Genome-wide signatures of complex introgression and adaptive evolution in the big cats Figueiró, H., G. Li, F. Trindade, J. Assis, et. al. 2017. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Science Advances. 3(7): e1700299.

Q&A: Where did the Neanderthals go? Harris K., R. Nielsen. 2017. Q&A: Where did the Neanderthals go? BMC Biology. 15:73.

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice Wang, H., F.G. Vieira, J.E. Crawford, C. Chu, R. Nielsen. 2017. Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice. Genome Research.gr.204800.116

The Evolutionary Pathway to Virulence of an RNA Virus Stern, Adi, M.T. Yeh, T. Zinger, R. Nielsen, A. Macadam, R. Andino. 2017. The Evolutionary Pathway to Virulence of an RNA virus. Cell. 169:35-46.

Tracing the peopling of the world through genomics Nielsen, R., J.M. Akey, M. Jakobsson, J.K. Pritchard, S. Tishkoff, E. Willerslev. 2017. Tracing the peopling of the world through genomics. Nature. 541: 302-310.

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., R. Nielsen. 2017. A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy. PLoS Genet 13(1): e1006529.

Archaic adaptive introgression in TBX15/WARS2 Racimo, F., D. Gokhman, M. Fumagalli, A. Ko, et. al. 2016. Archaic adaptive introgression in TBX15/WARS2. Molecular Biology and Evolution. Molecular Biology and Evolution, Oxford University Press. doi: 10.1093/molbev/msw283.

Genomic analyses inform on migration events during the peopling of Eurasia Pagani, L., D.J. Lawson, E. Jagoda, et. al. 2016. Genomic analyses inform on migration events during the peopling of Eurasia. Nature 538: 238-242.

Fumio Tajima and the Origin of Modern Population Genetics Nielsen, R. 2016. Fumio Tajima and the Origin of Modern Population Genetics. Genetics 204: 389-390.

A genomic history of Aboriginal Australia Malaspinas, A.S., M.C. Westaway, C. Muller, V. Sousa, et. al. 2016. A genomic history of Aboriginal Australia. Nature 538: 207-214.

Postglacial viability and colonization in North America’s ice-free corridor Pedersen, M.W., A. Ruter, C. Schweger, H. Friebe, et al. 2016. Postglacial viability and colonization in North America’s ice-free corridor. Nature 537: 45-49.

The genetic cost of Neanderthal introgression Harris, K., R. Nielsen. 2016. The genetic cost of Neanderthal introgression. Genetics 203(2): 881-891.

The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication Wang, H., X. Xu, F.G. Vieira, Y. Xiao, Z. Li, J. Wang, R. Nielsen, and C. Chu. 2016. The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication. Molecular Plant 9(7): 975-985.

Estimating IBD tracts from low coverage NGS data
Vieira, F. G., A. Albrechtsen, and R. Nielsen. 2016. Estimating IBD tracts from low coverage NGS data. Bioinformatics doi: 10.1093/bioinformatics/btw212.

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads
Chu, C., R. Nielsen, and Y. Wu. 2016. REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads. PloS one http://dx.doi.org/10.1371/journal.pone.0150719.

Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae sl, and its impact on susceptibility to Plasmodium infection
Crawford, J. C., M. M. Riehle, K. Markianos, E. Bischoff, et al. 2016. Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae sl, and its impact on susceptibility to Plasmodium infection. Molecular ecology doi: 10.1111/mec.13572.

Detecting recent selective sweeps while controlling for mutation rate and background selection
Huber, C. D., M. Degiorgio, I. Hellmann and R. Nielsen. 2015. Detecting recent selective sweeps while controlling for mutation rate and background selection. Molecular Ecology 25: 142-156.

Fitting the Balding–Nichols model to forensic databases
Rohlfs, R. V., V. R.C. Aguiar, K. E. Lohmueller, A. M. Castro et al. 2015. Fitting the Balding-Nichols model to forensic databases. Forensic Science International: Genetics 19: 86-91.

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago
Rasmussen, S., M. E. Allentoft, K. Nielsen, L. Orlando et al. 2015. Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago. Cell 163: 571-582.

Reticulate Speciation and Barriers to Introgression in the Anopheles gambiae Species Complex
Crawford, J. E., M. M. Riehle, W. M. Guelbeogo, A. Gneme et al. 2015. Reticulate Speciation and Barriers to Introgression in the Anopheles gambiae Species Complex. Genome biology and evolution 7: 3116-3131.

Tracking the origins of Yakutian horses and the genetic basis for their adaptation to subarctic environments
Librado, P., C. D. Sarkissian, L. Ermini, M. Schubert et al. 2015. Tracking the origins of Yakutian horses and the genetic basis for their adaptation to subarctic environments. Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1513696112.

Greenlandic Inuit show genetic signatures of diet and climate adaptation
Fumagalli, M., I. Moltke, N. Grarup, F. Racimo et al. 2015. Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science: 349: 1343-1347.

Genomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan, M., M. Steinrücken, K. Harris, S. Schiffels et al. 2015. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science DOI: 10.1126/science.aab3884.

Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution
Rohlfs, R. V. and R. Nielsen. 2015. Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution. Systematic Biology 64: 695-708.

The ancestry and affiliations of Kennewick Man
Rasmussen, M., M. Sikora, A. Albrechtsen, T. S. Korneliussen et al. 2015. The ancestry and affiliations of Kennewick Man. Nature DOI:10.1038/nature14625.

Population genomics of Bronze Age Eurasia
Allentoft, M. E., M. Sikora, K. Sjögren, S. Rasmussen et al. 2015. Population genomics of Bronze Age Eurasia. Nature 522: 167-172.

De novo assembly of a haplotype-resolved human genome
Cao, H., H. Wu, R. Luo, S. Huang et al. 2015. De novo assembly of a haplotype-resolved human genome. Nature Biotechnology 33: 617-622.

