Publications

Preprints

  • Y Hoang, C.A. Azaldegui, M. Ghalmi, J.S. Biteen, A.G. Vecchiarelli, “An experimental framework to assess biomolecular condensates in bacteria,” Nature Communications in press (2024). bioRxiv
  • Z. Chen, M. Seman, A. Farhat, Y. Fyodorova, S. Biswas, A. Levashkevich, P.L. Freddolino, J.S. Biteen, K. Ragunathan, “Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions,” submitted (2023). bioRxiv
  • J.F. Williams, I.V. Surovtsev, S.M. Schreiner, Z. Chen, G. Raiymbek, H. Nguyen, Y. Hu, J.S. Biteen, S. Mochrie, K. Ragunathan, M.C. King, “The condensation of HP1-α/Swi6 imparts nuclear stiffness,” submitted (2023). bioRxiv
  • A. Ames, M. Seman, A. Larkin, G. Raiymbek, Z. Chen, A. Levashkevich, J.S. Biteen, K. Ragunathan, “Identification of a novel, tunable interface in the S. pombe HP1 protein, Swi6, that underpins epigenetic inheritance,” submitted (2023). bioRxiv

Publications

  • J.-Y. Kim, C. McGlothin, M. Cha, Z.J. Pfaffenberger, E.S.T. Emre, W. Choi, S. Kim, J.S. Biteen, N.A. Kotov, “Direct Printing of Helical Metal Arrays by Circularly Polarized Light,” Proceedings of the National Academy of Sciences USA 121, e2312082121 (2024). DOI
  • S. Chattopadhyay, M. Lipok, Z.J. Pfaffenberger, J. Olesiak-Bańska, J.S. Biteen, “Single-particle photoluminescence measures a heterogenous distribution of differential circular absorbance of gold nanoparticle aggregates near constricted thioflavin T molecules,” Journal of Physical Chemistry Letters 15, 1618–1622 (2024). DOI
  • V. Nandana, et al., “The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions,” Cell Reports 42,113229 (2023). DOI
  • Z.J. Pfaffenberger, S. Chattopadhyay, and J.S. Biteen, “Far-field polarization optics control the nanometer-scale pattern of high fluorescence dissymmetry emission from achiral molecules near plasmonic nanodimers,” Journal of Physical Chemistry C 127, 9663–9672 (2023). DOI
    *Special Issue: Xiaoliang Sunney Xie Festschrift
  • N.L. Fernandez, Z. Chen, D.E.H. Fuller, L.A. van Gijtenbeek, T.M. Nye, J.S. Biteen, and L.A. Simmons, “DNA methylation and RNA-DNA hybrids regulate the single-molecule localization of a DNA methyltransferase on the bacterial nucleoid,” mBio, 14, e03185-22 (2023). DOI
  • A.L. Calkins, L.M. Demey, B.M. Rosenthal, V.J. DiRita, and J.S. Biteen, “Achieving Single-Molecule Tracking of Subcellular Regulation in Bacteria During Real-Time Environmental Perturbations,” Analytical Chemistry 95, 774–78 (2023). DOI
  • L. Geffroy, H.A. Brown, A.L. DeVeaux, N.M. Koropatkin, and J.S. Biteen, “Single-Molecule Dynamics of Surface Lipoproteins in Bacteroides Indicate Similarities and Cooperativity,” Biophysical Journal 121, 4644–4655 (2022). DOI
  • S. Biswas, et al., “Mapping biochemical states associated with HP1 target recognition at sites of heterochromatin formation in living cells,” Science Advances 8, eabk0793 (2022). DOI
  • A. Anandhi Rangarajan, H.E. Chia, C.A. Azaldegui, M.H. Olszewski, G. Pereira, N.M. Koropatkin, and J.S. Biteen, “Ruminococcus bromii enables the growth of proximal Bacteroides thetaiotaomicron by releasing glucose during starch degradation,” Microbiology 168:001180 (2022). DOI
    *Microbiology best paper of the year award.
  • S.J. Budiardjo, et al., “Colicin E1 opens its hinge to plug TolC,” eLife 11:e73297 (2022). DOI
  • F. Beaufay, et al., “Polyphosphate drives bacterial heterochromatin formation,” Science Advances 7, eabk0233 (2021). DOI
  • T. Zuo, H.J. Goldwyn, D.J. Masiello, and J.S. Biteen, “Model-Based Insight into Single-Molecule Plasmonic Mislocalization,” Journal of Physical Chemistry C 125, 24531-24539 (2021). DOI
  • H.E. Chia, K.J. Koebke, A. Anandhi Rangarajan, N.M. Koropatkin, E.N.G. Marsh, and J.S. Biteen, “A new orange ligand-dependent fluorescent reporter for anaerobic imaging,” ACS Chemical Biology 16, 2109-2115 (2021). DOI
  • Z. Chen, L. Geffroy, and J.S. Biteen, “NOBIAS: Analyzing anomalous diffusion in single-molecule tracks with nonparametric Bayesian inference,” Frontiers in Bioinformatics 1:742073 (2021). DOI; Accompanying code on Github.
