Recommended Readings: Louis M. Staudt, M.D., Ph.D. January 9

Friday Lecture Series
Friday, January 9, 2015
3:45 p.m., Caspary Auditorium

Louis M. Staudt, M.D., Ph.D.
Director, Center for Cancer Genomics
Co-chief, Lymphoid Malignancies Branch
Head, Molecular Biology of Lymphoid Malignancies Section,
Center for Cancer Research,
National Cancer Institute at the National Institutes of Health

Therapy of Lymphoma Inspired by Functional and Structural Genomics

Recommended Readings

Empirical Articles

Alizadeh, A., Eisen, M., Davis, R., & Ma, C. (2000). Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403(6769), 503-511.

Ngo, V. N., Davis, R. E., Lamy, L., Yu, X., Zhao, H., Lenz, G., … Staudt, L. M. (2006). A loss-of-function RNA interference screen for molecular targets in cancer. Nature, 441(7089), 106–110. doi:10.1038/nature04687

Rosenwald, A., Wright, G., Chan, W. C., Connors, J. M., Campo, E., Fisher, R. I., … Staudt, L. M. (2002). The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. The New England Journal of Medicine, 346(25), 1937–1947. doi:10.1056/NEJMoa012914

Yang, Y., III, A. S., Emre, N., & Ceribelli, M. (2012). Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma. Cancer Cell, 21(6), 723–737. doi:10.1016/j.ccr.2012.05.024.Exploiting

Review Papers

Lenz, G., & Staudt, L. M. (2010). Aggressive lymphomas. The New England Journal of Medicine, 362(15), 1417–1429. doi:10.1056/NEJMra0807082

Shaffer, A. L., Young, R. M., & Staudt, L. M. (2012). Pathogenesis of human B cell lymphomas. Annual Review of Immunology, 30, 565–610. doi:10.1146/annurev-immunol-020711-075027

Recommended Readings: Stephen Quake, Ph.D. November 12

Special Seminar Series
Wednesday, November 12, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Stephen Quake, Ph.D.
Lee Otterson Professor,
Bioengineering and Applied Physics,
Stanford University
Howard Hughes Medical Institute

Single Cell Genomics

Recommended Readings

Empirical Papers

Ashley, E. a, Butte, A. J., Wheeler, M. T., Chen, R., Klein, T. E., Dewey, F. E., … Altman, R. B. (2010). Clinical assessment incorporating a personal genome. Lancet, 375(9725), 1525–1535. doi:10.1016/S0140-6736(10)60452-7

Fan, H. C., Gu, W., Wang, J., Blumenfeld, Y. J., El-Sayed, Y. Y., & Quake, S. R. (2012). Non-invasive prenatal measurement of the fetal genome. Nature, 487(7407), 320–324. doi:10.1038/nature11251

Pushkarev, D., Neff, N. F., & Quake, S. R. (2009). Single-molecule sequencing of an individual human genome. Nature Biotechnology, 27(9), 847–850. doi:10.1038/nbt.1561

Wang, J., Fan, H. C., Behr, B., & Quake, S. R. (2012). Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell, 150(2), 402–412. doi:10.1016/j.cell.2012.06.030

Review Papers

Kalisky, T., Blainey, P., & Quake, S. R. (2011). Genomic analysis at the single-cell level. Annual Review of Genetics, 45, 431–445. doi:10.1146/annurev-genet-102209-163607

Melin, J., & Quake, S. R. (2007). Microfluidic large-scale integration: the evolution of design rules for biological automation. Annual Review of Biophysics and Biomolecular Structure, 36, 213–231. doi:10.1146/annurev.biophys.36.040306.132646

Recommended Readings: Amédée des Georges, Ph.D. October 20

Special Lecture Series
Monday, October 20, 2014
4:00 p.m., Carson Family Auditorium

Amédée des Georges, Ph.D.
Postdoctoral Associate,
Department of Biochemistry and Molecular Biophysics,
Columbia University

Structures of Eukaryotic Translation Initiation Complexes by Single-Particle Cryo-EM, a Powerful Tool for the Study of Heterogeneous Samples

Recommended Readings

Empirical Articles

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. Nature, 503(7477), 539–543. doi:10.1038/nature12658

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29. Cell, 153(5), 1108–1119. doi:10.1016/j.cell.2013.04.036

Hashem, Y., des Georges, A., Fu, J., Buss, S. N., Jossinet, F., Jobe, A., … Frank, J. (2013). High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature, 494(7437), 385–389. doi:10.1038/nature11872

