2019

• Perspectives on defining cell types in the brain.

  Eran A. Mukamel and John Ngai (2019)
  Current Opinion in Neurobiology 56:61-68
  [Article]

2018

• A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons.

  Alexey Kozlenkov, Junhao Li, Pasha Apontes, Yasmin L. Hurd, William M. Byne, Eugene V. Koonin, Michael Wegner, Eran A. Mukamel*, Stella Dracheva* (2018)
  Science Advances 4:eaau6190 DOI: 10.1126/sciadv.aau6190, PMC6157969
  *Corresponding authors
  [Pubmed] [Article]

• A transient cortical state with sleep-like sensory responses precedes emergence from general anesthesia in humans.

  Laura D Lewis*, Giovanni Piantoni, Robert A Peterfreund, Emad N Eskandar, Priscilla Grace Harrell, Oluwaseun Akeju, Linda S Aglio, Sydney S Cash, Emery N Brown, Eran A Mukamel*, Patrick L Purdon* (2018)
  eLife 7:e33250 DOI: 10.7554/eLife.33250
  *Corresponding authors
  [Pubmed] [Article]

• Environmental enrichment increases transcriptional and epigenetic differentiation between mouse dorsal and ventral dentate gyrus.

  Tie-Yuan Zhang†*, Christopher L. Keown†, Xianglan Wen, Junhao Li, Dulcie A. Vousden, Christoph Anacker, Urvashi Bhattacharyya, Richard Ryan, Josie Diorio, Nicholas O'Toole, Jason P. Lerch, Eran A. Mukamel*, Michael J. Meaney. (2018)
  Nature Communications 9:298, doi:10.1038/s41467-017-02748-x
  †Equal contributions
  *Corresponding authors
  Data browser: http://brainome.ucsd.edu/mouse_dentategyrus
  

2017

• Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex.

  Chongyuan Luo†, Christopher L. Keown†, Laurie Kurihara, Jingtian Zhou, Yupeng He, Junhao Li, Rosa Castanon, Jacinta Lucero, Joseph R. Nery, Justin P. Sandoval, Brian Bui, Terrence J. Sejnowski, Timothy T. Harkins, Eran A. Mukamel*, M. Margarita Behrens*, Joseph R. Ecker* Science 357:600-604
  †Equal contributions
  *Corresponding authors
  [Pubmed] [Article]
  Project website, including data and browsers: http://brainome.org
  

• Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain.

  Keown, C.L., Berletch, J.B., Castanon, R., Nery, J.R., Disteche, C.M., Ecker, J.R., Mukamel, E.A. (2017) PNAS. 2017; E2882-E2890, doi: 10.1073/pnas.1611905114. [Pubmed] [Article]

2016

• Epigenomic landscapes of retinal rods and cones.

  Mo, A., Luo, C., Davis, F.P., Mukamel, E.A., Henry, G.L., Nery, J.R., Urich, M.A., Picard, S., Lister, R., Eddy, S.R., Beer, M.A., Ecker, J.R. and Nathans, J. (2016) eLife. 2016;5:e11613.
  [Article]

2015

• Disruption of mGluR5 in parvalbumin-positive interneurons induces core features of neurodevelopmental disorders.

  Barnes SA, Pinto-Duarte A, Kappe A, Zembrzycki A, Metzler A, Mukamel EA, Lucero J, Wang X, Sejnowski TJ, Markou A, Behrens MM. (2015) Molecular Psychiatry. doi: 10.1038/mp.2015.113.
  [PubMed] [Article]




• Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

  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) Neuron. 86:1369.
  [Article]
  (*These authors contributed equally to this work.)

  See also Preview by Steven Henikoff.

• Human body epigenome maps reveal noncanonical DNA methylation variation.

  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) Nature (in press) DOI: 10.1038/nature14465. PMID: 26030523 [Pubmed] [Article]

2014

• Mukamel, E.A., Pirondini, E., Babadi, B., Wong, K.F.K., 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, 839–845. [Article]

2013

• Lister*, R., Mukamel*, E.A., Huang, N., Nery, J., Urich, M., Tonti-Filipini, J., Huang, N., Zaman, S., Heyn, H., Schultz, M., Hu, S. Lin, S. Tapella, R., Wu, J., Esteller, M., Rao, A., Haghighi, F.G., Se-jnowski, T.J., Behrens, M., Ecker, J.R., Widespread epigenomic reconfiguration during mammalian brain development. Science. DOI: 10.1126/science.1237905 [Pubmed] [Abstract] [Movie]
  (*These authors contributed equally to this work.)

  See also Preview by Harrison Gabel and Michael Greenberg.

