Research

I am a CNRS research fellow (chargé de recherche) in the team of Pascal Martin at the Curie Institute Physics of Cells and Cancer Laboratory. I study the emergence of complex dynamic structures in minimal actomyosin systems.

Previously, I was a post-doctoral researcher in the team of Laurent Cognet at the Laboratoire Photonique, Numérique et Nanosciences (Institut d’Optique d’Aquitaine), with support from the ARC Foundation for Cancer Research. There, I used carbon nanotubes as near-infrared fluorophores to probe the extracellular matrix.

I completed my Ph. D. in (bio)physics in the lab of Carlos Bustamante at UC Berkeley. The title of my thesis is Improving the resolution and accuracy of optical tweezers through algorithmic and instrumental advances.

During the first half of my Ph. D., I worked on the development of quantitative methods and fluorescent protein engineering for photoactivated localization microscopy. During the second half, I used optical tweezers to perform high resolution studies of the transcription dynamics of RNA polymerase at the single-molecule level.

Before my Ph. D., I worked on contrast agents for magnetic resonance imaging at Guerbet.

Publications

  1. Identification of early stage liver fibrosis by modifications in the interstitial space diffusive microenvironment using fluorescent single-walled carbon nanotubes.
    A. Lee*#, A. Simon*, A. Boyreau, N. Allain-Courtois, B. Lambert, J.-P. Pradère, F. Saltel#, L. Cognet#.
    Nano Lett. (2024). bioRxiv:10.1101/2024.02.06.579133v1
  1. Characterization of the asymmetrical stepwise disassembly of nucleosomes and chromatosomes by high-speed atomic force microscopy.
    B. Onoa, C. Díaz-Celis, C. Cañari-Chumpitaz, A. Lee, C. Bustamante.
    ACS Cent. Sci., 10, 122-137 (2024).
  1. A binary annular phase mask to regulate spherical aberration and allow super-localization in single-particle tracking over extended depth-of-focus.
    Q. Gresil, A. Lee, O. Lévêque, K. Caicedo, B. Martín Muñoz, C. Kulcsár, F. Goudail, P. Bon, L. Cognet.
    Opt. Commun., 545, 129699 (2023). arXiv:2304.12774 [physics.optics]
  1. Nanoscale and functional heterogeneity of the hippocampal extracellular space.
    D. Grassi, A. Idziak*, A. Lee*, I. Calaresu, J.-B. Sibarita, L. Cognet, U. V. Nägerl, L. Groc.
    Cell Rep., 42, 112478 (2023).
  1. Near-infrared carbon nanotube tracking reveals the nanoscale extracellular space around synapses.
    C. Paviolo, J. S. Ferreira, A. Lee, D. Hunter, L. Groc, L. Cognet.
    Nano Lett., 22, 6849–6856 (2022). bioRxiv:10.1101/2021.10.29.466461
  1. The Astropy Project: Sustaining and growing a community-oriented open-source project and the latest major release (v5.0) of the core package.
    The Astropy Collaboration et al.
    Astrophys. J., 935, 167 (2022). arXiv:2206.14220 [astro-ph]
  1. On the validity domain of maximum likelihood estimators for depth-of-field extension in single-molecule localization microscopy.
    O. Lévêque, C. Kulcsár, A. Lee, P. Bon, L. Cognet, F. Goudail.
    J. Opt. Soc. Am. A, 39, 37–43 (2022).
  1. Length measurement of single-walled carbon nanotubes from translational diffusion and intensity fluctuations.
    A. Lee, L. Cognet.
    J. Appl. Phys., 128, 224301 (2020).
  1. Co-designed annular binary phase masks for depth-of-field extension in single-molecule localization microscopy.
    O. Lévêque, C. Kulcsár, A. Lee, H. Sauer, A. Aleksanyan, P. Bon, L. Cognet, F. Goudail.
    Opt. Express, 28, 32426–32446 (2020).
  1. Synucleinopathy alters nanoscale organization and diffusion in the brain extracellular space through hyaluronan remodeling.
    F. N. Soria, C. Paviolo, E. Doudnikoff, M.-L. Arotcarena, A. Lee, N. Danné, A. K. Mandal, P. Gosset, B. Dehay, L. Groc, L. Cognet.
    Nat. Commun., 11, 3440 (2020).
  1. Nanoscale exploration of the extracellular space in the live brain by combining single carbon nanotube tracking and super-resolution imaging analysis.
    C. Paviolo*, F. N. Soria*, J. S. Ferreira*, A. Lee, L. Groc, E. Bezard, L. Cognet.
    Methods, 174, 91–99 (2020).
  1. SciPy 1.0: Fundamental algorithms for scientific computing in Python.
    P. Virtanen, …, the SciPy 1.0 Contributors.
    Nat. Methods, 17, 261–272 (2020). arXiv:1907.10121 [cs]
  1. Co-temporal force and fluorescence measurements reveal a ribosomal gear-shift mechanism of translation regulation by mRNA secondary structures.
    V. P. Desai*, F. Frank*, A. Lee, M. Righini, L. Lancaster, H. Noller, I. Tinoco, C. Bustamante.
    Mol. Cell, 75, 1007–1019 (2019).
  1. High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier.
    Z. Chen*, R. Gabizon*, A. I. Brown, A. Lee, A. Song, C. Díaz-Celis, C. D. Kaplan, E. F. Koslover, T. Yao, C. Bustamante.
    eLife, 8, e48281 (2019). bioRxiv:10.1101/641506v1
  1. Programming chain-growth copolymerization of DNA hairpin tiles for in-vitro hierarchical supramolecular organization.
    H. Zhang*, Y. Wang*, H. Zhang*, X. Liu*, A. Lee, Q. Huang, F. Wang, J. Chao, H. Liu, J. Li, J. Shi, X. Zuo, L. Wang, L. Wang, X. Cao, C. Bustamante, Z. Tian, C. Fan.
    Nat. Commun., 10, 1006 (2019).
  1. The Astropy Project: Building an open-science project and status of the v2.0 core package.
    The Astropy Collaboration et al.
    Astronom. J., 156, 123 (2018). arXiv:1801.02634 [astro-ph]
  1. Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates.
    R. Gabizon*, A. Lee*, H. Vahedian-Mohaved, RH. Ebright, C. Bustamante.
    Nat. Commun., 9, 2930 (2018).
  1. Full molecular trajectories of RNA polymerase at single base pair resolution.
    M. Righini*, A. Lee*, C. Cañari-Chumpitaz*, T. Lionberger*, R. Gabizon, Y. Coello, I. Tinoco, C. Bustamante.
    Proc. Nat. Acad. Sci. USA., 115, 1285–1291 (2018).
  1. Unraveling the thousand word picture: an introduction to super-resolution data analysis.
    A. Lee, K. Tsekouras, C. Calderon, C. Bustamante, S. Pressé.
    Chem. Rev., 117, 7276–7330 (2017).
  1. Identification of a minimal peptide tag for emphin vivo and emphin vitro loading of encapsulin.
    C. Cassidy-Amstutz, L. Oltrogge, C. Going, A. Lee, P. Teng, D. Quintanilla, A. East-Seletsky, E. Williams, D. Savage.
    Biochem., 55, 3461–3468 (2016).
  1. Optimized two-color super resolution imaging of Drp1 during mitochondrial fission with a slow-switching Dronpa variant.
    A. B. Rosenbloom, S.-H. Lee, M. To, A. Lee, J. Y. Shin, C. Bustamante.
    Proc. Nat. Acad. Sci. USA., 111, 13093–13098 (2014).
  1. Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM).
    S.-H. Lee, J. Y. Shin, A. Lee, C. Bustamante.
    Proc. Nat. Acad. Sci. USA., 109, 17436–17441 (2012).

