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.

Recommended Readings: Titia de Lange, Ph.D., December 7th

Monday Lecture Series
Monday, December 7, 2015
4:00 p.m., Carson Family Auditorium (CRC)

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

Telomere-derived Genome Instability in Cancer

Recommended Readings

Davoli, T., & de Lange, T. (2011). The causes and consequences of polyploidy in normal development and cancer. Annual review of cell and developmental biology, 27, 585-610. doi:10.1146/annurev-cellbio-092910-154234

Davoli, T., & de Lange, T. (2012). Telomere-driven tetraploidization occurs in human cells undergoing crisis and promotes transformation of mouse cellsCancer Cell, 21(6), 765-776. doi:10.1016/j.ccr.2012.03.044

de Lange, T. (2005). Telomere-related genome instability in cancer. Cold Spring Harbor Symposia on Quantitative Biology, 70, 197-204. doi:10.1101/sqb.2005.70.032

Recommended Readings: Joanna Wysocka, Ph.D., November 13th

Friday Lecture Series
Friday, November 13, 2015
3:45 p.m., Caspary Auditorium

Joanna Wysocka, Ph.D.
Professor,
Department of Chemical and Systems Biology,
Department of Developmental Biology,
Stanford University

On Peculiarities of Being a Human: Gene Regulatory Mechanisms in Human Development and Evolution

Recommended Readings

Empirical Articles

Buecker, C., Srinivasan, R., Wu, Z., Calo, E., Acampora, D., Faial, T., … & Wysocka, J. (2014). Reorganization of enhancer patterns in transition from naive to primed pluripoteny. Cell Stem Cell, 14(6), 838-853. doi:10.1016/j.stem.2014.04.003

Grow, E. J., Flynn, R. A., Chavez, S. L., Bayless, N. L., Wossidlo, M., Wesche, D. J., … & Wysocka, J. (2015). Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature. 522(7555), 221-225. doi:10.1038/nature14308

Prescott, S. L., Srinivasan, R., Marchetto, M. C., Grishina, I., Narvaiza, I., Selleri, L., … & Wysocka, J. (2015). Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell, 163(1), 68-83. doi:10.1016/j.cell.2015.08.036

Review Papers

Calo, E., & Wysocka, J. (2013). Modification of enhancer chromatin: what, how, and why?. Molecular Cell, 49(5), 825-837. doi:10.1016/j.molcel.2013.01.038

Buecker, C., & Wysocka, J. (2012). Enhancers as information integration hubs in development: lessons from genomics. Trends in Genetics, 28(6), 276-284. doi:10.1016/j.tig.2012.02.008

Recommended Readings: Seth Darst, Ph.D., November 2nd

Monday Lecture Series
Monday, November 2, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Seth Darst, Ph.D.
Jack Fishman Professor and Head,
Laboratory of Molecular Biophysics,
The Rockefeller University

CarD, an Essential Transcription Factor in Mycobacterium Tuberculosis, Uses a Minor Groove Wedge Mechanism to Stabilize the RNA Polymerase Open Promoter Complex

Recommended Readings

Empirical Articles

Bae, B., Chen, J., Davis, E., Leon, K., Darst, S. A., & Campbell, E. A. (2015). CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. eLife, e08505. doi:10.7554/eLife.08505

Davis, E., Chen, J., Leon, K., Darst, S. A., & Campbell, E. A. (2014). Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD. Nucleic Acids Research, gku1231. doi: 10.1093/nar/gku1231

Srivastava, D. B., Leon, K., Osmundson, J., Garner, A. L., Weiss, L. A., Westblade, L. F., … & Campbell, E. A. (2013). Structure and function of CarD, an essential mycobacterial transcription factor. Proceedings of the National Academy of Sciences, 110(31), 12619-12624. doi:10.1073/pnas.1308270110

Review Papers

Feklístov, A., Sharon, B. D., Darst, S. A., & Gross, C. A. (2014). Bacterial sigma factors: a historical, structural, and genomic perspective. Annual Review of Microbiology, 68, 357-376. doi:0.1146/annurev-micro-092412-155737

Recommended Readings: Stephen Quake, Ph.D., October 19th

Monday Lecture Series
Monday, October 19, 2015
4:00 p.m., Carson Family Auditorium (CRC)

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

Single Cell Genomics

Recommended Readings

Empirical Articles

Braslavsky, I., Hebert, B., Kartalov, E., & Quake, S. R. (2003). Sequence information can be obtained from single DNA molecules. Proceedings of the National Academy of Sciences, 100(7), 3960-3964. doi:10.1073/pnas.0230489100.

Dalerba, P., Kalisky, T., Sahoo, D., Rajendran, P. S., Rothenberg, M. E., Leyrat, A. A., … & Quake, S. R. (2011). Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nature Biotechnology, 29(12), 1120-1127. doi:10.1126/science.1150427.

