Recommended Readings: David Kingsley, Ph.D.

Friday Lecture Series

The Fairfield Osborn Memorial Lecture

Fishing for the Secrets of Vertebrate Evolution

David Kingsley, Ph.D., professor, developmental biology, Stanford University;

investigator, Howard Hughes Medical Institute

April 18, 2014

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

Caspary Auditorium

Recommended Readings

han, Y. F., Marks, M. E., Jones, F. C., Villarreal Jr., G., Shapiro, M. D., Brady, S. D., . . . Kingsley, D. M. (2010). Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a pitxl enhancer. Science, 327(5963), 302-305

Haussler, D., O’Brien, S. J., Ryder, O. A., Keith Barker, F., Clamp, M., Crawford, A. J., . . . Turner, S. (2009). Genome 10K: A proposal to obtain whole-genome sequence for 10000 vertebrate species. Journal of Heredity, 100(6), 659-674

Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., . . . Kingsley, D. M. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55-61

Kingsley, D. M., Zhu, B., Osoegawa, K., De Jong, P. J., Schein, J., Marra, M., . . . Myers, R. (2004). New genomic tools for molecular studies of evolutionary change in threespine sticklebacks. Behaviour, 141(11-12), 1331-1344

Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., . . . Haussler, D. (2011). Three periods of regulatory innovation during vertebrate evolution. Science, 333(6045), 1019-1024

Shapiro, M. D., Bell, M. A., & Kingsley, D. M. (2006). Parallel genetic origins of pelvic reduction in vertebrates. Proceedings of the National Academy of Sciences of the United States of America, 103(37), 13753-13758

 

Recommended Readings: Titia de Lange, Ph.D.

Friday Lecture Series

Breaking Bad: How Telomeres Hide from the DNA Damage Response

Titia de Lange, Ph.D., Leon Hess Professor, Head of the Laboratory of Cell Biology and Genetics, The Rockefeller University

February 28, 2014

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

Caspary Auditorium

Recommended Readings

Davoli, T., Denchi, E. L., & de Lange, T. (2010). Persistent telomere damage induces bypass of mitosis and tetraploidy. Cell, 141(1), 81-93

Hockemeyer, D., Sfeir, A. J., Shay, J. W., Wright, W. E., & De Lange, T. (2005). POT1 protects telomeres from a transient DNA damage response and determines how human chromosomes end. EMBO Journal, 24(14), 2667-2678

Jacobs, J. J. L., & De Lange, T. (2005). p16INK4a as a second effector of the telomere damage pathway. Cell Cycle, 4(10), 1364-1368

Konishi, A., & De Lange, T. (2008). Cell cycle control of telomere protection and NHEJ revealed by a ts mutation in the DNA-binding domain of TRF2. Genes and Development, 22(9), 1221-1230

Sfeir, A., & De Lange, T. (2012). Removal of shelterin reveals the telomere end-protection problem. Science, 336(6081), 593-597

Sfeir, A., Kabir, S., Van Overbeek, M., Celli, G. B., & De Lange, T. (2010). Loss of Rap1 induces telomere recombination in the absence of NHEJ or a DNA damage signal. Science, 327(5973), 1657-1661

Wu, P., Takai, H., & De Lange, T. (2012). Telomeric 3′ overhangs derive from resection by Exo1 and apollo and fill-in by POT1b-associated CST. Cell, 150(1), 39-52

 

Recommended Readings: Michael Strand, Ph.D.

Friday Lecture Series

Polydnaviruses: Viral Mutualists and Nature’s Genetic Engineers

Michael Strand, Ph.D., Regents Professor, department of entomology,

University of Georgia

February 21, 2014

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

Caspary Auditorium

Recommended Readings

Beck, M. H., & Strand, M. R. (2007). A novel polydnavirus protein inhibits the insect prophenoloxidase activation pathway. Proceedings of the National Academy of Sciences of the United States of America, 104(49), 19267-19272

Burke, G. R., Thomas, S. A., Eum, J. H., & Strand, M. R. (2013). Mutualistic polydnaviruses share essential replication gene functions with pathogenic ancestors. PLoS Pathogens, 9(5)

Strand, M. R., & Burke, G. R. (2012). Polydnaviruses as symbionts and gene delivery systems. PLoS Pathogens, 8(7), 5

Thoetkiattikul, H., Beck, M. H., & Strand, M. R. (2005). Inhibitor κB-like proteins from a polydnavirus inhibit NF-κB activation and suppress the insect immune response. Proceedings of the National Academy of Sciences of the United States of America, 102(32), 11426-11431

Webb, B. A., Strand, M. R., Dickey, S. E., Beck, M. H., Hilgarth, R. S., Barney, W. E., . . . Witherell, R. A. (2006). Polydnavirus genomes reflect their dual roles as mutualists and pathogens. Virology, 347(1), 160-174

 

Recommended Readings: Poornima Parameswaran Ph.D. February 10

SPECIAL SEMINAR
Monday, February 10, 2014
4:00 p.m., Carson Family Auditorium

Poornima Parameswaran, Ph.D.

