Research Topics
Genomes and Genes
| Rasmus NielsenSummaryAffiliation: Cornell University Country: USA Publications
| Collaborators
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Detail Information
Publications
Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominanceScott Williamson
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
Genetics 168:463-75. 2004..This nonintuitive result has major implications for the interpretation of several popular tests of neutrality...
A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patientsScott Williamson
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
Mol Biol Evol 22:456-68. 2005....
Localizing recent adaptive evolution in the human genomeScott H Williamson
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
PLoS Genet 3:e90. 2007..In general, we find that recent adaptation is strikingly pervasive in the human genome, with as much as 10% of the genome affected by linkage to a selective sweep...- Natural selection on protein-coding genes in the human genomeCarlos D Bustamante
Department of Biological Statistics and Computational Biology, 101 Biotechnology Building, Cornell University, Ithaca, New York 14853, USA
Nature 437:1153-7. 2005.... - Assessing the evolutionary impact of amino acid mutations in the human genomeAdam R Boyko
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
PLoS Genet 4:e1000083. 2008.... - A scan for positively selected genes in the genomes of humans and chimpanzeesRasmus Nielsen
Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
PLoS Biol 3:e170. 2005..The polymorphism analysis further supports the presence of positive selection in these genes by showing an excess of high-frequency derived nonsynonymous mutations... - Patterns of positive selection in six Mammalian genomesCarolin Kosiol
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
PLoS Genet 4:e1000144. 2008..This study provides additional evidence for widespread positive selection in mammalian evolution and new genome-wide insights into the functional implications of positive selection... - Proportionally more deleterious genetic variation in European than in African populationsKirk E Lohmueller
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
Nature 451:994-7. 2008..Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa... - Genomic scans for selective sweeps using SNP dataRasmus Nielsen
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
Genome Res 15:1566-75. 2005..Evidence for selective sweeps is also found in many other regions, including genes known to be associated with disease risk such as DPP10 and COL4A3... - Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sitesWendy S W Wong
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
Genetics 168:1041-51. 2004..The parsimony method has a very low rate of false positives but very little power for detecting positive selection or identifying positively selected sites... - Simultaneous inference of selection and population growth from patterns of variation in the human genomeScott H Williamson
Department of Biological Statistics and Computational Biology, 101 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
Proc Natl Acad Sci U S A 102:7882-7. 2005.... - Detecting coevolving amino acid sites using Bayesian mutational mappingMatthew W Dimmic
Department of Biological Statistics and Computational Biology, Cornell University Ithaca, NY 13101, USA
Bioinformatics 21:i126-35. 2005..A coevolutionary Markov model for codon substitution is also described, and this model is used as the basis of several test statistics... - Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov modelsWendy S W Wong
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
Bioinformatics 23:2031-7. 2007..There are numerous methods available for solving this problem, however, very few of them take advantage of the increasing availability of comparative genomic data... - Targets of balancing selection in the human genomeAida M Andres
Department of Molecular Biology and Genetics, Cornell University, USA
Mol Biol Evol 26:2755-64. 2009.... - Evolution of genes and genomes on the Drosophila phylogenyAndrew G Clark
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
Nature 450:203-18. 2007..These may prove to underlie differences in the ecology and behaviour of these diverse species... - Bayesian and maximum likelihood estimation of genetic mapsThomas L York
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
Genet Res 85:159-68. 2005..We also re-analyse a recently published set of data from the eggplant and show that the use of the MCMC-based method leads to smaller estimates of genetic distances... - Ascertainment bias in studies of human genome-wide polymorphismAndrew G Clark
Molecular Biology and Genetics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
Genome Res 15:1496-502. 2005.... - Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genomeAndrew G Clark
