Research Topics
Species | Magnus NordborgSummaryAffiliation: University of Southern California Country: USA Publications
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Publications
Molecular population geneticsMagnus 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...- Linkage disequilibrium: what history has to tell usMagnus 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... 
Next-generation genetics in plantsMagnus Nordborg
Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
Nature 456:720-3. 2008....
The genealogy of sequences containing multiple sites subject to strong selection in a subdivided populationMagnus 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...- The pattern of polymorphism in Arabidopsis thalianaMagnus 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... - An Arabidopsis example of association mapping in structured samplesKeyan 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... - Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred linesSusanna 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... - Association mapping with single-feature polymorphismsSung 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... - Estimating recombination rates from single-nucleotide polymorphisms using summary statisticsBadri 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... - Recombination and linkage disequilibrium in Arabidopsis thalianaSung 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... - A nonparametric test reveals selection for rapid flowering in the Arabidopsis genomeChristopher 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... - The evolution of selfing in Arabidopsis thalianaChunlao 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... - Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thalianaVincent 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... - Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time lociJenny 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... - The pattern of polymorphism on human chromosome 21Hideki Innan
Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
Genome Res 13:1158-68. 2003.... - Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genesMaria 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... - The extent of linkage disequilibrium in Arabidopsis thalianaMagnus 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... - The extent of linkage disequilibrium and haplotype sharing around a polymorphic siteHideki 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... - 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... - The scale of population structure in Arabidopsis thalianaAlexander 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... - Haplotype block structure and its applications to association studies: power and study designsKui 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... - Strong signature of natural selection within an FHIT intron implicated in prostate cancer riskYan 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... - Conditions under which genome-wide association studies will be positively misleadingAlexander Platt
Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
Genetics 186:1045-52. 2010.... - Estimating the rate of gene conversion on human chromosome 21Badri 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... - Genealogical trees, coalescent theory and the analysis of genetic polymorphismsNoah 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... - Hot and cold spots of recombination in the human genome: the reason we should find them and how this can be achievedNorman 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 - The Arabidopsis lyrata genome sequence and the basis of rapid genome size changeTina 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... - Genome-wide association mapping using mixed-models: application to GAW15 Problem 3Keyan 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.... - Genetic variation at nuclear loci fails to distinguish two morphologically distinct species of AquilegiaElizabeth 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... - Adjust quality scores from alignment and improve sequencing accuracyMing 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... - Selection on amino acid substitutions in ArabidopsisJohn 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... - Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thalianaJenny Hagenblad
Department of Genetics, Lund University, , 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... - The impact of genomics on the study of natural variation in ArabidopsisJustin O Borevitz
Plant Biology, Salk Institute, 10010 North Torrey Pines Rd, La Jolla, California 92037, USA
Plant Physiol 132:718-25. 2003 - Exploring population genetic models with recombination using efficient forward-time simulationsBadri Padhukasahasram
Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
Genetics 178:2417-27. 2008.... - Evolution and control of imprinted FWA genes in the genus ArabidopsisRyo 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... - Common sequence polymorphisms shaping genetic diversity in Arabidopsis thalianaRichard 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... - Genome-wide patterns of single-feature polymorphism in Arabidopsis thalianaJustin 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... - Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization responseChikako 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... - Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of ArabidopsisChikako 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... - A single IGF1 allele is a major determinant of small size in dogsNathan 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... - A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markersMattias 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... - The probability and chromosomal extent of trans-specific polymorphismCarsten 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... - The impact of Arabidopsis on human health: diversifying our portfolioAlan 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... - 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 - A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populationsNoah 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...