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
- Published
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
- Published
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
- Published
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
- 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, , 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
- 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
- Published
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
- Published
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
- Published
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
- 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
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
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
- Published
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
- 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-i135Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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
- Published
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
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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