Rasmus Nielsen

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing
    Ying Hui Li
    Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement NFCRI Key Lab of Germplasm Utilization MOA, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
    BMC Genomics 14:579. 2013
  2. pmc Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data
    Thorfinn Sand Korneliussen
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oestervoldgade 5 7, DK 1350, Copenhagen, Denmark
    BMC Bioinformatics 14:289. 2013
  3. pmc Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes
    A Albrechtsen
    Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
    Diabetologia 56:298-310. 2013
  4. pmc SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data
    Rasmus Nielsen
    BGI Shenzhen, Shenzhen, China
    PLoS ONE 7:e37558. 2012
  5. pmc Genotype and SNP calling from next-generation sequencing data
    Rasmus Nielsen
    Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
    Nat Rev Genet 12:443-51. 2011
  6. doi request reprint Statistical inferences in phylogeography
    Rasmus Nielsen
    Departments of Integrative Biology and Statistics, University of California, Berkeley, 94720, USA
    Mol Ecol 18:1034-47. 2009
  7. doi request reprint Design of association studies with pooled or un-pooled next-generation sequencing data
    Su Yeon Kim
    Department of Integrative Biology, UC Berkeley, Berkeley, California 94720, USA
    Genet Epidemiol 34:479-91. 2010
  8. pmc Quantifying population genetic differentiation from next-generation sequencing data
    Matteo Fumagalli
    Department of Integrative Biology, University of California, Berkeley, California 94720
    Genetics 195:979-92. 2013
  9. pmc Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome
    Kirk E Lohmueller
    Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
    PLoS Genet 7:e1002326. 2011
  10. doi request reprint Statistical assignment of DNA sequences using Bayesian phylogenetics
    Kasper Munch
    Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
    Syst Biol 57:750-7. 2008

