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Eran Mukamel, PhD

Assistant Professor
Department of Cognitive Science

Contact Information

Phone: 858.822.3713

Location: Social Sciences Research Building, room 251

Mailing Address:
University of California, San Diego
9500 Gilman Drive #0515
La Jolla, CA 92093

Lab Website

Research in our lab uses computational modeling and analysis of large-scale data sets to understand complex biological networks, from the genome to brain circuits. These networks are sophisticated collections of thousands to billions of elements, such as genes or individual brain cells, working together to achieve a biological function. Whereas we know a great deal about the working of individual network elements, putting this information together to understand how networks function is a challenge that requires combining empirical data with new computational, statistical and conceptual approaches. We develop statistical and machine learning approaches for discovery and hypothesis testing in high-dimensional electrophysiology and epigenomics data sets, and combine these with realistic biophysical modeling of brain dynamics. These techniques address critical questions about the organization of complex brain networks, including how the genetic regulation of brain cell types helps form brain circuits and how their communication via electrical and chemical signaling generates global brain states such as waking and unconsciousness.

One focus of our research is understanding the genetic and epigenetic networks that regulate brain cells’ development and maintain their mature phenotypes. We develop large-scale computational analysis and machine learning algorithms to extract biological insight from whole-genome DNA methylation data sets related to the development and maturation of human and mouse brain cells.

A second focus of our lab’s research is the temporal structure of cortical electrical activity during the induction of and recovery from general anesthesia. We use computational analysis and statistical signal processing of intra- and extracranial recordings in human subjects to discover and characterize transitions between distinct global brain states. By going beyond traditional power spectral analyses, we identified specific patterns of cross-frequency coupling that organize the low-frequency (<20 Hz) dynamics of cortical circuits during propofol-induced unconsciousness.

Overall we are dedicated to using computation to expand our empirical understanding of complex biological networks and brain function.

Lister, R. and Mukamel, E.A. (2015) Turning over DNA methylation in the mind. Frontiers in Neuroscience. doi: 10.3389/fnins.2015.00252. [PubMed Article]

Barnes SA, Pinto-Duarte A, Kappe A, Zembrzycki A, Metzler A, Mukamel EA, Lucero J, Wang X, Sejnowski TJ, Markou A, Behrens MM. (2015) Disruption of mGluR5 in parvalbumin-positive interneurons induces core features of neurodevelopmental disorders. Molecular Psychiatry. doi: 10.1038/mp.2015.113.[Article]

Mo*, A., Mukamel*, E.A., Davis*, F.P., Luo*, C., Henry, G.L., Picard, S., Urich, M.A., Nery, J.R., Sejnowski, T.J., Lister, R., Eddy, S.R., Ecker, J.R. and Nathans, J. (2015) Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron. 86:1369. [Article]
(*These authors contributed equally to this work.)

Schultz*, M.D., He*, Y., Whitaker, J.W., Hariharan, M., Mukamel, E.A., Leung, D., Rajagopal, N., Nery, J.R., Urich, M.A., Chen, H., Lin, S., Lin, Y., Jung, I., Schmitt, A.D., Selvaraj, S., Ren, B., Sejnowski, T.J., Wang, W., Ecker, J.R. (2015) Human body epigenome maps reveal noncanonical DNA methylation variation. Nature (in press) DOI: 10.1038/nature14465. PMID: 26030523 [Pubmed] [Article]

Mukamel E.A., Pirondini E., Babadi B., Wong K.F., Pierce E.T., Harrell P.G., Walsh J.L., Salazar-Gomez A.F., Cash S.S., Eskandar E.N., Weiner V.S., Brown E.N., Purdon P.L. (2014) “A Transition in Brain State during Propofol-Induced Unconsciousness.” J Neurosci. 34(3):839-45. PMC3891963. [Article]

Lister* R., Mukamel* E.A., Nery J.R., Urich M., Puddifoot C.A., Johnson N.D., Lucero J., Huang Y., Dwork A.J., Schultz M.D., Yu M., Tonti-Filippini J., Heyn H., Hu S., Wu J.C., Rao A., Esteller M., He C., Haghighi F.G., Sejnowski T.J., Behrens M.M., Ecker J.R. (2013) “Global epigenomic reconfiguration during mammalian brain development.” Science. 341(6146):1237905. PMC3785061. [Pubmed] [Abstract] [Movie]
(*These authors contributed equally to this work.)

Lewis L.D., Weiner V.S., Mukamel E.A., Donoghue J.A., Eskandar E.N., Madsen J.R., Anderson W.S., Hochberg L.R., Cash S.S., Brown E.N., Purdon P.L. (2012) “Rapid fragmentation of neuronal networks at the onset of propofol-induced unconsciousness.” Proc Natl Acad Sci U S A. 109(49):E3377-86. PMC3523833. [Pubmed] [Author summary] [PDF]

Mukamel, E.A., Babcock, H. and Zhuang, X. (2012) “Statistical deconvolution for super-resolution fluorescence microscopy.” Biophysical Journal. 102(10):2391. PMC3353000. [Abstract] [Article]

Mukamel, E.A. and Schnitzer, M.J. (2012) “Unified resolution bounds for conventional and stochastic localization fluorescence microscopy.” Phys. Rev. Lett. 109(16):168102. PMC3521605. [Abstract] [PDF]

Mukamel, E.A., Wong, K.F., Brown, E.N. and Purdon, P.L. (2011) “Phase-based measures of cross- frequency coupling in brain electrical dynamics under general anesthesia.” Conf. Proc. IEEE Eng. Med. Biol. Soc. 2011; 2011:1981-4. NIHMS353900. PMC3282123. [Pubmed] [PDF]

Mukamel, E.A., Nimmerjahn, A., and Schnitzer, M.J. (2009). “Automated analysis of cellular signals from large-scale calcium-imaging data.” Neuron. 63(6):747-760. NIHMS150319. PMC3282191. [Pubmed] [Free PMC article] [PDF]

Wetmore*, D.Z., Mukamel*, E.A., and Schnitzer, M.J. (2008). “Lock-and-key mechanisms of cerebellar memory recall based on rebound currents.” J. Neurophysiology. 100:2328-2347. PMC2576199. [Pubmed] [Free PMC article] [PDF]
(*These authors contributed equally to this work.)