Recommended Readings: Edward S. Boyden Ph.D. Friday February 17, 2017

Friday Lectures

Friday, February 17, 2017   3:45 p.m.

Caspary Auditorium

Edward S. Boyden,  Ph.D.

Associate Professor

MIT Media Lab

Optical Tools for Analyzing and Repairing

Complex Biological Systems

Recommended Readings:

Boyden, Edward S. (2015). Optogenetics and the future of neuroscience. NATURE NEUROSCIENCE. 18(12): 1862-1862

Chen, Fei; Tillberg, Paul W.; Boyden, Edward S. (2015). Expansion microscopy. SCIENCE. 347(6221): 543-548   

Madisen, Linda; Mao, Tianyi; Koch, Henner; et al. (2012). A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing. NATURE NEUROSCIENCE. 15(5): 793-802

Bernstein, Jacob G.; Garrity, Paul A.; Boyden, Edward S.  (2012). Optogenetics and thermogenetics: technologies for controlling the activity of targeted cells within intact neural circuits. CURRENT OPINION IN NEUROBIOLOGY.   22(1): 61-71



Recommended Readings: Shixin Liu Ph.D. Monday November 14 2016

Monday Lectures

Monday November 14, 2016   3:45 p.m.

Caspary Auditorium

Shixin Liu   Ph.D.

Assistant Professor, The Rockefeller University

Laboratory of Nanoscale Biophysics and Biochemistry

Watching Biological Machines in Action

Recommended Readings:

 Liu, Shixin; Chistol, Gheorghe; Hetherington, Craig L.; et al.  A Viral Packaging Motor Varies Its DNA Rotation and Step Size to Preserve Subunit Coordination as the Capsid Fills.  CELL    157 (3):702-713     APR 24 2014

Chemla, Yann R.  High-Resolution, Hybrid Optical Trapping Methods, and Their Application to Nucleic Acid Processing Proteins.  BIOPOLYMERS   105(10): 704-714    OCT 2016

Ha, Taekjip.  Single-molecule methods leap aheadNATURE METHODS    11(10)1015-1018    OCT 2014

Guo, Peixuan; Grainge, Ian; Zhao, Zhengyi; et al.  Two classes of nucleic acid translocation motors: rotation and revolution without rotation. CELL AND BIOSCIENCE  4:54     SEP 16 2014

Casjens, Sherwood R.  The DNA-packaging nanomotor of tailed bacteriophages.  NATURE REVIEWS MICROBIOLOGY   9(9):647-657   SEP 2011

Chemla, YR; Aathavan, K; Michaelis, J; et al.  Mechanism of force generation of a viral DNA packaging motor. CELL   122(5 ): 683-692   : SEP 9 2005 

Recommended Readings: Joel E. Cohen Ph.D. Monday November 7 2016

Monday Lectures

Monday October 31, 2016   3:45 p.m.

Caspary Auditorium

Joel E. Cohen   Ph.D.

Abby Rockefeller Mauzé Professor of Populations

The Rockefeller University


Departments of International and Public Affairs;
Earth and Environmental Sciences; Ecology, Evolution and Environmental Biology; and Statistics of Columbia University

The Variation is the Theme:

Taylor’s law from Chagas Disease Vector Control to Tornado Outbreaks

Recommended Readings:

Taylor, L. R. Aggregation, variance and the mean.  Nature.  178:732-735    1961

Anderson, Sean C.; Cooper, Andrew B.; Dulvy, Nicholas K.   Ecological prophets: quantifying metapopulation portfolio effects. METHODS IN ECOLOGY AND EVOLUTION  4(10): 971-981      OCT 2013

Meng, Xu. Taylor’s power law: Before and after 50 years of scientific scrutiny.  ArXiv.      2011

Taylor, L. R. and I. P. Woiwod  Temporal Stability as a Density-Dependent Species Characteristic.  Journal of Animal Ecology.   49(1): 209-224   February 1980

Kalyuzhny, Michael; Schreiber, Yishai; Chocron, Rachel; et al.  Temporal fluctuation scaling in populations and communities. ECOLOGY.   95(6):1701-1709   JUN 2014

