Recommended Readings: Eran Segal Ph.D. October 9, 2013

Special Seminar Series
Deciphering the Code of Gene Regulation
Eran Segal, Ph.D.
Incumbent of the Soretta and Henry Shapiro Career Development Chair
Department of Computer Science and Applied Mathematics
4:00 p.m. – 5:00 p.m. Carson Family Auditorium (CRC)
Refreshments: 3:45 p.m. – 4:00 p.m., Lower Level Greenberg Building (CRC)

Recommended Readings:

Review Papers

Coulon, A., Chow, C. C., Singer, R. H., & Larson, D. R. (2013). Eukaryotic transcriptional dynamics: from single molecules to cell populationsNature Reviews Genetics14(8), 572-584. doi: 10.1038/nrg3484.

De Smet, R., & Marchal, K. (2010). Advantages and limitations of current network inference methodsNature Reviews Microbiology8(10), 717-729. doi: 10.1038/nrmicro2419

Segal, E., & Widom, J. (2009). From DNA sequence to transcriptional behaviour: a quantitative approachNature Reviews Genetics10(7), 443-456. doi: 10.1038/nrg2591

Jiang, C., & Pugh, B. F. (2009). Nucleosome positioning and gene regulation: advances through genomicsNature Reviews Genetics10(3), 161-172. doi: 10.1038/nrg2522

Empirical Articles

Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A. J., Tillo, D., Field, Y., … & Segal, E. (2008). The DNA-encoded nucleosome organization of a eukaryotic genomeNature458(7236), 362-366. doi: 10.1038/nature07667

Schones, D. E., Cui, K., Cuddapah, S., Roh, T. Y., Barski, A., Wang, Z., … & Zhao, K. (2008). Dynamic regulation of nucleosome positioning in the human genomeCell132(5), 887-898. doi: 10.1016/j.cell.2008.02.022

Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thåström, A., Field, Y., Moore, I. K., … & Widom, J. (2006). A genomic code for nucleosome positioningNature,442(7104), 772-778. doi: 10.1038/nature04979

Segal, E., Shapira, M., Regev, A., Pe’er, D., Botstein, D., Koller, D., & Friedman, N. (2003). Module networks: identifying regulatory modules and their condition-specific regulators from gene expression dataNature Genetics34(2), 166-176. doi: 10.1038/ng1165

Valouev, A., Johnson, S. M., Boyd, S. D., Smith, C. L., Fire, A. Z., & Sidow, A. (2011). Determinants of nucleosome organization in primary human cellsNature474(7352), 516-520. doi: 10.1038/nature10002