Research

I am currently a post-doctoral researcher in the team of Laurent Cognet at the Laboratoire Photonique, Numérique et Nanosciences (Institut d’Optique d’Aquitaine).

Previously, I was a (bio)physics graduate student in the Bustamante lab 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 starting my Ph. D. at UC Berkeley, I worked on contrast agents for magnetic resonance imaging at Guerbet.

Publications

  1. Direct observation of cotranscriptional wrapping dynamics in nucleosomes at near base-pair resolution.
    R. Gabizon, Z. Chen, A. Lee, C. Díaz Celis, R. Sosa, T. Yao, C. Kaplan, C. Bustamante.
    In preparation.
  1. Co-temporal force and fluorescence measurements reveal a ribosomal gear-shift mechanism of translation regulation by mRNA secondary structures.
    VP. Desai*, F. Frank*, A. Lee, M. Righini, L. Lancaster, H. Noller, I. Tinoco, C. Bustamante.
    Submitted.
  1. Nanoscale exploration of the extracellular space in the live brain by combining single carbon nanotube tracking and super-resolution imaging analysis.
    C. Paviolo*, FN. Soria*, JS. Ferreira*, A. Lee, L. Groc, E. Bezard, L. Cognet.
    Methods (2019). (PubMed).
  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). (PubMed)
  1. The Astropy Project: Building an inclusive, open-science project and status of the 2.0 core package.
    The Astropy Collaboration [including A. Lee].
    Astronom. J., 156, 123 (2018) [arXiv:1801.02634 [astro-ph.IM]].
  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). (PubMed)
  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). (PubMed)
  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). (PubMed)
  1. Identification of a minimal peptide tag for in vivo and in 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). (PubMed)
  1. Optimized two-color super resolution imaging of Drp1 during mitochondrial fission with a slow-switching Dronpa variant.
    AB. Rosenbloom, SH. Lee, M. To, A. Lee, JY. Shin, C. Bustamante.
    Proc. Natl. Acad. Sci. USA, 111, 13093–13098 (2014). (PubMed)
  1. Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM).
    SH. Lee, JY. Shin, A. Lee, C. Bustamante.
    Proc. Natl. Acad. Sci. USA, 109, 17436–17441 (2012). (PubMed)

(asterisks denote equal contribution)

Talks

  1. Super-resolution imaging of protein-protein interactions by bimolecular complementation of photoactivatable fluorescent proteins.
    A. Lee, AB. Rosenbloom, SH. 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, RH. 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, AB. Rosenbloom, SH. Lee, YW. Seo, C. Bustamante.
    Single Molecule Biophysics Aspen Meeting (2015).

Other abstracts

  1. Simultaneous force and fluorescence measurements on single ribosomes demonstrate that mRNA secondary structures do not restrict EF-G catalyzed translocation.
    VP. Desai, F. Frank, M. Righini, A. Lee, I. Tinoco, C. Bustamante.
    Biophysical Society Annual Meeting (2018).
  1. New insights into transcriptional pausing using ultra-high resolution optical tweezers and novel analysis methods.
    R. Gabizon, A. Lee, H. Vahedian-Mohaved, RH. Ebright, C. Bustamante.
    Biophysical Society Annual Meeting (2018).
  1. RNA polymerase translocation in processive transcription elongation and pausing: dynamics, force-dependence, and modulation by sequence-specific RNAP-DNA interactions.
    R. Gabizon, A. Lee, H. Vahedian-Mohaved, RH. Ebright, C. Bustamante.
    Single Molecule Biophysics Aspen Meeting (2017).
  1. Quantification of photoactivatable fluorescent proteins by PALM.
    JY. Shin, SH. Lee, A. Lee, C. Bustamante.
    Biophysical Society Annual Meeting (2012).
  1. WASSR imaging of iron oxide particles at 2.35 and 7T.
    JS. Raynaud, A. Lee, C. Robic, E. Giaccomini, I. Raynal, P. Robert, F. Lethimonier, M. Port, C. Corot.
    International Society for Magnetic Resonance in Medecine Annual Meeting (2011).
  1. WASSR imaging of \(\alpha_\text{V}\beta_\text{3}\) targeted USPIO at 2.35T on U87 mice tumors: feasibility study.
    JS. Raynaud, A. Lee, X. Violas, R. Santus, G. Louin, I. Raynal, P. Robert, M. Port, C. Corot.
    International Society for Magnetic Resonance in Medecine Annual Meeting (2011).