• Purdon P.L., Pierce E.T., Mukamel E.A., Prerau M.J., Walsh J.L., Wong K.F., Salazar-Gomez A.F., Harrell P.G., Sampson A.L., Cimenser A., Ching S., Kopell N.J., Tavares-Stoeckel C., Ha-beeb K., Merhar R., Brown E.N. (2013) Electroencephalogram signatures of loss and recovery of consciousness from propofol. Proc. Natl. Acad. Sci. 110:E1142-51. [Pubmed] [Text]

2012

• Mukamel, E.A. and Schnitzer, M.J. (2012) Unified performance limits for conventional and stochastic localization fluorescence microscopy. Physical Review Letters, 109:168102. [Abstract] [PDF]

• Mukamel, E.A., Babcock, H. and Zhuang, X. (2012) Statistical deconvolution for super-resolution fluorescence microscopy. Biophysical Journal, 102(10):2391-2400. [Abstract] [PDF] .

• Lewis, L., 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. and Purdon, P.L. (2012) Rapid fragmentation of neuronal networks at the onset of propofol-induced unconsciousness. Proc. Natl. Acad. of Sci. Plus, 109(49):E3377-86 [Pubmed] [Author summary] [PDF]

2011

• 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.
  [Pubmed] [PDF]

• Wong, K.F., Mukamel, E.A., Salazar, A.F., Pierce, E.T., Harrell, P.G., Walsh, J.L., Sampson, A., Brown, E.N. and Purdon, P.L. (2011) Robust Time-Varying Multivariate Coherence Estimation:  Application to Electroencephalogram Recordings During General Anesthesia. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2011; 2011:4725-28.
  [Pubmed] [PDF]

• Wong, K.F., Smith, A.C., Pierce, E.T., Harrell, P.G., Walsh, J.L., Salazar, A.F., Tavares, C.L., Cimenser, A., Prerau, M.J., Mukamel, E.A., Sampson, A., Purdon, P.L. and Brown, E.N. (2011) Bayesian Analysis of Trinomial Data in Behavioral Experiments and Its Application to Human Studies of General Anesthesia. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2011; 2011:4705-08.[Pubmed] [PDF]

2009

• 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.
  [Pubmed] [Free PMC article] [PDF]

• Nimmerjahn, A., Mukamel, E.A., and Schnitzer, M.J. (2009). Motor behavior activates Bergmann glial networks. Neuron. 62(3):400-412.
  [Pubmed] [Free PMC article] [PDF]

2008

• 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.
  (*These authors contributed equally to this work.)
  [Pubmed] [Free PMC article] [PDF]

• Flusberg, B.A., Nimmerjahn, A., Cocker, E.D., Mukamel, E.A., Barretto, R.P., Ko, T.H., Burns, L.D., Jung, J.C., and Schnitzer, M.J. (2008). High-speed, miniaturized fluorescence microscopy in freely moving mice. Nature Methods. 5:935-938.
  [Pubmed] [Free PMC article] [PDF]

2004 and earlier

• Bernevig, B.A., Hu, J.P, Mukamel, E.A., and Zhang, S.C. (2004). Dissipationless Spin Current in Anisotropic p–Doped Semiconductors. Physical Review B. 70:113301.
  [APS]

• Mukamel, E.A., Banaszek, K., Walmsley, I.A., and Dorrer, C. (2003). Direct Measurement of the Spatial Wigner Function with Area–Integrated Detection. Optics Letters. 28:1317.
  [Pubmed] [PDF]

• URen, A.B., Mukamel, E.A., Banaszek, K., and Walmsley, I.A. (2003). Managing Photons for Quantum Information Processing. Philosophical Transactions of the Royal Society of London, Series A: Mathematical, Physical and Engineering Sciences. 261:1493.
  [Pubmed] [PDF]

• Mukamel, E.A., and Shakhnovich, E.I. (2002). Phase Diagram for Unzipping DNA with Long–Range Interactions. Physical Review E. 66:32901.
  [Pubmed] [PDF]

• Iaconis, C., Mukamel, E.A., and Walmsley, I.A. (2000). Temporal Heterodyne Detector for Multitemporal Mode Quantum State Measurement. Journal of Optics B: Quantum and Semiclassical Optics. 2:510–16.
  [IOP]

Opinion and review articles

• Lister, R. and Mukamel, E.A. (2017) Beyond mCG: DNA Methylation in Non-Canonical Sequence Context. DNA Modifications in the Brain: Neuroepigenetic regulation of gene expression, Ed. T.W. Bredy. Elsevier. ISBN 978-0-12-801596-4. [DOI].
  

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

• Wilt, B.A., Burns, L.D., Wei Ho, E.T., Ghosh, K.K., Mukamel, E.A., and Schnitzer, M.J. (2009). Advances in light microscopy for neuroscience. Annual Review of Neuroscience. 32:435-506.
  [Pubmed] [Free PMC article] [PDF]

• Mukamel, E.A., and Schnitzer, M.J. (2005). Retinal coding of visual scenes –– repetitive and redundant too? Neuron. 46(3):357–9.
  [Pubmed] [PDF]

Thesis

• Mukamel, E.A. (2009) "Biophysical modeling and optical imaging tools for studies of cerebellar motor learning". Stanford University Dept. of Physics. (PDF; abstract only)

Patent

• Brown, E.N., Purdon, P.L., Cimenser, A., Mukamel, E.A., Prerau, M.J., and Wong, K.F. System and method for tracking brain states during administration of anesthesia, US Patent WO/2012/154701.