Recommended Readings: Svante Pääbo, Ph.D.

Friday Lecture Series

Fairfield Osborn Memorial Lecture

A Molecular Perspective on Human Origins

Svante Pääbo, Ph.D., director, department of genetics,

Max Planck Institute for Evolutionary Anthropology

 December 14, 2012

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

Caspary Auditorium

Recommended Readings

Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., . . . Kaessmann, H. (2011). The evolution of gene expression levels in mammalian organs. Nature, 478(7369), 343-348

Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., . . . Pääbo, S. (2010). A draft sequence of the neandertal genome. Science, 328(5979), 710-722

Hu, H. Y., Guo, S., Xi, J., Yan, Z., Fu, N., Zhang, X., . . . Khaitovich, P. (2011). MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PLoS Genetics, 7(10)

Krause, J., Briggs, A. W., Kircher, M., Maricic, T., Zwyns, N., Derevianko, A., & Pääbo, S. (2010). A complete mtDNA genome of an early modern human from kostenki, russia. Current Biology, 20(3), 231-236

Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern siberia. Nature, 464(7290), 894-897

Xu, A. G., He, L., Li, Z., Xu, Y., Li, M., Fu, X., . . . Khaitovich, P. (2010). Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-seq. PLoS Computational Biology, 6(7), 37


Recommended Readings: Victor Ambros, Ph.D.

Friday Lecture Series

microRNA Pathways in Animal Development

Joshua Lederberg Distinguished Lectureship in Molecular Genetics

Victor Ambros, Ph.D., Silverman Professor of Natural Science, co-director,

RNA Therapeutics Institute,

University of Massachusetts Medical School

February 3, 2012

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

Caspary Auditorium

Recommended Readings:

Ambros, V. 2010. MicroRNAs: Genetically sensitized worms reveal new secrets. Current Biology 20, (14): R598-R600

Hammell, C. M., X. Karp, and V. Ambros. 2009. A feedback circuit involving let-7-family miRNAs and DAF-12 integrates environmental signals and developmental timing in caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America 106, (44): 18668-18673

Hammell, C. M., I. Lubin, P. R. Boag, T. K. Blackwell, and V. Ambros. 2009. Nhl-2 modulates MicroRNA activity in caenorhabditis elegans. Cell 136, (5): 926-938

Hammell, M., D. Long, L. Zhang, A. Lee, C. S. Carmack, M. Han, Y. Ding, and V. Ambros. 2008. mirWIP: MicroRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nature Methods 5, (9): 813-819

Miska, E. A., E. Alvarez-Saavedra, A. L. Abbott, N. C. Lau, A. B. Hellman, S. M. McGonagle, D. P. Bartel, V. R. Ambros, and H. R. Horvitz. 2007. Most caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genetics 3, (12): 2395-2403

Sokol, N. S., P. Xu, Y. -N Jan, and V. Ambros. 2008. Drosophila let-7 microRNA is required for remodeling of the neuromusculature during metamorphosis. Genes and Development 22, (12): 1591-1596

Recommended Readings: Anthony Leung Ph.D. April 12, 2010

Monday Lecture Series

Poly(ADP-ribose) Regulates microRNA Activity and

Stress Responses in the Cytoplasm

Anthony Leung, Ph.D.,

Senior Postdoctoral Fellow

Koch Institute for Integrative Cancer Research

Massachusetts Institute of Technology

Special Fellow of Leukemia and Lymphoma Society 

April 12, 2010

Welch Hall,  Level Two

4:00 p.m.-5:00 p.m

Recommended Readings:

Pothof J, Verkaik NS, Hoeijmakers JHJ, et al.  2009.    MicroRNA responses and stress granule formation modulate the DNA damage response.  CELL CYCLE    8(21):3462-3468   

Pothof J, Verkaik NS, van IJcken W, et al.   2009.   MicroRNA-mediated gene silencing modulates the UV-induced DNA-damage response.   EMBO JOURNAL   28(14):2090-2099

Andersson MK, Stahlberg A, Arvidsson Y, et al.  2008.   The multifunctional FUS, EWS and TAF15 proto-oncoproteins show cell type-specific expression patterns and involvement in cell spreading and stress response.   BMC CELL BIOLOGY   9(Article No. 37)

 Leung AKL.  2008.   MicroRNA and stress: Cellular and molecular perspectives.    BIOLOGICAL PSYCHIATRY    63(7): 52S-53S   Supplement: Suppl. S   

Leung AKL, Calabrese JM, Sharp PA.  2006.   Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA    103(48):18125-18130   

Balzer E, Moss EG.  2007.  Localization of the developmental timing regulator Lin28 to mRNP complexes, P-bodies and stress granules.     RNA BIOLOGY    4(1):16-25   

