What's New?
Document Actions
Sequence Variation
Analyzing a huge set of hybridization data from resequencing arrays with discriminative state-of-the-art machine learning methods, we identified hundreds of thousands polymorphisms (SNPs, deletions and highly polymorphic regions) in the genome of 20 varieties of two model plant organisms, Arabidopsis thaliana and Oryza sativa (rice). Such an inventory of sequence variation constitutes an unprecedented resource for further functional and large-scale evolutionary studies and is a fundamental step towards answering the key question: How is genetic variation linked to complex traits?
Research Projects
Publications
-
McNally, KL, Childs, KL, Bohnert, R, Davidson, RM, Zhao, K, Ulat, VJ, Zeller, G, Clark, RM, Hoen, DR, Bureau, TE, Stokowski, R, Ballinger, DG, Frazer, KA, Cox, DR, Padhukasahasram, B, Bustamante, CD, Weigel, D, Mackill, DJ, Bruskiewich, RM, Rätsch, G, Buell, CR, Leung, H, and Leach, JE (2009).
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice
Proceedings of the National Academy of Sciences, 106(30):12273-8.
http://www.pnas.org/content/106/30/12273.full
Printable file
-
Bohnert, R, Zeller, G, Clark, RM, Childs, KL, Ulat, V, Stokowski, R, Ballinger, D, Frazer, K, Cox, D, Bruskiewich, R, Buell, CR, Leach, J, Leung, H, McNally, KL, Weigel, D, and Rätsch, G (2008).
Revealing Sequence Variation Patterns in Rice with Machine Learning Methods
BMC Bioinformatics, 9(S10):O8.
http://www.biomedcentral.com/1471-2105/9/S10/O8
Printable file
-
Zeller, G, Clark, R, Schneeberger, K, Bohlen, A, Weigel, D, and Rätsch, G (2008).
Detecting Polymorphic Regions in Arabidopsis thaliana with Resequencing Microarrays
Genome Research, 18(6):918-929.
http://www.fml.tuebingen.mpg.de/raetsch/projects/mppr
Printable file
-
Bohnert, R (2007).
Polymorphism Detection in Rice
Diplom thesis, Friedrich Miescher Laboratory of the Max Planck Society and Eberhard Karls Universität Tübingen.
Printable file
-
Clark, R, Schweikert, G, Toomajian, C, Ossowski, S, Zeller, G, Shinn, P, Warthmann, N, Hu, T, Fu, G, Hinds, D, Chen, H, Frazer, K, Huson, D, Schölkopf, B, Nordborg, M, Rätsch, G, Ecker, J, and Weigel, D (2007).
Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana
Science, 317(5836):338 - 342.
Printable file
