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]
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]
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
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
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]
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.)
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]
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.
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.