Selected Publications

See the full publication list here.

Structural insights into human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins

J. Zhao*, S. Makhija*, C. Zhou, H. Zhang, Y. Wang, M. Muralidharan, B. Huang, Y. Cheng

PNAS 119, e2207200119 (2022) [link] [Preprint: bioRxiv/2021.06.25.449985]

CELL-E: Biological zero-shot text-to-image synthesis for protein localization prediction

E. Khwaja, Y.S. Song, B. Huang

bioRxiv 2022.05.27.493774 (2022) [Preprint]


OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization

N.H. Cho, K.C. Cheveralls, A. Brunner, K. Kim, A.C. Michaelis, P. Raghavan, H. Kobayashi, L. Savy, J.Y. Li, H. Canaj, J.Y.S. Kim, E.M. Stewart, C. Gnann, F. McCarthy, J.P. Cabrera, R.M. Brunetti, B.B. Chhun, G. Dingle, M.Y. Hein, B. Huang, S.B. Mehta, J.S. Weissman, R. Gómez-Sjöberg, D.N. Itzhak, L.A. Royer, M. Mann, M.D. Leonetti

Science 375, eabi6983 (2022) [Link] [Preprint: bioRxiv/2021.03.29.437450]

Image denoising for fluorescence microscopy by supervised to self-supervised transfer learning

Y. Wang, H. Pinkard, E. Khwaja, S. Zhou, L. Waller, B. Huang

Opt. Express 29, 41303-41312 (2021) [link] [Preprint: bioRxiv/2021.02.01.429188]
Code and Data: [GitHub]

 Label-retention expansion microscopy

X. Shi*, Q. Li*, Z. Dai, A.A. Tran, S. Feng, A.D. Ramirez, Z. Lin, X. Wang, T.T. Chow, J. Chen, D. Kumar, A.R. McColloch, J.F. Reiter, E.J. Huang, I.B. Seiple, B. Huang

J. Cell Biol. 220, e202105067 (2021) [link] [Preprint: bioRxiv/2019/687954]
Also see our collaborations to apply LR-ExM in resolving ciliary structures [J. Cell Biol. (2021)] and in zebrafish [Sci. Adv. (2021)]


Cytoplasmic protein granules organize kinase-mediated RAS signaling

A. Tulpule*, J. Guan*, D.S. Neel*, H.R. Allegakoen, Y.P. Lin, A. Heslin, D. Brown, Y.-T. Chou, A. Heslin, N. Chatterjee, S. Perati, S. Menon, T.A. Nguyen, J. Debnath, A.D. Ramirez, X. Shi, B. Yang, S. Feng, S. Makhija, D. Brown, B. Huang, T.G. Bivona

Cell 184, 2649-2664.e18 (2021) [Link] [Preprint: bioRxiv/2019/704312]
Spotlight in Molecular Cell
Highlight by Cancer Discovery


Versatile labeling and detection of endogenous proteins using tag-assisted split enzyme complementation

S. Makhija, D. Brown, R.M. Rudlaff, J. Doh, S. Bourke, Y. Wang, S. Zhou, R. Cheloor-Kovilakam, B. Huang

ACS Chem. Biol. 16, 671-681 (2021) [Link] [Preprint: bioRxiv/2020.12.01.407072]


HP1 proteins compact DNA into mechanically and positionally stable phase separated domains

M.M. Keenen, D. Brown, L.D. Brennan, R. Renger, H. Khoo, C.R. Carlson, B. Huang, S.W. Grill, G.J. Narlikar, S. Redding

eLife 10, e64563 (2021) [Link]

Deep profiling reveals substantial heterogeneity of integration outcomes in CRISPR knock-in experiments

H. Canaj, J.A. Hussmann, H. Li, K.A. Beckman, L. Goodrich, N.H. Cho, Y.J. Li, D.A. Santos, A. McGeever, E.M. Stewart, V. Pessino, M.A. Mandeger, C. Huang, L. Gan, B. Panning, B. Huang, J.S. Weissman, M.D. Leonetti

[Preprint: bioRxiv/2019/841098] [Preprint: bioRxiv/2017/178905]


Improved yellow-green split fluorescent proteins for protein labeling and signal amplification

