• 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

2025

• Cell type-specific enrichment of somatic aneuploidy in the mammalian brain

  Eran A. Mukamel, Hanqing Liu, M. Margarita Behrens, Joseph R. Ecker

  Neuron 113:2814-2821

• False positives in study of memory-related gene expression

  Eran A. Mukamel and Zhaoxia Yu

  Nature. https://www.nature.com/articles/s41586-025-08988-y

• Maternal Immune Activation Disrupts Epigenomic and Functional Maturation of Cortical Excitatory Neurons

  Chi-Yu Lai, Jessica Arzavala, Antonio Pinto-Duarte, Shiyuan Wang, Junhao Li, Hanqing Liu, Julia Osteen, Rosa Gomez Castanon, Joseph Nery, Susan B. Powell, Joseph R. Ecker, Eran A. Mukamel, M. Margarita Behrens

  BioRxiv, doi: https://doi.org/10.1101/2025.04.28.651094

• Single-cell spatial transcriptomics reveals distinct patterns of dysregulation in non-neuronal and neuronal cells induced by the Trem2R47H Alzheimer's risk gene mutation

  Kevin G. Johnston, Bereket T. Berackey, Kristine M. Tran, Alon Gelber, Zhaoxia Yu, Grant R. MacGregor, Eran A. Mukamel, Zhiqun Tan, Kim N. Green and Xiangmin Xu

  Molecular Psychiatry 30:461-477. PubMed PMCID: PMC10723554.

2024

• Cell type-specific effects of age and sex on human cortical neurons

  Jo-Fan Chien, Hanqing Liu, Bang-An Wang, Chongyuan Luo, Anna Bartlett, Rosa Castanon, Nicholas D. Johnson, Joseph R. Nery, Julia Osteen, Junhao Li, Jordan Altshul, Mia Kenworthy, Cynthia Valadon, Michelle Liem, Naomi Claffey, Carolyn O'Connor, Luise A Seeker, Joseph R. Ecker, M. Margarita Behrens, Eran A. Mukamel

  Neuron. https://doi.org/10.1016/j.neuron.2024.05.013

  • Preview in Nature Reviews Neuroscience: Mapping the cell-type-specific effects of ageing in the human cortex

• Gene expression changes in long-term memory unlikely to replicate in the long term

  Eran A. Mukamel, Zhaoxia Yu

  Biorxiv doi: https://doi.org/10.1101/2024.07.22.604349

• Temporally distinct 3D multi-omic dynamics in the developing human brain

  Matthew G. Heffel, Jingtian Zhou, Yi Zhang, Dong-Sung Lee, Kangcheng Hou, Oier Pastor Alonso, Kevin Abuhanna, Joseph Galasso, Colin Kern, Chi-Yu Tai, Carlos Garcia-Padilla, Mahsa Nafisi, Yi Zhou, Anthony D. Schmitt, Terence Li, Maximilian Haeussler, Brittney Wick, Martin Jinye Zhang, Fangming Xie, Ryan S. Ziffra, Eran A. Mukamel, Eleazar Eskin, Bogdan Pasaniuc, Joseph R. Ecker, Jesse Dixon, Tomasz J Nowakowski, Mercedes F. Paredes, Chongyuan Luo

  Nature doi: doi.org/10.1038/s41586-024-08030-7

• Single cell spatial transcriptomics reveals distinct patterns of dysregulation in non-neuronal and neuronal cells induced by the Trem2R47H Alzheimer's risk gene mutation

  Kevin Johnston, Bereket B Berackey, Kristine Minh Tran, Alon Gelber, Zhaoxia Yu, Grant MacGregor, Eran A Mukamel, Zhiqun Tan, Kim Green, Xiangmin Xu

  Molecular Psychiatry in press. preprint

• The single-cell opioid responses in the context of HIV (SCORCH) consortium

  Seth Ament, ..., Eran A. Mukamel, ..., et al.

  Molecular Psychiatry https://doi.org/10.1038/s41380-024-02620-7

2023

• Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation

  Junhao Li, Manoj K Jaiswal, Jo-Fan Chien, Alexey Kozlenkov, Jinyoung Jung, Ping Zhou, Mahammad Gardashli, Luc J. Pregent, Erica Engelberg-Cook, Dennis W. Dickson, Veronique V. Belzil, Eran A Mukamel, Stella Dracheva

  Nature Communications 14, Article number: 5714

• Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

  Fangming Xie, Ethan J. Armand, Zizhen Yao, Hanqing Liu, Anna Bartlett, M. Margarita Behrens, Yang Eric Li, Jacinta D. Lucero, Chongyuan Luo, Joseph R. Nery, Antonio Pinto-Duarte, Olivier Poirion, Sebastian Preissl, Angeline C. Rivkin, Bosiljka Tasic, Hongkui Zeng, Bing Ren, Joseph R. Ecker, Eran A. Mukamel

  Cell Genomics 3, 100342 (2023) https://doi.org/10.1016/j.xgen.2023.100342 (open access)

• A guide to the BRAIN Initiative Cell Census Network data ecosystem

  Michael Hawrylycz, Maryann E. Martone, et al.

  PLoS Biol 21(6): e3002133 (2023) https://doi.org/10.1371/journal.pbio.3002133

2022

• 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
  eLife 11, e66909; doi: https://doi.org/10.7554/eLife.66909 (Original version posted December 2019; current version includes new data and analysis.)

• 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

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

  Winston H. Cuddleston, Junhao Li, Xuanjia Fan, Alexey Kozenkov, Matthew Lalli, Shahrukh Khalique, Stella Dracheva, Eran A. Mukamel, Michael S. Breen

  Nature Commun. 13, Article number: 2997; doi: https://www.nature.com/articles/s41467-022-30531-0

• EpiAttend: A transformer model of gene regulation combining single cell epigenomes with DNA sequence

  Russell Li, Heng Xu, Eran A. Mukamel

  NeurIPS 2022 Workshop on Learning Meaningful Representations of Life (LMRL) [PDF]

2021

• 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:

    1. Overview of BICCN
    2. Mouse primary motor cortex (MOp) atlas
    3. DNA methylation atlas
    4. Open chromatin (ATAC-seq) atlas
    5. Projection neurons
    6. Cross-species analysis of motor cortex evolution

  • 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]

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.)
  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.