Fan, H. C., Wang, J., Potanina, A., & Quake, S. R. (2011). Whole-genome molecular haplotyping of single cells. Nature Biotechnology, 29(1), 51-57. doi:10.1038/nbt.1739.

Harris, T. D., Buzby, P. R., Babcock, H., Beer, E., Bowers, J., Braslavsky, I., … & Xie, Z. (2008). Single-molecule DNA sequencing of a viral genome. Science, 320(5872), 106-109. doi:10.1038/nbt.2038.

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.

Recommended Readings: Michael Lenardo, M.D., October 23rd

Friday Lecture Series
Friday, October 23, 2015
3:45 p.m., Caspary Auditorium

Michael Lenardo, M.D.
Chief, Molecular Development Section,
Laboratory of Immunology,
Director, NIAID Clinical Genomics Program,
National Institute of Allergy and Infectious Diseases,
National Institutes of Health

Genomic Approaches to Solving Primary Immune Disorders

Recommended Readings

Empirical Articles

Kuehn, H. S., Ouyang, W., Lo, B., Deenick, E. K., Niemela, J. E., Avery, D. T., … & Uzel, G. (2014). Immune dysregulation in human subjects with heterozygous germline mutations in CTLA4. Science, 345(6204), 1623-1627. doi:10.1126/science.1255904.

Lo, B., Zhang, K., Lu, W., Zheng, L., Zhang, Q., Kanellopoulou, C., … & Jordan, M. B. (2015). Patients with LRBA deficiency show CTLA4 loss and immune dysregulation responsive to abatacept therapy. Science, 349(6246), 436-440. doi:10.1126/science.aaa1663.

Lucas, C. L., Zhang, Y., Venida, A., Wang, Y., Hughes, J., McElwee, J., … & Lenardo, M. J. (2014). Heterozygous splice mutation in PIK3R1 causes human immunodeficiency with lymphoproliferation due to dominant activation of PI3K. The Journal of Experimental Medicine, 211(13), 2537-2547. doi:10.1084/jem.20141759.

Review Papers

Grönholm, J., & Lenardo, M. J. (2015). Novel diagnostic and therapeutic approaches for autoimmune diabetes- A prime time to treat insulitis as a disease. Clinical Immunology, 156(2), 109-118. doi:10.1016/j.clim.2014.11.007.

Zhang, Y., Su, H. C., & Lenardo, M. J. (2015). Genomics is rapidly advancing precision medicine for immunological disorders. Nature Immunology, 16(10), 1001-1004. doi:10.1038/ni.3275

Recommended Readings: Erich Jarvis, Ph.D., September 28th

Special Lecture
Monday, September 28th, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Erich Jarvis, Ph.D.
Associate Professor,
Department of Neurobiology,
Duke University Medical Center
Investigator, Howard Hughes Medical Institute

Dissecting the Molecular Mechanisms of Vocal Learning and Spoken Language

Recommended Readings

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … & Samaniego, J. A. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320-1331. doi:10.1126/science.1253451.

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … & Avian Phylogenomics Consortium. (2015). Phylogenomic analyses data of the avian phylogenomics project. GigaScience, 4(1), 1-9. doi:10.1186/s13742-014-0038-1.

Pfenning, A. R., Hara, E., Whitney, O., Rivas, M. V., Wang, R., Roulhac, P. L., … & Jarvis, E. D. (2014). Convergent transcriptional specializations in the brains of humans and song-learning birds. Science, 346(6215), 1256846. doi:10.1126/science.1256846.

Whitney, O., Pfenning, A. R., Howard, J. T., Blatti, C. A., Liu, F., Ward, J. M., … & Jarvis, E. D. (2014). Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science, 346(6215), 1256780. doi: 10.1126/science.1256780.

Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … & Ganapathy, G. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311-1320. doi:10.1126/science.1251385.

Recommended Readings: John Stamatoyannopoulos, M.D., May 11th

Special Lecture
Monday, May 11, 2015
4:00 p.m., Carson Family Auditorium (CRC)

John Stamatoyannopoulos, M.D.
Associate Professor of Genome Sciences and Medicine,
University Washington School of Medicine

New Insights into Human Genome Function

Recommended Readings

Empirical Articles

ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74. doi:10.1038/nature11247

Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., … & Kulkarni, A. (2015). Integrative analysis of 111 reference human epigenomes. Nature, 518(7539), 317-330. doi:10.1038/nature14248

Mayer, A., di Iulio, J., Maleri, S., Eser, U., Vierstra, J., Reynolds, A., … & Churchman, L. S. (2015). Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell, 161(3), 541-554. doi:10.1016/j.cell.2015.03.010

Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., … & Morrissey, C. S. (2014). A comparative encyclopedia of DNA elements in the mouse genome. Nature, 515(7527), 355-364. doi:10.1038/nature13992

Review Paper

Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., … & Hardison, R. C. (2014). Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences, 111(17), 6131-6138. doi:10.1073/pnas.1318948111