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Rasmus Nielsen
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Research Profile (preview)
Concepts & Ideas
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Genes & Molecular Sequences
Physiology
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Network (preview)
17
Hubisz, Melissa
14
clark, andrew
12
Bustamante, Carlos
7
White, Thomas
7
Willerslev, Eske
6
Adams, Mark
5
Bollback, Jonathan
5
Bustamante, Carlos
5
Durrett, Richard
5
Gilbert, Thomas
5
Glanowski, Stephen
5
Hernandez, Ryan
5
Sninsky, John
5
York, Thomas
5
Williamson, Scott
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Geonetwork of Rasmus Nielsen (preview)
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All Publications
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2009: Andrés Aida M; Hubisz Melissa J; Indap Amit; Torgerson Dara G; Degenhardt Jeremiah D; Boyko Adam R; Gutenkunst Ryan N; White Thomas J; Green Eric D; Bustamante Carlos D; Clark Andrew G; Nielsen Rasmus
Targets of balancing selection in the human genome.
Molecular biology and evolution 2009;26(12):2755-64.
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2009: Nielsen Rasmus
Adaptionism-30 years after Gould and Lewontin.
Evolution; international journal of organic evolution 2009;63(10):2487-90.
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2009: Nielsen Rasmus; Hubisz Melissa J; Hellmann Ines; Torgerson Dara; Andrés Aida M; Albrechtsen Anders; Gutenkunst Ryan; Adams Mark D; Cargill Michele; Boyko Adam; Indap Amit; Bustamante Carlos D; Clark Andrew G
Darwinian and demographic forces affecting human protein coding genes.
Genome research 2009;19(5):838-49.
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2009: Albrechtsen Anders; Sand Korneliussen Thorfinn; Moltke Ida; van Overseem Hansen Thomas; Nielsen Finn Cilius; Nielsen Rasmus
Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium.
Genetic epidemiology 2009;33(3):266-74.
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2009: Nielsen Rasmus; Beaumont Mark A
Statistical inferences in phylogeography.
Molecular ecology 2009;18(6):1034-47.
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2009: Ramírez-Soriano Anna; Nielsen Rasmus
Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process.
Genetics 2009;181(2):701-10.
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2009: Pool John E; Nielsen Rasmus
Inference of historical changes in migration rate from the lengths of migrant tracts.
Genetics 2009;181(2):711-9.
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2009: Zhai Weiwei; Nielsen Rasmus; Slatkin Montgomery
An investigation of the statistical power of neutrality tests based on comparative and population genetic data.
Molecular biology and evolution 2009;26(2):273-83.
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2008: Munch Kasper; Boomsma Wouter; Willerslev Eske; Nielsen Rasmus
Fast phylogenetic DNA barcoding.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2008;363(1512):3997-4002.
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2008: Munch Kasper; Boomsma Wouter; Huelsenbeck John P; Willerslev Eske; Nielsen Rasmus
Statistical assignment of DNA sequences using Bayesian phylogenetics.
Systematic biology 2008;57(5):750-7.
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2008: Axelsson Erik; Willerslev Eske; Gilbert M Thomas P; Nielsen Rasmus
The effect of ancient DNA damage on inferences of demographic histories.
Molecular biology and evolution 2008;25(10):2181-7.
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2008: Pool John E; Nielsen Rasmus
The impact of founder events on chromosomal variability in multiply mating species.
Molecular biology and evolution 2008;25(8):1728-36.
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2008: Hellmann Ines; Mang Yuan; Gu Zhiping; Li Peter; de la Vega Francisco M; Clark Andrew G; Nielsen Rasmus
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals.
Genome research 2008;18(7):1020-9.
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2008: Boyko Adam R; Williamson Scott H; Indap Amit R; Degenhardt Jeremiah D; Hernandez Ryan D; Lohmueller Kirk E; Adams Mark D; Schmidt Steffen; Sninsky John J; Sunyaev Shamil R; White Thomas J; Nielsen Rasmus; Clark Andrew G; Bustamante Carlos D
Assessing the evolutionary impact of amino acid mutations in the human genome.
