S., Ebenesersdóttir, S. S., Lundstrøm, I. K. C., Turner-Walker, G., Moore, K. H. S., Luisi, P., Margaryan, A., Martin, M. D., Ellegaard, M. R., Magnússon, Ó., Sigurðsson, Á., Snorradóttir, S., Magnúsdóttir, D. N., Laffoon, J. E., van Dorp, L., Liu, X., Moltke, I., Ávila-Arcos, M. C., Schraiber, J. G., Rasmussen, S. & 40 others, , 2022, In: Current Biology. 32, 21, p. 4743-4751.e6Research 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
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, , 2010, In: Science. 328, 5979, p. 710-722 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Covariance of pairwise differences on a multi-species coalescent tree and implications for FST
Guerra, G. & Nielsen, Rasmus, 2022, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 377, 1852, 14 p., 20200415.Research output: Contribution to journal › Journal article › Research › peer-review
Association mapping for compound heterozygous traits using phenotypic distance and integer programming
Gusfield, D. & Nielsen, Rasmus, 1 Jan 2015, Algorithms in Bioinformatics - 15th International Workshop, WABI 2015, Proceedings. Pop, M. & Touzet, H. (eds.). Springer Verlag, p. 136-147 12 p. A1. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 9289).Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
Ancient DNA reveals late survival of mammoth and horse in interior Alaska
Haile, James Seymour, Froese, D. G., Macphee, R. D. E., Roberts, R. G., Arnold, L. J., Reyes, A. V., Rasmussen, M., Nielsen, Rasmus, Brook, B. W., Robinson, S., Demuro, M., Gilbert, M Thomas P, Munch, K., Austin, J. J., Cooper, A., Barnes, I., Möller, P. & Willerslev, Eske, 2009, In: Proceedings of the National Academy of Science of the United States of America. 106, 52, p. 22352-7 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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
- 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
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
Error-prone polymerase activity causes multinucleotide mutations in humans
Harris, K. & Nielsen, Rasmus, 1 Sep 2014, In: Genome Research. 24, 9, p. 1445-1454 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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
- 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
Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques
Hernandez, R. D., Hubisz, M. J., Wheeler, D. A., Smith, D. G., Ferguson, B., Rogers, J., Nazareth, L., Indap, A., Bourquin, T., McPherson, J., Muzny, D., Gibbs, R., Nielsen, Rasmus & Bustamante, C. D., 2007, In: Science. 316, 5822, p. 240-3 3 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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
- Published
CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato
Hobolth, A., Nielsen, Rasmus, Wang, Y., Wu, F. & Tanksley, S. D., 2006, In: Molecular Biology and Evolution. 23, 6, p. 1318-1323Research 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
Effect of nonindependent substitution on phylogenetic accuracy
Huelsenbeck, J. P. & Nielsen, Rasmus, 1999, In: Systematic Biology. 48, 2, p. 317-328 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
Variation in the pattern of nucleotide substitution across sites
Huelsenbeck, J. P. & Nielsen, Rasmus, 1999, In: Journal of Molecular Evolution. 48, 1, p. 86-93 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 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, , 2014, In: Nature. 512, 7513, p. 194-197 4 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
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
SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing
Hui, S. & Nielsen, Rasmus, 2022, In: Bioinformatics. 38, 7, p. 1801-1808 8 p.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
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
- Published
The Selection Landscape and Genetic Legacy of Ancient Eurasians
Irving-Pease, E., Refoyo Martínez, A., Ingason, A., Pearson, A., Fischer, A., Barrie, W., Sjögren, K-G., Halgren, A. S., Macleod, R., Demeter, F., Henriksen, R. H. A., Vimala, T., McColl, H., Vaughn, A., Stern, A. J., Speidel, L., Scorrano, G., Ramsøe, A., Schork, A. J., Rosengren, A. & 12 others, , 2022, bioRxiv, 26 p.Research output: Working paper › Preprint › Research
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
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
- Published
Ancient bacteria show evidence of DNA repair.
Johnson, S. S., Hebsgaard, M. B., Christensen, T. R., Mastepanov, M., Nielsen, Rasmus, Munch, K., Brand, T., Gilbert, M Thomas P, Zuber, M. T., Bunce, M., Rønn, Regin, Gilichinsky, D., Froese, D. & Willerslev, Eske, 2007, In: Proceedings of the National Academy of Science of the United States of America. 104, 36, p. 14401-5 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 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, , 2015, In: Genome Research. 25, 4, p. 459-466 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)
Key, F. M., Peter, B., Dennis, M. Y., Huerta-Sánchez, E., Tang, W., Prokunina-Olsson, L., Nielsen, Rasmus & Andrés, A. M., 2014, In: PLOS Genetics. 10, 10, 12 p., e1004681.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimation of allele frequency and association mapping using next-generation sequencing data
Kim, S. Y., Lohmueller, K. E., Albrechtsen, Anders, Li, Y., Korneliussen, Thorfinn Sand, Tian, G., Grarup, Niels, Jiang, T., Andersen, G., Witte, D., Jorgensen, T., Hansen, Torben, Pedersen, Oluf Borbye, Wang, J. & Nielsen, Rasmus, 2011, In: B M C Bioinformatics. 12, p. 231 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Design of association studies with pooled or un-pooled next-generation sequencing data
Kim, S. Y., Li, Y., Guo, Y., Li, R., Holmkvist, J., Hansen, Torben, Pedersen, Oluf Borbye, Wang, J. & Nielsen, Rasmus, 2010, In: Genetic Epidemiology. 34, 5, p. 479-491 13 p.Research output: Contribution to journal › Journal article › 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
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
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
- Published
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data
Korneliussen, Thorfinn Sand, Moltke, Ida, Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: B M C Bioinformatics. 14, 14 p., 289.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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
- Published
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
- Published
The genetic architecture of sporadic and multiple consecutive miscarriage
Laisk, T., Soares, A. L. G., Ferreira, T., Painter, J. N., Censin, J. C., Laber, S., Bacelis, J., Chen, C. Y., Lepamets, M., Lin, K., Liu, S., Millwood, I. Y., Ramu, A., Southcombe, J., Andersen, M. S., Yang, L., Becker, C. M., Børglum, A. D., Gordon, S. D., Bybjerg-Grauholm, J. & 35 others, , 2020, In: Nature Communications. 11, 5980.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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
Evidence for Positive Selection on a Number of MicroRNA Regulatory Interactions during Recent Human Evolution
Li, J., Liu, Y., Xin, X., Kim, T. S., Cabeza, E. A., Ren, J., Nielsen, Rasmus, Wrana, J. L. & Zhang, Z., 1 Mar 2012, In: P L o S Genetics (Online). 8, 3Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., Zhang, Z., Zhang, Y., Wang, W., Li, J., Wei, F., Li, H., Jian, M., Li, J., Zhang, Z., Nielsen, R. & 103 others, , 2010, In: Nature. 463, 7279, p. 311-317 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population
Li, S., Besenbacher, S., Li, Y., Kristiansen, Karsten, Grarup, Niels, Albrechtsen, Anders, Sparsø, T. H., Korneliussen, Thorfinn Sand, Hansen, Torben, Wang, J., Nielsen, Rasmus, Pedersen, Oluf Borbye, Bolund, L. & Schierup, M. H., 2014, In: European Journal of Human Genetics. 22, p. 1040-1045 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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
- 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
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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