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

2021

• 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.)

• 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]

2020

• An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

  Zizhen Yao†, Hanqing Liu†, Fangming Xie†, Stephan Fischer†, A. Sina Booeshaghi, Ricky S Adkins, Andrew I. Aldridge, Seth A. Ament, Antonio Pinto-Duarte, Anna Bartlett, M. Margarita Behrens, Koen Van den Berge, Darren Bertagnolli, Tommaso Biancalani, Hector Corrada Bravo, Tamara Casper, Carlo Colantuoni, Heather Creasy, Kirsten Crichton, Megan Crow, Nick Dee, Elizabeth L Dougherty, Wayne I. Doyle, Sandrine Dudoit, Rongxin Fang, Victor Felix, Olivia Fong, Michelle Giglio, Jeff Goldy, Mike Hawrylycz, Hector Roux de Bezieux, Brian R. Herb, Ronna Hertzano, Xiaomeng Hou, Qiwen Hu, Jonathan Crabtree, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Yang Eric Li, Jacinta D. Lucero, Chongyuan Luo, Anup Mahurkar, Delissa McMillen, Naeem Nadaf, Joseph R. Nery, Sheng-Yong Niu, Joshua Orvis, Julia K. Osteen, Thanh Pham, Olivier Poirion, Sebastian Preissl, Elizabeth Purdom, Christine Rimorin, Davide Risso, Angeline C. Rivkin, Kimberly Smith, Kelly Street, Josef Sulc, Thuc Nghi Nguyen, Michael Tieu, Amy Torkelson, Herman Tung, Eeshit Dhaval Vaishnav, Valentine Svensson, Charles R. Vanderburg, Vasilis Ntranos, Cindy van Velthoven, Xinxin Wang, Owen R. White, Z. Josh Huang, Peter V. Kharchenko, Lior Pachter, John Ngai, Aviv Regev, Bosiljka Tasic, Joshua D. Welch, Jesse Gillis, Evan Z. Macosko, Bing Ren, Joseph R. Ecker, Hongkui Zeng*, Eran A. Mukamel*
  †Equal contributions
  *Corresponding authors
  

  Nature (2021) in press.
  bioRxiv 2020.02.29.970558v2 doi: https://doi.org/10.1101/2020.02.29.970558
  
  Data browser: https://brainome.ucsd.edu/annoj/BICCN_MOp/

• DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution

  Hanqing Liu, Jingtian Zhou, Wei Tian, Chongyuan Luo, Anna Bartlett, Andrew Aldridge, Jacinta Lucero, Julia K. Osteen, Joseph R. Nery, Huaming Chen, Angeline Rivkin, Rosa G Castanon, Ben Clock, Yang Eric Li, Xiaomeng Hou, Olivier B. Poirion, Sebastian Preissl, Carolyn O'Connor, Lara Boggeman, Conor Fitzpatrick, Michael Nunn, Eran A. Mukamel, Zhuzhu Zhang, Edward M. Callaway, Bing Ren, Jesse R. Dixon, M. Margarita Behrens, Joseph R. Ecker
  

  Nature (2021) in press.
  bioRxiv 2020.04.30.069377v1 doi: doi.org/10.1101/2020.04.30.069377

• An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

  Yang Eric Li, Sebastian Preissl, Xiaomeng Hou, Ziyang Zhang, Kai Zhang, Rongxin Fang, Yunjiang Qiu, Olivier Poirion, Bin Li, Hanqing Liu, Xinxin Wang, Jee Yun Han, Jacinta Lucero, Yiming Yan, Samantha Kuan, David Gorkin, Michael Nunn, Eran A. Mukamel, M. Margarita Behrens, Joseph Ecker, Bing Ren

  bioRxiv 2020.05.10.087585v2 doi: doi: https://doi.org/10.1101/2020.05.10.087585

• Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain

  Zhuzhu Zhang, Jingtian Zhou, Pengcheng Tan, Yan Pang, Angeline Rivkin, Megan A. Kirchgessner, Elora Williams, Cheng-Ta Lee, Hanqing Liu, Alexis D. Franklin, Paula Assakura Miyazaki, Anna Bartlett, Andrew Aldridge, Minh Vu, Lara Boggeman, Conor Fitzpatrick, Joseph R. Nery, Rosa G. Castanon, Mohammad Rashid, Matthew Jacobs, Tony Ito, Bertha Dominguez, Sheng-Yong Niu, Jared B. Smith, Carolyn O'Connor, Kuo-Fen Lee, Xin Jin, Eran A. Mukamel, M. Margarita Behrens, Joseph R. Ecker, Edward M. Callaway
  Nature (2021) in press.

  bioRxiv 2020.04.01.019612v2 doi: https://doi.org/10.1101/2020.04.01.019612

• Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

  Trygve E. Bakken, Nikolas L. Jorstad, Qiwen Hu, Blue B. Lake, Wei Tian, Brian E. Kalmbach, Megan Crow, Rebecca D. Hodge, Fenna M. Krienen, Staci A. Sorensen, Jeroen Eggermont, Zizhen Yao, Brian D. Aevermann, Andrew I. Aldridge, Anna Bartlett, Darren Bertagnolli, Tamara Casper, Rosa G. Castanon, Kirsten Crichton, Tanya L. Daigle, Rachel Dalley, Nick Dee, Nikolai Dembrow, Dinh Diep, Song-Lin Ding, Weixiu Dong, Rongxin Fang, Stephan Fischer, Melissa Goldman, Jeff Goldy, Lucas T. Graybuck, Brian R. Herb, Xiaomeng Hou, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Baldur van Lew, Yang Eric Li, Christine S. Liu, Hanqing Liu, Jacinta D. Lucero, Anup Mahurkar, Delissa McMillen, Jeremy A. Miller, Marmar Moussa, Joseph R. Nery, Philip R. Nicovich, Joshua Orvis, Julia K. Osteen, Scott Owen, Carter R. Palmer, Thanh Pham, Nongluk Plongthongkum, Olivier Poirion, Nora M. Reed, Christine Rimorin, Angeline Rivkin, William J. Romanow, Adriana E. Sedeño-Cortes, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Xinxin Wang, Fangming Xie, Anna Marie Yanny, Renee Zhang, Seth A. Ament, M. Margarita Behrens, Hector Corrada Bravo, Jerold Chun, Alexander Dobin, Jesse Gillis, Ronna Hertzano, Patrick R. Hof, Thomas Höllt, Gregory D. Horwitz, C. Dirk Keene, Peter V. Kharchenko, Andrew L. Ko, Boudewijn P. Lelieveldt, Chongyuan Luo, Eran A. Mukamel, Sebastian Preissl, Aviv Regev, Bing Ren, Richard H. Scheuermann, Kimberly Smith, William J. Spain, Owen R. White, Christof Koch, Michael Hawrylycz, Bosiljka Tasic, Evan Z. Macosko, Steven A. McCarroll, Jonathan T. Ting, Hongkui Zeng, Kun Zhang, Guoping Feng, Joseph R. Ecker, Sten Linnarsson, Ed S. Lein

  bioRxiv 2020.03.31.016972 doi: https://doi.org/10.1101/2020.03.31.016972

2019

• Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

  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

  bioRxiv 2019.12.11.873398; doi: https://doi.org/10.1101/2019.12.11.873398

• 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.)
  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

• 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.)
  See also Preview by Harrison Gabel and Michael Greenberg.

• 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.