Review Papers

Jackson, R. J., Hellen, C. U. T., & Pestova, T. V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews Molecular Cell Biology, 11(2), 113–127. doi:10.1038/nrm2838

Recommended Readings: Gary Ruvkun, Ph.D. October 24

Friday Lecture Series
Friday, October 24, 2014
3:45 p.m., Caspary Auditorium

Gary Ruvkun, Ph.D.
Hans-Hermann Schoene Distinguished Investigator and Professor,
Department of Genetics,
Harvard Medical School

C. elegans Surveillance of Conserved Cellular Components to Detect and Defend Pathogen Attacks, Real or Imagined

Recommended Readings

Empirical Articles

Liu, Y., Samuel, B. S., Breen, P. C., & Ruvkun, G. (2014). Caenorhabditis elegans pathways that surveil and defend mitochondria. Nature, 508(7496), 406–410. doi:10.1038/nature13204

Melo, J. A, & Ruvkun, G. (2012). Inactivation of conserved C. elegans genes engages pathogen- and xenobiotic-associated defenses. Cell, 149(2), 452–466. doi:10.1016/j.cell.2012.02.050

Shore, D. E., Carr, C. E., & Ruvkun, G. (2012). Induction of cytoprotective pathways is central to the extension of lifespan conferred by multiple longevity pathways. PLoS Genetics, 8(7), e1002792. doi:10.1371/journal.pgen.1002792

Review Papers

Shore, D. E., & Ruvkun, G. (2013). A cytoprotective perspective on longevity regulation. Trends in Cell Biology, 23(9), 409–420. doi:10.1016/j.tcb.2013.04.007

Recommended Readings: James E. Darnell, Jr., M.D. May 19

Monday Lecture Series
Monday, May 19, 2014
4:00 p.m., Carson Family Auditorium

James E. Darnell, Jr., M.D.
Vincent Astor Professor Emeritus 
Head, Laboratory of Molecular Cell Biology
The Rockefeller University

Then and now – making mRNA: an unbiased (?) look at pre-mRNA synthesis and processing

Recommended Readings:

Empirical Papers

Brenner, S., Jacob, F., & Meselson, M. (1961). An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature, 180(4776), 576–581.

Gros, F., Hiatt, H., Gilbert, W., & Kurland, C. (1961). Unstable ribonucleic acid revealed by pulse labelling of Escherichia coli. Nature, 190(4776), 581–585.

Jacob, F., & Monod, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology, 3, 318–356.

Scherrer, K., Latham, H., & Darnell, J. E. (1963). Demonstration of an unstable RNA and of a precursor to ribosomal RNA in HeLa cells. Proceedings of the National Academy of Sciences, 49(2), 240–248.

Review Articles

Darnell, J. E. (1968). Ribonucleic acids from animal cells. Bacteriological Reviews, 32(3), 262–290.

Darnell, J. E. (2013). Reflections on the history of pre-mRNA processing and highlights of current knowledge: a unified picture. RNA, 19(4), 443–60. doi:10.1261/rna.038596.113

Licatalosi, D. D., & Darnell, R. B. (2010). RNA processing and its regulation: global insights into biological networks. Nature Reviews Genetics, 11(1), 75–87. doi:10.1038/nrg2673

Recommended Readings: Lei Stanley Qi, Ph.D. Monday, January 13

Monday, January 13, 2014
4:00 p.m., Carson Family Auditorium

Lei Stanley Qi, Ph.D.
UCSF Systems Biology Fellow
Department of Cellular and Molecular Pharmacology and
UCSF Center for Systems and Synthetic Biology
University of California, San Francisco

Repurposing CRISPR/Cas as a versatile platform for genome engineering and imaging

Recommended Readings:

Empirical Articles

Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., … Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121), 819–823. doi:10.1126/science.1231143

Gilbert, L. a, Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., … Qi, L. S. (2013). CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell, 154(2), 442–451. doi:10.1016/j.cell.2013.06.044

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816–21. doi:10.1126/science.1225829

Qi, L., Haurwitz, R. E., Shao, W., Doudna, J. A., & Arkin, A. P. (2012). RNA processing enables predictable programming of gene expression. Nature Biotechnology, 30(10), 1002–6. doi:10.1038/nbt.2355

Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell, 152(5), 1173–83. doi:10.1016/j.cell.2013.02.022

Review Articles

Gaj, T., Gersbach, C. A., & Barbas, C. F. (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in Biotechnology, 31(7), 397–405. doi:10.1016/j.tibtech.2013.04.004

Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J. J., Charpentier, E., Horvath, P., … Koonin, E. V. (2011). Evolution and classification of the CRISPR-Cas systems. Nature Reviews Microbiology, 9(6), 467–477. doi:10.1038/nrmicro2577

Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012). RNA-guided genetic silencing systems in bacteria and archaea. Nature, 482(7385), 331–338. doi:10.1038/nature10886

Recommended Readings: Gerry Rubin, Ph.D.

