Recent Publications

• Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation.
  Peter, Benjamin M., Huerta-Sanchez, Emilia and Nielsen, Rasmus. 2012. Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation. PLOS Genetics: Volume 8, issue 10.
• Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes.
  Albrechtsen, A. et al. 2012. Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes. Diabetologiadoi: 10.1007/s00125-012-2756-1.
• SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data.
  Nielsen R, et al. 2012. SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data. PLoS ONE; 7(7): e37558. doi:10.1371/journal.pone.0037558.
• Looking for Darwin in Genomic Sequences—Validity and Success of Statistical Methods.
  Weiwei Zhai, Rasmus Nielsen , Nick Goldman and Ziheng Yang. 2012. Looking for Darwin in Genomic Sequences—Validity and Success of Statistical Methods. Mol. Biol. Evol. 29; (10): 2889-2893. doi: 10.1093.
• A metagenome-wide association study of gut microbiota in type 2 diabetes.
  Junjie Qin, et al. 2012. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490; 55–60 doi:10.1038/nature11450.
• Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias.
  Wang, Y. and Nielsen, R. 2012. Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias. Molecular Ecology
• Evidence for Positive Selection on a Number of MicroRNA Regulatory Interactions during Recent Human Evolution
  Li, J. et al. 2012. Evidence for Positive Selection on a Number of MicroRNA Regulatory Interactions during Recent Human Evolution PLoS Genet 8(3): e1002578. doi:10.1371/journal.pgen.1002578.
• Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
  Xun Xu et al. 2011. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology doi: 10. 1038/nbt.2050.
• Species-specific responses of Late Quaternary megafauna to climate and humans
  Lorenzen, Eline D. et al. 2011. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479(7373): 359-64. doi: 10.1038/nature10574.
• Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques.
  Yan, G. 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. et al. 2011. The evolution of gene expression levels in mammalian organs. Nature 478: 343–348.
• Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution
  Fumagalli, M. et al. 2011. Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution. PLoS Genetics 7(11): e1002355. doi:10.1371/journal.pgen.1002355.
• Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome
  Lohmueller, K.E. et al. 2011. Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome. PLoS Genet 7(10): e1002326. doi:10.1371/journal.pgen.1002326.
• An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
  Rasmussen, M. et al. 2011. An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Science 7: Vol. 334 no. 6052 pp. 94-98, DOI:10.1126/science.1211177.
• A method for detecting IBD regions simultaneously in multiple individuals—with applications to disease genetics
  Moltke, I. et al. 2011. A method for detecting IBD regions simultaneously in multiple individuals—with applications to disease genetics. Genome Res. 21: 1168-1180.
• Genotype and SNP calling from next-generation sequencing data.
  Nielsen, R. et al (2011). Genotype and SNP calling from next-generation sequencing data.Nature Reviews Genetics, 12:443-451.
• Estimation of allele frequency and association mapping using next-generation sequencing data
  Kim, Su Yeon. et al. 2011. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Biology 9: 20-24.
• Q & A: Who is H. sapiens really, and how do we know?
  Liang, M. and Nielsen, R. 2011. Q & A: Who is H. sapiens really, and how do we know?- Bmc Biology: Volume 9 Published.
• A Draft Sequence of the Neandertal Genome
  Green et al. 2010. A Draft Sequence of the Neandertal Genome. Science 328: 710-722.
• Ancient human genome sequence of an extinct Palaeo-Eskimo
  Rasmussen, M. et al. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463: 757-762 .
• Population genetic inference from genomic sequence variation
  Pool, J.E. et al. 2010. Population genetic inference from genomic sequence variation. Genome Res. 20: 291-300.
• Radiation of extant cetaceans driven by restructuring of the oceans
  Steeman, M.E. et al. 2010. Radiation of extant cetaceans driven by restructuring of the oceans. Syst Biol. 58: 573-585.
• Design of association studies with pooled or un-pooled next-generation sequencing data
  Kim, S.Y. et al. 2010. Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol 34: 79-91.
