Rasmus Nielsen

Rasmus Nielsen

Professor

ORCID: 0000-0003-0513-6591

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  1. Classic Selective Sweeps Revealed by Massive Sequencing in Cattle

    Qanbari, S., Pausch, H., Jansen, S., Somel, M., Strom, T. M., Fries, R., Nielsen, Rasmus & Simianer, H., 2014, In: PLOS Genetics. 10, 2, 13 p., e1004148.

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

  2. Published

    Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

    Richards, S., Liu, Y., Bettencourt, B. R., Hradecky, P., Letovsky, S., Nielsen, Rasmus & et al., 2005, In: Genome Research. 15, 1, p. 1-18

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

  3. Published

    Comparative genomics: Difference of expression

    Nielsen, Rasmus, 2006, In: Nature. 440, 7081, p. 161-161

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

  4. Published

    Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)

    Xia, Q., Guo, Y., Zhang, Z., Li, D., Xuan, Z., Li, Z., Dai, F., Li, Y., Cheng, D., Li, R., Cheng, T., Jiang, T., Becquet, C., Xu, X., Liu, C., Zha, X., Fan, W., Lin, Y., Shen, Y., Jiang, L. & 38 others, Jensen, J., Hellmann, I., Tang, S., Zhao, P., Xu, H., Yu, C., Zhang, G., Li, J., Cao, J., Liu, S., He, N., Zhou, Y., Liu, H., Zhao, J., Ye, C., Du, Z., Pan, G., Zhao, A., Shao, H., Zeng, W., Wu, P., Li, C., Pan, M., Li, J., Yin, X., Li, D., Wang, J., Zheng, H., Wang, W., Zhang, X., Li, S., Yang, H., Lu, C., Nielsen, Rasmus, Zhou, Z., Wang, J., Xiang, Z. & Wang, J., 2009, In: Science. 326, 5951, p. 433-6 3 p.

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

  5. 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

  6. Published

    Convergent evolution of increased urine-concentrating ability in desert mammals

    Rocha, J. L., Brito, J. C., Nielsen, Rasmus & Godinho, R., 2021, In: Mammal Review. 51, 4, p. 482-491 10 p.

    Research output: Contribution to journal › Review › Research › peer-review

  7. Published

    Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process

    Ramírez-Soriano, A. & Nielsen, Rasmus, 2009, In: Genetics. 181, 2, p. 701-10 9 p.

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

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

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

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

  9. Costs and benefits of mutational robustness in RNA viruses

    Stern, A., Bianco, S., Yeh, M. T., Wright, C., Butcher, K., Tang, C., Nielsen, Rasmus & Andino, R., 2014, In: Cell Reports. 8, 4, p. 1026-1036 11 p.

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

  10. Published

    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

  11. 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. 1318-1323

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

  12. Published

    Darwinian and demographic forces affecting human protein coding genes.

    Nielsen, Rasmus, Hubisz, M. J., Hellmann, I., Torgerson, D., Andres, A. M., Albrechtsen, Anders, Gutenkunst, R., Adams, M. D., Cargill, M., Boyko, A., Indap, A., Bustamante, C. D. & Clark, A. G., 2009, In: Genome Research. 19, 5, p. 838-49 12 p.

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

  13. 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

  14. Published

    Dependence of paracentric inversion rate on tract length

    York, T. L., Durrett, R. & Nielsen, Rasmus, 2007, In: BMC Bioinformatics. 8, p. 115

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

  15. 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

  16. Published

    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

  17. Published

    Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System

    Sainudiin, R., Wong, W. S. W., Yogeeswaran, K., Nasrallah, J. B., Yang, Z. & Nielsen, Rasmus, 2005, In: Journal of Molecular Evolution. 60, 3, p. 315-326

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

  18. 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

  19. Published

    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-i135

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

  20. 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

  21. Published

    Detecting selection needs comparative data

    Nielsen, Rasmus & Hubisz, M. J., 2005, In: Nature. 433, 7023, p. E6

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

  22. Published

    Disclosure of variation

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

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

  23. Disentangling selection on genetically correlated polygenic traits via whole-genome genealogies

    Stern, A. J., Speidel, L., Zaitlen, N. A. & Nielsen, Rasmus, 2021, In: American Journal of Human Genetics. 108, 2, p. 219-239 21 p.