  • A.L. Calkins, L.M. Demey, J.D. Karslake, E.D. Donarski, J.S. Biteen, and V.J. Dirita, “Independent Promoter Recognition by TcpP Precedes Cooperative Promoter Activation by TcpP and ToxR,” mBio 12:e02213-21 (2021). DOI
  • C.A. Azaldegui, A.G. Vecchiarelli and J.S. Biteen, “The emergence of phase separation as an organizing principle in bacteria,” Biophysical Journal 120, 1123-1138 (2021). DOI Science Direct
    *Special Issue: Phase Separation in Nucleic Acid Biochemistry and Signal Transduction
  • S. Chattopadhyay and J.S. Biteen, “Super-resolution characterization of heterogeneous light-matter interactions between single dye molecules and plasmonic nanoparticles,” Analytical Chemistry 93, 430-444 (2021). DOI
    *Special Issue: Fundamental and Applied Reviews in Analytical Chemistry
  • J.D. Karslake, E.D. Donarski, S.A. Shelby, L.M. Demey, V.J. DiRita, S.L. Veatch and J.S. Biteen, “SMAUG: Analyzing single-molecule tracks with nonparametric Bayesian statistics,” Methods 193 16-26 (2021). DOI; Accompanying code on Github.
    *Special Issue: Correlative approaches in single-molecule biophysics
  • A. Anandhi Rangarajan, N.M. Koropatkin and J.S. Biteen, “Nutrient-dependent morphological variability of Bacteroides thetaiotaomicron,” Microbiology, 166 624–628 (2020). DOI
  • H.E. Chia, T. Zuo, N.M. Koropatkin, E.N.G. Marsh and J.S. Biteen, “Imaging living obligate anaerobic bacteria with bilin-binding fluorescent proteins,” Current Research in Microbial Sciences, 1 1-6 (2020). DOI
  • N. Al-Husini, et al., “BR-bodies provide selectively permeable condensates that stimulate mRNA decay and prevent release of decay intermediates,” Molecular Cell, 78 670-682 (2020). DOI
  • S.A. Lee and J.S. Biteen, “Spectral Reshaping of Single Dye Molecules Coupled to Single Plasmonic Nanoparticles,” Journal of Physical Chemistry Letters, 10 5764-5769 (2019). DOI
  • T. Zuo, H.J. Goldwyn, B.P. Isaacoff, D.J. Masiello* and J.S. Biteen*, “Rotation of Single-Molecule Emission Polarization by Plasmonic Nanorods,” Journal of Physical Chemistry Letters, 10 5047-5054 (2019). DOI
  • H.E. Chia, E.N.G. Marsh, and J.S. Biteen, “Extending Fluorescence Microscopy into Anaerobic Environments,” Current Opinion in Chemical Biology, 51 98-104 (2019). DOI
  • B.P. Isaacoff, Y. Li, S.A. Lee and J.S. Biteen, “SMALL-LABS: An algorithm for measuring single-molecule intensity and position in the presence of obscuring backgrounds,” Biophysical Journal, 116 975-982 (2019). DOI; Accompanying code on Github.
  • Y. Li, Z. Chen, L.A. Matthews, L.A. Simmons* and J.S. Biteen*, “Dynamic Exchange of Two Essential DNA Polymerases during Replication and after Fork Arrest,” Biophysical Journal, 116 684-693 (2019). DOI
    *Cover Art, BPS Blog Post
  • H.L. Klein, et al., “Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes,” Microbial Cell, 6 65-101 (2019). DOI
  • D.A. Hinton, et al., “Mapping Forbidden Emission to Structure in Self-Assembled Organic Nanoparticles,” Journal of the American Chemical Society, 140 15827-15841 (2018). DOI
  • S.A. Lee and J.S. Biteen, “Interplay of Nanoparticle Resonance Frequency and Array Surface Coverage in Live-Cell Plasmon-Enhanced Single-Molecule Imaging,” Journal of Physical Chemistry C, 122 5705-5709 (2018). DOI
  • H.H. Tuson, M.H. Foley, N.M. Koropatkin* and J.S. Biteen*, “The Starch Utilization System Assembles around Stationary Starch-Binding Proteins,” Biophysical Journal, 115 242-250 (2018). DOI
  • Y. Li, J.W. Schroeder, L.A. Simmons, and J.S. Biteen, “Visualizing bacterial DNA replication and repair with molecular resolution,” Current Opinion in Microbiology, 43 38-45 (2018). DOI
  • B. Fu, B.P. Isaacoff, and J.S. Biteen, “Super-Resolving the Actual Position of Single Fluorescent Molecules Coupled to a Plasmonic Nanoantenna,” ACS Nano 11 8978-8987 (2017). DOI
  • J.S. Biteen and K.A. Willets, “Introduction: Super-Resolution and Single-Molecule Imaging,” Chemical Reviews, 117 7241-7243 (2017). DOI
  • D.J. Rowland and J.S. Biteen, “Measuring molecular motions inside single cells with improved analysis of single-particle trajectories,” Chemical Physics Letters, 674 173-178 (2017). DOI; Accompanying code on Github.