Collaborators

Detail Information

Publications44

  1. pmc Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing
    Ying Hui Li
    Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement NFCRI Key Lab of Germplasm Utilization MOA, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
    BMC Genomics 14:579. 2013
    ....
  2. pmc Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data
    Thorfinn Sand Korneliussen
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oestervoldgade 5 7, DK 1350, Copenhagen, Denmark
    BMC Bioinformatics 14:289. 2013
    ....
  3. pmc Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes
    A Albrechtsen
    Centre of Bioinformatics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
    Diabetologia 56:298-310. 2013
    ..Here we applied exome sequencing to identify novel associations of coding polymorphisms at minor allele frequencies (MAFs) >1% with common metabolic phenotypes...
  4. pmc SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data
    Rasmus 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...
  5. pmc Genotype and SNP calling from next-generation sequencing data
    Rasmus 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...
  6. doi request reprint Statistical inferences in phylogeography
    Rasmus 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...
  7. doi request reprint Design of association studies with pooled or un-pooled next-generation sequencing data
    Su 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...
  8. pmc Quantifying population genetic differentiation from next-generation sequencing data
    Matteo Fumagalli
    Department of Integrative Biology, University of California, Berkeley, California 94720
    Genetics 195:979-92. 2013
    ..We find that we can infer the fine-scale genetic structure of the sampled individuals, suggesting that employing this new method is useful for investigating the genetic relationships of populations sampled at low coverage. ..
  9. pmc Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome
    Kirk 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...
  10. doi request reprint Statistical assignment of DNA sequences using Bayesian phylogenetics
    Kasper 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...
  11. pmc Estimation of allele frequency and association mapping using next-generation sequencing data
    Su 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...
  12. pmc Sequencing of 50 human exomes reveals adaptation to high altitude
    Xin 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...
  13. pmc ngsTools: methods for population genetics analyses from next-generation sequencing data
    Matteo Fumagalli
    Department of Integrative Biology, Department of Statistics, University of California, Berkeley, CA 94720, USA and Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
    Bioinformatics 30:1486-7. 2014
    ..The methods implemented in these programs do not rely on single-nucleotide polymorphism or genotype calling and are particularly suitable for low sequencing depth data...
  14. pmc Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA
    Emilia Huerta-Sanchez
    1 BGI Shenzhen, Shenzhen 518083, China 2 Department of Integrative Biology, University of California, Berkeley, California 94720 USA 3 School of Natural Sciences, University of California, Merced, California 95343 USA 4
    Nature 512:194-7. 2014
    ..Our findings illustrate that admixture with other hominin species has provided genetic variation that helped humans to adapt to new environments. ..
  15. pmc Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population
    Shengting Li
    1 Bioinformatics Research Centre, Aarhus University, C F Mollers Alle, 8000 Aarhus C, Denmark 2 BGI Shenzhen, Shenzhen, China
    Eur J Hum Genet 22:1040-5. 2014
    ..Population genetics analysis using Bayesian skyline plot shows a recent history of rapid population growth in the Danish population in accordance with the fact that >40% of variable sites are observed as singletons. ..
  16. pmc Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears
    Shiping Liu
    BGI Shenzhen, Shenzhen 518083, China School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510641, China
    Cell 157:785-94. 2014
    ....
  17. pmc Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes
    Kirk E Lohmueller
    Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Am J Hum Genet 93:1072-86. 2013
    ..Thus, we could reject a model for the genetic architecture of type 2 diabetes where rare nonsynonymous variants clustered in a modest number of genes (fewer than 20) are responsible for the majority of disease risk. ..
  18. pmc Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
    Filipe G Vieira
    Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA
    Genome Res 23:1852-61. 2013
    ..We demonstrate the applicability and efficacy of these methods in both simulated and real data sets. ..
  19. doi request reprint Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants
    Yingrui 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...
  20. pmc Inference of historical changes in migration rate from the lengths of migrant tracts
    John 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...
  21. pmc Unlocking the vault: next-generation museum population genomics
    Ke Bi
    Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, California, 94720, USA
    Mol Ecol 22:6018-32. 2013
    ..Such technical advances greatly enhance the value of museum collections, even where a pre-existing reference is lacking and points to a broad range of potential applications in evolutionary and conservation biology...
  22. pmc Natural selection reduced diversity on human y chromosomes
    Melissa A Wilson Sayres
    Statistics Department, University of California Berkeley, Berkeley, California, United States of America Integrative Biology Department, University of California Berkeley, Berkeley, California, United States of America
    PLoS Genet 10:e1004064. 2014
    ..Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area. ..
  23. ncbi request reprint Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virus
    Weiwei 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...
  24. pmc An investigation of the statistical power of neutrality tests based on comparative and population genetic data
    Weiwei 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...
  25. doi request reprint Detecting adaptive trait loci in nonmodel systems: divergence or admixture mapping?
    Jacob E Crawford
    Department of Integrative Biology, University of California, Berkeley, 4134 Valley Life Sciences Building, Berkeley, CA, 94720 3140, USA
    Mol Ecol 22:6131-48. 2013
    ..Together with high-throughput exome sequencing, admixture mapping could be used to map ATL in systems such as Heliconius butterflies or Gryllus crickets when experimental design and analytical approach are chosen accordingly...
  26. pmc Fast phylogenetic DNA barcoding
    Kasper 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
    ....
  27. pmc Distinguishing between selective sweeps from standing variation and from a de novo mutation
    Benjamin 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...
  28. pmc The sequence and de novo assembly of the giant panda genome
    Ruiqiang Li
    BGI Shenzhen, Shenzhen 518083, China
    Nature 463:311-7. 2010
    ....
  29. pmc Population genetic inference from genomic sequence variation
    John 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...
  30. ncbi request reprint 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
    Per 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...
  31. pmc bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)
    Anna Sapfo Malaspinas
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720 3140, Ancestry com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
    Bioinformatics 30:2962-4. 2014
    ..Our tool is aimed at determining the ancestry of unknown samples-typical of ancient DNA data-particularly when only low amounts of data are available for those samples...
  32. pmc A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes
    Mehmet Somel
    Department of Integrative Biology, University of California, Berkeley, CA, USA
    Mol Biol Evol 30:1808-15. 2013
    ..Human proteasome genes also bear no evidence of recent positive or balancing selection. These results suggest human-specific relaxation of negative selection in proteasome subunits; the exact biological causes, however, remain unknown. ..
  33. pmc The impact of founder events on chromosomal variability in multiply mating species
    John 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...
  34. pmc Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
    Ines 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...
  35. pmc Evidence for archaic adaptive introgression in humans
    Fernando Racimo
    Department of Integrative Biology, University of California, Berkeley, Berkeley, California 97420, USA
    Nat Rev Genet 16:359-71. 2015
    ..Finally, we discuss challenges and recommendations for inferring selection on introgressed regions. ..
  36. pmc Genetic signatures reveal high-altitude adaptation in a set of ethiopian populations
    Emilia Huerta-Sanchez
    Department of Integrative Biology, University of California, Berkeley, CA, USA
    Mol Biol Evol 30:1877-88. 2013
    ..These results support the view that Ethiopian, Andean, and Tibetan populations living at high altitude have adapted to hypoxia differently, with convergent evolution affecting different genes from the same pathway. ..
  37. pmc On detecting incomplete soft or hard selective sweeps using haplotype structure
    Anna Ferrer-Admetlla
    Department of Integrative Biology, University of California at Berkeley, Berkeley
    Mol Biol Evol 31:1275-91. 2014
    ..We propose that the underlying causes for the selection on these genes are pleiotropic effects relating to blood parasites rather than their role in lipid metabolism. ..
  38. pmc Inferring demographic history from a spectrum of shared haplotype lengths
    Kelley Harris
    Department of Mathematics, University of California Berkeley, Berkeley, CA, USA
    PLoS Genet 9:e1003521. 2013
    ....
  39. pmc Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias
    Yong 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...
  40. doi request reprint Greenlandic Inuit show genetic signatures of diet and climate adaptation
    Matteo Fumagalli
    Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
    Science 349:1343-7. 2015
    ..By analyzing membrane lipids, we found that the selected alleles modulate fatty acid composition, which may affect the regulation of growth hormones. Thus, the Inuit have genetic and physiological adaptations to a diet rich in PUFAs. ..
  41. pmc The lengths of admixture tracts
    Mason Liang
    University of California, Berkeley, California 94108
    Genetics 197:953-67. 2014
    ..This representation is useful for analyzing admixture tract-length distributions for populations with recent admixture, a scenario in which existing models perform poorly. ..
  42. pmc Error-prone polymerase activity causes multinucleotide mutations in humans
    Kelley Harris
    Department of Mathematics, University of California Berkeley, Berkeley, California 94703, USA
    Genome Res 24:1445-54. 2014
    ..We develop statistical estimates of MNM prevalence that can be used to correct phylogenetic and population genetic inferences for the presence of complex mutations. ..
  43. doi request reprint A metagenome-wide association study of gut microbiota in type 2 diabetes
    Junjie 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...
  44. doi request reprint Positive selection on apoptosis related genes
    Rute 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...