PLoS genetics 2008;4(5):e1000083.
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2008: Bollback Jonathan P; York Thomas L; Nielsen Rasmus
Estimation of 2Nes from temporal allele frequency data.
Genetics 2008;179(1):497-502.
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2008: Yang Ziheng; Nielsen Rasmus
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage.
Molecular biology and evolution 2008;25(3):568-79.
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2008: Lohmueller Kirk E; Indap Amit R; Schmidt Steffen; Boyko Adam R; Hernandez Ryan D; Hubisz Melissa J; Sninsky John J; White Thomas J; Sunyaev Shamil R; Nielsen Rasmus; Clark Andrew G; Bustamante Carlos D
Proportionally more deleterious genetic variation in European than in African populations.
Nature 2008;451(7181):994-7.
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2008: Kosiol Carolin; Vinar Tomás; da Fonseca Rute R; Hubisz Melissa J; Bustamante Carlos D; Nielsen Rasmus; Siepel Adam
Patterns of positive selection in six Mammalian genomes.
PLoS genetics 2008;4(8):e1000144.
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2007: Singh Nadia D; Bauer DuMont Vanessa L; Hubisz Melissa J; Nielsen Rasmus; Aquadro Charles F
Patterns of mutation and selection at synonymous sites in Drosophila.
Molecular biology and evolution 2007;24(12):2687-97.
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2007: Pool John E; Nielsen Rasmus
Population size changes reshape genomic patterns of diversity.
Evolution; international journal of organic evolution 2007;61(12):3001-6.
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2007: Nielsen Rasmus; Hellmann Ines; Hubisz Melissa; Bustamante Carlos; Clark Andrew G
Recent and ongoing selection in the human genome.
Nature reviews. Genetics 2007;8(11):857-68.
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2007: Caicedo Ana L; Williamson Scott H; Hernandez Ryan D; Boyko Adam; Fledel-Alon Adi; York Thomas L; Polato Nicholas R; Olsen Kenneth M; Nielsen Rasmus; McCouch Susan R; Bustamante Carlos D; Purugganan Michael D
Genome-wide patterns of nucleotide polymorphism in domesticated rice.
PLoS genetics 2007;3(9):1745-56.
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2007: Johnson Sarah Stewart; Hebsgaard Martin B; Christensen Torben R; Mastepanov Mikhail; Nielsen Rasmus; Munch Kasper; Brand Tina; Gilbert M Thomas P; Zuber Maria T; Bunce Michael; Rønn Regin; Gilichinsky David; Froese Duane; Willerslev Eske
Ancient bacteria show evidence of DNA repair.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(36):14401-5.
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2007: Petersen Lise; Bollback Jonathan P; Dimmic Matt; Hubisz Melissa; Nielsen Rasmus
Genes under positive selection in Escherichia coli.
Genome research 2007;17(9):1336-43.
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2007: Wong Wendy S W; Nielsen Rasmus
Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models.
Bioinformatics (Oxford, England) 2007;23(16):2031-7.
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2007: Willerslev Eske; Cappellini Enrico; Boomsma Wouter; Nielsen Rasmus; Hebsgaard Martin B; Brand Tina B; Hofreiter Michael; Bunce Michael; Poinar Hendrik N; Dahl-Jensen Dorthe; Johnsen Sigfus; Steffensen Jørgen Peder; Bennike Ole; Schwenninger Jean-Luc; Nathan Roger; Armitage Simon; de Hoog Cees-Jan; Alfimov Vasily; Christl Marcus; Beer Juerg; Muscheler Raimund; Barker Joel; Sharp Martin; Penkman Kirsty E H; Haile James; Taberlet Pierre; Gilbert M Thomas P; Casoli Antonella; Campani Elisa; Collins Matthew J
Ancient biomolecules from deep ice cores reveal a forested southern Greenland.
Science (New York, N.Y.) 2007;317(5834):111-4.
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2007: Williamson Scott H; Hubisz Melissa J; Clark Andrew G; Payseur Bret A; Bustamante Carlos D; Nielsen Rasmus
Localizing recent adaptive evolution in the human genome.