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Am J Hum Genet 73:285-300. 2003..This result is consistent with differences in the genealogical depth of local genomic regions, a finding that has direct bearing on the design and utility of LD mapping and on the National Institutes of Health HapMap project... - 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 systemRaazesh Sainudiin
Department of Statistical Science, Cornell University, Ithaca, NY14853, USA
J Mol Evol 60:315-26. 2005..An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins... - Identification of physicochemical selective pressure on protein encoding nucleotide sequencesWendy S W Wong
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
BMC Bioinformatics 7:148. 2006..However, they have been limited by not taking the physiochemical properties of amino acids into account... - Linkage disequilibrium as a signature of selective sweepsYuseob Kim
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
Genetics 167:1513-24. 2004..However, the improvement made by including LD is rather small, suggesting that most of the relevant information regarding selective sweeps is captured by the spatial distribution and marginal allele frequencies of polymorphisms... - Inferring nonneutral evolution from human-chimp-mouse orthologous gene triosAndrew G Clark
Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Science 302:1960-3. 2003..In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders... - Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism dataRasmus Nielsen
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
Genetics 168:2373-82. 2004..Appropriate treatment of SNP ascertainment is vital to our ability to make correct inferences from the data of the International HapMap Project... - Patterns of mutation and selection at synonymous sites in DrosophilaNadia D Singh
Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA
Mol Biol Evol 24:2687-97. 2007.... - Bayesian estimation of the number of inversions in the history of two chromosomesThomas L York
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
J Comput Biol 9:805-18. 2002..melanogaster comparison, the lower boundary of a 95% highest posterior density credible interval for the number of inversions is considerably larger than the most parsimonious number of inversions... - Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaquesRyan D Hernandez
Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
Science 316:240-3. 2007..15 at 10 kilobases) versus Indian (r(2) approximately 0.52 at 10 kilobases) macaque populations... - Dependence of paracentric inversion rate on tract lengthThomas L York
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
BMC Bioinformatics 8:115. 2007..We develop a Bayesian method based on MCMC for estimating the relative rates of pericentric and paracentric inversions from marker data from two species. The method also allows estimation of the distribution of inversion tract lengths... - Estimating effective paternity number in social insects and the effective number of alleles in a populationRasmus Nielsen
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
Mol Ecol 12:3157-64. 2003..It should also be of use in population genetic studies in which the effective number of alleles is of interest... - Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiationRichard W Jobson
Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
Proc Natl Acad Sci U S A 101:18064-8. 2004.... - Population genetic analysis of ascertained SNP dataRasmus Nielsen
Department of Biological Statistics and Computational Biology, Cornell University, 439 Warren Hall, Ithaca, NY 14853 7801, USA
Hum Genomics 1:218-24. 2004..Several recently developed methods for correcting for the ascertainment bias will also be discussed... - Microsatellite mutation models: insights from a comparison of humans and chimpanzeesRaazesh Sainudiin
Department of Statistical Science, Cornell University, Ithaca, New York 14853, USA
Genetics 168:383-95. 2004..In general, models that allow chimps to have a larger per-repeat unit slippage rate and/or a shorter focal length compared to humans give a better fit to the human-chimp data as well as the human genomic data... - Mapping mutations on phylogeniesRasmus Nielsen
Department of Biological Statistics, Cornell University, 439 Warren Hall, Ithaca, New York 14853 7801, USA
Syst Biol 51:729-39. 2002..Applications include a method for testing for variation in the substitution rate along the sequence and a method for testing whether the d(N)/d(S) ratio varies among lineages in the phylogeny... - Evolution of the integral membrane desaturase gene family in moths and fliesDouglas C Knipple
Department of Entomology, New York State Agricultural Experiment Station, Cornell University, Geneva, New York 14456, USA
Genetics 162:1737-52. 2002.... - Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism dataCarlos D Bustamante
Mathematical Genetics Group, Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, UK OX1 3TG
Theor Popul Biol 63:91-103. 2003.... - Statistical approaches for DNA barcodingRasmus Nielsen
Department of Biological Statistics and Computational Biology, Center for Bioinformatics, University of Copenhagen Universitetsparken 15, 2100 Copenhagen, Denmark