Evidence for archaic adaptive introgression in humans
Racimo, F., S. Sankararaman, R. Nielsen, and E. Huerta-Sánchez. 2015. Evidence for archaic adaptive introgression in humans. Nature Reviews Genetics 16: 359-371.

Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator
Vestergaard, J. S., E. Twomey, R. Larsen, K. Summers, and R. Nielsen. 2015. Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator. Proceedings of the Royal Society of London B: Biological Sciences DOI: 10.1098/rspb.2014.1950.

Introduction: Genomics and philosophy of race
Winther, R. G., R. L. Millstein, and R. Nielsen. 2015. Introduction: Genomics and philosophy of race. Studies in History and Philosophy of Biological and Biomedical Sciences 52: 1-4.

A recent bottleneck of Y chromosome diversity coincides with a global change in culture
Karmin, M., L. Saag, M. Vicente, M. A. W. Sayres et al. 2015. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Research DOI: 10.1101/gr.186684.114.

The mind, the lab, and the field: Three kinds of populations in scientific practice
Winther, R. G., R. Giordano, M. D. Edge, and R. Nielsen. 2015. The mind, the lab, and the field: Three kinds of populations in scientific practice. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 52: 12-21.

A genome-wide scan for signatures of directional selection in domesticated pigs
Moon, S., T. Kim, K. Lee, W. Kwak et al. 2015. A genome-wide scan for signatures of directional selection in domesticated pigs. BMC Genomics DOI: 10.1186/s12864-015-1330-x.

Convergent evolution of the genomes of marine mammals
Foote, A. D., Y. Liu, G. W. C. Thomas, T. Vinař et al. 2015. Convergent evolution of the genomes of marine mammals. Nature genetics 47: 272-275.

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing
Ai, H., X. Fang, B. Yang, Z. Huang, H. Chen et al. 2015. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nature genetics 47: 217-225.

The origin and evolution of maize in the Southwestern United States
da Fonseca, R. R., B. D. Smith, N. Wales, E. Cappellini et al. 2015. The origin and evolution of maize in the Southwestern United States. Nature plants DOI:10.1038/nplants.2014.3.

Uncovering the Genetic History of the Present-Day Greenlandic Population
Moltke, I., M. Fumagalli, T. S. Korneliussen, J. E. Crawford et al. 2014. Uncovering the Genetic History of the Present-Day Greenlandic Population. The American Journal of Human Genetics 96: 54-69.

Prehistoric genomes reveal the genetic foundation and cost of horse domestication
Schubert, M., H. Jónsson, D. Chang, C. D. Sarkissian et al. 2014. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1416991111.

Speciation with gene flow in equids despite extensive chromosomal plasticity
Jónsson, H., M. Schubert, A. Seguin-Orlando, A. Ginolhac et al. 2014. Speciation with gene flow in equids despite extensive chromosomal plasticity. Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1412627111.

ANGSD: Analysis of Next Generation Sequencing Data
Korneliussen, T. S., A. Albrechtsen, and R. Nielsen. 2014. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics DOI:10.1186/s12859-014-0356-4.

Genomic structure in Europeans dating back at least 36,200 years
Seguin-Orlando, A., T. S. Korneliussen, M. Sikora, A. Malaspinas et al. 2014. Genomic structure in Europeans dating back at least 36,200 years. Science 346: 1113-1118.

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil
Malaspinas, A., O. Lao, H. Schroeder, M. Rasmussen et al. 2014. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Current Biology 24: R1035-R1037.

Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans
Moreno-Mayar, J. V., S. Rasmussen, A. Seguin-Orlando, M. Rasmussen et al. 2014. Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans. Current Biology 24: 2518-2525.

A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations
Clemente, F. J., A. Cardona, C. E. Inchley, B. M. Peter et al. 2014. A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations. The American Journal of Human Genetics 95: 584-589.

Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)
Key, F. M., B. Peter, M. Y. Dennis, E. Huerta-Sánchez et al. 2014. Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4). PLOS Genetics DOI: 10.1371/journal.pgen.1004681.

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA
Rebolledo-Jaramillo, B., M. S. Su, N. Stoler, J. A. McElhoe et al. 2014. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proceedings of the National Academy of Sciences 111: 15474-15479.

The genetic prehistory of the New World Arctic
Raghavan, M., M. DeGiorgio, A. Albrechtsen, I. Moltke et al. 2014. The genetic prehistory of the New World Arctic. Science DOI: 10.1126/science.1255832. {Link broken}

A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data
DeGiorgio, M., K. E. Lohmueller, and R. Nielsen. 2014. A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data. PLOS Genetics DOI: 10.1371/journal.pgen.1004561.

Costs and Benefits of Mutational Robustness in RNA Viruses
Stern, A., S. Bianco, M. T. Yeh, C. Wright et al. 2014. Costs and Benefits of Mutational Robustness in RNA Viruses. Cell reports 8: 1026-1036.

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA
Huerta-Sánchez, E., X. Jin, Asan, Z. Bianba et al. 2014. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512: 194-197.

Error-prone polymerase activity causes multinucleotide mutations in humans
Harris, K. and R. Nielsen. 2014. Error-prone polymerase activity causes multinucleotide mutations in humans. Genome Research DOI: 10.1101/gr.170696.113.

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)
Malaspinas, A., O. Tange, J. V. Moreno-Mayar, M. Rasmussen et al. 2014. bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). Bioinformatics 30: 2962-2964.

A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes
Moltke, I., N. Grarup, M. E. Jørgensen, P. Bjerregaard et al. 2014. A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes. Nature 512: 190-193.

Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population
Li, S., S. Besenbacher, Y. Li, K. Kristiansen et al. 2014. Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population. European Journal of Human Genetics 22: 1040-1045.

