Recommended Readings: Michael Levine Ph.D. Sept 30, 2016

Friday Lecture Series

Norton Zinder Lecture

Michael Levine, Ph.D.

Director, Lewis-Sigler Institute for Integrative Genomics, Princeton Univ.

Anthony B. Evnin Professor, Dept Molecular Biology, Princeton Univ.

Visualization and evolution of transcriptional enhancers

Recommended Readings:

Bothma, J.P., Garcia, H.G., Ng, S., Perry, M.W., Gregor, T., and Levine, M. (2015). Enhancer additivity and nonadditivity are determined by enhancer strength in the Drosophila embryo. eLife 4, 07956.

Farley, E.K., Olson, K.M., Zhang, W., Brandt, A.J., Rokhsar, D.S., and Levine, M. (2015). Suboptimization of developmental enhancers. Science 350, 325-328.

Fukaya, T., Lim, B., and Levine, M. 2016. Enhancer control of transcriptional bursting. Cell 166, 358-368.

Bothma, J., Garcia, H., Gavin, S., Esposito, E., Gregor, T., and Levine, M. (2014). Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. PNAS 111, 10598-10603.

Evans, Nicole C.; Swanson, Christina I.; Barolo, Scott.  Sparkling Insights into Enhancer Structure, Function, and Evolution.  TRANSCRIPTIONAL SWITCHES DURING DEVELOPMENT   Book Series: Current Topics in Developmental Biology .  98: 97-120   2012

Gordon, Kacy L.; Ruvinsky, Ilya.  Tempo and Mode in Evolution of Transcriptional Regulation.  PLOS GENETICS.   8(1): e1002432    2012

Recommended Readings: Richard Lifton, M.D., Ph.D., June 10

Friday Lecture Series
Friday, June 10, 2016
3:45 p.m., Caspary Auditorium

Richard Lifton, M.D., Ph.D.
President-elect, The Rockefeller University
Sterling Professor of Genetics and Professor of Medicine (Nephrology),
Chair, Department of Genetics, Yale University
Investigator, Howard Hughes Medical Institute

From Genes and Genomes to Biology and Health

Recommended Readings:

Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., … & Lifton, R. O. (2009). Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proceedings of the National Academy of Sciences, 106(45), 19096-19101. doi: 10.1073/pnas.0910672106.

Ji, W., Foo, J. N., O’Roak, B. J., Zhao, H., Larson, M. G., Simon, D. B., … & Lifton, R. P. (2008). Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nature Genetics, 40(5), 592-599. doi: 10.1038/ng.118.

Lifton, R. P., Gharavi, A. G., & Geller, D. S. (2001). Molecular mechanisms of human hypertension. Cell, 104(4), 545-556. doi:10.1016/S0092-8674(01)00241-0

Shimkets, R. A., Warnock, D. G., Bositis, C. M., Nelson-Williams, C., Hansson, J. H., Schambelan, M., … & Lifton, R. O. (1994). Liddle’s syndrome: heritable human hypertension caused by mutations in the β subunit of the epithelial sodium channel. Cell, 79(3), 407-414. doi:10.1016/0092-8674(94)90250-X

Recommended Readings: Sean Brady, Ph.D., May 16

Monday Lecture Series
Monday, May 16, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Sean Brady, Ph.D.
Tri-Institutional Associate Professor,
Evnin Associate Professor and Head,
Laboratory of Genetically Encoded Small Molecules,
The Rockefeller University
Early Career Scientist, Howard Hughes Medical Institute

Bioactive Metabolites from the Human Microbiome: Natural Cures or Snake Oil

Recommended Readings:

Cohen, L. J., Kang, H. S., Chu, J., Huang, Y. H., Gordon, E. A., Reddy, B. V. B., … & Brady, S. F. (2015). Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist. Proceedings of the National Academy of Sciences, 112(35), E4825-E4834. doi: 10.1073/pnas.1508737112.

Charlop-Powers, Z., Milshteyn, A., & Brady, S. F. (2014). Metagenomic small molecule discovery methods. Current Opinion in Microbiology, 19, 70-75. doi: 10.1016/j.mib.2014.05.021.

Recommended Readings: Angelika Amon, Ph.D., May 27

Friday Lecture Series
Friday, May 27, 2016
3:45 p.m., Caspary Auditorium

Angelika Amon, Ph.D.
Kathleen and Curtis Marble Professor of Cancer Research,
Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology
Investigator, Howard Hughes Medical Institute

The Causes and Consequences of Aneuploidy

Recommended Readings:

Sheltzer, J. M., Blank, H. M., Pfau, S. J., Tange, Y., George, B. M., Humpton, T. J., … & Amon, A. (2011). Aneuploidy drives genomic instability in yeast. Science, 333(6045), 1026-1030. doi: 10.1126/science.1206412.