• Balancing Selection Maintains a Form of ERAP2 that Undergoes Nonsense-Mediated Decay and Affects Antigen Presentation
  Andres, A.M. 2010. Balancing Selection Maintains a Form of ERAP2 that Undergoes Nonsense-Mediated Decay and Affects Antigen Presentation. PLoS Genetics 6: e1001157.
• Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds
  Axelsson, E, et al. 2010. Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds. Heredity 105: 290.
• Positive selection on apoptosis related genes
  da Fonseca, R.R. et al. 2010. Positive selection on apoptosis related genes. FEBS Lett. 584: 469-76.
• Ascertainment biases in SNP chips affect measures of population divergence
  Albrechtsen A., Nielsen F.C., and Nielsen, R. 2010. Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol. 27: 2534-2547.
• The sequence and de novo assembly of the giant panda genome
  Li, R. et al. 2010. The sequence and de novo assembly of the giant panda genome. Nature 463: 1106-1111.
• In search of rare human variants
  Nielsen, R. 2010. In search of rare human variants. Nature 467: 1050-1051.
• Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
  Yi, X. et al. 2010. Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude. Science 329: 75-78.
• Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants
  Li, Y. et al. 2010. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nature Genetics 42: 969-972.
• Natural selection and the distribution of identity-by-descent in the human genome
  Albrechtsen, A., Moltke, I. and Nielsen, R. 2010. Natural selection and the distribution of identity-by-descent in the human genome. Genetics 186: 295-308.
• In defence of model-based inference in phylogeography
  Beaumont, M.A. et al. 2010. In defence of model-based inference in phylogeography. Mol Ecol. 19: 436-446.
• An Investigation of the Statistical Power of Neutrality Tests Based on Comparative and Population Genetic Data
  Zhai, W.W., Nielsen, R., and Slatkin, M. 2009. An Investigation of the Statistical Power of Neutrality Tests Based on Comparative and Population Genetic Data. Mol. Biol. Evol. 26: 273-283.
• Statistical inferences in phylogeography
  Nielsen, R. and Beaumont, M. A. 2009. Statistical inferences in phylogeography. Mol. Ecol. 18: 1034-1047.
• Darwinian and demographic forces affecting human protein coding genes
  Nielsen, R. et al. 2009. Darwinian and demographic forces affecting human protein coding genes. Genome Res. 19: 838-849.
• Inference of historical changes in migration rate from the lengths of migrant tracts
  Pool, J.E., and Nielsen, R. 2009. Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181: 711-719.
• Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process
  Ramírez-Soriano, A, and Nielsen, R. 2009. Correcting estimators of theta and Tajima’s D for ascertainment biases caused by the single-nucleotide polymorphism discovery process. Genetics 181:701-710.
• The diploid genome sequence of an Asian individual
  Wang et al. 2009. The diploid genome sequence of an Asian individual. Nature 456: 60-65.
• Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium
  Albrechtsen, A. et al. 2009. Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium. Genet Epidemiol. 33: 266-274.
• Adaptionism-30 years after Gould and Lewontin
  Nielsen, R. 2009. Adaptionism-30 years after Gould and Lewontin. Evolution 10: 2487-90.
• In defense of statistical methods for detecting positive selection
  Yang, Z., Nielsen, R. and Goldman, N. 2009. In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci U S A. 106: 36.
• Targets of balancing selection in the human genome
  Andres, A.M., et al. 2009. Targets of balancing selection in the human genome. Mol. Biol. Evol. 26(12): 2755–2764.
• Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)
  Xia, Q. et al. (2009). Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326: 433-436.
• Ancient DNA reveals late survival of mammoth and horse in interior Alaska
  Haile J. et al. 2009. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proc Natl Acad Sci U S A. 106: 22352-7.
• Patterns of positive selection in six mammalian genomes
  Kosiol, C., T. et al. 2008. Patterns of positive selection in six mammalian genomes. PLoS- Genetics 4(8): e1000144.
