Nordborg Group Publications
Beleza S, Johnson NA, Candille SI, Absher DM, Coram MA, Lopes J, Campos J, Araujo II, Anderson TM, Vilhjálmsson BJ, Nordborg M, Correia e Silva A, Shriver MD, Rocha J, Barsh GS, Tang H. (2013) Genetic Architecture of Skin and Eye Color in an African-European Admixed Population. PLoS Genet 9(3): e1003372. doi:10.1371/journal.pgen.1003372
Long Q, Zhang Q, Vilhjálmsson BJ, Seren Ü, Forai P, Nordborg M (2013) JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models. Bioinformatics: doi: 10.1093/bioinformatics/btt122
Platzer A. (2013) Visualization of SNPs with t-SNE. PLoS ONE 8(2): e56883. doi:10.1371/journal.pone.0056883
Chao DY, Silva A, Baxter I, Huang YS, Nordborg M, Lahner B, Yakubova E, Salt DE (2012) Genome-Wide Association Studies Identify Heavy Metal ATPase3 as the Primary Determinant of Natural Variation in Leaf Cadmium in Arabidopsis thaliana. PLoS Genet., 8(9):e1002923.
Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjálmsson BJ, Nordborg M, Borevitz JO, Bergelson J (2012) Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet 44:212-216.
Korte A, Vilhjálmsson B, Segura V, Platt A, Long Q, Nordborg M (2012) A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nat Genet 44:1066–1071.
Platzer A, Nizhynska V, Long Q (2012) TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data. Biology 2012 1:395-410.
Segura V, Vilhjálmsson B, Platt A, Korte A, Seren Ü, Long Q, Nordborg M (2012) An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nat Genet. 44(7): 825-30.
Seren Ü, Vilhjálmsson BJ, Horton MW, Meng D, Forai P, Huang YS, Long Q, Segura V, Nordborg M (2012) GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis. Plant Cell Online, December 2012 tpc.112.108068
Vilhjálmsson BJ, Nordborg M (2012) The nature of confounding in genome-wide association studies. Nature Reviews Genetics, 14:1-2.
Anastasio AE, Platt A, Horton M, Grotewold E, Scholl R, Borevitz JO, Nordborg M, Bergelson J (2011) Source verification of misidentified Arabidopsis thaliana accessions. Plant J 67:554-566.
Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J, Wilczek AM (2011) A map of local adaptation in Arabidopsis thaliana. Science 334:86-89.
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng J-F, Clark RM, Fahlgen N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KFX, van der Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo Y-L (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43:476-481.
Huang YS, Horton M, Vilhjálmsson BJ, Seren Ü, Meng D, Meyer C, Amer MA, Borevitz JO, Bergelson J, Nordborg M (2011) Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies. Database 2011: doi:10.1093/database/bar014.
Long Q, Jeffares DC, Zhang Q, Ye K, Nizhynska V, Ning Z, Tyler-Smith C, Nordborg M (2011) PoolHap: inferring haplotype frequencies from pooled samples by next-generation sequencing. PLoS ONE 6:e15292.
Strange A, Li P, Lister C, Anderson J, Warthmann N, Shindo C, Irwin J, Nordborg M, Dean C (2011) Major-effect alleles at relatively few loci underlie vernalization and flowering variation in Arabidopsis accessions. PLoS One 6:e19949.
Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue M, Spillane C, Nordborg M, Rehmsmeier M, Köhler C (2011) High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm. PLoS Genet 7:e1002126.
Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone A, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JDG, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz J, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627-631.
Baxter I, Brazelton JN, Yu D, Huang Y, Lahner B, Nordborg M, Vitek O, Salt DE (2010) A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genet 6:e1001193.
Brachi B, Faure N, Horton M, Flahauw E, Vazquez A, Nordborg M, Bergelson J Cuguen J, Roux F (2010) Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet 6:e1000940.
Cooper EA, Whittall JB, Hodges SA, Nordborg M (2010) Genetic variation at nuclear loci fails to distinguish two morphologically distinct species of Aquilegia. PLoS ONE 5:e8655.
Li Y, Huang Y, Bergelson J, Nordborg M, Borevitz JO (2010) Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana. Proc Natl Acad Sci USA 107: 21199-21204. Supporting information.
Nemri A, Atwell S, Tarone AM, Huang YS, Zhao K, Studholme DJ, Nordborg M, Jones JDG (2010) Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping. Proc Natl Acad Sci USA 107:10302-10307.
