Research Topics
Species | Rasmus NielsenSummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing dataRasmus Nielsen
BGI Shenzhen, Shenzhen, China
PLoS ONE 7:e37558. 2012..We evaluate the statistical properties of the methods using simulations and by application to a real data set...- Genotype and SNP calling from next-generation sequencing dataRasmus Nielsen
Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
Nat Rev Genet 12:443-51. 2011..We review these methods and provide a guide for their use in NGS studies... 
Statistical inferences in phylogeographyRasmus Nielsen
Departments of Integrative Biology and Statistics, University of California, Berkeley, 94720, USA
Mol Ecol 18:1034-47. 2009..In this review, we will describe the development of statistical methods in phylogeographic analysis, and discuss some of the challenges facing these methods...- Design of association studies with pooled or un-pooled next-generation sequencing dataSu Yeon Kim
Department of Integrative Biology, UC Berkeley, Berkeley, California 94720, USA
Genet Epidemiol 34:479-91. 2010..Our results provide guidelines for researchers who are developing association mapping studies based on next-generation sequencing... - Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genomeKirk E Lohmueller
Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
PLoS Genet 7:e1002326. 2011..This work suggests that natural selection has affected multiple aspects of linked neutral variation throughout the human genome and that positive selection is not required to explain these observations... - Statistical assignment of DNA sequences using Bayesian phylogeneticsKasper Munch
Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
Syst Biol 57:750-7. 2008..However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA... - Sequencing of 50 human exomes reveals adaptation to high altitudeXin Yi
BGI Shenzhen, Shenzhen 518083, China
Science 329:75-8. 2010..This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude... - Estimation of allele frequency and association mapping using next-generation sequencing dataSu Yeon Kim
Departments of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA 94720, USA
BMC Bioinformatics 12:231. 2011..g., < 15X). However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates... - Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variantsYingrui Li
BGI Shenzhen, Shenzhen, China
Nat Genet 42:969-72. 2010..This excess was more pronounced for X-linked SNPs, suggesting that deleterious substitutions are primarily recessive... - Inference of historical changes in migration rate from the lengths of migrant tractsJohn E Pool
Department of Statistics, University of California, Berkeley, California 94720, USA
Genetics 181:711-9. 2009..m. musculus, we find evidence for an increase in the rate of hybridization. Our findings could indicate an evolutionary trajectory toward fusion rather than speciation in these taxa... 
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...- An investigation of the statistical power of neutrality tests based on comparative and population genetic dataWeiwei Zhai
Department of Integrative Biology, University of California, Berkeley, USA
Mol Biol Evol 26:273-83. 2009..We discuss our findings in the light of the discordant results obtained in several recently published genomic scans... - Fast phylogenetic DNA barcodingKasper Munch
Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
Philos Trans R Soc Lond B Biol Sci 363:3997-4002. 2008.... - Distinguishing between selective sweeps from standing variation and from a de novo mutationBenjamin M Peter
Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
PLoS Genet 8:e1003011. 2012..We also confirm evidence of selection for one further gene, TRPV6. In one gene, G6PD, neither neutral models nor models of selective sweeps fit the data, presumably because this locus has been subject to balancing selection... - The sequence and de novo assembly of the giant panda genomeRuiqiang Li
BGI Shenzhen, Shenzhen 518083, China
Nature 463:311-7. 2010.... - Population genetic inference from genomic sequence variationJohn E Pool
Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA
Genome Res 20:291-300. 2010..Here, we assess the challenges to analyzing whole-genome sequence polymorphism data, and we discuss the potential of these data to yield new insights concerning population history and the genomic prevalence of natural selection... - 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... - The impact of founder events on chromosomal variability in multiply mating speciesJohn E Pool
Department of Integrative Biology, University of California, Berkeley, USA
Mol Biol Evol 25:1728-36. 2008..Investigating the potential of this process to account for sharply reduced X-linked diversity in European Drosophila melanogaster, we find that this model yields predictions that are compatible with the empirical data... - 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... - Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment biasYong Wang
Department of Integrative Biology, University of California, 3060 VLSB, Berkeley, CA 94720, USA
Mol Ecol 21:974-86. 2012..We evaluate the methods by simulations and by applying them to a large SNP data set of seven East Asian populations... - A metagenome-wide association study of gut microbiota in type 2 diabetesJunjie Qin
BGI Shenzhen, Shenzhen 518083, China
Nature 490:55-60. 2012..An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes... - Positive selection on apoptosis related genesRute R da Fonseca
Department of Integrative Biology, UC Berkeley, Berkeley, CA 94720, USA
FEBS Lett 584:469-76. 2010..Trade-offs in fitness are expected out of these selective pressures, which could explain the involvement of these genes in various diseases, including cancer...