• Assessing the evolutionary impact of amino acid mutations in the human genome
  Boyko, A. R., et al. 2008. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS-Genetics 4(5):e1000083.
• Proportionally more deleterious genetic variation in European than in African populations
  Lohmueller K.E. et al. 2008. Proportionally more deleterious genetic variation in European than in African populations. Nature 451:994-997.
• Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
  Hellmann, I. et al. 2008. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res. 18: 1020-1029.
• Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage
  Yang, Z. and Nielsen, R. 2008. Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage. Mol. Biol. Evol. 25: 568-579.
• Estimation of 2Nes From Temporal Allele Frequency Data
  Bollback, J. P, York, T. L. and Nielsen, R. 2008. Estimation of 2Nes From Temporal Allele Frequency Data. Genetics 179: 497-502.
• The Impact of Founder Events on Chromosomal Variability in Multiply Mating Species
  Pool, J. and Nielsen, R. 2008. The Impact of Founder Events on Chromosomal Variability in Multiply Mating Species. Mol. Biol. Evol. 25: 1728-1736.
• The effect of ancient DNA damage on inferences of demographic histories
  Axelsson, E., Willerslev, E., Gilbert, M.T.P., and Nielsen, R. 2008. The effect of ancient DNA damage on inferences of demographic histories. Mol. Biol. Evol 25: 2181-2187.
• Fast phylogenetic DNA barcoding
  Munch, K., Boomsma, W.,Willerslev, E. and Nielsen, R. 2008. Fast phylogenetic DNA barcoding. Phil. Trans. Royal Soc. B. 363: 3997-4002.
• Estimating human demographic parameters from genomic SNP data
  Nielsen. R. 2008. Estimating human demographic parameters from genomic SNP data. Pages 155-160 in Simulations, genetics and human prehistory, edited by Matsumura, S., Forster, P., and Renfrew, C. MacDonald Institute for Archaeological Research, Cambridge
• Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics
  Munch, K., Boomsma, W., Huelsenbeck, J.P. and Nielsen, R. 2008. Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics. Systematic Biology 57: 750-757.
• Maximum Likelihood Estimation of Ancestral Codon Usage Bias Parameters in Drosophila
  Nielsen R, et al. 2007. Maximum Likelihood Estimation of Ancestral Codon Usage Bias Parameters in Drosophila. Mol. Biol. Evol. 24: 228-35.
• Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible and is DNA Leaching a Factor?
  Haile, J. et al. 2007. Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible and is DNA Leaching a Factor? Mol. Biol. Evol. 24: 982-989.
• Adaptive genic evolution in the Drosophila genomes
  Shapiro, J.A. et al. 2007. Adaptive genic evolution in the Drosophila genomes. Proc Natl Acad Sci U S A. 104: 2271-6.
• The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.
  Binladen, J. et al. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE. 14;2:e197.
• Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata
  Pastene, L. A. et al. 2007. Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata Mol. Ecol. 16: 1481–1495.
• Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
  Hey, J. and Nielsen, R.2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A. 104: 2785–2790.
• Dependence of paracentric inversion rate on tract length.
  York TL, R. Durrett, R. and Nielsen, R. 2007. Dependence of paracentric inversion rate on tract length. BMC Bioinformatics 8: 115-123.
• Evolutionary and biomedical insights from the rhesus macaque genome.
  Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234.
• Bayesian multi-loci association method: allowing for higher-order interaction in association studies
  Albrechtsen A, S. et al. 2007. Bayesian multi-loci association method: allowing for higher-order interaction in association studies. Genetics 176: 1197-1208.
• Localizing recent adaptive evolution in the human genome
  Williamson, S. H. et al. 2007. Localizing recent adaptive evolution in the human genome. PLoS Genetics doi: 10.1371/journal.pgen.0030090.eor.
• Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques
  Hernandez, R.D. et al. 2007. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science 316: 240-243.
• 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.