Platt A, Horton M, Huang YS, Li Y, Anastasio AE, Mulyati NW, Agren J, Bossdorf O, Byers D, Donohue K, Dunning M, Holub EB, Hudson A, Le Corre V, Loudet O, Roux F, Warthmann N, Weigel D, Rivero L, Scholl R, Nordborg M, Bergelson J, Borevitz JO (2010) The scale of population structure in Arabidopsis thaliana. PLoS Genet 6:e1000843.
Platt A, Vilhjálmsson BJ, Nordborg M (2010) Conditions under which genome-wide association studies will be positively misleading. Genetics 186:1045-1052.
Todesco M, Balasubramanian S, Hu TT, Traw MB, Horton M, Epple P, Kuhns C, Sureshkumar S, Schwartz C, Lanz C, Laitinen RAE, Huang Y, Chory J, Lipka V, Borevitz JO, Dangl JL, Bergelson J, Nordborg M, Weigel D (2010) Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana. Nature 465:632-636.
Turner TL, Bourne EC, Wettberg EJ, Hu TT, Nuzhdin SV (2010) Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet 42:260-263.
Bakker EG, Traw MB, Toomajian C, Kreitman M, Bergelson J (2008) Low levels of polymorphism in genes that control the activation of defense response in Arabidopsis thaliana. Genetics 178:2031-2043.
Baxter I, Muthukumar B, Park H, Buchner P, Lahner B, Danku J, Zhao K, Lee J, Hawkesford M, Guerinot M, Salt DE (2008) Variation in molybdenum content across broadly distributed populations of Arabidopsis thaliana is controlled by a mitochondrial molybdenum transporter (MOT1). PLoS Genet 4:e1000004.
Ding Y, Larson G, Rivas G, Lundberg C, Geller L, Ouyang C, Weitzel J, Archambeau J, Slater J, Daly MB, Benson AB, Kirkwood JM, O'Dwyer PJ, Sutphen R, Stewart JA, Johnson D, Nordborg M, Krontiris TG (2008) Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk. PLoS ONE 3:e3533.
Foxe JP, Dar V-u-N, Zheng H, Nordborg M, Gaut BS, Wright SI (2008) Selection on amino acid substitutions in Arabidopsis. Mol Biol Evol 25:1375-1383.
Fujimoto R, Kinoshita Y, Kawabe A, Kinoshita T, Takashima K, Nordborg M, Nasrallah ME, Shimizu KK, Kudoh H, Kakutani T (2008) Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genet 4:e1000048.
Jones AM, Chory J, Dangl JL, Estelle M, Jacobsen SE, Meyerowitz EM, Nordborg M, Weigel D (2008) The impact of Arabidopsis on human health: diversifying our portfolio. Cell 133:939-943.
Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456:720-723.
Borevitz JO, Hazen SP, Michael TP, Morris GP, Baxter IR, Hu TT, Chen H, Werner JD, Nordborg M, Salt DE, Kay SA, Chory J, Weigel D, Jones JD, Ecker JR (2007) Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl Acad Sci USA 104:12057-12062.
Clark RM, Schweikert G, Ossowski S, Zeller G, Toomajian C, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH, Schölkopf B, Nordborg M, Rätsch G, Ecker JR, Weigel D (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317:338-342.
Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, Ossowski S, Ecker JR, Weigel D, Nordborg M (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nature Genet 39:1151-1155.
Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M (2007). Exploring population genetic models with recombination using effcient forward-time simulations. Genetics 178:2417-2427.
Sutter NB, Bustamante CD, Chase K, Gray MM, Zhao K, Zhu L, Padhukasahasram B, Karlins E, Davis S, Jones PG, Quignon P, Johnson GS, Parker HG, Fretwell N, Mosher DS, Lawler DF, Satyaraj E, Nordborg M, Lark KG, Wayne RK, Ostrander EA (2007) A single IGF1 allele is a major determinant of small size in dogs. Science 316:112.
Tang C, Toomajian C, Sherman-Broyles S, Plagnol V, Guo Y-L, Hu TT, Clark RM, Nasrallah JB, Weigel D, Nordborg M (2007) The evolution of selfing in Arabidopsis thaliana. Science 317:1070-1072.
Zhao K, Nordborg M, Marjoram P (2007) Genome-wide association mapping using mixed-models: application to GAW15 Problem 3. BMC Proc 2007 1(Suppl):164.
Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:e4.
Bakker EG, Stahl EA, Toomajian C, Nordborg M, Kreitman M, Bergelson J (2006) Distribution of genetic variation within and among local populations of Arabidopsis thaliana over its species range. Mol Ecol 15:1405-1418.
Bakker EG, Toomajian C, Kreitman M, Bergelson J (2006) A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell 18:1803-1818. downloads
Jakobsson M, Hagenblad J, Tavaré S, Säll T, Halldén C, Lind-Halldén C, Nordborg M (2006) A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers. Mol Biol Evol 23:1217-1231.