Talks

  1. Analyzing single-particle anomalous diffusion in heterogeneous environments.
    A. Lee, L. Cognet.
    Focus on Microscopy (2021)
  1. Super-resolution imaging of protein-protein interactions by bimolecular complementation of photoactivatable fluorescent proteins.
    A. Lee, A. B. Rosenbloom, S.-H. Lee, C. Bustamante.
    Biophysical Society Annual Meeting (2014)

Posters

  1. RNA polymerase translocation in processive transcription elongation and pausing: dynamics, force-dependence, and modulation by sequence-specific RNAP-DNA interactions.
    A. Lee, R. Gabizon, H. Vahedian-Mohaved, R. H. Ebright, C. Bustamante.
    Biophysical Society Annual Meeting (2017)
  1. Super-resolution imaging of protein-protein interactions in mitochondria by bimolecular complementation of photoactivatable fluorescent proteins.
    A. Lee, A. B. Rosenbloom, S.-H. Lee, Y.-W. Seo, C. Bustamante.
    Single Molecule Biophysics Aspen Meeting (2015)

Proceedings

  1. How to assess depth-of-field extension strategies applied to single-molecule super-resolution microscopes?
    O. Lévêque, C. Kulcsár, A. Lee, P. Bon, L. Cognet, F. Goudail.
    Computational Optical Sensing and Imaging; OSA Imaging and Applied Optics Congress (2021)
  1. Can phase masks extend depth-of-field in localization microscopy?
    O. Lévêque, C. Kulcsár, H. Sauer, A. Lee, P. Bon, L. Cognet, F. Goudail.
    Proceedings vol.11351, Unconventional Optical Imaging II, 113510E; SPIE Photonics Europe (2020)
  1. Correlative imaging of single carbon nanotubes and fluorescently labelled neuronal structures in the extracellular space of live brains.
    C. Paviolo, J. S. Ferreira, A. Lee, L. Groc, L. Cognet.
    Proceedings vol.11360, Neurophotonics, 113600B; SPIE Photonics Europe (2020)