Publications

Publications

Publications

Gan, X., Hay, A., Kwantes, M., Haberer, G., Hallab, A., Dello Ioio, R., Hofhuis, H., Pieper, B., Cartolano, M., Neumann, U., Nikolov, L. A., Song, B., Hajheidari, M., Briskine, R., Kougioumoutzi, E., Vlad, D., Broholm, S., Hein, J., Meksem, K., Lightfoot, D., Shimizu, K. K., Shimizu-Inatsugi, R., Imprialou, M., Kudrna, D., Wing, R., Sato, S., Huijser, P., Filatov, D., Mayer, K. F. X., Mott, R., Tsiantis, M. (2016) The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nature Plants 2, 16167. (co-corresponding author).

The 1001 Genomes Consortium. (2016). 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 166, 481-91.

CONVERGE Consortium. (2015). Sparse whole-genome sequencing identifies two loci for major depressive disorder. Nature 523, 588-91.

Mott R, Yuan W, Kaisaki P, Gan X, Cleak J, Edwards A, et al. (2014) The architecture of parent-of-origin effects in mice. Cell. 2014;156(1-2):332-42.

Vlad D, Kierzkowski D, Rast MI, Vuolo F, Dello Ioio R, Galinha C, et al. (2014) Leaf shape evolution through duplication, regulatory diversification, and loss of a homeobox gene. Science. 2014;343(6172):780-3.

Hay AS, Pieper B, Cooke E, Mandakova T, Cartolano M, Tattersall AD, et al. (2014) Cardamine hirsuta: a versatile genetic system for comparative studies. The Plant journal : for cell and molecular biology. 2014.

Belfield, E.J., Gan, X., Mithani, A., Brown, C., Jiang, C., Franklin, K., Wibowo, A., Jung, M., Bailey, K., Kalwani, S., Ragoussis, J., Mott, R., and Harberd, N.P. (2012). Genome-Wide Analysis of Arabidopsis Mutations Induced by Ionizing Radiation. Genome Res 22, 1306-1315

Gan, X., Stegle, O., Behr, J., Steffen, J.G., Drewe, P., Hildebrand, K.L., Lyngsoe, R., Schultheiss, S.J., Osborne, E.J., Sreedharan, V.T., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E.J., Harberd, N.P., Kemen, E., Toomajian, C., Kover, P.X., Clark, R.M., Ratsch, G., and Mott, R. (2011). Multiple Reference Genomes and Transcriptomes for Arabidopsis Thaliana. Nature 477, 419-423.

Keane, T.M., Goodstadt, L., Danecek, P., White, M.A., Wong, K., Yalcin, B., Heger, A., Agam, A., Slater, G., Goodson, M., Furlotte, N.A., Eskin, E., Nellaker, C., Whitley, H., Cleak, J., Janowitz, D., Hernandez-Pliego, P., Edwards, A., Belgard, T.G., Oliver, P.L., McIntyre, R.E., Bhomra, A., Nicod, J., Gan, X., Yuan, W., van der Weyden, L., Steward, C.A., Bala, S., Stalker, J., Mott, R., Durbin, R., Jackson, I.J., Czechanski, A., Guerra-Assuncao, J.A., Donahue, L.R., Reinholdt, L.G., Payseur, B.A., Ponting, C.P., Birney, E., Flint, J., and Adams, D.J. (2011). Mouse Genomic Variation and Its Effect on Phenotypes and Gene Regulation. Nature 477, 289-294.

Yalcin, B., Wong, K., Agam, A., Goodson, M., Keane, T.M., Gan, X., Nellaker, C., Goodstadt, L., Nicod, J., Bhomra, A., Hernandez-pliego, P., Whitley, H., Cleak, J., Dutton, R., Janowitz, D., Mott, R., Adams, D.J., and Flint, J. (2011). Sequence-Based Characterization of Structural Variation in the Mouse Genome. Nature 477, 326-329.

Jiang, C., Mithani, A., Gan, X., Belfield, E.J., Klingler, J.P., Zhu, J.K., Ragoussis, J., Mott, R., and Harberd, N.P. (2011). Regenerant Arabidopsis Lineages Display a Distinct Genome-Wide Spectrum of Mutations Conferring Variant Phenotypes. Current biology  CB 21, 1385-1390.

Gan, X., Liew, A.W.C., and Yan, H. (2010). Representation and Extraction of Bicluster from Data Arrays. US Patent US784908, granted on Dec 7, 2010.

Yalcin, B., Nicod, J., Bhomra, A., Davidson, S., Cleak, J., Farinelli, L., Osteras, M., Whitley, A., Yuan, W., Gan, X., Goodson, M., Klenerman, P., Satpathy, A., Mathis, D., Benoist, C., Adams, D.J., Mott, R., and Flint, J. (2010). Commercially Available Outbred Mice for Genome-Wide Association Studies. PLoS genetics 6.

Liew, A.W., and Gan, X. (2009). Microarray Gene Expression Data Analysis. In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, M. Elloumi and A.Y. Zomaya, eds. (John Wiley & Sons).

Kapsokalivas, L., Gan, X., Albrecht, A.A., and Steinhofel, K. (2009). Population-Based Local Search for Protein Folding Simulation in the Mj Energy Model and Cubic Lattices. Computational biology and chemistry 33, 283-294.

Gan, X., Liew, A.W., and Yan, H. (2008). Discovering Biclusters in Gene Expression Data Based on High-Dimensional Linear Geometries. BMC bioinformatics 9, 209.

Gan, X., Liew, A.W.-C., and Yan, H. (2006). Microarray Missing Data Imputation Based on a Set Theoretic Framework and Biological Knowledge. Nucleic acids research 34, 1608-1619.

 
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