Postdoctoral Research Fellow
School of Public Health
University of California, Berkeley

Virome & Immunome Diversity in Dengue & other Infectious Diseases

Recommended Readings:

Empirical Papers

Parameswaran, P., Charlebois, P., Tellez, Y., Nunez, A., Ryan, E. M., Malboeuf, C. M., … Henn, M. R. (2012). Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity. Journal of Virology, 86(16), 8546–8558. doi:10.1128/JVI.00736-12

Parameswaran, P., Liu, Y., Roskin, K. M., Jackson, K. K. L., Dixit, V. P., Lee, J.-Y., … Fire, A. Z. (2013). Convergent antibody signatures in human dengue. Cell Host & Microbe, 13(6), 691–700. doi:10.1016/j.chom.2013.05.008

Parameswaran, P., Sklan, E., Wilkins, C., Burgon, T., Samuel, M. a, Lu, R., … Fire, A. Z. (2010). Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems. PLoS pathogens, 6(2), e1000764. doi:10.1371/journal.ppat.1000764

Review Articles

Fontana, J. M., Alexander, E., & Salvatore, M. (2012). Translational research in infectious disease: current paradigms and challenges ahead. Translational Research, 159(6), 430–453. doi:10.1016/j.trsl.2011.12.009

Wylie, K. M., Weinstock, G. M., & Storch, G. a. (2012). Emerging view of the human virome. Translational Research, 160(4), 283–290. doi:10.1016/j.trsl.2012.03.006

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

SPECIAL SEMINAR
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: Lei Stanley Qi, Ph.D. Monday, January 13

SPECIAL SEMINAR
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: Scott Lowe, Ph.D.

Friday Lecture Series

Cancer Initiation and Maintenance Genes

Scott Lowe, Ph.D., chair, Geoffrey Beene Cancer Research Center,

Memorial Sloan Kettering Cancer Center;

investigator, Howard Hughes Medical Institute

January 3, 2014

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

Caspary Auditorium

Recommended Readings

Chicas, A., Kapoor, A., Wang, X., Aksoy, O., Evertts, A. G., Zhang, M. Q., . . . Lowe, S. W. (2012). H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proceedings of the National Academy of Sciences of the United States of America, 109(23), 8971-8976

Dow, L. E., & Lowe, S. W. (2012). Life in the fast lane: Mammalian disease models in the genomics era. Cell, 148(6), 1099-1109

Premsrirut, P. K., Dow, L. E., Kim, S. Y., Camiolo, M., Malone, C. D., Miething, C., . . . Lowe, S. W. (2011). A rapid and scalable system for studying gene function in mice using conditional RNA interference. Cell, 145(1), 145-158

Sawey, E., Chanrion, M., Cai, C., Wu, G., Zhang, J., Zender, L., . . . Powers, S. (2011). Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by oncogenomic screening. Cancer Cell, 19(3), 347-358

Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., . . . Lowe, S. W. (2012). A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proceedings of the National Academy of Sciences of the United States of America, 109(21), 8212-8217

Zuber, J., Rappaport, A. R., Luo, W., Wang, E., Chen, C., Vaseva, A. V., . . . Lowe, S. W. (2011). An integrated approach to dissecting oncogene addiction implicates a myb-coordinated self-renewal program as essential for leukemia maintenance. Genes and Development, 25(15), 1628-1640

 

Recommended Readings: Harmit S. Malik, Ph.D.

Friday Lecture Series

Genetic Conflicts: Beyond the Usual Suspects

Harmit S. Malik, Ph.D., principal investigator, basic sciences division,

Fred Hutchinson Cancer Research Center;

early career scientist, Howard Hughes Medical Institute

December 13, 2013

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

Caspary Auditorium

Recommended Readings

Malik, H. S. (2009). Evolution of TRIM antiviral genes in primate genomes. Retrovirology, 6(SUPPL. 2)

Malik, H. S., & Bayes, J. J. (2006). Genetic conflicts during meiosis and the evolutionary origins of centromere complexity. Biochemical Society Transactions, 34(4), 569-573

Malik, H. S., & Henikoff, S. (2002). Conflict begets complexity: The evolution of centromeres. Current Opinion in Genetics and Development, 12(6), 711-718

Moran, J. V., & Malik, H. S. (2009). Diamonds and rust: How transposable elements influence mammalian genomes. conference on mobile elements in mammalian genomes. EMBO Reports, 10(12), 1306-1310

Oliver, P. L., Goodstadt, L., Bayes, J. J., Birtle, Z., Roach, K. C., Phadnis, N., . . . Ponting, C. P. (2009). Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genetics, 5(12)

