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Genetics|July 23, 2003
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sitesMaria Anisimova, Rasmus Nielsen, Ziheng YangGenetics|July 9, 2004
Detecting selection in noncoding regions of nucleotide sequencesWendy S W Wong, Rasmus NielsenPlos One|March 16, 2016
REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence ReadsChong Chu, Rasmus Nielsen, Yufeng WuJournal of Molecular Evolution|September 12, 2007
Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virusWeiwei Zhai, Montgomery Slatkin, Rasmus NielsenBMC Bioinformatics|November 26, 2014
ANGSD: Analysis of Next Generation Sequencing DataThorfinn Sand Korneliussen, Anders Albrechtsen, Rasmus NielsenBioinformatics (Oxford, England)|May 7, 2016
Estimating IBD tracts from low coverage NGS dataFilipe G Vieira, Anders Albrechtsen, Rasmus NielsenGenetics|December 16, 2024
A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifactYun Deng, Rasmus Nielsen, Yun S SongBioinformatics (Oxford, England)|March 24, 2017
Fast admixture analysis and population tree estimation for SNP and NGS dataJade Yu Cheng, Thomas Mailund, Rasmus NielsenNature Genetics|September 8, 2025
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomesYun Deng, Rasmus Nielsen, Yun S SongNature Reviews. Genetics|September 30, 2024
Inference and applications of ancestral recombination graphsRasmus Nielsen, Andrew H Vaughn, Yun DengPageof 34