• Population Size Changes Reshape Genomic Patterns of Diversity
  Pool, J. and Nielsen, R. 2007. Population Size Changes Reshape Genomic Patterns of Diversity. Evolution 61: 3001-6.
• Genes under positive selection in Escherichia coli
  Petersen, L. J. et al. 2007. Genes under positive selection in Escherichia coli. Genome Res. 17: 1336-1343.
• Exploring variation in the dN/dS ratio among sites and lineages using mutational mappings: applications to the Influenza virus
  Zhai, W., Slatkin, M. and Nielsen, R.2007. Exploring variation in the dN/dS ratio among sites and lineages using mutational mappings: applications to the Influenza virus. J. Mol. Evol. 65: 340-8.
• Ancient bacteria show evidence of DNA repair
  Johnson, S.S. et al. 2007. Ancient bacteria show evidence of DNA repair. Proc. Natl. Acad. Sci. USA 104: 14401-14.
• Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice
  Caicedo, A.L. et al. 2007. Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice. PLoS Genetics Vol. 3: No. 9, e163 doi:10.1371/journal.pgen.0030163.
• Recent and ongoing selection in the human genome
  Nielsen, R. et al. 2007. Recent and ongoing selection in the human genome. Nat. Rev Genet. 8: 857-68.
• Patterns of Mutation and Selection at Synonymous Sites in Drosophila
  Singh N.D. et al. 2007. Patterns of Mutation and Selection at Synonymous Sites in Drosophila. Mol Biol Evol. 2007, Nov 13; [Epub ahead of print].
• Evolution of genes and genomes on the Drosophila phylogeny
  Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-18.
• Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences
  Nightingale, K. K.et al. 2006. Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences. J. Clin. Microbiol. 44: 3742-3751.
• CpG+CpNpG analysis of protein coding sequences from tomato
  Hobolth A, and Nielsen, R. et al. 2006. CpG+CpNpG analysis of protein coding sequences from tomato. Mol. Biol. Evol. 23: 1318-1323.
• Identification of physicochemical selective pressure on protein encoding nucleotide sequences
  Wong, W. S., Sainudiin, R. and Nielsen, R. 2006. Identification of physicochemical selective pressure on protein encoding nucleotide sequences. BMC Bioinformatics 7 (1): 148.
• Reducing an intellectual deficit: coalescent theory for (almost) everyone.
  Nielsen, R. 2006. Reducing an intellectual deficit: coalescent theory for (almost) everyone. Evolution 60: 208–209 (Book review).
• Statistical Approaches for DNA barcoding
  Nielsen, R. and Matz, M. 2006. Statistical Approaches for DNA barcoding. Syst. Biol 55: 162-169.
• Difference of Expression
  Nielsen, R. 2006. Difference of Expression. Nature 440: 161-161.
• Why sex?
  Nielsen, R. 2006. Why sex? Science 311: 960-961.
• Statistical Methods in Molecular Evolution
  Nielsen, R. (Ed.) 2005. Statistical Methods in Molecular Evolution, Springer-Verlag, New York (Edited Book – 504 pages).
• Composite likelihood estimation in population genetics
  Nielsen, R and Wiuf, C. 2005. Composite likelihood estimation in population genetics. Proc. 55th Ses. ISI. (Invited paper).
• Mapping Mutations on Phylogenies
  Nielsen, R. 2005. Mapping Mutations on Phylogenies. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinfornatics, John Wiley and Sons.
• Bayesian and maximum likelihood estimation of genetic maps
  York, T. L., Durrett, R. T., Tanksley, S. and R. Nielsen. 2005. Bayesian and maximum likelihood estimation of genetic maps. Genetical Research 85: 159-168.
• 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 (Awarded best paper ISMB 2005).
• Bayes Empirical Bayes Inference of Amino Acid Sites under Positive Selection
  Yang, Z., Wong, W.S.W. and Rasmus Nielsen 2005. Bayes Empirical Bayes Inference of Amino Acid Sites under Positive Selection. Mole. Biol. Evol 22: 1107-1118.