PLoS genetics 2007;3(6):e90.
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2007: Albrechtsen Anders; Castella Sofie; Andersen Gitte; Hansen Torben; Pedersen Oluf; Nielsen Rasmus
A Bayesian multilocus association method: allowing for higher-order interaction in association studies.
Genetics 2007;176(2):1197-208.
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2007: Hernandez Ryan D; Hubisz Melissa J; Wheeler David A; Smith David G; Ferguson Betsy; Rogers Jeffrey; Nazareth Lynne; Indap Amit; Bourquin Traci; McPherson John; Muzny Donna; Gibbs Richard; Nielsen Rasmus; Bustamante Carlos D
Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques.
Science (New York, N.Y.) 2007;316(5822):240-3.
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2007: Pastene Luis A; Goto Mutsuo; Kanda Naohisa; Zerbini Alexandre N; Kerem Dan; Watanabe Kazuo; Bessho Yoshitaka; Hasegawa Masami; Nielsen Rasmus; Larsen Finn; Palsbøll Per J
Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata.
Molecular ecology 2007;16(7):1481-95.
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2007: Haile James; Holdaway Richard; Oliver Karen; Bunce Michael; Gilbert M Thomas P; Nielsen Rasmus; Munch Kasper; Ho Simon Y W; Shapiro Beth; Willerslev Eske
Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?
Molecular biology and evolution 2007;24(4):982-9.
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2007: Shapiro Joshua A; Huang Wei; Zhang Chenhui; Hubisz Melissa J; Lu Jian; Turissini David A; Fang Shu; Wang Hurng-Yi; Hudson Richard R; Nielsen Rasmus; Chen Zhu; Wu Chung-I
Adaptive genic evolution in the Drosophila genomes.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(7):2271-6.
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2007: Nielsen Rasmus; Bauer DuMont Vanessa L; Hubisz Melissa J; Aquadro Charles F
Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila.
Molecular biology and evolution 2007;24(1):228-35.
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2007: York Thomas L; Durrett Rick; Nielsen Rasmus
Dependence of paracentric inversion rate on tract length.
BMC bioinformatics 2007;8():115.
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2007: Binladen Jonas; Gilbert M Thomas P; Bollback Jonathan P; Panitz Frank; Bendixen Christian; Nielsen Rasmus; Willerslev Eske
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.
PloS one 2007;2(2):e197.
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2006: Nightingale K K; Lyles K; Ayodele M; Jalan P; Nielsen R; Wiedmann M
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 2006;44(10):3742-51.
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2006: Hobolth Asger; Nielsen Rasmus; Wang Ying; Wu Feinan; Tanksley Steven D
CpG + CpNpG analysis of protein-coding sequences from tomato.
Molecular biology and evolution 2006;23(6):1318-23.
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2006: Nielsen Rasmus; Matz Mikhail
Statistical approaches for DNA barcoding.
Systematic biology 2006;55(1):162-9.
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2006: Nielsen Rasmus
Evolution. Why sex?
Science (New York, N.Y.) 2006;311(5763):960-1.
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2006: Wong Wendy S W; Sainudiin Raazesh; Nielsen Rasmus
Identification of physicochemical selective pressure on protein encoding nucleotide sequences.
BMC bioinformatics 2006;7():148.
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2005: Wang Y; van der Hoeven R S; Nielsen R; Mueller L A; Tanksley S D
Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 2005;112(1):72-84.
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2005: Nielsen Rasmus; Williamson Scott; Kim Yuseob; Hubisz Melissa J; Clark Andrew G; Bustamante Carlos
Genomic scans for selective sweeps using SNP data.
Genome research 2005;15(11):1566-75.
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2005: Clark Andrew G; Hubisz Melissa J; Bustamante Carlos D; Williamson Scott H; Nielsen Rasmus
Ascertainment bias in studies of human genome-wide polymorphism.
Genome research 2005;15(11):1496-502.