Sheltzer, J. M., Torres, E. M., Dunham, M. J., & Amon, A. (2012). Transcriptional consequences of aneuploidy. Proceedings of the National Academy of Sciences, 109(31), 12644-12649. doi: 10.1073/pnas.1209227109.

Tang, Y. C., & Amon, A. (2013). Gene copy-number alterations: a cost-benefit analysis. Cell, 152(3), 394-405. doi: 10.1016/j.cell.2012.11.043.

Torres, E. M., Sokolsky, T., Tucker, C. M., Chan, L. Y., Boselli, M., Dunham, M. J., & Amon, A. (2007). Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science, 317(5840), 916-924. doi: 10.1126/science.1142210

Recommended Readings: Mary Jeanne Kreek, M.D., May 2

Monday Lecture Series
Monday, May 2, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Mary Jeanne Kreek, M.D.
Senior Attending Physician,
The Rockefeller University Hospital
Patrick E. and Beatrice M. Haggerty Professor and Head,
Laboratory of the Biology of Addictive Diseases,
The Rockefeller University

50th Anniversary of First Research Paper on Methadone Maintenance Treatment: Update on Molecular, Neurobiological, Behavioral, and Genetic Research

Recommended Readings:

Bond, C., LaForge, K. S., Tian, M., Melia, D., Zhang, S., Borg, L., … & Tischfield, J. A. (1998). Single-nucleotide polymorphism in the human mu opioid receptor gene alters β-endorphin binding and activity: possible implications for opiate addiction. Proceedings of the National Academy of Sciences, 95(16), 9608-9613.

Butelman, E. R., Yuferov, V., & Kreek, M. J. (2012). κ-opioid receptor/dynorphin system: genetic and pharmacotherapeutic implications for addiction. Trends in Neurosciences, 35(10), 587-596. doi:10.1016/j.tins.2012.05.005.

Dole, V. P., Nyswander, M. E., & Kreek, M. J. (1966). Narcotic blockade. Archives of Internal Medicine, 118(4), 304-309. doi:10.1001/archinte.1966.00290160004002

Kreek, M. J., Nielsen, D. A., Butelman, E. R., & LaForge, K. S. (2005). Genetic influences on impulsivity, risk taking, stress responsivity and vulnerability to drug abuse and addiction. Nature Neuroscience, 8(11), 1450-1457. doi:10.1038/nn1583

Reed, B., Butelman, E. R., Yuferov, V., Randesi, M., & Kreek, M. J. (2014). Genetics of opiate addiction. Current Psychiatry Reports, 16(11), 1-12. doi:10.1007/s11920-014-0504-6.

Recommended Readings: Bruce Beutler, M.D., March 25

Friday Lecture Series
Friday, March 25
3:45 p.m., Caspary Auditorium

Bruce Beutler, M.D.
Regental Professor,
Director, Center for the Genetics of Host Defense,
Raymond and Ellen Willie Distinguished Chair in Cancer Research,
University of Texas Southwestern Medical Center

Saturation Mutagenesis of the Mouse Genome with Real-time Identification of Causative Mutations

Recommended Readings

Empirical Articles

Shi, H., Wang, Y., Li, X., Zhan, X., Tang, M., Fina, M., … & Beutler, B. (2015). NLRP3 activation and mitosis are mutually exclusive events coordinated by NEK7, a new inflammasome component. Nature Immunology. 17(3), 250-258. doi: 10.1038/ni.3333.

Wang, T., Zhan, X., Bu, C. H., Lyon, S., Pratt, D., Hildebrand, S., … & Beutler, B. (2015). Real-time resolution of point mutations that cause phenovariance in mice. Proceedings of the National Academy of Sciences, 112(5), E440-E449. doi: 10.1073/pnas.1423216112.

Review Paper

Simon, M. M., Moresco, E. M. Y., Bull, K. R., Kumar, S., Mallon, A. M., Beutler, B., & Potter, P. K. (2015). Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. Mammalian Genome, 26(9-10), 486-500. doi: 10.1007/s00335-015-9603-x

Recommended Readings: Anne Brunet, Ph.D., March 11

Friday Lecture Series
Friday, March 11
3:45 p.m., Caspary Auditorium

Anne Brunet, Ph.D.
Michele and Timothy Barakett Endowed Professor,
Department of Genetics,
Stanford University School of Medicine

Epigenetic and Metabolic Regulation of Aging

Recommended Readings

Empirical Articles

Benayoun, B. A., Pollina, E. A., Ucar, D., Mahmoudi, S., Karra, K., Wong, E. D., … & Brunet, A. (2014). H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell, 158(3), 673-688. doi: 10.1016/j.cell.2014.06.027

Greer, E. L., Maures, T. J., Hauswirth, A. G., Green, E. M., Leeman, D. S., Maro, G. S., … & Brunet, A. (2010). Members of the H3K4 trimethylation complex regulate lifespan in a germline-dependent manner in C. elegans. Nature, 466(7304), 383-387. doi: 10.1038/nature09195