Kim S, Zhao K, Jiang R, Molitor J, Borevitz JO, Nordborg M, Marjoram P (2006) Association mapping with single-feature polymorphisms. Genetics 173:1125-1133.
Padhukasahasram B, Wall JD, Marjoram P, Nordborg M (2006) Estimating recombination rates from single-nucleotide polymorphisms using summary statistics. Genetics 174:1517-1528.
Plagnol V, Padhukasahasram B, Wall JD, Marjoram P, Nordborg M (2006) Relative influences of crossing-over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana. Genetics 172:2441-2448.
Rosenberg N, Nordborg M (2006) A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed, or spatially distributed populations. Genetics 173:1665-1678.
Shindo C, Lister C, Crevillen P, Nordborg M, Dean C (2006) Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization response. Genes Devel 20:3079-3083.
Toomajian C, Hu TT, Aranzana MJ, Lister C, Tang C, Zheng H, Calabrese P, Dean C, Nordborg M (2006) A non-parametric test reveals selection for rapid flowering in the Arabidopsis genome. PLoS Biol 4:e137. downloads
Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1:e60. downloads
Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall J, Wang J, Zhao K, Kalbfleisch T, Schultz V, Kreitman M, Bergelson J (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3:e196. downloads
Shindo C, Aranzana MJ, Lister C, Baxter C, Nicholls C, Nordborg M, Dean C (2005) Role of FRIGIDA and FLC in determining variation in flowering time of Arabidopsis thaliana. Plant Physiol 138:1163-1173.
Sjödin P, Kaj I, Krone S, Lascoux M, Nordborg M (2005) On the meaning and existence of an effective population size. Genetics 169:1061-1070.
Weigel D, Nordborg M (2005) Natural variation in Arabidopsis. How do we find the causal genes? Plant Physiol 138:567-568.
Hagenblad J, Tang C, Molitor J, Werner J, Zhao K, Zheng H, Marjoram P, Weigel D, Nordborg M (2004) Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci. Genetics 168:1627-1638.
Li M, Nordborg M, Li LM (2004) Adjust quality scores from alignment and improve sequencing accuracy. Nucleic Acids Res 32:5183-5191.
Nordborg M (2004) Were Neanderthals and anatomically modern humans different species? In: Jobling MA, Hurles ME, Tyler-Smith C (Eds), Human Evolutionary Genetics, p. 264. Garland Science, Abingdon, UK.
Padhukasahasram B, Marjoram P, Nordborg M (2004) Estimating the rate of gene conversion on human chromosome 21. Am J Hum Genet 75:386-397.
Wiuf C, Zhao K, Innan H, Nordborg M (2004) The probability and chromosomal extent of trans-specific polymorphism. Genetics 168:2363-2372.
Arnheim N, Calabrese P, Nordborg M (2003) Hot and cold spots of recombination in the human genome: The reason we should find them and how this can be achieved. Am J Hum Genet 73:5-16.
Borevitz JO, Nordborg M (2003) The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiol 132:718-725.
Innan H, Nordborg M (2003) The extent of linkage disequilibrium and haplotype sharing around a polymorphic site. Genetics 165:437-444.
Innan H, Padhukasahasram B, Nordborg M (2003) The pattern of polymorphism on human chromosome 21. Genome Res 13:1158-1168.
Nordborg M, Innan H (2003) The genealogy of sequences containing multiple sites sub ject to strong selection in a subdivided population. Genetics 163:1201-1213.
Hagenblad J, Nordborg M (2002) Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana. Genetics 161:289-298.
Innan H, Nordborg M (2002) Recombination or mutational hotspots in human mtDNA? Mol Biol Evol 19:1122-1127.
Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D(2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nature Genet 30:190-193.
Nordborg M, Innan H (2002) Molecular population genetics. Curr Opin Plant Biol 5:69-73.
Nordborg M, Krone SM (2002) Separation of time scales and convergence to the coalescent in structured populations. In: Slatkin M, Veuille M (Eds) Modern Developments in Theoretical Population Genetics: The Legacy of Gustave Malécot, p 194-232, Oxford University Press, Oxford.
Nordborg M, Tavaré S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18:83-90.
Rosenberg NA, Nordborg M (2002) Genealogical trees, coalescent theory, and the analysis of genetic polymorphisms. Nature Rev Genet 3:380-390.
Zhang K, Calabrese P, Nordborg M, Sun F (2002) Haplotype block structure and its applications to association studies: Power and study designs. Am J Hum Genet 71:1386-1394.