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

  24. Published

    DistAngsd: Fast and Accurate Inference of Genetic Distances for Next-Generation Sequencing Data

    Zhao, Lei, Nielsen, Rasmus & Korneliussen, Thorfinn Sand, 2022, In: Molecular Biology and Evolution. 39, 6, 14 p., msac119.

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

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

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

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

  26. Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation

    Peter, B. M., Huerta-Sanchez, E. & Nielsen, Rasmus, 2012, In: P L o S Genetics (Online). 8, 10, p. 1-14 14 p., e1003011.

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

  27. Published

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

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

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

  28. Published

    Early human dispersals within the Americas

    Moreno-Mayar, J. V., Vinner, L., de Barros Damgaard, P., de la Fuente, C., Allentoft, M. E., Vimala, T., Racimo, F., Rasmussen, S., Margaryan, A., Iraeta Orbegozo, M., Mylopotamitaki, D., Alexandersen, V., Primeau, C., Gregersen, K., Hansen, K. L., Lynnerup, N., Kjær, K., Schroeder, H., Malaspinas, A. S., Sikora, M. & 2 others, Nielsen, Rasmus & Willerslev, Eske, 7 Dec 2018, In: Science (New York, N.Y.). 362, 6419, p. 1, 1-11 12 p., eaav2621.

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

  29. 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

  30. Published

    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, Vinner, Lasse, Korneliussen, Thorfinn Sand, Allentoft, Morten Erik, Sikora, Martin, Kristiansen, Kristian, Rodriguez, S., Nielsen, Rasmus, Iversen, A. K. N., Lawson, D. J., Fugger, Lars & Willerslev, Eske, 2024, In: Nature. 625, 7994, p. 321-328

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

  31. Published

    Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

    Rascovan, N., Sjogren, K., Kristiansen, K., Nielsen, Rasmus, Willerslev, Eske, Desnues, C. & Rasmussen, Simon, 2019, In: Cell. 176, 1-2, p. 295-305.e10

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

  32. 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

  33. Published

    Estimating IBD tracts from low coverage NGS data

    Vieira, Filipe Garrett, Albrechtsen, Anders & Nielsen, Rasmus, 2016, In: Bioinformatics. 32, 14, p. 2096-2102 7 p.

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

  34. Published

    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

  35. Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias

    Wang, Y. & Nielsen, Rasmus, 2012, In: Molecular Ecology. 21, 4, p. 974-986 13 p.

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

  36. Published

    Estimating the relative proportions of SARS-CoV-2 haplotypes from wastewater samples

    Pipes, L., Chen, Z., Afanaseva, S. & Nielsen, Rasmus, 2022, In: Cell Reports Methods. 2, 10, 100313.

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

  37. Published

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

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

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

  38. Published

    Estimating the timing of multiple admixture pulses during local ancestry inference

    Medina, P., Thornlow, B., Nielsen, Rasmus & Corbett-Detig, R., 2018, In: Genetics. 210, 3, p. 1089-1107 19 p.

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

  39. Published

    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

  40. 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

  41. Published

    Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level

    Zhang, J., Nielsen, Rasmus & Yang, Z., 2005, In: Molecular Biology and Evolution. 22, 12, p. 2472-2479

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

  42. Published

    Evaluation of methods for estimating coalescence times using ancestral recombination graphs

    Y C Brandt, D., Wei, X., Deng, Y., Vaughn, A. H. & Nielsen, Rasmus, 2022, In: Genetics. 221, 1, 13 p., iyac044.