Recommended Readings: Michael Rosbash, Ph. D. Oct. 9, 2009

Friday Lecture Series

Circadian Rhythms and the Transcriptional Feedback Loop

Michael Rosbach, Ph. D., professor and director

National Center for Behavioral Genomics, Brandeis University;

Howard Hughes Medical Institute, investigator

October 9, 2009

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

Caspary Auditorium

Recommended Articles:

Kadener, S., J. S. Menet, K. Sugino, M. D. Horwich, U. Weissbein, P. Nawathean, V. V. Vagin, P. D. Zamore, S. B. Nelson, and M. Rosbash. 2009. A role for microRNAs in the drosophila circadian clock. Genes and Development 23, (18): 2179-219

Kadener, S., D. Stoleru, M. McDonald, P. Nawathean, and M. Rosbash. 2007. Clockwork orange is a transcriptional repressor and a new drosophila circadian pacemaker component. Genes and Development 21, (13): 1675-168

Rosbash, M. 2009. The implications of multiple circadian clock origins. PLoS Biology 7, (3): 0421-0425

Shang, Y., L. C. Griffith, and M. Rosbash. 2008. Light-arousal and circadian photoreception circuits intersect at the large PDF cells of the drosophila brain. Proceedings of the National Academy of Sciences of the United States of America 105, (50): 19587-19594

Stoleru, D., P. Nawathean, M. d. l. P. Fernández, J. S. Menet, M. F. Ceriani, and M. Rosbash. 2007. The drosophila circadian network is a seasonal timer. Cell 129, (1): 207-219

Recommended Readings: Jennifer A. Doudna, Ph.D.; May 8, 2009

Friday Lecture Series

“Dicer and Beyond: Regulatory RNA Processing and Function”

Jennifer A. Doudna, Ph.D., professor, departments of molecular and cell biology and of chemistry; investigator, Howard Hughes Medical Institute

University of California, Berkeley

May 8, 2009

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

Caspary Auditorium

Recommended Articles:

Aggarwal, A. K., and J. A. Doudna. 2005. Protein-nucleic acid interactions: Unlocking mysteries old and new. Current opinion in structural biology. 15(1 SPEC. ISS.):65-67.


Fukunaga, R., and J. A. Doudna. 2009. dsRNA with 5′ overhangs contributes to endogenous and antiviral RNA silencing pathways in plants. EMBO Journal. 28(5):545-555.


Jinek, M., and J. A. Doudna. 2009. A three-dimensional view of the molecular machinery of RNA interference. Nature. 457(7228):405-412.


Ma, E., I. J. MacRae, J. F. Kirsch, and J. A. Doudna. 2008. Autoinhibition of human dicer by its internal helicase domain. Journal of Molecular Biology. 380(1):237-243.


MacRae, I. J., and J. A. Doudna. 2007. Ribonuclease revisited: Structural insights into ribonuclease III family enzymes. Current opinion in structural biology. 17(1):138-145.


MacRae, I. J., K. Zhou, and J. A. Doudna. 2007. Structural determinants of RNA recognition and cleavage by dicer. Nature Structural and Molecular Biology. 14(10):934-940.


MacRae, I. J., K. Zhou, F. Li, A. Repic, A. N. Brooks, W. Z. Cande, P. D. Adams, and J. A. Doudna. 2006. Structural basis for double-stranded RNA processing by dicer. Science. 311(5758):195-198.

Recommended Readings: Andrew Grimson, Ph.D.

Monday Lecture Series

Animal microRNAs: their ancient origin and contemporary targets

Andrew Grimson, Ph.D.

Postdoctoral Fellow

Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute

Monday, March 2, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Glazov, E. A., S. McWilliam, W. C. Barris, and B. P. Dalrymple. 2008. Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Molecular Biology and Evolution. 25(5):939-948.

Farh, K. K. -H, A. Grimson, C. Jan, B. P. Lewis, W. K. Johnston, L. P. Lim, C. B. Burge, and D. P. Bartel. 2005. Biochemistry: The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science. 310(5755):1817-1821.

Grimson, A., K. K. -H Farh, W. K. Johnston, P. Garrett-Engele, L. P. Lim, and D. P. Bartel. 2007. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Molecular Cell. 27(1):91-105.

Grimson, A., M. Srivastava, B. Fahey, B. J. Woodcroft, H. R. Chiang, N. King, B. M. Degnan, D. S. Rokhsar, and D. P. Bartel. 2008. Early origins and evolution of microRNAs and piwi-interacting RNAs in animals. Nature. 455(7217):1193-1197.

Piriyapongsa, J., L. Mariño-Ramírez, and I. K. Jordan. 2007. Origin and evolution of human microRNAs from transposable elements. Genetics. 176(2):1323-1337.