Friday Lecture Series

Richard M. Furlaud Distinguished Lecture

A Molecular Geneticist’s Approach to Understanding the Fly Brain

Gerry Rubin, Ph.D., vice president and executive director,

Howard Hughes Medical Institute Janelia Farm Research Campus

October 19, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Aboobaker, A. A., Tomancak, P., Patel, N., Rubin, G. M., & Lai, E. C. (2005). Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proceedings of the National Academy of Sciences of the United States of America, 102(50), 18017-18022

Ashburner, M., Misra, S., Roote, J., Lewis, S. E., Blazej, R., Davis, T., . . . Rubin, G. M. (1999). An exploration of the sequence of a 2.9-mb region of the genome of drosophila melanogaster: The adh region. Genetics, 153(1), 179-219

Bellen, H. J., Levis, R. W., Liao, G., He, Y., Carlson, J. W., Tsang, G., . . . Spradling, A. C. (2004). The BDGP gene disruption project: Single transposon insertions associated with 40% of drosophila genes. Genetics, 167(2), 761-781

Miklos, G. L. G., & Rubin, G. M. (1996). The role of the genome project in determining gene function: Insights from model organisms. Cell, 86(4), 521-529

Pfeiffer, B. D., Jenett, A., Hammonds, A. S., Ngo, T. -. B., Misra, S., Murphy, C., . . . Rubin, G. M. (2008). Tools for neuroanatomy and neurogenetics in drosophila. Proceedings of the National Academy of Sciences of the United States of America, 105(28), 9715-9720

Pfeiffer, B. D., Ngo, T. -. B., Hibbard, K. L., Murphy, C., Jenett, A., Truman, J. W., & Rubin, G. M. (2010). Refinement of tools for targeted gene expression in drosophila. Genetics, 186(2), 735-755


Recommended Readings: Mitchell Guttman, Monday, February 27, 2012

Monday lecture Series

Functional Integration of Large ncRNAs in the Molecular

Circuitry Controlling Cell State

Mitchell Guttman

Graduate Fellow

Broad Institute of MIT and Harvard

   Massachusetts Institute of Technology

Monday, February 27, 2012

4 p.m, Caspary Auditorium.   Refreshments 3:45 p.m.

Recommended Readings:

Yang, LG; Lin CR; Rosebfeld MG. 2011.  A lincRNA switch for embryonic stem cell fate.  Cell Research  21(12):1646-1648.  DOI:10.1038/cr.2011.166

Guttman M; Donachey J; Carey BW; et al. 2011.  lincRNAs act in the circuitry controlling pluripotency and differentiation.  NATURE.  477(7364):295-U60.   DOI:10.1038/nature10398

Loewer S; Cabili MN; Guttman M: et al.  2010.  Large intergenic non-coding RNA-RoR modeulates reprogramming of human induced pluripotent stem cells.  NATURE Genetics.  42(12):1113-   DOI: 10.1038/ng.710

Huarte M; Guttman M; Feldser D; et al.  2010.  A large intergenic noncoding RNA induced by p53 mediates global gene repression in thep53 response. Cell.  142(3):409-419.   DOI:10.1016/j.cell.2010.06.040

Guttman, M; Garber M; Levin JZ; et al.  2010.  Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.  NATURE Biotechnology.  28(5):503-U166.  DOI: 10.1038/nbt.1633

Khalil AM; Guttman M; Huarte M; et al.  2009.  Many human large intergenic noncoding RNAs associate with Chromatin-modifying complexes and affect gene expression.  PNAS.  106(28):11667-11672   DOI: 10.1073/pnas.0904715106

Guttman M; Amit I; Garber M; et al.  2009.  Chromatin signature reveals over a thousand highly conserved large no-coding RNAs in mammals.  NATURE.  458(7235):223-227.  DOI: 10.1038/nature07672