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

  43. 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, 3

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

  44. Published

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

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

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

  45. Evidence for archaic adaptive introgression in humans

    Racimo, Fernando, Sankararaman, S., Nielsen, Rasmus & Huerta-Sánchez, E., 18 May 2015, In: Nature Reviews Genetics. 16, 6, p. 359-371 13 p.

    Research output: Contribution to journal › Review › Research › peer-review

  46. 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

  47. Published

    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, Aquadro, C. F., Ardell, D. H., Arguello, R., Artieri, C. G., Barbash, D. A., Barker, D., Barsanti, P., Batterham, P., Batzoglou, S., Begun, D., Bhutkar, A., Blanco, E., Bosak, S. A., Bradley, R. K., Brand, A. D., Brent, M. R., Brooks, A. N., Brown, R. H., Butlin, R. K., Caggese, C., Calvi, B. R., Bernardo de Carvalho, A., Caspi, A., Castrezana, S., Celniker, S. E., Chang, J. L., Garcia, A. C. L., Nielsen, Rasmus, Pedersen, Jakob Skou, Vieira, Filipe Garrett & Drosophila 12 Genomes Consortium, D. 1. G. C., 2007, In: Nature. 450, 7167, p. 203-18 15 p.

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

  48. Published

    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, Sikela, J. M., Attaway, T., Bell, S., Bernard, K. E., Buhay, C. J., Chandrabose, M. N., Dao, M., Davis, C., Delehaunty, K. D., Ding, Y., Dinh, H. H., Dugan-Rocha, S., Fulton, L. A., Gabisi, R. A., Garner, T. T., Godfrey, J., Hawes, A. C., Hernandez, J., Hines, S., Holder, M., Hume, J., Jhangiani, S. N., Joshi, V., Khan, Z. M., Kirkness, E. F., Cree, A., Fowler, R. G., Lee, S., Lewis, L. R., Nielsen, Rasmus & Rhesus Macaque Genome Sequencing and Analysis Consortium, R. M. G. S. A. A. C., 2007, In: Science. 316, 5822, p. 222-34 12 p.

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

  49. Published

    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, Bennett, A. J., Bolund, L., Charpentier, G., Chen, Y., Dekker, J. M., Doney, A. S. F., Dorkhan, M., Forsen, T., Frayling, T. M., Groves, C. J., Gui, Y., Hallmans, G., Hattersley, A. T., He, K., Hitman, G. A., Holmkvist, J., Huang, S., Jiang, H., Jin, X., Justesen, Johanne Marie, Kristiansen, Karsten, Kuusisto, J., Lajer, M., Lantieri, O., Li, W., Liang, H., Liao, Q., Liu, X., Ma, T., Ma, X., Manijak, M. P., Marre, M., Mokrosinski, J., Morris, A. D., Mu, B., Nielsen, A. A., Nijpels, G., Nilsson, P., Palmer, C. N. A., Rayner, N. W., Renström, F., Ribel-Madsen, R., Robertson, N., Rolandsson, O., Rossing, P., Schwartz, Thue W., Slagboom, P. E., Sterner, M., Tang, M., Tarnow, L., Tuomi, T., Van't Riet, E., van Leeuwen, N., V Varga, Tibor, Vestmar, M. A., Walker, M., Wang, B., Wang, Y., Wu, H., Xi, F., Yengo, L., Yu, C., Zhang, X., Zhang, J., Zhang, Q., Zhang, W., Zheng, H., Zhou, Y., Altshuler, D., 't Hart, L. M., Franks, P. W., Balkau, B., Froguel, P., McCarthy, M. I., Laakso, M., Groop, L., Christensen, C., Brandslund, I., Lauritzen, T., Witte, D. R., Linneberg, A., Jørgensen, T., Hansen, Torben, Wang, J., Nielsen, Rasmus & Pedersen, Oluf Borbye, 2013, In: Diabetologia. 56, 2, p. 298-310 13 p.

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

  50. Published

    Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virus

    Zhai, W., Slatkin, M. & Nielsen, Rasmus, 2007, In: Journal of Molecular Evolution. 65, 3, p. 340-8 8 p.

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

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