    * Chemical Physical Letters Frontiers Article
  • Y. Liao, Y. Li, J.W. Schroeder, L.A. Simmons* and J.S. Biteen*, “Single-molecule DNA polymerase dynamics at a bacterial replisome in live cells,” Biophysical Journal, 111 2562-2569 (2016). DOI
    * Included in Biophysical Journal Best of 2016
  • E.A. Wertz, B.P. Isaacoff and J.S. Biteen, “Wavelength-dependent super-resolution images of dye molecules coupled to plasmonic nanotriangles,” ACS Photonics, 3 1733-1740 (2016). DOI
  • S.A. Lee, A. Ponjavic, C. Siv, S.F. Lee and J.S. Biteen, “Nanoscopic Cellular Imaging: Confinement Broadens Understanding,” ACS Nano, 10 8143-8153 (2016). DOI
  • J.D. Flynn, B.L. Haas and J.S. Biteen, “Plasmon-Enhanced Fluorescence from Single Proteins in Living Bacteria,” Journal of Physical Chemistry C, 120 20512-20517 (2016). DOI
  • H.H. Tuson, A. Aliaj, E.R. Brandes, L.A. Simmons and J.S. Biteen, “Addressing the Requirements of High Sensitivity Single-Molecule Imaging of Low-Copy Number Proteins in Bacteria,” ChemPhysChem, 17 1435-1440 (2016). DOI
  • D.J. Rowland, H.H. Tuson and J.S. Biteen, “Resolving fast, confined diffusion in bacteria with image correlation spectroscopy,” Biophysical Journal, 110 2241-2251 (2016). DOI
  • J.S. Biteen, et al., “Tools for the Microbiome: Nano and Beyond.” ACS Nano, 10 6-37 (2016). DOI
    * Highlighted as an ACS Editors’ Choice
    * Most read paper of the year 2016 at ACS Nano 
  • J.S. Lenhart, M.C. Pillon, A. Guarné*, J.S. Biteen* and L.A. Simmons*, “Mismatch repair in Gram-positive bacteria,” Research in Microbiology, 167 4-12 (2016). DOI
  • Y. Liao, J.W. Schroeder, B. Gao, L.A. Simmons* and J.S. Biteen*, “Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair,” Proceedings of the National Academy of Sciences USA, 112 E6898-E6906 (2015). DOI
    * Highlighted by a PNAS Commentary HERE!
  • A.P. Alivisatos, M.J. Blaser, E.L. Brodie, M. Chun, J.L. Dangl, T.J. Donohue, P.C. Dorrestein, J.A. Gilbert, J.L. Green, J.K. Jansson, R. Knight, M.E. Maxon, M.J. McFall-Ngai, J.F. Miller, K.S. Pollard, E.G. Ruby, S.A. Taha, Unified Microbiome Initiative Consortium*, “A unified initiative to harness Earth’s microbiomes.” Science, 350 507-508 (2015). DOI
    * Julie S. Biteen is a member of the Unified Microbiome Initiative Consortium.
  • B. Fu, J.D. Flynn, B.P. Isaacoff, D.J. Rowland and J.S. Biteen, “Super-resolving the distance-dependent plasmon-enhanced fluorescence of single dye and fluorescent protein molecules.” Journal of Physical Chemistry C, 119 19350-19358 (2015). DOI
  • E. Wertz, B.P. Isaacoff, J.D. Flynn and J.S. Biteen, “Single-Molecule Super-Resolution Microscopy Reveals How Light Couples to a Plasmonic Nanoantenna on the Nanometer Scale.” Nano Letters, 15 2662-2670 (2015). DOI
  • B.L. Haas, J.S. Matson, V.J. DiRita* and J.S. Biteen*, “Single-molecule tracking in live Vibrio cholerae reveals that ToxR recruits the membrane-bound virulence regulator TcpP to the toxT promoter.” Molecular Microbiology, 96 4-13 (2015). DOI
    * Highlighted by a MicroCommentary HERE!
