Recommended Readings: Martin Kampmann Ph.D. Monday, January 27

Monday, January 27, 2014
4:00 p.m., Carson Family Auditorium

Martin Kampmann, Ph.D.
Postdoctoral Scholar
University of San Francisco

Toward a Systematic Understanding of the Mammalian Proteostasis Network and its Therapeutic Potential

Recommended Readings:

Empirical Papers

Bassik, M. C., Kampmann, M., Lebbink, R. J., Wang, S., Hein, M. Y., Poser, I., … Weissman, J. S. (2013). A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell, 152(4), 909–922. doi:10.1016/j.cell.2013.01.030

Kampmann, M., Bassik, M. C., & Weissman, J. S. (2013). Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America, 110(25), E2317–2326. doi:10.1073/pnas.1307002110

Review Articles

Balch, W. E., Morimoto, R. I., Dillin, A., & Kelly, J. W. (2008). Adapting proteostasis for disease intervention. Science, 319(5865), 916–919. doi:10.1126/science.1141448

Hartl, F. U., Bracher, A., & Hayer-Hartl, M. (2011). Molecular chaperones in protein folding and proteostasis. Nature, 475(7356), 324–332. doi:10.1038/nature10317

Recommended Readings: Madeline Lancaster, Ph.D. Monday, Dec. 11

Special Lecture
The Human Brain in a Dish: Using Cerebral Organoids to Model Development and Disease
Madeline A. Lancaster, Ph.D.
Postdoctoral Fellow
Institute of Molecular Biotechnology
4:00 p.m., Carson Family Auditorium

Recommended Readings

Review Papers

Eiraku, M., & Sasai, Y. (2012). Self-formation of layered neural structures in three-dimensional culture of ES cells. Current Opinion in Neurobiology, 22(5), 768–777. doi:10.1016/j.conb.2012.02.005

Gage, F. H., & Temple, S. (2013). Neural stem cells: generating and regenerating the brain. Neuron, 80(3), 588–601. doi:10.1016/j.neuron.2013.10.037

Han, S. S. W., Williams, L. a, & Eggan, K. C. (2011). Constructing and deconstructing stem cell models of neurological disease. Neuron, 70(4), 626–644. doi:10.1016/j.neuron.2011.05.003

Lui, J. H., Hansen, D. V, & Kriegstein, A. R. (2011). Development and evolution of the human neocortex. Cell, 146(1), 18–36. doi:10.1016/j.cell.2011.06.030

Empirical Articles

Espuny-Camacho, I., Michelsen, K. a, Gall, D., Linaro, D., Hasche, A., Bonnefont, J., … Vanderhaeghen, P. (2013). Pyramidal neurons derived from human pluripotent stem cells integrate efficiently into mouse brain circuits in vivo. Neuron, 77(3), 440–456. doi:10.1016/j.neuron.2012.12.011

Lancaster, M. a, Renner, M., Martin, C.-A., Wenzel, D., Bicknell, L. S., Hurles, M. E., … Knoblich, J. a. (2013). Cerebral organoids model human brain development and microcephaly. Nature, 501(7467), 373–379. doi:10.1038/nature12517

Mariani, J., Simonini, M. V., Palejev, D., Tomasini, L., Coppola, G., Szekely, A. M., … Vaccarino, F. M. (2012). Modeling human cortical development in vitro using induced pluripotent stem cells. Proceedings of the National Academy of Sciences of the United States of America, 109(31), 12770–12775. doi:10.1073/pnas.1202944109

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