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2005: Bustamante Carlos D; Fledel-Alon Adi; Williamson Scott; Nielsen Rasmus; Hubisz Melissa Todd; Glanowski Stephen; Tanenbaum David M; White Thomas J; Sninsky John J; Hernandez Ryan D; Civello Daniel; Adams Mark D; Cargill Michele; Clark Andrew G
Natural selection on protein-coding genes in the human genome.
Nature 2005;437(7062):1153-7.
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2005: Nielsen Rasmus
Demography: peopling the Americas.
European journal of human genetics : EJHG 2005;13(10):1100-1.
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2005: Dimmic Matthew W; Hubisz Melissa J; Bustamante Carlos D; Nielsen Rasmus
Detecting coevolving amino acid sites using Bayesian mutational mapping.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i126-35.
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2005: Nielsen Rasmus; Bustamante Carlos; Clark Andrew G; Glanowski Stephen; Sackton Timothy B; Hubisz Melissa J; Fledel-Alon Adi; Tanenbaum David M; Civello Daniel; White Thomas J; J Sninsky John; Adams Mark D; Cargill Michele
A scan for positively selected genes in the genomes of humans and chimpanzees.
PLoS biology 2005;3(6):e170.
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2005: Williamson Scott H; Hernandez Ryan; Fledel-Alon Adi; Zhu Lan; Nielsen Rasmus; Bustamante Carlos D
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 2005;102(22):7882-7.
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2005: York Thomas L; Durrett Richard T; Tanksley Steven; Nielsen Rasmus
Bayesian and maximum likelihood estimation of genetic maps.
Genetical research 2005;85(2):159-68.
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2005: Sainudiin Raazesh; Wong Wendy Shuk Wan; Yogeeswaran Krithika; Nasrallah June B; Yang Ziheng; Nielsen Rasmus
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 2005;60(3):315-26.
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2005: Nielsen Rasmus; Hubisz Melissa J
Evolutionary genomics: detecting selection needs comparative data.
Nature 2005;433(7023):E6; discussion E7-8.
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2005: Nielsen Rasmus
Molecular signatures of natural selection.
Annual review of genetics 2005;39():197-218.
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2004: Jobson Richard W; Nielsen Rasmus; Laakkonen Liisa; Wikström Mårten; Albert Victor A
Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(52):18064-8.
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2004: Nielsen Rasmus; Hubisz Melissa J; Clark Andrew G
Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data.
Genetics 2004;168(4):2373-82.
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2004: Wong Wendy S W; Yang Ziheng; Goldman Nick; Nielsen Rasmus
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites.
Genetics 2004;168(2):1041-51.
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2004: Sainudiin Raazesh; Durrett Richard T; Aquadro Charles F; Nielsen Rasmus
Microsatellite mutation models: insights from a comparison of humans and chimpanzees.
Genetics 2004;168(1):383-95.
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2004: Kim Yuseob; Nielsen Rasmus
Linkage disequilibrium as a signature of selective sweeps.
Genetics 2004;167(3):1513-24.
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2004: Wong Wendy S W; Nielsen Rasmus
Detecting selection in noncoding regions of nucleotide sequences.
Genetics 2004;167(2):949-58.
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2004: Nielsen Rasmus
Population genetic analysis of ascertained SNP data.
Human genomics 2004;1(3):218-24.
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2004: Palsbøll Per J; Bérubé Martine; Aguilar Alex; Notarbartolo-Di-Sciara Giuseppe; Nielsen Rasmus
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) populations.
Evolution; international journal of organic evolution 2004;58(3):670-5.
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2004: Durrett Richard; Nielsen Rasmus; York Thomas L
Bayesian estimation of genomic distance.
Genetics 2004;166(1):621-9.
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2003: Clark Andrew G; Glanowski Stephen; Nielsen Rasmus; Thomas Paul D; Kejariwal Anish; Todd Melissa A; Tanenbaum David M; Civello Daniel; Lu Fu; Murphy Brian; Ferriera Steve; Wang Gary; Zheng Xianqgun; White Thomas J; Sninsky John J; Adams Mark D; Cargill Michele
Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios.
Science (New York, N.Y.) 2003;302(5652):1960-3.