Unlocking the vault: next-generation museum population genomics
Bi, K., T. Linderoth, D. Vanderpool, J. M. Good et al. 2013. Unlocking the vault: next-generation museum population genomics. Molecular ecology DOI: 10.1111/mec.12516.

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
Vieira, F. G., M. Fumagalli, A. Albrechtsen, and R. Nielsen. 2013. Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Research 23: 1852-1861.

Quantifying population genetic differentiation from next-generation sequencing data
Fumagalli, M., F. G. Vieira, T. S. Korneliussen, T. Linderoth et al. 2013. Quantifying population genetic differentiation from next-generation sequencing data. Genetics 195: 979-992.

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data
Korneliussen, T. S., I. Moltke, A. Albrechtsen, and R. Nielsen. 2013. Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics 14: 289.

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing
Li, Y., S. Zhao, J. Ma, D. Li et al. 2013. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics 14: 579.

A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes Somel, M., M. A. W. Sayres, G. Jordan, E. Huerta-Sanchez et al. 2013. A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes. Molecular biology and evolution 30: 1808-1815.

Genetic signatures reveal high-altitude adaptation in a set of Ethiopian populations
Huerta-Sánchez, E., M. DeGiorgio, L. Pagani, A. Taretegn et al. 2013. Genetic signatures reveal high-altitude adaptation in a set of Ethiopian populations. Molecular biology and evolution 30: 1877-1888.

A model-based approach for identifying signatures of balancing selection in genetic data
DeGiorgio, M., K. E. Lohmueller, and R. Nielsen. 2013. A model-based approach for identifying signatures of balancing selection in genetic data. arXiv preprint arXiv:1307.4137.

The Lengths of Admixture Tracts
Liang, M. and R. Nielsen. 2014. The lengths of admixture tracts. Genetics 197: 953-967.

ngsTools: methods for population genetics analyses from next-generation sequencing data
Fumagalli, M., F. G. Vieira, T. Linderoth, and R. Nielsen. 2014. ngsTools: methods for population genetics analyses from next-generation sequencing data. Bioinformatics 30: 1486-1487.

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears
Liu, S., E. D. Lorenzen, M. Fumagalli, B. Li et al. 2014. Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears. Cell 157: 785-794.

On detecting incomplete soft or hard selective sweeps using haplotype structure
Ferrer-Admetlla, A., M. Liang, T. Korneliussen, and R. Nielsen. 2014. On detecting incomplete soft or hard selective sweeps using haplotype structure. Molecular biology and evolution 31: 1275-1291.

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
Olalde, I., M. E. Allentoft, F. Sánchez-Quinto, G. Santpere. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507: 225-228.

Classic selective sweeps revealed by massive sequencing in cattle
Qanbari, S., H. Pausch, S. Jansen, M. Somel et al. 2014. Classic selective sweeps revealed by massive sequencing in cattle. PLoS Genetics doi:10.1371/journal.pgen.1004148.

The genome of a Late Pleistocene human from a Clovis burial site in western Montana
Rasmussen, M., S. L. Anzick, M. R. Waters, P. Skoglund et al. 2014. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506: 225-229.

Natural selection reduced diversity on human Y chromosomes
Sayres, M. A. W., K. E. Lohmueller, and R. Nielsen. 2014. Natural selection reduced diversity on human Y chromosomes. PLoS Genetics doi:10.1371/journal.pgen.1004064.

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Raghavan, M. P. Skoglund, K. E. Graf, M. Metspalu et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505: 87-91.

Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex
Crawford, J. M. M. Riehle, W. M. Guelbeogo, A. Gneme et al. 2014. Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex. bioRxiv doi: http://dx.doi.org/10.1101/009837.

Understanding admixture fractions
Liang, M and R. Nielsen. 2014. Understanding admixture fractions. bioRxiv doi: http://dx.doi.org/10.1101/008078.

Identifying adaptive and plastic gene expression levels using a unified model for expression variance between and within species
Rohlfs, R. and R. Nielsen. 2014. Identifying adaptive and plastic gene expression levels using a unified model for expression variance between and within species. bioRxiv doi: http://dx.doi.org/10.1101/004374.

Modeling gene expression evolution with an extended Ornstein–Uhlenbeck process accounting for within-species variation
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Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes
Lohmueller, K. E., T. Sparsø, Q. Li, E. Andersson et al. 2013. Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes. The American Journal of Human Genetics 6: 1072-1086.

Detecting adaptive trait loci in nonmodel systems: divergence or admixture mapping?
Crawford, J. E. and R. Nielsen. 2013. Detecting adaptive trait loci in nonmodel systems: divergence or admixture mapping? Molecular ecology 22: 6131-6148.

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
Orlando, L. A. Ginolhac, G. Zhang, D. Froese et al. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499: 74-78.

Genetic Architecture of Vitamin B 12 and Folate Levels Uncovered Applying Deeply Sequenced Large Datasets
Grarup, N. P. Sulem, C. H. Sandbolt, G. Thorleifsson et al. 2013. Genetic Architecture of Vitamin B 12 and Folate Levels Uncovered Applying Deeply Sequenced Large Datasets. PLoS Genetics http://dx.doi.org/10.1371/journal.pgen.1003530.

Inferring demographic history from a spectrum of shared haplotype lengths
Harris, K. and R. Nielsen. 2013. Inferring demographic history from a spectrum of shared haplotype lengths. PLoS Genetics http://dx.doi.org/10.1371/journal.pgen.1003521.

Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes
Albrechtsen, A., N. Grarup, Y. Li, T. Sparsø et al. 2013. Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes. Diabetologia 56: 298-310.

Distinguishing between selective sweeps from standing variation and from a de novo mutation
Peter, B. M., E. Huerta-Sanchez and R. Nielsen. 2012. Distinguishing between selective sweeps from standing variation and from a de novo mutation. PLoS Genetics http://dx.doi.org/10.1371/journal.pgen.1003011.

