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

Recommended Readings: Robert G. Roeder, Ph.D., April 13

Monday Lecture Series
Monday, April 13, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Robert G. Roeder, Ph.D.
Arnold and Mabel Beckman Professor and Head,
Laboratory of Biochemistry and Molecular Biology,
The Rockefeller University

Transcriptional Regulatory Mechanisms in Animal Cells

Recommended Readings

Empirical Articles

Jiang, H., Lu, X., Shimada, M., Dou, Y., Tang, Z., & Roeder, R. G. (2013). Regulation of transcription by the MLL2 complex and MLL complex–associated AKAP95. Nature Structural & Molecular Biology, 20(10), 1156-1163. doi:10.1038/nsmb.2656

Sabari, B. R., Tang, Z., Huang, H., Yong-Gonzalez, V., Molina, H., Kong, H. E., … & Allis, C. D. (2015). Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. Molecular Cell. doi:10.1016/j.molcel.2015.02.029

Zhang, P., Tu, B., Wang, H., Cao, Z., Tang, M., Zhang, C., … & Zhu, W. G. (2014). Tumor suppressor p53 cooperates with SIRT6 to regulate gluconeogenesis by promoting FoxO1 nuclear exclusion. Proceedings of the National Academy of Sciences, 111(29), 10684-10689. doi:10.1073/pnas.1411026111

Review Papers

Malik, S., & Roeder, R. G. (2010). The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nature Reviews Genetics, 11(11), 761-772. doi:10.1038/nrg2901

Roeder, R. G. (2005). Transcriptional regulation and the role of diverse coactivators in animal cells. FEBS letters, 579(4), 909-915. doi:10.1016/j.febslet.2004.12.007

Recommended Readings: Agata Smogorzewska, M.D., Ph.D., April 24

Friday Lecture Series
Friday, April 24, 2015
3:45 p.m., Caspary Auditorium

Agata Smogorzewska, M.D., Ph.D.
Assistant Professor and Head,
Laboratory of Genome Maintenance,
The Rockefeller University

DNA Interstrand Crosslink Repair: from Genetics to Mechanism

Recommended Readings

Empirical Articles

Flynn, E. K., Kamat, A., Lach, F. P., Donovan, F. X., Kimble, D. C., Narisu, N., … & Chandrasekharappa, S. C. (2014). Comprehensive analysis of pathogenic deletion variants in Fanconi anemia genes. Human Mutation, 35(11), 1342-1353. doi:10.1002/humu.22680

Kim, Y., Spitz, G. S., Veturi, U., Lach, F. P., Auerbach, A. D., & Smogorzewska, A. (2013). Regulation of multiple DNA repair pathways by the Fanconi anemia protein SLX4. Blood, 121(1), 54-63. doi:10.1182/blood-2012-07-441212

Ouyang, J., Garner, E., Hallet, A., Nguyen, H. D., Rickman, K. A., Gill, G., … & Zou, L. (2015). Noncovalent interactions with SUMO and ubiquitin orchestrate distinct functions of the SLX4 complex in genome maintenance. Molecular Cell, 57(1), 108-122. doi:10.1016/j.molcel.2014.11.015

Wang, R., Persky, N. S., Yoo, B., Ouerfelli, O., Smogorzewska, A., Elledge, S. J., & Pavletich, N. P. (2014). Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1. Science, 346(6213), 1127-1130. doi:10.1126/science.1258973

Review Paper

Kottemann, M. C., & Smogorzewska, A. (2013). Fanconi anaemia and the repair of Watson and Crick DNA crosslinks. Nature, 493(7432), 356-363. doi:10.1038/nature11863

Recommended Readings: Michael W. Young, Ph.D., April 20

Monday Lecture Series
Monday, April 20, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Michael W. Young, Ph.D.
Vice President for Academic Affairs,
Richard and Jeanne Fisher Professor and Head,
Laboratory of Genetics,
The Rockefeller University

Genes that Regulate Sleep and Circadian Rhythms

Recommended Readings

Empirical Articles

Levy, C., Zoltowski, B. D., Jones, A. R., Vaidya, A. T., Top, D., Widom, J., … & Leys, D. (2013). Updated structure of Drosophila cryptochrome. Nature, 495(7441), E3-E4. doi:10.1038/nature11995.