• The population structure of African cultivated rice (Oryza Glaberrima (Steud.): evidence for elevated levels of LD caused by admixture with O. sativa and ecological adaptation
  Semon, M., Nielsen, R., Jones, M. and McCouch, S. 2005. The population structure of African cultivated rice (Oryza Glaberrima (Steud.): evidence for elevated levels of LD caused by admixture with O. sativa and ecological adaptation. Genetics 169 no. 3:
• 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. 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. J. Mol. Evol. 60: 3
• Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
  Richards, S., et al. (50 authors). 2005. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Res. 15: 1-18.
• Simultaneous inference of selection and population growth from patterns of variation in the human genome
  Williamson, S. H. et al. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc. Natl. Acad. Sci. 102: 7882-7887.
• A scan for positively selected genes in the genomes of humans and chimpanzees
  Nielsen, R., et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology 3(6): e170.
• Human Genomics – Disclosure of Variation
  Nielsen, R. 2005. Human Genomics – Disclosure of Variation. Nature 434: 288-288. (News and Views).
• Peopling of the Americas
  Nielsen R. 2005. Peopling of the Americas. Eur. J. Hum. Genet. 13:1100-1101 News and Comment).
• Comparative data is needed to detect selection
  Nielsen, R and M. J. Hubitz. 2005. Comparative data is needed to detect selection. Nature 433(7023):E6.
• Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level
  Zhang, J.,Nielsen, R. and Yang, Z. 2005. Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level. Mol. Biol. Evol. 22: 2472-2479.
• A likelihood ratio test for species membership based on DNA sequence data
  Matz, M. V. and Nielsen, R. 2005. A likelihood ratio test for species membership based on DNA sequence data. Phil. Trans. Royal. Soc. 360: 1969-1974.
• Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments
  Wang, Y, et al. 2005. Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor Appl Genet. 2005 Oct 6;:1-13 [Epub ahead of print].
• Molecular signatures of natural selection
  Nielsen, R. 2005. Molecular signatures of natural selection. Ann. Rev. Genet. 39: 197-218.
• Natural Selection on Protein Coding Genes in the Human Genome
  Bustamante, C. D. et al. 2005. Natural Selection on Protein Coding Genes in the Human Genome. Nature 437: 1153-1157.
• Ascertainment bias in studies of human genome-wide polymorphism
  Clark, A. G.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. et al. 2005. Genomic scans for selective sweeps using SNP data. Genome Research 15: 1566-1575.
• Action of purifying selection on silent sites in the human genome.
  Nielsen, R. and Akashi, H. 2004. Action of purifying selection on silent sites in the human genome. In The Encyclopedia of the Human Genome. Nature Publishing Group.
• Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
  Wong, W. et al. . 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., Aquadro, C. F., Durrett, R. T. 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., Todd, M. J. and Nielsen, R. 2004. Is Haplotype Block Identification Useful for Association Mapping Studies? Genetic Epidemiology 27: 80-83.
• Population genetic analysis of ascertained SNP data
  Nielsen, R. 2004. Population genetic analysis of ascertained SNP data. Human Genomics 3: 218-224.
• Paternity estimation in social insects. Insectes Sociaux
  Tarpy, D. R., Nielsen, R. and Nielsen, D.I.. 2004. Paternity estimation in social insects. Insectes Sociaux. 51: 203-204.
• Discerning between re-current gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale
  Palsbøll, P. J, et al. 2004. Discerning between re-current gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations. Evolution 58: 670-675.
• Detecting positive selection in non-coding regions of DNA sequences. Genetics
  Wong, W.H. and Nielsen, R. 2004. Detecting positive selection in non-coding regions of DNA sequences. Genetics 167: 949-958.
• Bayesian estimation of genomic distance
  Durrett, R., R. Nielsen and T. F. York 2004. Bayesian estimation of genomic distance. Genetics 166: 621-629.