Vermaak, D., & Malik, H. S. (2009). Multiple roles for heterochromatin protein 1 genes in drosophila. Annual Review of Genetic 43 , pp. 467-492

 

Recommended Readings: Pardis Sabeti M.D., Ph.D. Friday, Nov 8

FRIDAY LECTURE SERIES
Friday, November 8, 2013
3:45 p.m., Caspary Auditorium

Pardis Sabeti M.D., Ph.D.
Senior Associate Member, Broad Institute of MIT and Harvard;
Associate Professor, Center for Systems Biology, Harvard University Department of Organismic and Evolutionary Biology, and Department of Immunology and Infectious Disease at Harvard School of Public Health

Evolutionary Forces in Humans and Pathogens

Recommended Readings:

Empirical Articles

The 100 Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061–1073. doi:10.1038/nature09534

The International MapMap Consortium. (2005). A haplotype map of the human genome. Nature, 437(7063), 1299–1320. doi:10.1038/nature04226

Grossman, S. R., Andersen, K. G., Shlyakhter, I., Tabrizi, S., Winnicki, S., Yen, A., … Sabeti, P. C. (2013). Identifying recent adaptations in large-scale genomic data. Cell, 152(4), 703–713. doi:10.1016/j.cell.2013.01.035

Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z., Richter, D. J., Schaffner, S. F., … & Lander, E. S. (2002). Detecting recent positive selection in the human genome from haplotype structureNature419(6909), 832-837. doi:10.1038/nature01140

Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., … Gaudet, R. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449(7164), 913–8. doi:10.1038/nature06250

Review Papers

Biswas, S., Akey, J. M. (2006) Genomic insights into positive selection. Trends in Genetics, 22(8), 437-445. doi:10.1016/j.tig.2006.06.005

Kreitman, M. (2000). Methods to detect selection in populations with applications to the human. Annual Review of Genomics and Human Genetics, 1, 539-559. doi: 10.1146/annurev.genom.1.1.539

Nielsen, R., Hellmann, I., Hubisz, M., Bustamante, C., & Clark, A. G. (2007). Recent and ongoing selection in the human genome. Nature Reviews Genetics,8(11), 857-868. doi:10.1038/nrg2187

Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., … & Lander, E. S. (2006). Positive natural selection in the human lineage .Science, 312(5780), 1614-1620. doi:10.1126/science.1124309

Vitti, J. J., Cho, M. K., Tichkoff, S. A., Sabeti, P. C. (2012). Human evolutionary genomics: ethical and interpretive issues. Trends in Genetics, 28(3), 137-145. doi:10.1016/j.tig.2011.12.001

Recommended Readings: Frederick Cross Ph.D. September 23, 2013

Monday Lecture Series
A Fast Route to Cell Cycle Control in the Plant Superkingdom
Frederick Cross, Ph.D.
Professor, Laboratory of Cell Cycle Genetics
The Rockefeller University
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

Bloom, J., & Cross, F. R. (2007). Multiple levels of cyclin specificity in cell-cycle control. Nature Reviews Molecular and Cell Biology, 8(2), 1491–1560. doi:10.1038/nrm2105

Cross, F. R., Buchler, N. E., & Skotheim, J. M. (2011). Evolution of networks and sequences in eukaryotic cell cycle control. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 366(1584), 3532–3544. doi:10.1098/rstb.2011.0078

Harris, E. (2001). Chlamydomonas as a model organism. Annual Review of Plant Biology, 52, 363–406. doi:10.1146/annurev.arplant.52.1.363

Empirical Papers

Bisova, K., Krylov, D. M., & Umen, J. G. (2005). Genome-wide annotation and expression profiling of cell cycle regulatory genes in Chlamydomonas reinhardtii. Plant Physiology, 137, 475–491. doi:10.1104/pp.104.054155.G1-S-G2-M

Fang, S.-C., de los Reyes, C., & Umen, J. G. (2006). Cell size checkpoint control by the retinoblastoma tumor suppressor pathway. PLoS Genetics, 2(10), e167. doi:10.1371/journal.pgen.0020167

Koff, a, Cross, F., Fisher, a, Schumacher, J., Leguellec, K., Philippe, M., & Roberts, J. M. (1991). Human cyclin E, a new cyclin that interacts with two members of the CDC2 gene family. Cell, 66(6), 1217–1228.

Olson, B. J. S. C., Oberholzer, M., Li, Y., Zones, J. M., Kohli, H. S., Bisova, K., … Umen, J. G. (2010). Regulation of the Chlamydomonas cell cycle by a stable, chromatin-associated retinoblastoma tumor suppressor complex. The Plant Cell, 22(10), 3331–3347. doi:10.1105/tpc.110.076067

Richardson, H. E., Wittenberg, C., Cross, F., & Reed, S. I. (1989). An essential G1 function for cyclin-like proteins in yeast. Cell, 59(6), 1127–1133.