Greer, E. L., Maures, T. J., Ucar, D., Hauswirth, A. G., Mancini, E., Lim, J. P., … & Brunet, A. (2011). Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature, 479(7373), 365-371. doi: 10.1038/nature10572

Review Papers

Benayoun, B. A., Pollina, E. A., & Brunet, A. (2015). Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nature Reviews Molecular Cell Biology, 16(10), 593-610. doi:10.1038/nrm4048

Lim, J. P., & Brunet, A. (2013). Bridging the transgenerational gap with epigenetic memory. Trends in Genetics, 29(3), 176-186. doi: 10.1016/j.tig.2012.12.008

Recommended Readings: David A. Relman, M.D., February 19

Friday Lecture Series
Friday, February 19
3:45 p.m., Caspary Auditorium

David A. Relman, M.D.
Thomas C. and Joan M. Merigan Professor,
Department of Medicine,
Department of Microbiology and Immunology,
Stanford University

The Human Microbiome Across Space and Time

Recommended Readings

Empirical Article

DiGiulio, D. B., Callahan, B. J., McMurdie, P. J., Costello, E. K., Lyell, D. J., Robaczewska, A., … & Stevenson, D. K. (2015). Temporal and spatial variation of the human microbiota during pregnancy. Proceedings of the National Academy of Sciences, 112(35), 11060-11065. doi: 10.1073/pnas.1502875112.

Hoy, Y. E., Bik, E. M., Lawley, T. D., Holmes, S. P., Monack, D. M., Theriot, J. A., & Relman, D. A. (2015). Variation in taxonomic composition of the fecal microbiota in an inbred mouse strain across individuals and time. PLOS ONE, 10(11), e0142825. doi: 10.1371/journal.pone.0142825.

Lin, A., Bik, E. M., Costello, E. K., Dethlefsen, L., Haque, R., Relman, D. A., & Singh, U. (2013). Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLOS ONE, 8(1), e53838. doi: 10.1371/journal.pone.0053838.

Review Paper

Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J., & Relman, D. A. (2012). The application of ecological theory toward an understanding of the human microbiome. Science, 336(6086), 1255-1262. doi: 10.1126/science.1224203.

Recommended Readings: Li Zhao, Ph.D., March 2

Special Lecture Series
Wednesday, March 2, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Li Zhao, Ph.D.
Postdoctoral Researcher,
Department of Evolution and Ecology,
University of California Davis

Evolution of Genetic Novelties in Drosophila

Recommended Reading

Li, X., Fan, D., Zhang, W., Liu, G., Zhang, L., Zhao, L., … & Ding, Y. (2015). Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. Nature Communications, 6(8212). doi:10.1038/ncomms9212

Zhao, L., Saelao, P., Jones, C. D., & Begun, D. J. (2014). Origin and spread of de novo genes in Drosophila melanogaster populations. Science, 343(6172), 769-772. doi: 10.1126/science.1248286.

Zhao, L., Wit, J., Svetec, N., & Begun, D. J. (2015). Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans. PLOS Genetics, 11(5), e1005184. doi: 10.1371/journal.pgen.1005184.

Recommended Readings: Xiaoliang “Sunney” Xie, Ph.D, January 15

Friday Lecture Series
Friday, January 15, 2016
3:45 p.m., Caspary Auditorium

Xiaoliang “Sunney” Xie, Ph.D.
Mallinckrodt Professor of Chemistry and Chemical Biology,
Harvard University

Life at the Single Molecule Level: From Single Molecule  Enzymology to MALBAC Babies

Recommended Reading

Empirical Articles

Hou, Y., Fan, W., Yan, L., Li, R., Lian, Y., Huang, J., … & Qiao, J. (2013). Genome analyses of single human oocytes. Cell, 155(7), 1492-1506. doi: 10.1016/j.cell.2013.11.040.

Lu, S., Zong, C., Fan, W., Yang, M., Li, J., Chapman, A. R., … & Bai, F. (2012). Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science, 338(6114), 1627-1630. doi: 10.1126/science.1229112.

Taniguchi, Y., Choi, P. J., Li, G. W., Chen, H., Babu, M., Hearn, J., … & Xie, X. S. (2010). Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science, 329(5991), 533-538. doi: 10.1126/science.1188308.

Zong, C., Lu, S., Chapman, A. R., & Xie, X. S. (2012). Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338(6114), 1622-1626. doi: 10.1126/science.1229164.

Review Papers

Li, G. W., & Xie, X. S. (2011). Central dogma at the single-molecule level in living cells. Nature, 475(7356), 308-315. doi: 10.1038/nature10315.

Xie, X. S. (2010). Enzymology and life at the single molecule level. In Single Molecule Spectroscopy in Chemistry, Physics and Biology (pp. 435-448). Springer Berlin Heidelberg.