• Using Haplotypes with microsatellites to study gene flow between recently separated populations
  Hey, J. et al. 2004. Using Haplotypes with microsatellites to study gene flow between recently separated populations. Molecular Ecology 13: 909-919.
• 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 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.
• Adaptive evolution of cytochrome c oxidase: infrastructure for a carnivorous plant radiation
  Jobson, R. W. et al. 2004. Adaptive evolution of cytochrome c oxidase: infrastructure for a carnivorous plant radiation. Proc. Natl. Acad. Sci. 101: 18064-18068.
• Reconstituting the frequency spectrum of ascertained SNP data
  Nielsen, R., Todd, M. J. and Clark, A. G. 2004. Reconstituting the frequency spectrum of ascertained SNP data. Genetics 168: 2373-2382.
• Distinguishing Migration from Isolation: an MCMC Approach
  Nielsen, R. and Wakeley, J. W. 2001. Distinguishing Migration from Isolation: an MCMC Approach. Genetics 158: 885-896.
• Positive selection in the human genome inferred from human-chimp-mouse orthologous gene alignments
  Clark, A. G. 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: 471-477.
• Estimating the effective paternity numbdetecter in social insects and the effective number of alleles in a population
  Nielsen, R., Tarpy, D. R. and Reeve, H. K. 2003. Estimating the effective paternity numbdetecter in social insects and the effective number of alleles in a population. Molecular Ecology 12: 3157-3164.
• 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. Theor. Pop. Biol. 63: 245-255.
• Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.
  Anisimova, M.,Nielsen, R. and Yang, Z. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164: 1229-1236.
• Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data
  Bustamante, C. D., Nielsen, R. and Hartl, D. L. 2003. Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theor. Pop. Biol 63: 105-114.
• Pervasive Adaptive Evolution in Mammalian Fertilization Proteins
  Swanson, W. J., Nielsen, R. and Yang, Q. 2003. Pervasive Adaptive Evolution in Mammalian Fertilization Proteins. Mol. Biol. Evol. 20: 18-20.
• Stochastic Mapping of Morphological Characters
  Huelsenbeck, J. P., Nielsen, R. and Bollback, J. P. 2003. Stochastic Mapping of Morphological Characters. Syst. Biol. 52 (2): 131-158.
• Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA
  Nielsen, R. and Yang, Z.2003. Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol. Biol. Evol. 20: 1231-1239.
• Linkage Disequilibrium and Inference of Ancestral Recombination in 538 Single-Nucleotide Polymorphism Clusters across the Human Genome
  Clark, A. G. and Nielsen, R. et al. 2003. Linkage Disequilibrium and Inference of Ancestral Recombination in 538 Single-Nucleotide Polymorphism Clusters across the Human Genome. Am. J. Hum. Genet. 73:285-300.
• Inferring non-neutral evolution from human-chimp-mouse orthologous gene trios.
  Clark, A. G. et al. 2003. Inferring non-neutral evolution from human-chimp-mouse orthologous gene trios. Science 302: 1960-1961.
• Invited comment on “Inference from DNA data: population histories evolutionary processes and forensic match probabilities”
  Nielsen, R and Hey, J. 2003. Invited comment on “Inference from DNA data: population histories evolutionary processes and forensic match probabilities” by I. A. Wilson, M. E. Weale and D. J. Balding. J. R. Statist. Soc. A. 166: 155.
• Invited comment on “Bayesian phylogenetic inference from animal mitochondrial genome arrangements
  Durrett, R. and Nielsen, R. 2002. Invited comment on “Bayesian phylogenetic inference from animal mitochondrial genome arrangements” by B. Larget, D. L. Simon and J. B. Kadane. J. R. Statist. Soc. B. 64: 748.
• 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. J. Comp. Biol. 9: 805-818.
• Rational Design of DNA Sequence-Based Strategies for Subtyping Listeria monocytogenes.
  Cai S, et al. 2002. Rational Design of DNA Sequence-Based Strategies for Subtyping Listeria monocytogenes. J. Clin. Microbiol. 40: 3319-3325.