Rogulja, D., & Young, M. W. (2012). Control of sleep by cyclin A and its regulator. Science, 335(6076), 1617-1621. doi:10.1126/science.1212476.

Stavropoulos, N., & Young, M. W. (2011). insomniac and Cullin-3 regulate sleep and wakefulness in Drosophila. Neuron, 72(6), 964-976. doi:10.1016/j.neuron.2011.12.003.

Zoltowski, B. D., Vaidya, A. T., Top, D., Widom, J., Young, M. W., & Crane, B. R. (2011). Structure of full-length Drosophila cryptochrome. Nature, 480(7377), 396-399. doi:10.1038/nature10618.

Review Papers

Boothroyd, C. E., & Young, M. W. (2008). The in (put)s and out (put)s of the Drosophila circadian clock. Annals of the New York Academy of Sciences, 1129(1), 350-357. doi:10.1196/annals.1417.006

Crane, B. R., & Young, M. W. (2014). Interactive features of proteins composing eukaryotic circadian clocks. Annual Review of Biochemistry, 83, 191-219. doi:10.1146/annurev-biochem-060713-035644

Recommended Readings: David Baker, Ph.D., April 29

Special Lecture Series
Wednesday, April 29, 2015
3:45 p.m., Carson Family Auditorium (CRC)

David Baker, Ph.D.,
Professor of Biochemistry,
University of Washington
Investigator, Howard Hughes Medical Institute

Post-Evolutionary Biology: Design of Novel Protein Structures, Functions and Assemblies

Recommended Readings

Empirical Articles

Bradley, P., Misura, K. M., & Baker, D. (2005). Toward high-resolution de novo structure prediction for small proteins. Science, 309(5742), 1868-1871.

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., … & Popović, Z. (2010). Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. doi:10.1038/nature09304

Eiben, C. B., Siegel, J. B., Bale, J. B., Cooper, S., Khatib, F., Shen, B. W., … & Baker, D. (2012). Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology, 30(2), 190-192. doi:10.1038/nbt.2109

Jiang, L., Althoff, E. A., Clemente, F. R., Doyle, L., Röthlisberger, D., Zanghellini, A., … & Baker, D. (2008). De novo computational design of retro-aldol enzymes. Science, 319(5868), 1387-1391. doi:10.1126/science.1152692

Review Papers

Adams, P. D., Baker, D., Brunger, A. T., Das, R., DiMaio, F., Read, R. J., … & Terwilliger, T. C. (2013). Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics, 42, 265-287.doi: 10.1146/annurev-biophys-083012-130253

Das, R., & Baker, D. (2008). Macromolecular modeling with Rosetta. Annual Review of Biophysics, 77, 363-382. doi:10.1146/annurev.biochem.77.062906.171838

Recommended Readings: Jef Boeke, Ph.D., March 13

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

Jef Boeke, Ph.D.
Professor,
Department of Biochemistry and Molecular Pharmacology,
Director, Institute for systems genetics,
New York University

Synthesis of Designer Chromosomes from Scratch

Recommended Readings

Empirical Articles

Annaluru, N., Muller, H., Mitchell, L. a, Ramalingam, S., Stracquadanio, G., Richardson, S. M., … Chandrasegaran, S. (2014). Total synthesis of a functional designer eukaryotic chromosome. Science, 344(6179), 55–58. doi:10.1126/science.1249252

Dymond, J. S., Richardson, S. M., Coombes, C. E., Babatz, T., Muller, H., Annaluru, N., … Boeke, J. D. (2011). Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 477(7365), 471–476. doi:10.1038/nature10403

Mitchell, L. a., & Boeke, J. D. (2014). Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Proceedings of the National Academy of Sciences, 111(48), 17003–17010. doi:10.1073/pnas.1414399111

Reviews and Protocols

Cooper, E. M., Müller, H., Chandrasegaran, S., Bader, J. S., & Boeke, J. D. (2012). The build-a-genome course. Methods in Molecular Biology, 852, 273–283. doi:10.1007/978-1-61779-564-0_20

Recommended Readings: Liangcai Gu, Ph.D. January 7

Special Lecture
Wednesday, January 7, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Liangcai Gu, Ph.D.
Research Fellow,
Department of Genetics,
Harvard Medical School