A metagenome-wide association study of gut microbiota in type 2 diabetes
Qin, J., Y. Li, Z. Cai, S. Li et al. 2012. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490: 55-60.

Looking for Darwin in genomic sequences—validity and success of statistical methods
Zhai, W., R. Nielsen, N. Goldman and Z. Yang. 2012. Looking for Darwin in genomic sequences—validity and success of statistical methods. Molecular biology and evolution 29: 2889-2893.

SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data
Nielsen, R. T. Korneliussen, A. Albrechtsen, Y. Li et al. 2012. SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. PloS one http://dx.doi.org/10.1371/journal.pone.0037558.

Evidence for positive selection on a number of microRNA regulatory interactions during recent human evolution
Li, J., Y. Liu, X. Xin, T. S. Kim et al. 2012. Evidence for positive selection on a number of microRNA regulatory interactions during recent human evolution. PLoS Genetics http://dx.doi.org/10.1371/journal.pgen.1002578.

Estimating population divergence time and phylogeny from single‐nucleotide polymorphisms data with outgroup ascertainment bias
Wang, Y. and R. Nielsen. 2012. Estimating population divergence time and phylogeny from single‐nucleotide polymorphisms data with outgroup ascertainment bias. Molecular ecology 4: 974-986.

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
Xu, X., X. Liu, S. Ge, J. D. Jensen et al. 2012. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature biotechnology 30: 105-111.

Species-specific responses of Late Quaternary megafauna to climate and humans
Lorenzen, E. D., D. Nogués-Bravo, L. Orlando, J. Weinstock et al. 2011. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479: 359-364.

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution
Fumagalli, M., M. Sironi, U. Pozzoli, A. Ferrer-Admettla et al. 2011. Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution. PLoS Genetics 7: http://dx.doi.org/10.1371/journal.pgen.1002355.

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques
Yan, G. G. Zhang, X. Fang, Y. Zhang et al. 2011. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nature biotechnology 29: 1019-1023.

The evolution of gene expression levels in mammalian organs
Brawand, D. M. Soumillon, A. Necsulea, P. Julien et al. 2011. The evolution of gene expression levels in mammalian organs. Nature 478: 343-348.

Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome
Lohmueller, K. E., A. Albrechtsen, Y. Li, S. Y. Kim et al. 2011. Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genetics 7: http://dx.doi.org/10.1371/journal.pgen.1002326.

An Aboriginal Australian genome reveals separate human dispersals into Asia
Rasmussen, M., X. Guo, Y. Wang, K. E. Lohmueller et al. 2011. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334: 94-98.

A method for detecting IBD regions simultaneously in multiple individuals—with applications to disease genetics
Moltke, I., A. Albrechtsen, T. v. Hansen., F. C. Nielsen et al. 2011. A method for detecting IBD regions simultaneously in multiple individuals—with applications to disease genetics. Genome Research 21: 1168-1180.

Estimation of allele frequency and association mapping using next-generation sequencing data
Kim, S. Y., K. E. Lohmueller, A. Albrechtsen, Y. Li et al. 2011. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC bioinformatics 12: DOI: 10.1186/1471-2105-12-231.

Genotype and SNP calling from next-generation sequencing data
Nielsen, R., J. S. Paul, A. Albrechtsen, and Y. S. Song. 2011. Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics 12: 443-451.

Q&A: Who is H. sapiens really, and how do we know?
Liang, M. and R. Nielsen. 2011. Q&A: Who is H. sapiens really, and how do we know? BMC Biology 9: DOI: 10.1186/1741-7007-9-20.

Ascertainment biases in SNP chips affect measures of population divergence
Albrechtsen, A., F. C. Nielsen, and R. Nielsen. 2010. Ascertainment biases in SNP chips affect measures of population divergence. Molecular biology and evolution 27: 2534-2547.

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants
Li, Y., N. Vinckenbosch, G. Tien, E. Huerta-Sanchez et al. 2010. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nature genetics 42: 969-972.

Genomics: In search of rare human variants
Nielsen, Rasmus. 2010. Genomics: In search of rare human variants. Nature 467: 1050-1051.

Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation
Andrés, A. M., M. Y. Dennis, W. W. Kretzschmar, J. L. Cannons et al. 2010. Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. PLoS Genetics 6: http://dx.doi.org/10.1371/journal.pgen.1001157.

Archaeology Augments Tibet’s Genetic History—Response
Yi, X., Y. Liang, E. Huerta-Sanchez, X. Jin et al. 2010. Archaeology Augments Tibet’s Genetic History—Response. Science 329: 1467-1468.

Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds
Axelsson, E., A. Albrechtsen, L. Li, H. Megens et al. 2010. Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds. Heredity 105: 290-298.

Natural selection and the distribution of identity-by-descent in the human genome
Albrechtsen, A., I. Moltke, and R. Nielsen. 2010. Natural selection and the distribution of identity-by-descent in the human genome. Genetics 186: 295-308.

Sequencing of 50 human exomes reveals adaptation to high altitude
Yi, X., Y. Liang, E. Huerta-Sanchez, X. Jin et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329: 75-78.

Design of association studies with pooled or un‐pooled next‐generation sequencing data
Kim, S. Y., Y. Li, Y. Guo, R. Li et al. 2010. Design of association studies with pooled or un‐pooled next‐generation sequencing data. Genetic epidemiology 34: 479-491.

A draft sequence of the Neandertal genome
Green, R. E., J. Krause, A. W. Briggs, T. Maricic et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710-722.

Population genetic inference from genomic sequence variation
Pool, J. E., I. Hellmann, J. D. Jensen, and R. Nielsen. 2010. Population genetic inference from genomic sequence variation. Genome research 20: 291-300.

Ancient human genome sequence of an extinct Palaeo-Eskimo
Rasmussen, M., Y. Li, S. Lindgreen, J. S. Pedersen et al. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463: 757-762.