• Mapping Mutations on Genealogies
  Nielsen, R. 2002. Mapping Mutations on Genealogies. Syst. Biol. 51: 729-739.
• Codon Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages
  Yang, Z. and Nielsen, R. 2002. Codon Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages. Mol. Biol. Evol. 19: 908-17.
• Detecting positively selected sites using posterior predictive p-values
  Nielsen, R. and Huelsenbeck, J. P. 2002. Detecting positively selected sites using posterior predictive p-values. Pac. Symp. Biocomp. 2002 (Eds. R. B. Altman, K. Dunker, L. Hunter, K. Lauderdal and T. E. Klein), pp. 576-578.
• A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents
  Bustamente, 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. Mol. Biol. Evol. 16: 110-117.
• The cost of inbreeding in Arabidopsis
  Bustamente, C. D. et al. 2002. The cost of inbreeding in Arabidopsis. Nature 416: 531-534.
• Evolution of the Integral Membrane Desaturase Gene Family in Moths and Flies
  Knipple, D. C. et al. 2002. Evolution of the Integral Membrane Desaturase Gene Family in Moths and Flies. Genetics. Genetics 162: 1737-1752.
• PATRI – paternity inference in natural populations
  Signorovitch, J. and Nielsen, R. 2002. PATRI – paternity inference in natural populations. Bioinformatics. 18: 341-342.
• Bayesian inference of phylogeny: Reverend Bayes meets Darwin
  Huelsenbeck, J. P. et al. 2001. Bayesian inference of phylogeny: Reverend Bayes meets Darwin. Science 294: 2310-2314.
• The discovery of single nucleotide polymorphisms and inferences about human demographic history
  Wakeley, J., Nielsen, R, Ardlie, K. and Liu-Cordero, S. N. 2001. The discovery of single nucleotide polymorphisms and inferences about human demographic history, Am. J. Hum. Genet. 69: 1332-1347.
• 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: 413-422.
• Statistical tests of neutrality in the age of genomics. Heredity
  Nielsen, R. 2001. Statistical tests of neutrality in the age of genomics. Heredity 86: 641-647.
• Statistical Approaches to Paternity Analysis in Natural Populations and Applications to the North Atlantic Humpback Whale
  Nielsen, R., Mattila D. K., Clapham, P. J. and Palsbøll, P. J. 2001. Statistical Approaches to Paternity Analysis in Natural Populations and Applications to the North Atlantic Humpback Whale. Genetics 157: 1673-1682.
• Detecting Selection in Protein Coding Genes Using the Rate of Nonsynonymous and Synonymous Divergence
  Nielsen, R. 2000. Detecting Selection in Protein Coding Genes Using the Rate of Nonsynonymous and Synonymous Divergence. In Computational and Evolutionary Analysis of HIV Molecular Sequences, eds. A.G. Rodrigo and G.H Learn, Kluwer Academic Publishers, B
• Codon-Substitution Models for Variable Selection Pressure at Amino Acid Sites
  Yang, Z.,Nielsen, R. Goldman, N. and Pedersen, A.-M. K. 2000. Codon-Substitution Models for Variable Selection Pressure at Amino Acid Sites. Genetics 155: 431-449.
• Analysis of Population Subdivision using Di-Allelic Models
  Nielsen, R. and Slatkin, M. 2000. Analysis of Population Subdivision using Di-Allelic Models. Evolution 54: 44-50.
• Estimating Synonymous and Nonsynonymous Substitution Rates under Realistic Evolutionary Models.
  Yang, Z. and Nielsen, R. 2000. Estimating Synonymous and Nonsynonymous Substitution Rates under Realistic Evolutionary Models. Mol. Biol. Evol. 17: 32-43.
• Estimation of Population Parameters and Recombination Rates using Single Nucleotide Polymorphisms
  Nielsen, R. 2000. Estimation of Population Parameters and Recombination Rates using Single Nucleotide Polymorphisms. Genetics 154: 931-942.
