Magnus Nordborg

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. ncbi request reprint Molecular population genetics
    Magnus Nordborg
    Department of Biological Sciences, University of Southern California, 835 W 37th St, SHS 172, Los Angeles, California 90089 1340, USA
    Curr Opin Plant Biol 5:69-73. 2002
  2. ncbi request reprint Linkage disequilibrium: what history has to tell us
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, 835 W 37th St, SHS172, Los Angeles, CA 90089 134, USA
    Trends Genet 18:83-90. 2002
  3. pmc The pattern of polymorphism in Arabidopsis thaliana
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    PLoS Biol 3:e196. 2005
  4. pmc The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 163:1201-13. 2003
  5. doi request reprint Next-generation genetics in plants
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nature 456:720-3. 2008
  6. pmc An Arabidopsis example of association mapping in structured samples
    Keyan Zhao
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 3:e4. 2007
  7. pmc Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    Susanna Atwell
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nature 465:627-31. 2010
  8. pmc Association mapping with single-feature polymorphisms
    Sung Kim
    Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089 2910, USA
    Genetics 173:1125-33. 2006
  9. pmc Estimating recombination rates from single-nucleotide polymorphisms using summary statistics
    Badri Padhukasahasram
    Molecular and Computational Biology and Biostatistics Division, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
    Genetics 174:1517-28. 2006
  10. ncbi request reprint Recombination and linkage disequilibrium in Arabidopsis thaliana
    Sung Kim
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nat Genet 39:1151-5. 2007