Positive selection on apoptosis related genes
Fonseca, R. R., C. Kosiol, T. Vinař, A. Siepel et al. 2010. Positive selection on apoptosis related genes. Febs Letters 584: 469-476.

In defence of model‐based inference in phylogeography
Beaumont, M. A., R. Nielsen, C. Robert, J. Hey et al. 2010. In defence of model‐based inference in phylogeography. Molecular Ecology 19: 436-446.

The sequence and de novo assembly of the giant panda genome
Li, R., W. Fan, G. Tian, H. Zhu et al. 2010. The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317.

Ancient DNA reveals late survival of mammoth and horse in interior Alaska
Haile, J., D. G. Froese, R. D. E. MacPhee, R. G. Roberts et al. 2009. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proceedings of the National Academy of Sciences 2009: 22352-22357.

Targets of balancing selection in the human genome
Andrés, A. M., M. J. Hubisz, A. Indap, D. G. Torgerson et al. 2009. Targets of balancing selection in the human genome. Molecular biology and evolution 26: 2755-2764.

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)
Xia, Q., Y. Guo, Z. Zhang, D. Li et al. 2009. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326: 433-436.

Adaptionism—30 years after Gould and Lewontin
Nielsen, Rasmus. 2009. Adaptionism—30 years after Gould and Lewontin. Evolution 63: 2487-2490.

In defense of statistical methods for detecting positive selection
Yang, Z., R. Nielsen, and N. Goldman. 2009. In defense of statistical methods for detecting positive selection. Proceedings of the National Academy of Sciences 106: E95-E95.

Darwinian and demographic forces affecting human protein coding genes
Nielsen, R., M. J. Hubisz, I. Hellmann, D. Torgerson et al. 2009. Darwinian and demographic forces affecting human protein coding genes. Genome research 19: 838-849.

Relatedness mapping and tracts of relatedness for genome‐wide data in the presence of linkage disequilibrium
Albrechtsen, A., T. S. Korneliussen, I. Moltke, T. v. O. Hansen et al. 2009. Relatedness mapping and tracts of relatedness for genome‐wide data in the presence of linkage disequilibrium. Genetic epidemiology 33: 266-274.

Statistical inferences in phylogeography
Nielsen, R. and M. A. Beaumont. 2009. Statistical inferences in phylogeography. Molecular Ecology 18: 1034-1047.

Inference of historical changes in migration rate from the lengths of migrant tracts
Pool, J. E. and R. Nielsen. 2009. Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181: 711-719.

An investigation of the statistical power of neutrality tests based on comparative and population genetic data
Zhai, W., R. Nielsen, and M. Slatkin. 2009. An investigation of the statistical power of neutrality tests based on comparative and population genetic data. Molecular biology and evolution 29: 273-283.

Correcting estimators of θ and Tajima’s D for ascertainment biases caused by the single-nucleotide polymorphism discovery process
Ramírez-Soriano, A. and R. Nielsen. 2009. Correcting estimators of θ and Tajima’s D for ascertainment biases caused by the single-nucleotide polymorphism discovery process. Genetics 181: 701-710.

Radiation of extant cetaceans driven by restructuring of the oceans
Steeman, M. E., M. B. Hebsgaard, R. E. Fordyce, S. Y. w. Ho et al. 2009. Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology doi: 10.1093/sysbio/syp060.

Fast phylogenetic DNA barcoding
Munch, K., W. Boomsma, E. Willerslev, and R. Nielsen. 2008. Fast phylogenetic DNA barcoding. Philosophical Transactions of the Royal Society of London B: Biological Sciences 363: 3997-4002.

The diploid genome sequence of an Asian individual
Wang, J., W. Wang, R. Li, Y. Li et al. 2008. The diploid genome sequence of an Asian individual. Nature 456: 60-65.

Statistical assignment of DNA sequences using Bayesian phylogenetics
Munch, K., W. Boomsma, J. P. Huelsenbeck, E. Willerslev et al. 2008. Statistical assignment of DNA sequences using Bayesian phylogenetics. Systematic Biology 57: 750-757.

The effect of ancient DNA damage on inferences of demographic histories
Axelsson, E., E. Willerslev, M. T. P. Gilbert, and R. Nielsen. 2008. The effect of ancient DNA damage on inferences of demographic histories. Molecular Biology and Evolution 25: 2181-2187.

Patterns of positive selection in six mammalian genomes
Kosiol, C., T. Vinař, R. R. Fonseca, M. J. Hubisz et al. 2008. Patterns of positive selection in six mammalian genomes. PLoS Genetics http://dx.doi.org/10.1371/journal.pgen.1000144.

The impact of founder events on chromosomal variability in multiply mating species
Pool, J. E. and R. Nielsen. 2008. The impact of founder events on chromosomal variability in multiply mating species. Molecular biology and evolution 25: 1728-1736.

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
Hellmann, I., Y. Mang, Z. Gu, P. Li et al. 2008. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome research 18: 1020-1029.

Assessing the evolutionary impact of amino acid mutations in the human genome
Boyko, A. R., S. H. Williamson, A. R. Indap, J. D. Degenhardt et al. 2008. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genetics http://dx.doi.org/10.1371/journal.pgen.1000083.

Estimation of 2Nes from temporal allele frequency data
Bollback, J. P., T. L. York, and R. Nielsen. 2008. Estimation of 2Nes from temporal allele frequency data. Genetics 179: 497-502.

Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
Yang, Z. and R. Nielsen. 2008. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Molecular biology and evolution 25: 568-579.

Proportionally more deleterious genetic variation in European than in African populations
Lohmueller, K. E., A. R. Indap, S. Schmidt, A. R. Boyko et al. 2008. Proportionally more deleterious genetic variation in European than in African populations. Nature 451: 994-997.

Population size changes reshape genomic patterns of diversity
Pool, J. E. and R. Nielsen. 2007. Population size changes reshape genomic patterns of diversity. Evolution 61: 3001-3006.

