Rasmus Nielsen
Professor
Section for Geogenetics
Øster Voldgade 5-7, 1350 København K
Section for Geogenetics
Øster Voldgade 5-7
1350 København K
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
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
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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
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
Sequencing of 50 human exomes reveals adaptation to high altitude
Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X. P., Pool, J. E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T. S., Zheng, H., Liu, T., He, W., Li, K., Luo, R., Nie, X., Wu, H., Zhao, M., Cao, H., Zou, J. & 50 others, , 2 Jul 2010, In: Science. 329, 5987, p. 75-8 4 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
- Published
Simultaneous inference of selection and population growth from patterns of variation in the human genome
Williamson, S. H., Hernandez, R., Fledel-Alon, A., Zhu, L., Nielsen, Rasmus & Bustamente, C. D., 2005, In: Proceedings of the National Academy of Science of the United States of America. 102, 22, p. 7882-7887Research output: Contribution to journal › Journal article › Research › peer-review
- 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
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
- 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, , 2011, In: Nature. 479, 7373, p. 359-364 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Statistical Approaches for DNA Barcoding
Nielsen, Rasmus & Matz, M., 2006, In: Systematic Biology. 55, 1, p. 162-169Research output: Contribution to journal › Journal article › Research › peer-review
- 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
- Published
Statistical assignment of DNA sequences using Bayesian phylogenetics
Terkelsen, K. M., Boomsma, Wouter, Huelsenbeck, J. P., Willerslev, Eske & Nielsen, Rasmus, 2008, In: Systematic Biology. 57, 5, p. 750-757 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
Synonymous and nonsynonymous rate variation in nuclear genes of mammals
Yang, Z. & Nielsen, Rasmus, 23 Apr 1998, In: Journal of Molecular Evolution. 46, 4, p. 409-418 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Synonymous mutations and the molecular evolution of SARS-CoV-2 origins
Wang, H., Pipes, L. & Nielsen, Rasmus, 2021, In: Virus Evolution. 7, 1, 11 p., veaa098.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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
Taxon sampling and the accuracy of large phylogenies
Rannala, B., Huelsenbeck, J. P., Yang, Z. & Nielsen, Rasmus, 1 Jan 1998, In: Systematic Biology. 47, 4, p. 702-710 9 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
- Published
Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans
Moreno Mayar, J. Víctor, Potter, B. A., Vinner, Lasse, Steinrucken, M., Rasmussen, Simon, Terhorst, J., Kamm, J. A., Albrechtsen, Anders, Malaspinas, A., Sikora, Martin, Reuther, J. D., Irish, J. D., Malhi, R. S., Orlando, L. A. A., Song, Y. S., Nielsen, Rasmus, Meltzer, D. J. & Willerslev, Eske, 2018, In: Nature Genetics. 553, 7687, p. 203-207 5 p.Research output: Contribution to journal › Letter › Research › peer-review
The 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, , 2021, In: California Agriculture. 75, 1, p. 20-32 13 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
- Published
The Population Structure of African Cultivated Rice Oryza glaberrima (Steud.): Evidence for Elevated Levels of Linkage Disequilibrium Caused by Admixture with O. sativa and Ecological Adaptation
Semon, M., Nielsen, Rasmus, Jones, M. P. & McCouch, S. R., 2005, In: Genetics. 169, 3, p. 1639-1647Research 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
The Tibetan-Yi region is both a corridor and a barrier for human gene flow
Zhang, Z., Zhang, Y., Wang, Y., Zhao, Z., Yang, M., Zhang, L., Zhou, B., Xu, B., Zhang, H., Chen, T., Dai, W., Zhou, Y., Shi, S., Nielsen, Rasmus, Li, S. C. & Li, S., 2022, In: Cell Reports. 39, 4, 16 p., 110720.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The ancestry and affiliations of Kennewick Man
Rasmussen, M., Sikora, Martin, Albrechtsen, Anders, Korneliussen, Thorfinn Sand, Moreno Mayar, J. Víctor, Poznik, G. D., Zollikofer, C. P. E., Ponce de León, M. S., Allentoft, Morten Erik, Moltke, Ida, Jónsson, H., Valdiosera Morales, C. E., Malhi, R. S., Orlando, L. A. A., Bustamante, C. D., Stafford jr., T., Meltzer, D. J., Nielsen, Rasmus & Willerslev, Eske, 2015, In: Nature. 523, 7561, p. 455-458 4 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
The diploid genome sequence of an Asian individual
Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Zhang, J., Guo, Y., Feng, B., Li, H., Lu, Y., Fang, X., Liang, H., Du, Z., Li, D., Zhao, Y., Hu, Y. & 57 others, , 2008, In: Nature. 456, 7218, p. 60-65 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