• The molecular clock is gone but not forgotten (Meeting review).
  Nielsen, R. 1999. The molecular clock is gone but not forgotten (Meeting review). Trends in Genetics 15. 442-443.
• The Age of Nonsynonymous and Synonymous Mutations and Implications for the Slightly Deleterious Theory
  Nielsen, R. and Weinreich, D. M. 1999. The Age of Nonsynonymous and Synonymous Mutations and Implications for the Slightly Deleterious Theory. Genetics 153: 497-506.
• The Effect of Non-Independent Substitution on Phylogenetic Accuracy.
  Huelsenbeck, J. P. and Nielsen, R. 1999. The Effect of Non-Independent Substitution on Phylogenetic Accuracy. Syst. Biol. 48: 317-328.
• Changes in ds/dn in the HIV-1 Env Gene
  Nielsen, R. 1999. Changes in ds/dn in the HIV-1 Env Gene. Mol. Biol. Evol. 16: 711-714.
• Tests of Microsatellite Evolution: Multi-Step Mutations and Constraints on Allele Size
  Nielsen, R. and Palsboll, P. J. 1999. Tests of Microsatellite Evolution: Multi-Step Mutations and Constraints on Allele Size. Mol. Phyl. Evol. 11: 477-484.
• Variation in the Substitution Process along a DNA sequence
  Huelsenbeck, J. P. and R. Nielsen. 1999. Variation in the Substitution Process along a DNA sequence.J. Mol. Evol. 48: 86-93.
• Species Sampling and Estimation of Large Phylogenies.
  Rannala, B., Huelsenbeck, J. P., Yang, Z. and Nielsen, R.1998. Species Sampling and Estimation of Large Phylogenies. Syst. Biol. 47: 702-710.
• Models of Amino Acid Substitution and Applications to Mitochondrial Protein Evolution
  Yang, Z., Nielsen, R. and Hasegawa, M. 1998. Models of Amino Acid Substitution and Applications to Mitochondrial Protein Evolution. Mol. Biol. Evol. 15: 1600-1611.
• Maximum-Likelihood Estimation of Population Divergence Times and Population Phylogeny in Models without Mutation.
  Nielsen, R., Mountain, J. L., Huelsenbeck, J. P. and Slatkin, M. 1998. Maximum-Likelihood Estimation of Population Divergence Times and Population Phylogeny in Models without Mutation. Evolution 52: 669-677.
• Synonymous and Nonsynonymous Rate Variation in Nuclear Genes of Mammals
  Yang, Z. and Nielsen, R.1998. Synonymous and Nonsynonymous Rate Variation in Nuclear Genes of Mammals. J. Mol. Evol. 46: 409-418.
• Likelihood Models for Detecting Positive Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
  Nielsen, R. and Yang, Z. 1998. Likelihood Models for Detecting Positive Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene. Genetics 148: 929-936.
• 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. Theor. Pop. Biol. 53: 143-151.
• The Robustness of the Estimator of the Index of Dispersion for DNA Sequences
  Nielsen, R. 1997. The Robustness of the Estimator of the Index of Dispersion for DNA Sequences. Mol. Phyl. Evol. 7: 346-351.
• Site-by-Site Estimation of the Rate of Evolution and the Correlation of Rates in Mitochondrial DNA
  Nielsen, R. 1997. Site-by-Site Estimation of the Rate of Evolution and the Correlation of Rates in Mitochondrial DNA. Syst. Biol. 46: 346-353.
• A Maximum Likelihood Approach to Population Samples of Microsatellite alleles. Genetics
  Nielsen, R. 1997. A Maximum Likelihood Approach to Population Samples of Microsatellite alleles. Genetics 146: 711-716.
• A likelihood Ratio Test of Monophyly
  Huelsenbeck, J., Hillis D. M. and Nielsen, R.1997. A likelihood Ratio Test of Monophyly. Syst. Biol. 45: 546-558.
• 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. J. Evol. Biol. 10: 217-231.