Patterns of mutation and selection at synonymous sites in Drosophila
Singh, N. D., V. L. B. DuMont, M. J. Hubisz, R. Nielsen et al. 2007. Patterns of mutation and selection at synonymous sites in Drosophila. Molecular biology and evolution 24: 2687-2697.

Evolution of genes and genomes on the Drosophila phylogeny
Clark, A. G., M. B. Eisen, D. R. Smith, C. M. Bergman et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.

Recent and ongoing selection in the human genome
Nielsen, R., I. Hellmann, M. Hubisz, C. Bustamante et al. 2007. Recent and ongoing selection in the human genome. Nature Reviews Genetics 8: 857-868.

Genome-wide patterns of nucleotide polymorphism in domesticated rice
Caicedo, A. L., S. H. Williamson, R. D. Hernandez, A. Boyko et al. 2007. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics http://dx.doi.org/10.1371/journal.pgen.0030163.

Ancient bacteria show evidence of DNA repair
Johnson, S. S., M. B. Hebsgaard, T. R. Christensen, M. Mastepanov et al. 2007. Ancient bacteria show evidence of DNA repair. Proceedings of the National Academy of Sciences 104: 14401-14405.

Genes under positive selection in Escherichia coli
Petersen, L., J. P. Bollback, M. Dimmic, M. Hubisz et al. 2007. Genes under positive selection in Escherichia coli. Genome research 17: 1336-1343.

Exploring variation in the d N/d S ratio among sites and lineages using mutational mappings: applications to the influenza virus
Zhai, W., M. Slatkin, and R. Nielsen. 2007. Exploring variation in the d N/d S ratio among sites and lineages using mutational mappings: applications to the influenza virus. Journal of molecular evolution 65: 340-348.

Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models
Wong W. and R. Nielsen. 2007. Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models. Bioinformatics 23: 2031-2037.

Ancient biomolecules from deep ice cores reveal a forested southern Greenland
Willerslev, E., E. Cappellini, W. Boomsma, R. Nielsen et al. 2007. Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 317: 111-114.

Localizing recent adaptive evolution in the human genome
Williamson, S. H., M. J. Hubisz, A. G. Clark, B. A. Payseur et al. 2007. Localizing recent adaptive evolution in the human genome. PLoS Genetics http://dx.doi.org/10.1371/journal.pgen.0030090.

A Bayesian multilocus association method: allowing for higher-order interaction in association studies
Albrechtsen, A., S. Castella, G. Andersen, T. Hansen et al. 2007. A Bayesian multilocus association method: allowing for higher-order interaction in association studies. Genetics 176: 1197-1208.

Estimating the history of mutations on a phylogeny
Bollback, J. P., P. P. Gardner, and R. Nielsen. 2007. Estimating the history of mutations on a phylogeny. Ancestral Sequence Reconstruction. D. Liberles (ed.). Oxford University Press, UK.

Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques
Hernandez, R. D., M. J. Hubisz, D. A. Wheeler, D. G. Smith et al. 2007. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science 316: 240-243.

Evolutionary and biomedical insights from the rhesus macaque genome
Rhesus Macaque Genome Sequencing, R. A. Gibbs, J. Rogers, M. G. Katze et al. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234.

Dependence of paracentric inversion rate on tract length
York, T. L., R. Durrett, and R. Nielsen. 2007. Dependence of paracentric inversion rate on tract length. BMC bioinformatics 8: 115.

Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?
Haile, J., R. Holdaway, K. Oliver, M. Bunce et al. 2007. Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Molecular biology and evolution 24: 982-989.

Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata
Pastene, L. A., M. Goto, N. Kanda, A. N. Zerbini et al. 2007. Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata. Molecular Ecology 16: 1481-1495.

Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
Hey J. and R. Nielsen. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences 104: 2785-2790.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing
Binladen, J., M. T. P. Gilbert, J. P. Bollback, F. Panitz et al. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PloS one http://dx.doi.org/10.1371/journal.pone.0000197.

Adaptive genic evolution in the Drosophila genomes
Shapiro, J. A., W. Huang, C. Zhang, M. J. Hubisz et al. 2007. Adaptive genic evolution in the Drosophila genomes.

Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila
Nielsen, R., V. L. B. DuMont, M. J. Hubisz, and C. F. Aquadro. 2007. Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila. Molecular biology and evolution 24: 228-235.

Novel method to identify source-associated phylogenetic clustering shows that Listeria monocytogenes includes niche-adapted clonal groups with distinct ecological preferences
Nightingale, K. K., K. Lyles, M. Ayodele, P. Jalan, R. Nielsen et al. 2006. Novel method to identify source-associated phylogenetic clustering shows that Listeria monocytogenes includes niche-adapted clonal groups with distinct ecological preferences. Journal of clinical microbiology 44: 3742-3751.

Statistical Methods in Molecular Evolution
Whelan, S. and R. Nielsen. 2006. Statistical Methods in Molecular Evolution. Systematic Biology 55: 698-700.

CpG+ CpNpG analysis of protein-coding sequences from tomato
Hobolth, A., R. Nielsen, Y. Wang, F. Wu et al. 2006. CpG+ CpNpG analysis of protein-coding sequences from tomato. Molecular biology and evolution 23: 1318-1323.

Identification of physicochemical selective pressure on protein encoding nucleotide sequences
Wong, W. S. W., R. Sainudiin, and R. Nielsen. 2006. Identification of physicochemical selective pressure on protein encoding nucleotide sequences. Bmc Bioinformatics DOI: 10.1186/1471-2105-7-148.

Why sex?
Nielsen, R. 2006. Why sex? Science 311: 960-961.

Statistical approaches for DNA barcoding
Nielsen, R. and M. Matz. 2006. Statistical approaches for DNA barcoding. Systematic biology 55: 162-169.

Molecular signatures of natural selection
Nielsen, R. 2005. Molecular signatures of natural selection. Annu. Rev. Genet. 39: 197-218.

