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June 4, 2013

modENCODE Educational Supplement

Jonathan Pevsner (2009) Bioinformatics and Functional Genomics, Second Edition. Wiley-Blackwell.
(optional) Buy this at This is an outstanding text, although it is possible to complete this course without ever reading any of this book.

June 6, 2013

Leung, W, CD Shaffer, T Cordonnier, J Wong, MS Itano, EE Slawson-Tempel, E Kellmann, DM Desruisseau, C Cain, R Carrasquillo, TM Chusak, K Falkowska, KD Grim, R Guan, J Honeybourne, S Khan, L Lo, R McGaha, J Plunkett, JM Richner, R Richt, L Sabin, A Shah, A Sharma, S Singhal, F Song, C Swope, CB Wilen, J Buhler, ER Mardis, SCR Elgin (2010) Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis. Genetics 185: 1519-1534.

Stark et al (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-32.

modENCODE Educational Supplement

June 13, 2013

Kharchenko, PV, ..., M Kellis, SCR Elgin, MI Kuroda, V Pirrotta, G Karpen, PJ Park. (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471: 480-5.

Riddle, NC, ..., SCR Elgin, GH Karpen (2011) Plasticity in patterns of histone modifications and chromosomal proteins in the Drosophila heterochromatin. Genome Res 21: 147-63.

modENCODE Educational Supplement

June 18, 2013

Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.

Bhutkar, A, SW Schaeffer, SM Russo, M Xu, TF Smith, WM Gelbart. (2008) Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes. Genetics 179: 1697-1680.