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: Eve Marder, Ph.D., January 23

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

Eve Marder, Ph.D.
Victor and Gwendolyn Beinfield Professor of Neuroscience,
Volen National Center for Complex Systems,
Brandeis University

Robustness, Variability, and Neuromodulation in Neurons and Networks

Recommended Readings

Empirical Articles

Caplan, J. S., Williams, A. H., & Marder, E. (2014). Many parameter sets in a multicompartment model oscillator are robust to temperature perturbations. The Journal of Neuroscience, 34(14), 4963–4975. doi:10.1523/JNEUROSCI.0280-14.2014

O’Leary, T., Williams, A. H., Franci, A., & Marder, E. (2014). Cell types, network homeostasis, and pathological compensation from a biologically plausible ion channel expression model. Neuron, 82(4), 809–821. doi:10.1016/j.neuron.2014.04.002

Soofi, W., Goeritz, M. L., Kispersky, T. J., Prinz, A. A., Marder, E., & Stein, W. (2014). Phase maintenance in a rhythmic motor pattern during temperature changes in vivo. Journal of Neurophysiology, 111(12), 2603–2613. doi:10.1152/jn.00906.2013

Review Papers

Marder, E., O’Leary, T., & Shruti, S. (2014). Neuromodulation of circuits with variable parameters: single neurons and small circuits reveal principles of state-dependent and robust neuromodulation. Annual Review of Neuroscience, 37, 329–346. doi:10.1146/annurev-neuro-071013-013958

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.