Syst Biol 55:162-9. 2006 - Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNARasmus Nielsen
Department of Biometrics, Cornell University, USA
Mol Biol Evol 20:1231-9. 2003.... - 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 adaptationMande Semon
Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA
Genetics 169:1639-47. 2005..The remaining three O. glaberrima subpopulations were significantly associated with specific combinations of phenotypic traits-possibly reflecting ecological adaptation to different growing environments... - Detecting selection in noncoding regions of nucleotide sequencesWendy S W Wong
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
Genetics 167:949-58. 2004..Data analysis of both simulated and real viral data is presented. Using the new method we show that positive selection in viruses is acting primarily in protein-coding regions and is rare or absent in noncoding regions... - Bayesian estimation of genomic distanceRichard Durrett
Department of Mathematics, Cornell University, Ithaca, New York 14853, USA
Genetics 166:621-9. 2004..In the first case the most likely number of events is larger than the parsimony value. In the last two cases the parsimony solutions have very small probability... - Rational design of DNA sequence-based strategies for subtyping Listeria monocytogenesSteven Cai
Department of Food Science, Cornell University, Ithaca, New York 14853, USA
J Clin Microbiol 40:3319-25. 2002..Our specific results also show that inclusion of virulence gene target sequences in a DNA sequence-based subtyping scheme for L. monocytogenes is necessary to achieve maximum subtype differentiation... - Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibriumRasmus Nielsen
Department of Biometrics, Cornell University, 439 Warren Hall, Ithaca, NY 14853 7801, USA
Theor Popul Biol 63:245-55. 2003.... - A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype dataHong Gao
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
Genetics 176:1635-51. 2007..48-0.70)... - A likelihood ratio test for species membership based on DNA sequence dataMikhail V Matz
Whitney Laboratory for Marine Bioscience, Department of Molecular Genetics and Microbiology, University of Florida, 9505 Ocean Shore Blvd, Saint Augustine, FL 32080, USA
Philos Trans R Soc Lond B Biol Sci 360:1969-74. 2005.... - Ancient biomolecules from deep ice cores reveal a forested southern GreenlandEske Willerslev
Centre for Ancient Genetics, University of Copenhagen, Denmark
Science 317:111-4. 2007..The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections... - Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virusWeiwei Zhai
Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720 3140, USA
J Mol Evol 65:340-8. 2007..Our results suggest that it may be more difficult to use inferences regarding the strength of selection on mutations to make predictions regarding viral epidemics than previously thought... - Genome-wide patterns of nucleotide polymorphism in domesticated riceAna L Caicedo
Department of Genetics, North Carolina State University, Raleigh, North Carolina, USA
PLoS Genet 3:1745-56. 2007.... - Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid speciesJody Hey
Department of Genetics, Rutgers The State University of New Jersey, Piscataway, NJ 08854, USA
Mol Ecol 13:909-19. 2004..An example using Cichlid fishes from Lake Malawi is described. The analysis suggests that the species have been exchanging genes since the time they began to diverge... - Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sitesMaria Anisimova
Department of Biology, University College London, London WC1E 6BT, United Kingdom
Genetics 164:1229-36. 2003..Identification of sites under positive selection by the empirical Bayes method appears to be less affected than the LRT by recombination... - Stochastic mapping of morphological charactersJohn P Huelsenbeck
Section of Ecology, Behavior and Evolution, Division of Biology, University of California San Diego, La Jolla, California 92093 0116, USA
Syst Biol 52:131-58. 2003..Biol. 51:729-739) to the mapping of morphological characters under continuous-time Markov models and demonstrate here the utility of the method for mapping characters on trees and for identifying character correlation... - Population genetic analysis of shotgun assemblies of genomic sequences from multiple individualsInes Hellmann
Departments of Integrative Biology and Statistics, University of California, Berkeley, California 94720, USA
Genome Res 18:1020-9. 2008..Finally, we identify a number of genomic regions with increased or reduced diversity compared with the local level of human-chimpanzee divergence and the local recombination rate... - Codon-substitution models for detecting molecular adaptation at individual sites along specific lineagesZiheng Yang
Galton Laboratory, Department of Biology, University College London
Mol Biol Evol 19:908-17. 2002..Additional tests on several data sets suggest that the new models may be useful in detecting positive selection after gene duplication in gene family evolution... 
