For an introduction to our lab's research interests, please see these recent reviews/perspectives:

Mukamel and Ngai, Curr. Op. Neurobio (2019) Perspectives on defining cell types in the brain.
Armand, Li, Xie, Luo and Mukamel, Neuron (2021) Primer: Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes [Open access from eScholarship]

Full publication list: Google Scholar, NCBI/Pubmed

2022

Single nucleus multi-omics identifies human cortical cell regulatory genome diversity

Chongyuan Luo, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, Wayne I. Doyle, Rebecca D. Hodge, Lijuan Hu, Bang-An Wang, Zhuzhu Zhang, Sebastian Preissl, Dong-Sung Lee, Jingtian Zhou, Sheng-Yong Niu, Rosa Castanon, Anna Bartlett, Angeline Rivkin, Xinxin Wang, Jacinta Lucero, Joseph R. Nery, David A. Davis, Deborah C. Mash, Jesse R. Dixon, Sten Linnarsson, Ed Lein, M. Margarita Behrens, Bing Ren, Eran A. Mukamel, Joseph R. Ecker

Cell Genomics 2:100107 https://doi.org/10.1016/j.xgen.2022.100107
Preview by Che and Thienpoint

2021

Cellular and genetic drivers of RNA editing variation in the human brain

Ryn Cuddleston, Junhao Li, Xuanjia Fan, Alexey Kozenkov, Matthew Lalli, Shahrukh Khalique, Stella Dracheva, Eran A. Mukamel, Michael S. Breen
BioRxiv (2021) ; doi: https://doi.org/10.1101/2021.07.16.452690

Multiple Comparisons and Inappropriate Statistical Testing Lead to Spurious Sex Differences in Gene Expression

Eran A. Mukamel
Biological Psychiatry (2021) 91 (1), e1-e2 ; doi: https://doi.org/10.1016/j.biopsych.2021.06.026 [Text] [PDF]
- BRAIN Initiative Cell Census Network (BICCN)
  A package of papers published in October, 2021 reports findings from the first phase of the BICCN. Check out Nature's coverage of the BICCN, including commentaries, perspectives and links to all the papers. Our lab contributed to the following BICCN publications:
- A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
  
  Hongkui Zeng*, Eran A. Mukamel*
  †Equal contributions
  *Corresponding authors
  
  Nature (2021) 598:103. https://doi.org/10.1038/s41586-021-03500-8
  
  Data browser: https://brainome.ucsd.edu/annoj/BICCN_MOp/
- A multimodal cell census and atlas of the mammalian primary motor cortex
  BRAIN Initiative Cell Census Network (BICCN) [258 authors, including Mukamel lab members: Ethan Armand, Eran A. Mukamel, Fangming Xie]
  Nature 598:86 (2021) https://doi.org/10.1038/s41586-021-03950-0
- DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution
  
  Joseph R. Ecker
  
  Nature (2021) 598:120 https://doi.org/10.1038/s41586-020-03182-8
- An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum
  
  Bing Ren
  Nature (2021) 598:129 https://doi.org/10.1038/s41586-021-03604-1
- Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain
  
  Eran A. Mukamel, M. Margarita Behrens, Joseph R. Ecker, Edward M. Callaway
  Nature (2021) 598:167 https://doi.org/10.1038/s41586-021-03223-w
- Comparative cellular analysis of motor cortex in human, marmoset and mouse
  
  Sten Linnarsson, Ed S. Lein
  Nature (2021) 598:111 https://doi.org/10.1038/s41586-021-03465-8
Primer: Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes

Armand, Ethan J., Junhao Li, Fangming Xie, Chongyuan Luo, and Eran A. Mukamel
Neuron Vol. 109, 11-26 DOI: 10.1016/j.neuron.2020.12.010
Book review: Thermodynamics and the matter of life

Eran A. Mukamel and Amelia M. Glaser
Science 01 Jan 2021: Vol. 371, Issue 6524, pp. 38, DOI: 10.1126/science.abf5633
Comprehensive analysis of single cell ATAC-seq data with SnapATAC

Rongxin Fang, Sebastian Preissl, Yang Li, Xiaomeng Hou, Jacinta Lucero, Xinxin Wang, Amir Motamedi, Andrew K. Shiau, Xinzhu Zhou, Fangming Xie, Eran A. Mukamel, Kai Zhang, Yanxiao Zhang, M. Margarita Behrens, Joseph Ecker, Bing Ren
Nature Communications 615179; [Article]
Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and is partly compensated by repressive histone modification H3K27me3

Junhao Li, Antonio Pinto-Duarte, Mark Zander, Chi-Yu Lai, Julia Osteen, Linjing Fang, Chongyuan Luo, Jacinta D. Lucero, Rosa Gomez-Castanon, Joseph R. Nery, Isai Silva-Garcia, Yan Pang, Terrence J. Sejnowski, Susan B. Powell, Joseph R. Ecker, Eran A. Mukamel, M. Margarita Behrens
bioRxiv 2019.12.20.883694; doi: https://doi.org/10.1101/2019.12.20.883694 (Original version posted December 2019; current version includes new data and analysis.)

2020

Evolution of regulatory signatures in primate cortical neurons at cell-type resolution
Alexey Kozlenkov, Marit W. Vermunt, Pasha Apontes, Junhao Li, Ke Hao, Chet C. Sherwood, Patrick R. Hof, John J. Ely, Michael Wegner, Eran A. Mukamel, Menno P. Creyghton, Eugene V. Koonin, and Stella Dracheva.
Proc. Natl. Acad. Sci. U. S. A. (2020) 117, 28422-28432.

2019

Maternal immune activation impairs cognitive flexibility and alters transcription in frontal cortex.

Dionisio A. Amodeo, Chi-Yu Lai, Omron Hassan, Eran A. Mukamel, M. Margarita Behrens, Susan B. Powell (2019)
Neurobiology of Disease 125:211-218
[Pubmed] [Article]
Perspectives on defining cell types in the brain.

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

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
†Equal contributions
*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.)
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

A Transition in Brain State during Propofol-Induced Unconsciousness.
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).
J. Neurosci. 34, 839–845. [Article]

2013

Global epigenomic reconfiguration during mammalian brain development.
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., Sejnowski, T.J., Behrens, M., Ecker, J.R.
Science. DOI: 10.1126/science.1237905 [Pubmed] [Abstract] [Movie]
(*These authors contributed equally to this work.)
Electroencephalogram signatures of loss and recovery of consciousness from propofol.

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)
Proc. Natl. Acad. Sci. 110:E1142-51. [Pubmed] [Text]

2012

Unified performance limits for conventional and stochastic localization fluorescence microscopy.

Mukamel, E.A. and Schnitzer, M.J. (2012) Physical Review Letters, 109:168102. [Abstract] [PDF]
Statistical deconvolution for super-resolution fluorescence microscopy.

Mukamel, E.A., Babcock, H. and Zhuang, X. (2012) 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.

BRAIN Initiative Cell Census Network (BICCN)

Opinion and review articles

Thesis

Patent

Contact