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


Recommended Readings: Ila R. Fiete, Ph.D. April 7

Monday, April 7, 2014
4:00 p.m., Carson Family Auditorium

Ila R. Fiete, Ph.D.
Associate Professor, Department of Neuroscience
Fellow, The Institute for Neuroscience
The University of Texas at Austin

Neural Codes and Dynamics for Representation and Memory

Recommended Readings:

Empirical Papers

Burak, Y., & Fiete, I. R. (2012). Fundamental limits on persistent activity in networks of noisy neurons. Proceedings of the National Academy of Sciences, 109(43), 17645–17650. doi:10.1073/pnas.1117386109

Fiete, I. R., Burak, Y., & Brookings, T. (2008). What grid cells convey about rat location. The Journal of Neuroscience, 28(27), 6858–6871. doi:10.1523/JNEUROSCI.5684-07.2008

Sreenivasan, S., & Fiete, I. (2011). Grid cells generate an analog error-correcting code for singularly precise neural computation. Nature Neuroscience, 14(10), 1330–1337. doi:10.1038/nn.2901

Yoon, K., Buice, M. a, Barry, C., Hayman, R., Burgess, N., & Fiete, I. R. (2013). Specific evidence of low-dimensional continuous attractor dynamics in grid cells. Nature Neuroscience, 16(8), 1077–1084. doi:10.1038/nn.3450

Review Articles

Burak, Y. (2006). Do We Understand the Emergent Dynamics of Grid Cell Activity? Journal of Neuroscience, 26(37), 9352–9354. doi:10.1523/JNEUROSCI.2857-06.2006

Recommended Readings: Eran Segal Ph.D. October 9, 2013

Special Seminar Series
Deciphering the Code of Gene Regulation
Eran Segal, Ph.D.
Incumbent of the Soretta and Henry Shapiro Career Development Chair
Department of Computer Science and Applied Mathematics
4:00 p.m. – 5:00 p.m. Carson Family Auditorium (CRC)
Refreshments: 3:45 p.m. – 4:00 p.m., Lower Level Greenberg Building (CRC)

Recommended Readings:

Review Papers

Coulon, A., Chow, C. C., Singer, R. H., & Larson, D. R. (2013). Eukaryotic transcriptional dynamics: from single molecules to cell populationsNature Reviews Genetics14(8), 572-584. doi: 10.1038/nrg3484.

De Smet, R., & Marchal, K. (2010). Advantages and limitations of current network inference methodsNature Reviews Microbiology8(10), 717-729. doi: 10.1038/nrmicro2419

Segal, E., & Widom, J. (2009). From DNA sequence to transcriptional behaviour: a quantitative approachNature Reviews Genetics10(7), 443-456. doi: 10.1038/nrg2591

Jiang, C., & Pugh, B. F. (2009). Nucleosome positioning and gene regulation: advances through genomicsNature Reviews Genetics10(3), 161-172. doi: 10.1038/nrg2522

Empirical Articles

Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A. J., Tillo, D., Field, Y., … & Segal, E. (2008). The DNA-encoded nucleosome organization of a eukaryotic genomeNature458(7236), 362-366. doi: 10.1038/nature07667

Schones, D. E., Cui, K., Cuddapah, S., Roh, T. Y., Barski, A., Wang, Z., … & Zhao, K. (2008). Dynamic regulation of nucleosome positioning in the human genomeCell132(5), 887-898. doi: 10.1016/j.cell.2008.02.022

Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thåström, A., Field, Y., Moore, I. K., … & Widom, J. (2006). A genomic code for nucleosome positioningNature,442(7104), 772-778. doi: 10.1038/nature04979

Segal, E., Shapira, M., Regev, A., Pe’er, D., Botstein, D., Koller, D., & Friedman, N. (2003). Module networks: identifying regulatory modules and their condition-specific regulators from gene expression dataNature Genetics34(2), 166-176. doi: 10.1038/ng1165

Valouev, A., Johnson, S. M., Boyd, S. D., Smith, C. L., Fire, A. Z., & Sidow, A. (2011). Determinants of nucleosome organization in primary human cellsNature474(7352), 516-520. doi: 10.1038/nature10002

The State of Vaccine Development: Toughest Problems Remain Unsolved

Accelerating Next-Generation Vaccine Development for Global Disease Prevention

Koff, W. C. et all    Science  v. 340, 2013

Recent technological advances in molecular genetics, molecular and cellular immunology, structural biology, bioinformatics, computational biology, nanotechnology, formulation methods, and systems biology are ushering in a new era of discovery. However, translation of these advances into vaccines remains impeded by major gaps in our knowledge of human immune responses.

Recommended Readings: Tiago Branco M.D, Ph.D. Monday, March 12, 2012

Dendritic Computation in Cortical Pyramidal Cells

Tiago Branco, M.D, Ph.D.

Postdoctoral Research Associate

Wolfson Institute for Biomedical Research

University College London

4:00 p.m. Monday, March 12, 2012   refreshments 3:45 p.m.

Caspary Auditorium

Recommended Readings:

Takahashi N: Kitamura K; Matsuo N; et al.  2012.  Locally synchronized synaptic inputs. Science.  335(6066):353-356.  DOI:10.1126/science.1210362

George GA; Lyons-Warren AM; Ma XF; et al.  2011.  A diversity of synaptic filters are created by temporal summation of excitation and inhibition.  Journal of Neuroscience.  31(41):14721-14734.  DOI:10.1523/JNEUROSCI.1424-11.2011

Branco T.  2011.  The language of dendrites.   Science. 334(6056):615-616. DOI: 10.1126/science.1215079   

Branco T: Haeusser M.  2011.  Synaptic integration gradients in single cortical pyramidal sequences in cortical neurons.  Neuron. 69(5):885-895.  DOI:10.1016/j.neuron.2011.02.006

Branco T: Clark BA; Haeusser M.  2010.  Dendritic discrimination of temporal input sequences in cortical neurons.  Science.  329(5999):1671-1675.  DOI:10:1126/science.1189664

Branco T; Haeusser M.  2010.  The single dendritic branch as a fundamental functional unit in the nervous system. Current Opinion in Neurobiology.  20(4):494-502.  DOI:10.1016/j.conb.2010.07.009

Branco T; Staras K; Darcy KJ.; et al.  2008.  Local dendritic activity sets release probability at hippocampal synapses.  Neuron.  59(3):475-485.   DOI:10.1016/j.neuron.2008.07.006.