In Situ Sequencing of Molecular Interactomes

Recommended Readings

Empirical Articles

Gu, L., Li, C., Aach, J., Hill, D. E., Vidal, M., & Church, G. M. (2014). Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature, 515(7528), 554–557. doi:10.1038/nature13761

Gu, L., Wang, B., Kulkarni, A., Geders, T. W., Grindberg, R. V, Gerwick, L., … Sherman, D. H. (2009). Metamorphic enzyme assembly in polyketide diversification. Nature, 459(7247), 731–735. doi:10.1038/nature07870

Li, J., Gu, L., Aach, J., & Church, G. M. (2014). Improved cell-free RNA and protein synthesis system. PLOS ONE, 9(9), e106232. doi:10.1371/journal.pone.0106232

Review Papers

Jones, A. C., Gu, L., Sorrels, C. M., Sherman, D. H., & Gerwick, W. H. (2009). New tricks from ancient algae: natural products biosynthesis in marine cyanobacteria. Current Opinion in Chemical Biology, 13(2), 216–23. doi:10.1016/j.cbpa.2009.02.019

Recommended Readings: Louis M. Staudt, M.D., Ph.D. January 9

Friday Lecture Series
Friday, January 9, 2015
3:45 p.m., Caspary Auditorium

Louis M. Staudt, M.D., Ph.D.
Director, Center for Cancer Genomics
Co-chief, Lymphoid Malignancies Branch
Head, Molecular Biology of Lymphoid Malignancies Section,
Center for Cancer Research,
National Cancer Institute at the National Institutes of Health

Therapy of Lymphoma Inspired by Functional and Structural Genomics

Recommended Readings

Empirical Articles

Alizadeh, A., Eisen, M., Davis, R., & Ma, C. (2000). Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403(6769), 503-511.

Ngo, V. N., Davis, R. E., Lamy, L., Yu, X., Zhao, H., Lenz, G., … Staudt, L. M. (2006). A loss-of-function RNA interference screen for molecular targets in cancer. Nature, 441(7089), 106–110. doi:10.1038/nature04687

Rosenwald, A., Wright, G., Chan, W. C., Connors, J. M., Campo, E., Fisher, R. I., … Staudt, L. M. (2002). The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. The New England Journal of Medicine, 346(25), 1937–1947. doi:10.1056/NEJMoa012914

Yang, Y., III, A. S., Emre, N., & Ceribelli, M. (2012). Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma. Cancer Cell, 21(6), 723–737. doi:10.1016/j.ccr.2012.05.024.Exploiting

Review Papers

Lenz, G., & Staudt, L. M. (2010). Aggressive lymphomas. The New England Journal of Medicine, 362(15), 1417–1429. doi:10.1056/NEJMra0807082

Shaffer, A. L., Young, R. M., & Staudt, L. M. (2012). Pathogenesis of human B cell lymphomas. Annual Review of Immunology, 30, 565–610. doi:10.1146/annurev-immunol-020711-075027

Recommended Readings: Stephen Quake, Ph.D. November 12

Special Seminar Series
Wednesday, November 12, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

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

Single Cell Genomics

Recommended Readings

Empirical Papers

Ashley, E. a, Butte, A. J., Wheeler, M. T., Chen, R., Klein, T. E., Dewey, F. E., … Altman, R. B. (2010). Clinical assessment incorporating a personal genome. Lancet, 375(9725), 1525–1535. doi:10.1016/S0140-6736(10)60452-7

Fan, H. C., Gu, W., Wang, J., Blumenfeld, Y. J., El-Sayed, Y. Y., & Quake, S. R. (2012). Non-invasive prenatal measurement of the fetal genome. Nature, 487(7407), 320–324. doi:10.1038/nature11251

Pushkarev, D., Neff, N. F., & Quake, S. R. (2009). Single-molecule sequencing of an individual human genome. Nature Biotechnology, 27(9), 847–850. doi:10.1038/nbt.1561

Wang, J., Fan, H. C., Behr, B., & Quake, S. R. (2012). Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell, 150(2), 402–412. doi:10.1016/j.cell.2012.06.030

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

Melin, J., & Quake, S. R. (2007). Microfluidic large-scale integration: the evolution of design rules for biological automation. Annual Review of Biophysics and Biomolecular Structure, 36, 213–231. doi:10.1146/annurev.biophys.36.040306.132646

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