Recommended Readings: Tony Hunter, Ph.D., April 29

Friday Lecture Series
Friday, April 29, 2016
3:45 p.m., Caspary Auditorium

Tony Hunter, Ph.D.
Director, Molecular and Cell Biology Laboratory,
Renato Dulbecco Chair in Cancer Research,
American Cancer Society Professor,
Salk Institute for Biological Studies

Post-translational regulation of cell signaling

Recommended Readings

Hunter, T. (2014). The genesis of tyrosine phosphorylation. Cold Spring Harbor Perspectives in Biology, 6(5), a020644. doi: 10.1101/cshperspect.a020644

Hunter, T. (2015). Discovering the first tyrosine kinase. Proceedings of the National Academy of Sciences, 112(26), 7877–7882. doi: 10.1073/pnas.1508223112

Recommended Readings: Tom Muir, Ph.D., March 27

Friday Lecture Series
Friday, March 27, 2015
3:45 p.m., Caspary Auditorium

Tom Muir, Ph.D.
Van Zandt Williams Jr. Class of ‘65 Professor of Chemistry,
Chair, Department of chemistry
Princeton University

‘Houdini’ Proteins: Discovery and Applications of Ultrafast Inteins

Recommended Readings

Empirical Articles

Shah, N. H., Dann, G. P., Vila-Perelló, M., Liu, Z., & Muir, T. W. (2012). Ultrafast protein splicing is common among cyanobacterial split inteins: Implications for protein engineering. Journal of the American Chemical Society, 134(28), 11338–11341. doi:10.1021/ja303226x

Shah, N. H., Eryilmaz, E., Cowburn, D., & Muir, T. W. (2013). Naturally split inteins assemble through a “capture and collapse” mechanism. Journal of the American Chemical Society, 135(49), 18673–18681. doi:10.1021/ja4104364

Shah, N. H., Vila-Perelló, M., & Muir, T. W. (2011). Kinetic control of one-pot trans-splicing reactions by using a wild-type and designed split intein. Angewandte Chemie, 50(290, 6511–6515. doi:10.1002/anie.201102909

Vila-Perelló, M., Liu, Z., Shah, N. H., Willis, J. A., Idoyaga, J., & Muir, T. W. (2013). Streamlined expressed protein ligation using split inteins. Journal of the American Chemical Society, 135(1), 286–292. doi:10.1021/ja309126m

Review Papers

Eryilma, E., Shah, N. H., Muir, T. W., & Cowburn, D. (2014). Structural and dynamical features of Inteins and implications on protein splicing. Journal of Biological Chemistry, 289(21), 14506–14511. doi:10.1074/jbc.R113.540302

Shah, N. H., & Muir, T. W. (2014). Inteins: Nature’s Gift to Protein Chemists. Chemical Science, 5(1), 446–461. doi:10.1016/j.biotechadv.2011.08.021.Secreted

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: 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: Nathaniel Heintz, Ph.D. Monday, Oct. 21

Understanding Neuronal Diversity: TRAP, Molecular Phenotyping and 5-hydroxymethylcytosine
Nathaniel Heintz, Ph.D.
Investigator, Howard Hughes Medical Institute
James and Marilyn Simons Professor
Laboratory of Molecular Biology
The Rockefeller University
4:00 p.m., Carson Family Auditorium

Recommended Readings

Review Paper

Branco, M. R., Ficz, G., & Reik, W. (2012). Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nature reviews. Genetics, 13(1), 7–13. doi:10.1038/nrg3080

Empirical Articles

Doyle, J. P., Dougherty, J. D., Heiman, M., Schmidt, E. F., Stevens, T. R., Ma, G., … Heintz, N. (2008). Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell, 135(4), 749–762. doi:10.1016/j.cell.2008.10.029

Gong, S., Zheng, C., Doughty, M. L., Losos, K., Didkovsky, N., Schambra, U. B., … Heintz, N. (2003). A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature, 425(6961), 917–925. doi:10.1038/nature02033

Heiman, M., Schaefer, A., Gong, S., Peterson, J. D., Day, M., Ramsey, K. E., … Heintz, N. (2008). A translational profiling approach for the molecular characterization of CNS cell types. Cell, 135(4), 738–748. doi:10.1016/j.cell.2008.10.028

