June 4, 2013

modENCODE Educational Supplement

Jonathan Pevsner (2009) Bioinformatics and Functional Genomics, Second Edition. Wiley-Blackwell.
(optional) Buy this at Amazon.com. 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.