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2003: Nielsen Rasmus; Tarpy David R; Reeve H Kern
Estimating effective paternity number in social insects and the effective number of alleles in a population.
Molecular ecology 2003;12(11):3157-64.
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2003: Clark Andrew G; Nielsen Rasmus; Signorovitch James; Matise Tara C; Glanowski Stephen; Heil Jeremy; Winn-Deen Emily S; Holden Arthur L; Lai Eric
Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome.
American journal of human genetics 2003;73(2):285-300.
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2003: Nielsen Rasmus; Yang Ziheng
Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA.
Molecular biology and evolution 2003;20(8):1231-9.
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2003: Nielsen Rasmus; Signorovitch James
Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium.
Theoretical population biology 2003;63(3):245-55.
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2003: Huelsenbeck John P; Nielsen Rasmus; Bollback Jonathan P
Stochastic mapping of morphological characters.
Systematic biology 2003;52(2):131-58.
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2003: Bustamante Carlos D; Nielsen Rasmus; Hartl Daniel L
Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data.
Theoretical population biology 2003;63(2):91-103.
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2003: Clark A G; Glanowski S; Nielsen R; Thomas P; Kejariwal A; Todd M J; Tanenbaum D M; Civello D; Lu F; Murphy B; Ferriera S; Wang G; Zheng X; White T J; Sninsky J J; Adams M D; Cargill M
Positive selection in the human genome inferred from human-chimp-mouse orthologous gene alignments.
Cold Spring Harbor symposia on quantitative biology 2003;68():471-7.
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2002: Cai Steven; Kabuki Dirce Yorika; Kuaye Arnaldo Yoshiteru; Cargioli Theresa Gina; Chung Michael S; Nielsen Rasmus; Wiedmann Martin
Rational design of DNA sequence-based strategies for subtyping Listeria monocytogenes.
Journal of clinical microbiology 2002;40(9):3319-25.
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2002: Bustamante Carlos D; Nielsen Rasmus; Sawyer Stanley A; Olsen Kenneth M; Purugganan Michael D; Hartl Daniel L
The cost of inbreeding in Arabidopsis.
Nature 2002;416(6880):531-4.
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2002: Signorovitch J; Nielsen R
PATRI-paternity inference using genetic data.
Bioinformatics (Oxford, England) 2002;18(2):341-2.
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2002: Bustamante Carlos D; Nielsen Rasmus; Hartl Daniel L
A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents.
Molecular biology and evolution 2002;19(1):110-7.
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2002: York Thomas L; Durrett Richard; Nielsen Rasmus
Bayesian estimation of the number of inversions in the history of two chromosomes.
Journal of computational biology : a journal of computational molecular cell biology 2002;9(6):805-18.
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2001: Huelsenbeck J P; Ronquist F; Nielsen R; Bollback J P
Bayesian inference of phylogeny and its impact on evolutionary biology.
Science (New York, N.Y.) 2001;294(5550):2310-4.
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2001: Wakeley J; Nielsen R; Liu-Cordero S N; Ardlie K
The discovery of single-nucleotide polymorphisms--and inferences about human demographic history.
American journal of human genetics 2001;69(6):1332-47.
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2001: Nielsen R
Mutations as missing data: inferences on the ages and distributions of nonsynonymous and synonymous mutations.
Genetics 2001;159(1):401-11.
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2001: Nielsen R; Wakeley J
Distinguishing migration from isolation: a Markov chain Monte Carlo approach.
Genetics 2001;158(2):885-96.
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2001: Nielsen R; Mattila D K; Clapham P J; Palsbøll P J
Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale.
Genetics 2001;157(4):1673-82.
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2000: Nielsen R
Estimation of population parameters and recombination rates from single nucleotide polymorphisms.
Genetics 2000;154(2):931-42.
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1999: Nielsen R; Weinreich D M
The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory.
Genetics 1999;153(1):497-506.
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1999: Huelsenbeck J P; Nielsen R
Effect of nonindependent substitution on phylogenetic accuracy.
Systematic biology 1999;48(2):317-28.
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