The discovery of Single-Nucleotide Polymorphisms: and Inferences about Human Demographic History
Wakeley, J., Nielsen, Rasmus, Liu-Cordero, S. N. & Ardlie, K., 2001, In: American Journal of Human Genetics. 69, 6, p. 1332-1347 16 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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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
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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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The genetic architecture of phenotypic diversity in the Betta fish (Betta splendens)
Zhang, W., Wang, H., Brandt, D. Y. C., Hu, B., Sheng, J., Wang, M., Luo, H., Li, Y., Guo, S., Sheng, B., Zeng, Q., Peng, K., Zhao, D., Jian, S., Wu, D., Wang, J., Zhao, G., Ren, J., Shi, W., van Esch, J. H. M. & 3 others, , 2022, In: Science Advances. 8, 38, 13 p., eabm4955.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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
The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system
Stuckert, A. M. M., Chouteau, M., McClure, M., LaPolice, T. M., Linderoth, T., Nielsen, Rasmus, Summers, K. & MacManes, M. D., 2021, In: Molecular Ecology. 30, 16, p. 4039-4061 23 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans
Zhang, X., Witt, K. E., Banuelos, M. M., Ko, A., Yuan, K., Xu, S., Nielsen, Rasmus & Huerta-Sanchez, E., 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 22, 9 p., 2020803118.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The impact of founder events on chromosomal variability in multiply mating species
Pool, J. E. & Nielsen, Rasmus, 2008, In: Molecular Biology and Evolution. 25, 8, p. 1728-36 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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
The mind, the lab, and the field: Three kinds of populations in scientific practice
Winther, Rasmus, Giordano, R., Edge, M. D. & Nielsen, Rasmus, 1 Aug 2015, In: Studies in History and Philosophy of Science Part C :Studies in History and Philosophy of Biological and Biomedical Sciences. 52, p. 12-21 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
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
- Published
The origin and evolution of maize in the Southwestern United States: [+ erratum]
Rodrigues da Fonseca, Rute Andreia, Smith, B. D., Wales, N., Cappellini, Enrico, Skoglund, P., Fumagalli, M., Samaniego Castruita, J. A., Carøe, C., Avila Arcos, M. D. C., Hufnagel, D. E., Korneliussen, Thorfinn Sand, Vieira, Filipe Garrett, Jakobsson, M., Arriaza, B., Willerslev, Eske, Nielsen, Rasmus, Hufford, M. B., Albrechtsen, Anders, Ross-Ibarra, J. & Gilbert, M Thomas P, 2015, In: Nature Plants. 1, 5 p., 14003.Research output: Contribution to journal › Letter › Research › peer-review
- Published
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
- Published
The population history of northeastern Siberia since the Pleistocene
Sikora, M., Pitulko, V. V., Sousa, V. C., Allentoft, M. E., Vinner, L., Rasmussen, S., Margaryan, A., Damgaard, P. D. B., de la Fuente Castro, C., Renaud, G., Yang, M. A., Fu, Q., Dupanloup, I., Giampoudakis, K., Nogues, D. B., Rahbek, C., Kroonen, G., Peyrot, M., McColl, H., Vasilyev, S. V. & 27 others, , 2019, In: Nature. 570, p. 182–188Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The power of inbreeding: NGS-based GWAS of rice reveals convergent evolution during rice domestication
Wang, H., Xu, X., Vieira, Filipe Garrett, Xiao, Y., Li, Z., Wang, J., Nielsen, Rasmus & Chu, C., 6 Jul 2016, In: Molecular Plant. 9, 7, p. 975-985 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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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
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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
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Tracing the peopling of the world through genomics
Nielsen, Rasmus, Akey, J. M., Jakobsson, M., Pritchard, J. K., Tishkoff, S. & Willerslev, Eske, 19 Jan 2017, In: Nature. 541, 7637, p. 302-310 9 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
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, , 2014, In: Current biology : CB. 24, 21, p. R1035-R1037 3 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 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
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
ID: 3311
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Natural selection affects multiple aspects of genetic variation at putatively peutral sites across the human genome
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Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets
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SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data
Research output: Contribution to journal › Journal article › Research › peer-review
Published