  • H.H. Tuson and J.S. Biteen, “Unveiling the Inner Workings of Live Bacteria Using Super-Resolution Microscopy.” Analytical Chemistry, 87 42-63 (2015). DOI
  • T. Hu, B.P. Isaacoff, J.H. Bahng, C. Hao, Y. Zhou, J. Zhu, X. Li, Z. Wang, S. Liu, C. Xu, J.S. Biteen* and N.A. Kotov*, “Self-Organization of Plasmonic and Excitonic Nanoparticles into Resonant Chiral Supraparticle Assemblies.” Nano Letters, 14 6799-6810 (2014). DOI
  • K.S. Karunatilaka, E.A. Cameron, E.C. Martens, N.M. Koropatkin and J.S. Biteen, “Superresolution Imaging Captures Carbohydrate Utilization Dynamics in Human Gut Symbionts.” mBio, 5 e02172-14 (2014). DOI
  • B.L. Haas, J.S. Matson, V.J. Dirita and J.S. Biteen, “Imaging live cells at the nanometer-scale with single-molecule microscopy: Obstacles and achievements in experimental optimization for microbiology.” Molecules, 19 12116-12149 (2014). DOI
  • J.E. Donehue, E. Wertz, C.N. Talicska and J.S. Biteen, “Plasmon-Enhanced Brightness and Photostability from Single Fluorescent Proteins Coupled to Gold Nanorods.” Journal of Physical Chemistry C, 118 15027-15035 (2014). DOI
  • D.J. Rowland and J.S. Biteen, “Top-Hat and Asymmetric Gaussian-Based Fitting Functions for Quantifying Directional Single-Molecule Motion.” ChemPhysChem, 15 712-720 (2014). DOI
  • J.S. Biteen, “Intracellular Dynamics of Bacterial Proteins Are Revealed by Super-resolution Microscopy.” Biophysical Journal, 105 1547-1548 (2013). DOI
  • J.E. Donehue, B.L. Haas, E. Wertz, C.N. Talicska and J.S. Biteen, “Plasmon-enhanced emission from single fluorescent proteins.” SPIE Proceedings, 8597 85970J (2013). DOI
  • E. Wertz, J.E. Donehue, C. Hayes and J.S. Biteen, “Plasmon-enhanced fluorescence intensities and rates permit super-resolution imaging of enhanced local fields.” SPIE Proceedings, 8590 85900U (2013). DOI
  • K.S. Karunatilaka, B.R. Coupland, E.A. Cameron, E.C. Martens, N.M. Koropatkin and J.S. Biteen, “Single-Molecule Imaging Can Be Achieved in Live Obligate Anaerobic Bacteria.” SPIE Proceedings, 8590 85900K (2013). DOI
  • M.C. Cheng, A.T. Leske, T. Matsuoka, B.C. Kim, J. Lee, M.A. Burns, S. Takayama and J.S. Biteen, “Super-Resolution Imaging of PDMS Nanochannels by Single-Molecule Micelle-Assisted Blink Microscopy.” Journal of Physical Chemistry B, 117 4406-4411 (2013). DOI
  • J.S. Biteen, “Live-Cell Single-Molecule Imaging.” Encyclopedia of Biophysics, vol. 1, G. C. K. Roberts (ed.), Springer (Heidelberg, 2013). ISBN: 978-3-642-16711-9.
  • J.S. Biteen, “Photoactivated Localization Microscopy (PALM).” Encyclopedia of Biophysics, vol. 1, G. C. K. Roberts (ed.), Springer (Heidelberg, 2013). ISBN: 978-3-642-16711-9.
  • Y. Liao, S.K. Yang, K. Koh, A.J. Matzger and J.S. Biteen, “Heterogeneous Single-Molecule Diffusion in One-, Two-, and Three-Dimensional Microporous Coordination Polymers: Directional, Trapped, and Immobile Guests.” Nano Letters, 12 3080-3085 (2012). DOI
  • J.S. Biteen, “Extending the tools of single-molecule fluorescence imaging to real problems in microbiology.” Molecular Microbiology, 85 1-4 (2012). DOI
  • J.S. Biteen, “Moving Toward the Future of Single-Molecule-Based Super-Resolution Imaging.” Biopolymers, 95 287-289 (2011). DOI

Publications prior to University of Michigan