Collaborators

Detail Information

Publications45

  1. ncbi request reprint Molecular population genetics
    Magnus Nordborg
    Department of Biological Sciences, University of Southern California, 835 W 37th St, SHS 172, Los Angeles, California 90089 1340, USA
    Curr Opin Plant Biol 5:69-73. 2002
    ..Furthermore, population genetics is becoming increasingly relevant to other fields of biology, for example to genetic epidemiology, because of disease gene mapping in general populations...
  2. ncbi request reprint Linkage disequilibrium: what history has to tell us
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, 835 W 37th St, SHS172, Los Angeles, CA 90089 134, USA
    Trends Genet 18:83-90. 2002
    ..The stochastic process known as the coalescent is a convenient way to model such genealogies, and in this paper we set out the theory behind the coalescent and its implications for understanding linkage disequilibrium...
  3. pmc The pattern of polymorphism in Arabidopsis thaliana
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    PLoS Biol 3:e196. 2005
    ..Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics...
  4. pmc The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 163:1201-13. 2003
    ..We focus in particular on the statistical power to detect balancing selection when it is present...
  5. doi request reprint Next-generation genetics in plants
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nature 456:720-3. 2008
    ....
  6. pmc An Arabidopsis example of association mapping in structured samples
    Keyan Zhao
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 3:e4. 2007
    ..Ultimately, association mapping is a powerful tool for identifying a list of candidates that is short enough to permit further genetic study...
  7. pmc Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    Susanna Atwell
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nature 465:627-31. 2010
    ..Our study demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms...
  8. pmc Association mapping with single-feature polymorphisms
    Sung Kim
    Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089 2910, USA
    Genetics 173:1125-33. 2006
    ..Finally, we show how power depends on the accuracy with which single-feature polymorphisms are called...
  9. pmc Estimating recombination rates from single-nucleotide polymorphisms using summary statistics
    Badri Padhukasahasram
    Molecular and Computational Biology and Biostatistics Division, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
    Genetics 174:1517-28. 2006
    ..We used our method to analyze a human data set recently genotyped by Perlegen Sciences...
  10. ncbi request reprint Recombination and linkage disequilibrium in Arabidopsis thaliana
    Sung Kim
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nat Genet 39:1151-5. 2007
    ..LD also reflects the action of selection, and it is more extensive between nonsynonymous polymorphisms than between synonymous polymorphisms...
  11. ncbi request reprint The evolution of selfing in Arabidopsis thaliana
    Chunlao Tang
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    Science 317:1070-2. 2007
    ..An analysis of the genome-wide pattern of linkage disequilibrium suggests that selfing most likely evolved roughly a million years ago or more...
  12. pmc A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome
    Christopher Toomajian
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    PLoS Biol 4:e137. 2006
    ..We introduce a novel test statistic based on haplotype sharing that embraces the problem of population structure, and so should be widely applicable...
  13. pmc Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana
    Vincent Plagnol
    Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089 2910, USA
    Genetics 172:2441-8. 2006
    ..The ratio of gene conversion to crossing over is estimated to be around one. We also find evidence for fine-scale variations of the crossing-over rate...
  14. pmc Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci
    Jenny Hagenblad
    Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA
    Genetics 168:1627-38. 2004
    ..No clear evidence for previously unknown alleles at either locus was found, but the effect of population structure in causing false positives was evident...
  15. pmc Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes
    Maria Jose Aranzana
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 1:e60. 2005
    ..However, the false positive rates were always substantial regardless of the trait, highlighting the necessity of an appropriate genomic control in association studies...
  16. pmc The pattern of polymorphism on human chromosome 21
    Hideki Innan
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Genome Res 13:1158-68. 2003
    ....
  17. ncbi request reprint Recombination or mutational hot spots in human mtDNA?
    Hideki Innan
    Molecular and Computational Biology, University of Southern California, CA 90089 1340, USA
    Mol Biol Evol 19:1122-7. 2002
    ..Thus, there appears to be no evidence for recombination in the mtDNA polymorphism data. In conclusion, we discuss the possibility of detecting recombination in mtDNA and the implications of its existence...
  18. pmc The extent of linkage disequilibrium and haplotype sharing around a polymorphic site
    Hideki Innan
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 165:437-44. 2003
    ..The implications of our results for data analysis, and in particular for detecting selection, are discussed...
  19. ncbi request reprint The extent of linkage disequilibrium in Arabidopsis thaliana
    Magnus Nordborg
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    Nat Genet 30:190-3. 2002
    ..The combination of a relatively high level of polymorphism and extensive haplotype structure bodes well for developing a genome-wide LD map in A. thaliana...
  20. pmc The scale of population structure in Arabidopsis thaliana
    Alexander Platt
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    PLoS Genet 6:e1000843. 2010
    ..Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales...
  21. pmc Haplotype block structure and its applications to association studies: power and study designs
    Kui Zhang
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles 90089, USA
    Am J Hum Genet 71:1386-94. 2002
    ..Our study also indicates that haplotype-based analysis can be much more powerful than marker-by-marker analysis...
  22. pmc Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk
    Yan Ding
    Division of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
    PLoS ONE 3:e3533. 2008
    ..0049, Fay & Wu's H = 8.05, 14 SNPs), as well as in chimpanzees (Fay & Wu's H = 8.62, 12 SNPs). These results strongly support the involvement of the FHIT intronic region in an increased risk of prostate cancer...
  23. pmc Conditions under which genome-wide association studies will be positively misleading
    Alexander Platt
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Genetics 186:1045-52. 2010
    ....
  24. pmc Estimating the rate of gene conversion on human chromosome 21
    Badri Padhukasahasram
    Program in Molecular and Computational Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 1340, USA
    Am J Hum Genet 75:386-97. 2004
    ..Removal of the 5,696 SNPs that occur in known mutational hotspots (CpG sites) did not significantly change our conclusions, suggesting that recurrent mutations alone cannot explain our data...
