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Papers

Publications involving the Nordborg lab

2008

  1. M. Nordborg and D. Weigel. Next-generation genetics in plants. Nature, 456:720-723, 2008.
  2. J. P. Foxe, V.-u.-N. Dar, H. Zheng, M. Nordborg, B. S. Gaut, and S. I. Wright. Selection on amino acid substitutions in Arabidopsis. Published Mol. Biol. Evol., 25:1375-1383, 2008.
  3. A. M. Jones, J. Chory, J. L. Dangl, M. Estelle, S. E. Jacobsen, E. M. Meyerowitz, M. Nordborg, D. Weigel. The impact of Arabidopsis on human health: diversifying our portfolio. Cell, 133:939-43, 2008.
  4. Y. Ding, G. Larson, G. Rivas, C. Lundberg, L. Geller, C. Ouyang, J. Weitzel, J. Archambeau, J. Slater, M. B. Daly, A. B. Benson, J. M. Kirkwood, P. J. O'Dwyer, R. Sutphen, J. A. Stewart, D. Johnson, M. Nordborg, T. G. Krontiris. Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk. PLoS ONE, 3:e3533, 2008.
  5. E. G. Bakker, M. B. Traw, C. Toomajian, M. Kreitman, J. Bergelson.  Low Levels of Polymorphism in Genes That Control the Activation of Defense Response in Arabidopsis thaliana, Genetics, 178:2031-2043, 2008.
  6. R. Fujimoto, Y. Kinoshita, A. Kawabe, T. Kinoshita, K. Takashima, M. Nordborg, M. E. Nasrallah, K. K. Shimizu, H. Kudoh, and T. Kakutani. Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genet, 4:e1000048, 2008.
  7. I. Baxter, B. Muthukumar, H. Park, P. Buchner, B. Lahner, J. Danku, K. Zhao, J. Lee, M. Hawkesford, M. Guerinot, D. E. Salt. Variation in molybdenum content across broadly distributed populations of Arabidopsis thaliana is controlled by a mitochondrial molybdenum transporter (MOT1). PLoS Genet, 4:e1000004, 2008.
  8. B. Padhukasahasram, P. Marjoram, J. D. Wall, C. D. Bustamante, and M. Nordborg. Exploring population genetic models with recombination using efficient forward-time simulations. Genetics, 178:2417–27, 2008.

2007

  1. S. Kim, V. Plagnol, T. T. Hu, C. Toomajian, R. M. Clark, S. Ossowski, J. R. Ecker, D. Weigel, and M. Nordborg. Recombination and linkage disequilibrium in Arabidopsis thaliana. Nature Genet., 39:1151-1155, 2007.
  2. C. Tang, C. Toomajian, S. Sherman-Broyles, V. Plagnol, Y.-L. Guo, T. T. Hu, R. M. Clark, J. B. Nasrallah, D. Weigel, and M. Nordborg. The evolution of selfing in Arabidopsis thaliana. Science, 317:1070-1072, 2007.
  3. R. M. Clark, G. Schweikert, S. Ossowski, G. Zeller, C. Toomajian, P. Shinn, N. Warthmann, T. T. Hu, G. Fu, D. A. Hinds, H. Chen, K. A. Frazer, D. H. Huson, B. Schölkopf, M. Nordborg, G. Rätsch, J. R. Ecker, and D. Weigel. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science, 317:338–342, 2007.
  4. J. O. Borevitz, S. P. Hazen, T. P. Michael, G. P. Morris, I. R. Baxter, T. T. Hu, H. Chen, J. D. Werner, M. Nordborg, D. E. Salt, S. A. Kay, J. Chory, D. Weigel, J. D. Jones, and J. R. Ecker. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA, 104:12057–12062, 2007.
  5. N. B. Sutter, C. D. Bustamante, K. Chase, M. M. Gray, K. Zhao, L. Zhu, B. Padhukasahasram, E. Karlins, S. Davis, P. G. Jones, P. Quignon, G. S. Johnson, H. G. Parker, N. Fretwell, D. S. Mosher, D. F. Lawler, E. Satyaraj, M. Nordborg, K. G. Lark, R. K. Wayne, and E. A. Ostrander. A single IGF1 allele is a major determinant of small size in dogs. Science, 316:112, 2007.
  6. K. Zhao, M. J. Aranzana, S. Kim, C. Lister, C. Shindo, C. Tang, C. Toomajian, H. Zheng, C. Dean, P. Marjoram, and M. Nordborg. An Arabidopsis example of association mapping in structured samples. PLoS Genet., 3:e4, 2007. [downloads]

2006

  1. B. Padhukasahasram, J. D. Wall, P. Marjoram, and M. Nordborg. Estimating recombination rates from single-nucleotide polymorphisms using summary statistics. Genetics, 174:1517–1528, 2006.
  2. C. Shindo, C. Lister, P. Crevillen, M. Nordborg, and C. Dean. Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization response. Genes & Development, 20:3079–3083, 2006.
  3. N. Rosenberg and M. Nordborg. 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, 2006.
  4. M. Jakobsson, J. Hagenblad, S. Tavaré, T. Säll, C. Halldén, C. Lind-Halldén, and M. Nordborg. A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers. Mol. Biol. Evol., 23:1217–1231, 2006.
  5. E. G. Bakker, C. Toomajian, M. Kreitman, and J. Bergelson. A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell, 18:1803-1818, 2006. [downloads]
  6. C. Toomajian, T. T. Hu, M. J. Aranzana, C. Lister, C. Tang, H. Zheng, P. Calabrese, C. Dean, and M. Nordborg. A non-parametric test reveals selection for rapid flowering in the Arabidopsis genome. PLoS Biol., 4:e137, 2006. [downloads]
  7. S. Kim, K. Zhao, R. Jiang, J. Molitor, J. O. Borevitz, M. Nordborg, and P. Marjoram. Association mapping with single-feature polymorphisms. Genetics, 173:1125–1133, 2006.
  8. V. Plagnol, B. Padhukasahasram, J. D. Wall, P. Marjoram, and M. Nordborg. Relative influences of crossing-over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana. Genetics, 172:2441–2448, 2006.
  9. E. G. Bakker, E. A. Stahl, C. Toomajian, M. Nordborg, M. Kreitman, and J. Bergelson. Distribution of genetic variation within and among local populations of Arabidopsis thaliana over its species range. Mol. Ecol., 15:1405–1418, 2006.