Heintz, N. (2004). Gene expression nervous system atlas (GENSAT). Nature neuroscience, 7(5), 483. doi:10.1038/nn0504-483

Kriaucionis, S., & Heintz, N. (2009). The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science, 324(5929), 929–30. doi:10.1126/science.1169786

Recommended Readings: Leslie M Turner PhD Oct 22, 2012

Genomic Networks of Hybrid Sterility

Leslie M Turner  PhD

Postdoctoral Fellow

Laboratory of Genetics, University of Wisconsin – Madison

Monday, October 22,  2012

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

Recommended Readings:

Janousek, V; Wang, LY; Luzynski, K; et al.  2012.  Genome-wide architecture of reproductive isolation in naturally occurring hybrid zone between Mus musculus musculus and M. m. domesticus.   Molecular Ecology.  21(12):3032-3047.  DOI:10.111/j.1365-294X.2012.05583.x

White, MA; Steffy, B; Wiltshire, T; et al.  2011.  Genetic dissection of a key reproductive barrier between nascent species of house mice.  Genetics. 189(1):289-U988.  DOI:10.1534/genetics.111.129171

Turner, LM; Schwahn, DJ; Harr, B.  2012.  Reduced male fertility is common but highly variable in form and severity in a natural house mouse hybrid zone.   Evolution.  66(2):443-458 DOI:10.1111/j.1558-5646.2011.01445.x

Turner, LM; Young, AR; Roempler, H; et al.  2010.  Monogamy evolves through multiple mechanisms: evidence from V1aR in deer mice.  Molecular Biology and Evolution.  27(6)1269-1278.  DOI:10.1093/molbev/msq013

Harr, B; Turner, LM.  2010.  Genome-wide analysis of alternative splicing evolution among Mus subspecies.  Molecular Ecology.  19(suppl 1):228-239.  DOI:10.1111/j.1365-294X.04490.x

Gompert, Z; Buerkle, CA.  2009.  A powerful regression-based method for admixture mapping of isolation across the genome of hybrids.  Molecular Ecology.  18(6):1207-1224.  DOI:10.1111/j.1365-0294X.04098.x

Elliott, RW; Miller, DR; Pearsall, RS; et al.  2001.  Genetic analysis of testis weight and fertility in an interspecies hybrid congenic strain for chromosome X.   Mammalian Genome.  12(1):45-51.  DOI:10.1007/s003350010234

Recommended Readings: Marco Tripodi PhD Oct 8 2012

Spatiotemporal Control of Motor Circuit Assembly and Function

 Marco Tripodi, Ph.D.

Postdoctoral Fellow


University of Basel and

Friedrich Miescher Institute for Biomedical Research

 Monday, October 8, 2012

4:00 p.m., Caspary Auditorium

Recommended Readings:

Arber, Silvia.  2012.  Motor circuits in action: specification, connectivity and functionNeuron.  74(6):975-969  DOI: 10.1016/j.neuron.2012.05.011

Martin, John H.  2012.  Systems neurobiology of restorative neurology and future directions for repair of the damaged motor systems.  Clinical Neurobiology and Neurosurgery.  114(5, Sp.Issue S1):515-523.  DOI: 10.1016/j.clineuro.2012.01.011  Please request from Markus Library.

Denk, W.; K.L. Briggman; M. Helmstaedter.  2012.  Structural neurobiology: missing link t o a mechanistic understanding of neural computation.  Nature Reviews Neuroscience.  13(5):351-358.  DOI: 10.1038/nrn3169

Tripodi, M.; A. E. Stepien; and S. Arber.   2011.  Motor antagonism exposed by spatial segregation and timing of neurogenesis.  Nature.  479:7371:61-U84.  DOI:10.1038/nature1038

Simon, M.A.; S. J. Fusillo; K. Colman, et al. 2010.  Motor patterns associated with crawling in a soft-bodied arthropod.  Journal of Experimental Biology.  213(13):2302-2309.  DOI:10.1242/jeb.039206

Ugolini, G.  2010.  Advances in viral transneuronal tracing.  7th FENS Meeting on Neuroanatomical Tracing and Systems. Amsterdam, Netherlands, July 3, 2010.  Journal of Neuroscience Methods.  194(1):2-20.  DOI:10.1016/j.jneumeth.2009.12.001