  25. ncbi request reprint Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
    Noah A Rosenberg
    Program in Molecular and Computational Biology, University of Southern California, 835 West 37th Street, SHS172, Los Angeles, California 90089 1340, USA
    Nat Rev Genet 3:380-90. 2002
    ..Traditional analysis methods do not take this into account. A stochastic process known as the 'coalescent' presents a coherent statistical framework for analysis of genetic polymorphisms...
  26. pmc Hot and cold spots of recombination in the human genome: the reason we should find them and how this can be achieved
    Norman Arnheim
    Molecular and Computational Biology Program, University of Southern California, 835 West 37th Street, SHS 172, Los Angeles, CA 90089 1340, USA
    Am J Hum Genet 73:5-16. 2003
  27. pmc The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
    Tina T Hu
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    Nat Genet 43:476-81. 2011
    ..The high-quality reference genome sequence for A. lyrata will be an important resource for functional, evolutionary and ecological studies in the genus Arabidopsis...
  28. pmc Genome-wide association mapping using mixed-models: application to GAW15 Problem 3
    Keyan Zhao
    Molecular and Computational Biology Program, University of Southern California 1050 Childs Way Room 201B, Los Angeles, California 90089, USA
    BMC Proc 1:S164. 2007
    ....
  29. pmc Genetic variation at nuclear loci fails to distinguish two morphologically distinct species of Aquilegia
    Elizabeth A Cooper
    Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 5:e8655. 2010
    ..We conclude that the extremely low levels of genetic differentiation between A. formosa and A. pubescens at neutral loci will facilitate future genome-wide scans for speciation genes...
  30. pmc Adjust quality scores from alignment and improve sequencing accuracy
    Ming Li
    Computational Biology, University of Southern California, Los Angeles, CA, USA
    Nucleic Acids Res 32:5183-91. 2004
    ..Besides Phred scores obtained from ABI sequencers, we apply the same technique to calibrate quality values that come along with Beckman sequencers...
  31. pmc Selection on amino acid substitutions in Arabidopsis
    John Paul Foxe
    Department of Biology, York University, Toronto, Ontario, Canada
    Mol Biol Evol 25:1375-83. 2008
    ..Highly expressed genes show a reduced ratio of amino acid to synonymous change for both polymorphism and fixed differences, suggesting a general pattern of stronger purifying selection on high-expression proteins...
  32. pmc Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana
    Jenny Hagenblad
    Department of Genetics, Lund University, Solvegatan 29, S 223 62 Lund, Sweden
    Genetics 161:289-98. 2002
    ..In particular, recombination is evident within 35 kb of FRI in a haplotype associated with a functionally important allele. This suggests that A. thaliana may be highly suitable for linkage disequilibrium mapping...
  33. pmc The impact of genomics on the study of natural variation in Arabidopsis
    Justin O Borevitz
    Plant Biology, Salk Institute, 10010 North Torrey Pines Rd, La Jolla, California 92037, USA
    Plant Physiol 132:718-25. 2003
  34. pmc Exploring population genetic models with recombination using efficient forward-time simulations
    Badri Padhukasahasram
    Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
    Genetics 178:2417-27. 2008
    ....
  35. pmc Evolution and control of imprinted FWA genes in the genus Arabidopsis
    Ryo Fujimoto
    Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
    PLoS Genet 4:e1000048. 2008
    ..The possible significance of epigenetic variation in reproductive strategies during evolution is also discussed...
  36. ncbi request reprint Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana
    Richard M Clark
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Science 317:338-42. 2007
    ..Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana...
  37. pmc Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana
    Justin O Borevitz
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 104:12057-62. 2007
    ..SFPs identified with the gene expression array also provide an empirical hybridization polymorphism background for studies of gene expression polymorphism and are available through the genome browser http://signal.salk.edu/cgi-bin/AtSFP...
  38. pmc Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization response
    Chikako Shindo
    Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
    Genes Dev 20:3079-83. 2006
    ..This response was correlated with the rate of accumulation of FLC histone H3 Lys 27 trimethylation (H3K27me3). Thus, variation in epigenetic silencing of FLC appears to have contributed to Arabidopsis adaptation...
  39. pmc Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis
    Chikako Shindo
    Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
    Plant Physiol 138:1163-73. 2005
    ..These data reveal how useful these Arabidopsis accessions will be in dissecting the complex molecular variation that has led to the adaptive phenotypic variation in flowering time...
  40. pmc A single IGF1 allele is a major determinant of small size in dogs
    Nathan B Sutter
    National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892 8000, USA
    Science 316:112-5. 2007
    ..A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs...
  41. ncbi request reprint A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers
    Mattias Jakobsson
    Bioinformatics Program, Department of Human Genetics, University of Michigan, USA
    Mol Biol Evol 23:1217-31. 2006
    ..When combined with what is known about the history of glaciations, our results suggest that A. suecica originated south of its present distribution in Sweden and Finland and then migrated north, perhaps in the wake of the retreating ice...
  42. pmc The probability and chromosomal extent of trans-specific polymorphism
    Carsten Wiuf
    Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
    Genetics 168:2363-72. 2004
    ..When trans-specific polymorphism is obvious, on the other hand, it may be reasonable to argue that selection must be acting on multiple sites or that recombination is suppressed in the surrounding region...
  43. pmc The impact of Arabidopsis on human health: diversifying our portfolio
    Alan M Jones
    Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Cell 133:939-43. 2008
    ..Many discoveries with direct relevance to human health and disease have been elaborated using Arabidopsis, and several processes important to human biology are more easily studied in this versatile model plant...
  44. pmc Natural variation in Arabidopsis. How do we find the causal genes?
    Detlef Weigel
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, D 72076 Tuebingen, Germany
    Plant Physiol 138:567-8. 2005
  45. pmc A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations
    Noah A Rosenberg
    Department of Human Genetics, Bioinformatics Program and the Life Sciences Institute, University of Michigan, Michigan 48109 2218, USA
    Genetics 173:1665-78. 2006
    ..This observation, together with the results of simulations that examine the relative influences of various model parameters, has important implications for the design and analysis of genetic association studies in structured populations...