2005

  1. M. J. Aranzana, S. Kim, K. Zhao, E. Bakker, M. Horton, K. Jakob, C. Lister, J. Molitor, C. Shindo, C. Tang, C. Toomajian, B. Traw, H. Zheng, J. Bergelson, C. Dean, P. Marjoram, and M. Nordborg. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet., 1:e60, 2005. [downloads]
  2. C. Shindo, M. J. Aranzana, C. Lister, C. Baxter, C. Nicholls, M. Nordborg, and C. Dean. Role of FRIGIDA and FLC in determining variation in flowering time of Arabidopsis thaliana. Plant Physiol., 138:1163–1173, 2005.
  3. M. Nordborg, T. T. Hu, Y. Ishino, J. Jhaveri, C. Toomajian, H. Zheng, E. Bakker, P. Calabrese, J. Gladstone, R. Goyal, M. Jakobsson, S. Kim, Y. Morozov, B. Padhukasahasram, V. Plagnol, N. A. Rosenberg, C. Shah, J. Wall, J. Wang, K. Zhao, T. Kalbfleisch, V. Schultz, M. Kreitman, and J. Bergelson. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol., 3:e196, 2005. [downloads]
  4. P. Sjödin, I. Kaj, S. Krone, M. Lascoux, and M. Nordborg. On the meaning and existence of an effective population size. Genetics, 169:1061–1070, 2005.
  5. D. Weigel and M. Nordborg. Natural variation in Arabidopsis. how do we find the causal genes? Plant Physiol., 138:567–568, 2005.

2004

  1. M. Li, M. Nordborg, and L. M. Li. Adjust quality scores from alignment and improve sequencing accuracy. Nucleic Acids Res., 32:5183–5191, 2004.
  2. C. Wiuf, K. Zhao, H. Innan, and M. Nordborg. The probability and chromosomal extent of trans-specific polymorphism. Genetics, 168:2363–2372, 2004.
  3. J. Hagenblad, C. Tang, J. Molitor, J. Werner, K. Zhao, H. Zheng, P. Marjoram, D. Weigel, and M. Nordborg. Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci. Genetics, 168:1627–1638, 2004.
  4. B. Padhukasahasram, P. Marjoram, and M. Nordborg. Estimating the rate of gene conversion on human chromosome 21. Am. J. Hum. Genet., 75:386–397, 2004.
  5. M. Nordborg. Were Neanderthals and anatomically modern humans different species? In M. A. Jobling, M. E. Hurles, and C. Tyler-Smith, editors, Human Evolutionary Genetics, page 264. Garland Science, Abingdon, UK, 2004.

2003

  1. H. Innan and M. Nordborg. The extent of linkage disequilibrium and haplotype sharing around a polymorphic site. Genetics, 165:437–444, 2003.
  2. H. Innan, B. Padhukasahasram, and M. Nordborg. The pattern of polymorphism on human chromosome 21. Genome Res., 13:1158–1168, 2003.
  3. M. Nordborg and H. Innan. The genealogy of sequences containing multiple sites sub ject to strong selection in a subdivided population. Genetics, 163:1201–1213, 2003.
  4. N. Arnheim, P. Calabrese, and M. Nordborg. 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, 2003.
  5. J. O. Borevitz and M. Nordborg. The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiol., 132:718–725, 2003.

2002

  1. K. Zhang, P. Calabrese, M. Nordborg, and F. Sun. Haplotype block structure and its applications to association studies: Power and study designs. Am. J. Hum. Genet., 71:1386–1394, 2002.
  2. H. Innan and M. Nordborg. Recombination or mutational hotspots in human mtDNA? Mol. Biol. Evol., 19:1122–1127, 2002.
  3. J. Hagenblad and M. Nordborg. Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana. Genetics, 161:289–298, 2002.
  4. M. Nordborg, J. O. Borevitz, J. Bergelson, C. C. Berry, J. Chory, J. Hagenblad, M. Kreitman, J. N. Maloof, T. Noyes, P. J. Oefner, E. A. Stahl, and D. Weigel. The extent of linkage disequilibrium in Arabidopsis thaliana. Nature Genet., 30:190–193, 2002.
  5. N. A. Rosenberg and M. Nordborg. Genealogical trees, coalescent theory, and the analysis of genetic polymorphisms. Nature Rev. Genet., 3:380–390, 2002.
  6. M. Nordborg and H. Innan. Molecular population genetics. Curr. Opin. Plant Biol., 5:69–73, 2002.
  7. M. Nordborg and S. M. Krone. Separation of time scales and convergence to the coalescent in structured populations. In M. Slatkin and M. Veuille, editors, Modern Developments in Theoretical Population Genetics: The Legacy of Gustave Malécot, pages 194–232. Oxford University Press, Oxford, 2002.
  8. M. Nordborg and S. Tavaré. Linkage disequilibrium: What history has to tell us. TIG, 18:83–90, 2002.
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