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
Zhang, J., R. Nielsen, and Z. Yang. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular biology and evolution 22: 2472-2479.

Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments
Wang, Y., R. S. V. D. Hoeven, R. Nielsen, L. A. Mueller et al. 2005. Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theoretical and applied genetics 112: 72-84.

Ascertainment bias in studies of human genome-wide polymorphism
Clark, A. G., M. J. Hubisz, C. D. Bustamante, S. H. Williamson et al. 2005. Ascertainment bias in studies of human genome-wide polymorphism. Genome research 15: 1496-1502.

Genomic scans for selective sweeps using SNP data
Nielsen, R., S. Williamson, Y. Kim, M. J. Hubisz et al. 2005. Genomic scans for selective sweeps using SNP data. Genome Research 15: 1566-1575.

A likelihood ratio test for species membership based on DNA sequence data
Matz, M. V. and R. Nielsen. 2005. A likelihood ratio test for species membership based on DNA sequence data. Philosophical Transactions of the Royal Society of London B: Biological Sciences 360: 1969-1974.

Natural selection on protein-coding genes in the human genome
Bustamante, C. D., A. Fledel-Alon, S. Williamson, R. Nielsen et al. 2005. Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.

Detecting coevolving amino acid sites using Bayesian mutational mapping
Dimmic, M. W., M. J. Hubisz, C. D. Bustamante, and R. Nielsen. 2005. Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics 21: i126-i135.

Simultaneous inference of selection and population growth from patterns of variation in the human genome
Williamson, S. H., R. Hernandez, A. Fledel-Alon, L. Zhu, R. Nielsen et al. 2005. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proceedings of the National Academy of Sciences 102: 7882-7887.

A scan for positively selected genes in the genomes of humans and chimpanzees
Nielsen, R., C. Bustamante, A. G. Clark, S. Glanowski et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology http://dx.doi.org/10.1371/journal.pbio.0030170.

Statistical methods in molecular evolution
Statistical methods in molecular evolution. Nielsen, R. 2005.

Bayes empirical Bayes inference of amino acid sites under positive selection
Yang, Z., W. S. W. Wong, and R. Nielsen. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Molecular biology and evolution 22: 1107-1118.

Bayesian and maximum likelihood estimation of genetic maps
York, T. L., R. T. Durrett, S. Tanksley, and R. Nielsen. 2005. Bayesian and maximum likelihood estimation of genetic maps. Genetical research 85: 159-168.

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., W. S. W. Wong, K. Yogeeswaran, J. B. Nasrallah et al. 2005. 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. Journal of Molecular Evolution 60: 315-326.

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., R. Nielsen, M. P. Jones, and S. R. McCouch. 2005. 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. Genetics 169: 1639-1647.

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution
Richards, S., Y. Liu, B. R. Bettencourt, P. Hradecky et al. 2005. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome research 15: 1-18.

Simultaneous inference of selection and population growth from patterns of variation in the human genome
Bustamante, C. D., R. Nielsen, A. Fledel-Alon, R. Hernandez et al. 2005. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proceedings of the National Academy of Sciences of the United States of America 22: 7882-7887.

Adaptive evolution of cytochrome c oxidase: infrastructure for a carnivorous plant radiation
Jobson, R. W., R. Nielsen, L. Laakkonen, M. Wikström et al. 2004. Adaptive evolution of cytochrome c oxidase: infrastructure for a carnivorous plant radiation. Proceedings of the National Academy of Sciences 101: 18064-18068.

Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data
Nielsen, R., M. J. Hubisz, and A. G. Clark. 2004. Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data. Genetics 168: 2373-2382.

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
Wong, W. S. W., Z. Yang, N. Goldman, and R. Nielsen. 2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168: 1041-1051.

Microsatellite mutation models insights from a comparison of humans and chimpanzees
Sainudiin, R., R. T. Durrett, C. F. Aquadro, and R. Nielsen. 2004. Microsatellite mutation models insights from a comparison of humans and chimpanzees. Genetics 168: 383-395.

Linkage disequilibrium as a signature of selective sweeps
Kim, Y. and R. Nielsen. 2004. Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513-1524.

Is haplotype block identification useful for association mapping studies?
Zhai, W., M. J. Todd, and R. Nielsen. 2004. Is haplotype block identification useful for association mapping studies? Genetic epidemiology 27: 80-83.

Detecting selection in noncoding regions of nucleotide sequences
Wong, W. S. W. and R. Nielsen. 2004. Detecting selection in noncoding regions of nucleotide sequences. Genetics 167: 949-958.

Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis

Hey, J. and R. Nielsen. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167: 747-760.

Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species
Hey, J., Y. Won, A. Sivasundar, R. Nielsen, et al. 2004. Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species. Molecular Ecology 13: 909-919.

Population genetic analysis of ascertained SNP data
Nielsen, R. 2004. Population genetic analysis of ascertained SNP data. Human genomics 1: 1.

Bayesian estimation of genomic distance
Durrett, R., R. Nielsen, and T. L. York. 2004. Bayesian estimation of genomic distance. Genetics 166: 621-629.

Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios
Clark, A. G., S. Glanowski, R. Nielsen, P. D. Thomas et al. 2003. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302: 1960-1963.

Estimating effective paternity number in social insects and the effective number of alleles in a population
Nielsen, R., D. R. Tarpy, and H. K. Reeve. 2003. Estimating effective paternity number in social insects and the effective number of alleles in a population. Molecular ecology 12: 3157-3164.

Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome
Clark, A. G., R. Nielsen, J. Signorovitch, T. C. Matise et al. 2003. Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. The American Journal of Human Genetics 73: 285-300.

Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA
Nielsen, R. and Z. Yang. 2003. Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Molecular biology and evolution 20: 1231-1239.

Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
Anisimova, M., R. Nielsen, and Z. Yang. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164: 1229-1236.

Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium
Nielsen, R. and J. Signorovitch. 2003. Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. l
Theoretical population biology 63: 245-255.

Stochastic mapping of morphological characters
Huelsenbeck, J. P., R. Nielsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Systematic Biology 52: 131-158.

Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data
Bustamante, C. D., R. Nielsen, and D. L. Hartl. 2003. Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theoretical population biology 63: 91-103.

Pervasive adaptive evolution in mammalian fertilization proteins
Swanson, W. J., R. Nielsen, and Q. Yang. 2003. Pervasive adaptive evolution in mammalian fertilization proteins. Molecular biology and evolution 20: 18-20.

Positive selection in the human genome inferred from human–chimp–mouse orthologous gene alignments
Clark, A. G., S. Glanowski, R. Nielsen, P. Thomas et al. 2003. Positive selection in the human genome inferred from human–chimp–mouse orthologous gene alignments. Cold Spring Harbor symposia on quantitative biology 68: 479-486.

Evolution of the integral membrane desaturase gene family in moths and flies
Knipple, D. C., C. Rosenfield, R. Nielsen, K. M. You et al. 2002. Evolution of the integral membrane desaturase gene family in moths and flies. Genetics 162: 1737-1752.

Bayesian estimation of the number of inversions in the history of two chromosomes
York, T. L., R. Durrett, and R. Nielsen. 2002. Bayesian estimation of the number of inversions in the history of two chromosomes. Journal of Computational Biology 9: 805-818.

Rational design of DNA sequence-based strategies for subtyping Listeria monocytogenes
Cai, S., D. Y. Kabuki, A. Y. Kuaye, T. G. Cargioli et al. 2002. Rational design of DNA sequence-based strategies for subtyping Listeria monocytogenes. Journal of Clinical Microbiology 40: 3319-3325.

Mapping mutations on phylogenies
Nielsen, R. 2002. Mapping mutations on phylogenies. Systematic biology 51: 729-739.

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
Yang, Z. and R. Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular biology and evolution 19: 908-917.

The cost of inbreeding in Arabidopsis
Bustamante, C. D., R. Nielsen, S. A. Sawyer, K. M. Olsen et al. 2002. The cost of inbreeding in Arabidopsis. Nature 416: 531-534.

A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents
Bustamante, C. D., R. Nielsen, and D. L. Hartl. 2002. A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Molecular Biology and Evolution 19: 110-117.

The discovery of single-nucleotide polymorphisms—and inferences about human demographic history
Wakeley, J., R. Nielsen, S. Neen Liu-Cordero, and K. Ardlie. 2001. The discovery of single-nucleotide polymorphisms—and inferences about human demographic history. The American Journal of Human Genetics 69: 1332-1347.

Bayesian inference of phylogeny and its impact on evolutionary biology
Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314.

Mutations as missing data: inferences on the ages and distributions of nonsynonymous and synonymous mutations
Nielsen, R. 2001. Mutations as missing data: inferences on the ages and distributions of nonsynonymous and synonymous mutations. Genetics 159: 401-411.

Statistical tests of selective neutrality in the age of genomics
Nielsen, R. 2001. Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641-647.

Distinguishing migration from isolation: a Markov chain Monte Carlo approach
Nielsen, R. and J. Wakeley. 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158: 885-896.

Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale
Nielsen, R., D. K. Mattila, P. J. Clapham, and P. J. Palsbøll. 2001. Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale. Genetics 157: 1673-1682.

Codon-substitution models for heterogeneous selection pressure at amino acid sites
Yang, Z., R. Nielsen, N. Goldman, and A. K. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.

Estimation of population parameters and recombination rates from single nucleotide polymorphisms
Nielsen, R. 2000. Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154: 931-942.

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
Yang Z. and R. Nielsen. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular biology and evolution 17: 32-43.

The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory
Nielsen, R. and D. M. Weinreich. 1999. The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory. Genetics 153: 497-506.

Effect of nonindependent substitution on phylogenetic accuracy
Huelsenbeck, J. P. and R. Nielsen. 1999. Effect of nonindependent substitution on phylogenetic accuracy. Systematic Biology 48: 317-328.

Single-locus tests of microsatellite evolution: multi-step mutations and constraints on allele size
Nielsen, R. and P. J. Palsbøll. 1999. Single-locus tests of microsatellite evolution: multi-step mutations and constraints on allele size. Molecular phylogenetics and evolution 11: 477-484.

Variation in the pattern of nucleotide substitution across sites
Huelsenbeck, J. P. and R. Nielsen. 1999. Variation in the pattern of nucleotide substitution across sites. Journal of molecular evolution 48: 86-93.

Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation
Nielsen, R., J. L. Mountain, J. P. Huelsenbeck, and M. Slatkin. 1998. Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation. Evolution 669-677.

Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model
Nielsen. R. 1998. Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model. Theoretical population biology 53: 143-151.

Synonymous and nonsynonymous rate variation in nuclear genes of mammals
Yang, Z. and R. Nielsen. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. Journal of molecular evolution 46: 409-418.

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
Nielsen, R. and Z. Yang. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.

Robustness of the estimator of the index of dispersion for DNA sequences
Nielsen, R. 1997. Robustness of the estimator of the index of dispersion for DNA sequences. Molecular phylogenetics and evolution 7: 346-351.

A likelihood approach to populations samples of microsatellite alleles
Nielsen, R. 1997. A likelihood approach to populations samples of microsatellite alleles. Genetics 146: 711-716.

The ratio of replacement to silent divergence and tests of neutrality
Nielsen, R. 1997. The ratio of replacement to silent divergence and tests of neutrality. Journal of Evolutionary Biology 10: 217-231.

A likelihood-ratio test of monophyly
Huelsenbeck, J. P., D. M. Hillis, and R. Nielsen. 1996. A likelihood-ratio test of monophyly. Systematic Biology 45: 546-558.