Detecting Positively Selected Amino Acid Sites Using Posterior Predictive P-Values. - Rasmus Nielsen; John P. Huelsenbeck (Pacific Symposium on Biocomputing, 2002)

PATRI-paternity inference using genetic data. - J. Signorovitch; Rasmus Nielsen (Bioinform., 2002)

Bayesian Estimation of the Number of Inversions in the History of Two Chromosomes. - Thomas L. York; Richard Durrett; Rasmus Nielsen (J. Comput. Biol., 2002)

Detecting coevolving amino acid sites using Bayesian mutational mapping. - Matthew W. Dimmic; Melissa J. Hubisz; Carlos D. Bustamante; Rasmus Nielsen (ISMB (Supplement of Bioinformatics), 2005)

Identification of physicochemical selective pressure on protein encoding nucleotide sequences. - Wendy S. W. Wong; Raazesh Sainudiin; Rasmus Nielsen (BMC Bioinform., 2006)

Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models. - Wendy S. W. Wong; Rasmus Nielsen (Bioinform., 2007)

Dependence of paracentric inversion rate on tract length. - Thomas L. York; Richard Durrett; Rasmus Nielsen (BMC Bioinform., 2007)

Estimation of allele frequency and association mapping using next-generation sequencing data. - Su Yeon Kim; Kirk E. Lohmueller; Anders Albrechtsen; Yingrui Li; Thorfinn Korneliussen; Geng Tian; Niels Grarup; Tao Jiang; Gitte Andersen; Daniel Witte; Torben Jørgensen; Torben Hansen; et al. (BMC Bioinform., 2011)

Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. - Thorfinn Sand Korneliussen; Ida Moltke; Anders Albrechtsen; Rasmus Nielsen (BMC Bioinform., 2013)

ngsTools: methods for population genetics analyses from next-generation sequencing data. - Matteo Fumagalli 002; Filipe G. Vieira; Tyler Linderoth; Rasmus Nielsen (Bioinform., 2014)

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). - Anna-Sapfo Malaspinas; Ole Tange; José Víctor Moreno-Mayar; Morten Rasmussen; Michael Degiorgio; Yong Wang; Cristina E. Valdiosera; Gustavo Politis; Eske Willerslev; Rasmus Nielsen (Bioinform., 2014)

ANGSD: Analysis of Next Generation Sequencing Data. - Thorfinn Korneliussen; Anders Albrechtsen; Rasmus Nielsen (BMC Bioinform., 2014)

Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming. - Dan Gusfield; Rasmus Nielsen (WABI, 2015)

Workshop message: IoT-SoS 2016. - Elias Z. Tragos; Rasmus Nielsen; Adam Kapovits; Claudio Cicconetti; Enzo Mingozzi; Jaudelice Cavalcante de Oliveira; Xiaohua Jia; Stefano Iellamo; Vangelis Angelakis (WoWMoM, 2016)

SweepFinder2: increased sensitivity, robustness and flexibility. - Michael Degiorgio; Christian D. Huber; Melissa J. Hubisz; Ines Hellmann; Rasmus Nielsen (Bioinform., 2016)

Estimating IBD tracts from low coverage NGS data. - Filipe G. Vieira; Anders Albrechtsen; Rasmus Nielsen (Bioinform., 2016)

A genomic history of Aboriginal Australia. - Anna-Sapfo Malaspinas; Michael C. Westaway; Craig Muller; Vitor C. Sousa; Oscar Lao; Isabel Alves; Anders Bergström; Georgios Athanasiadis; Jade Yu Cheng; Jacob E. Crawford; Tim H. Heupink; Enrico Macholdt; et al. (Nat., 2016)

Fast admixture analysis and population tree estimation for SNP and NGS data. - Jade Yu Cheng; Thomas Mailund; Rasmus Nielsen (Bioinform., 2017)

A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data. - José Víctor Moreno-Mayar; Thorfinn Sand Korneliussen; Jyoti Dalal; Gabriel Renaud; Anders Albrechtsen; Rasmus Nielsen; Anna-Sapfo Malaspinas (Bioinform., 2020)

Inferring the ancestry of parents and grandparents from genetic data. - Jingwen Pei; Yiming Zhang 007; Rasmus Nielsen; Yufeng Wu (PLoS Comput. Biol., 2020)

SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing. - Sandra Hui; Rasmus Nielsen (Bioinform., 2022)

AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees. - Lenore Pipes; Rasmus Nielsen (Bioinform., 2022)

SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances. - Sandra Hui; Rasmus Nielsen (BMC Bioinform., 2022)