The effect of ancient DNA damage on inferences of demographic historiesErik Axelsson
Department of Biology, Evolutionary Biology, Copenhagen University, Copenhagen, Denmark
Mol Biol Evol 25:2181-7. 2008..Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution...- The cost of inbreeding in ArabidopsisCarlos D Bustamante
Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
Nature 416:531-4. 2002.... - A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodentsCarlos D Bustamante
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Mol Biol Evol 19:110-7. 2002.... - Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populationsPer J Palsbøll
Ecosystem Science Division ESPM, University of California at Berkeley, 151 Hilgard Hall, 3110, Berkeley, California 94720 3110, USA
Evolution 58:670-5. 2004..Intensive commercial shore-based whaling during the 1920s removed substantial numbers of fin whales in the Strait of Gibraltar and this local population has seemingly since failed to recover... - Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular levelJianzhi Zhang
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
Mol Biol Evol 22:2472-9. 2005..Bayes empirical Bayes identification of amino acid sites under positive selection along the foreground branches was found to be reliable, but lacked power... - Human genomics: disclosure of variationRasmus Nielsen
Nature 434:288-9. 2005 - Maximum likelihood estimation of ancestral codon usage bias parameters in DrosophilaRasmus Nielsen
Institute of Biology and Centre for Bioinformatics, University of Copenhagen, Copenhagen, Denmark
Mol Biol Evol 24:228-35. 2007..melanogaster lineage. For example, we also confirm previous results showing that the Notch locus has experienced positive selection for previously classified unpreferred mutations... - Adaptive genic evolution in the Drosophila genomesJoshua A Shapiro
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
Proc Natl Acad Sci U S A 104:2271-6. 2007..Finally, we discuss the theories and data pertaining to the interpretation of adaptive evolution in genomic studies... - Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population geneticsJody Hey
Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08846, USA
Proc Natl Acad Sci U S A 104:2785-90. 2007..Several examples, including an application to the divergence of chimpanzee subspecies, are provided... - Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrataLuis A Pastene
Institute of Cetacean Research, 4 5 Toyomi cho, Chuo Ku, Tokyo 104 0055, Japan
Mol Ecol 16:1481-95. 2007..Our hypothesis that prolonged periods of global warming facilitate speciation in pelagic marine species that depend on upwelling should be tested by comparative analyses in other pelagic species... - Bayes empirical bayes inference of amino acid sites under positive selectionZiheng Yang
Department of Biology, University College London, London, UK
Mol Biol Evol 22:1107-18. 2005..The results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach, while in large data sets it retains the good power of the NEB approach for inferring positively selected sites... - Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolutionStephen Richards
Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas 77030, USA
Genome Res 15:1-18. 2005..Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila... - Is haplotype block identification useful for association mapping studies?Weiwei Zhai
Genet Epidemiol 27:80-3. 2004 - A Bayesian multilocus association method: allowing for higher-order interaction in association studiesAnders Albrechtsen
Bioinformatics Centre, University of Copenhagen, 2100 Copenhagen, Denmark
Genetics 176:1197-208. 2007..It is computationally feasible even for a large number of possible interactions and differs fundamentally from most previous approaches by entertaining nonlinear interactions and by directly addressing the multiple-testing problem... - Evolutionary and biomedical insights from the rhesus macaque genomeRichard A Gibbs
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
Science 316:222-34. 2007..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...