S. Zhou, S. Feng, D. Brown, B. Huang

PLoS ONE 15, e0241592 (2020) [link] [Preprint: bioRxiv/2020/315679]


Bright split red fluorescent proteins for the visualization of endogenous proteins and synapses

S. Feng, A. Varshney, D. Coto Villa, C. Modavi, J. Kohler, F. Farah, S. Zhou, N. Ali, J.D. Müller, M. VanHoven, B. Huang

Commun. Biol. 2, 344 (2019) [link] [Preprint: bioRxiv/2018/454041]


Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution

B. Yang, X. Chen, Y. Wang, S. Feng, V. Pessino, N. Stuurman, N.H. Cho, K.W. Cheng, S.J. Lord, L. Xu, D. Xie, R.D. Mullins, M.D. Leonetti, B. Huang

Nat. Methods 16, 501-504 (2019) [link] [Preprint: bioRxiv/2018/273359]


Deformed alignment of super-Resolution images for semi-flexible structures in 3D

X. Shi, G. Garcia III, Y. Wang, J.F. Reiter, B. Huang

PLoS One 0212735 (2019) [link] [Preprint: bioRxiv/2018/461913]


Multicolor fluorescent imaging by space-constrained computational spectral imaging

Y. Wang, B. Yang, S. Feng, V. Pessino, B. Huang

Opt. Express 27, 5393 (2019) [link] [Preprint: bioRxiv/2018/458869]

Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-Tag

B. Chen#, W. Zou, H. Xu, Y. Liang, B. Huang#

Nat. Commun. 9, 5065 (2018) [link] [Preprint: bioRxiv/2018/280495]


Local enrichment of HP1alpha at telomeres alters their structure and regulation of telomere protection

T.T. Chow, X. Shi, J.H. Wei, J. Guan, G. Stadler, B. Huang, E. Blackburn

Nat. Commun. 9, 3583 (2018) [link]


A LINE1-nucleolin partnership regulates early development and ESC identity

M. Percharde, C. Lin, Y. Yin, J. Guan, G.A. Peixoto, A. Bulut-Karslioglu, S. Biechele, B. Huang, X. Shen, M. Ramalho-Santos

Cell 174, 391-405 (2018) [link]


Co-translational protein targeting facilitates centrosomal recruitment of PCNT during centrosome maturation

G. Sepulveda, M. Antkowiak, I. Brust-Mascher, K. Mahe, T. Ou, N. Castro, L.N. Christensen, L. Cheung, D. Yoon, B. Huang, L.E. Jao

eLife 7, e34959 (2018) [link] [Preprint: bioRxiv/2017/241083]


Correlation analysis framework for localization-based superresolution microscopy

J. Schnitzbauer, Y. Wang, M. Bakalar, B. Chen, T. Nuwal, S. Zhao, B. Huang

Proc. Nat. Acad. Sci. USA 115, 3219-3224 (2018) [link] [Preprint: bioRxiv/2017/125005]
--- Research Highlights in Nat. Methods


The centrosomin CM2 domain is a multi-functional binding domain with distinct cell cycle roles

Y.R. Citron, C.J. Fagerstrom, B. Keszthelyi, B. Huang, N.M. Rusan, M.J.S. Kelly, D.A. Agard

PLoS One 13, e0190530 (2018) [link] [Preprint: bioRxiv/2017/200204]

Super-resolution microscopy reveals that disruption of ciliary transition-zone architecture causes Joubert syndrome

X. Shi*, G. Garcia*, J.C. Van De Weghe, R. McGorty, G.J. Pazour, D. Doherty, B. Huang#, J.F. Reiter#

Nat. Cell Biol. 19, 1178-1188 (2017) [link] [Preprint: bioRxiv/2017/142042]


High-NA open-top selective-plane illumination microscopy for biological imaging

R. McGorty, D. Xie, B. Huang

Opt. Express, 25, 17798-17810 (2017) [link] [Preprint: bioRxiv/2017/140418]


Improved split fluorescent proteins for endogenous protein labeling

S. Feng, S. Sekine, V. Pessino, H. Li, M.D. Leonetti, B. Huang

Nat. Commun. 8, 370 (2017) [link] [Preprint: bioRxiv/2017/137059]
--- Tools in Brief by Nature Methods


Woofer-tweeter adaptive optical structured illumination microscopy

Q. Li, M. Reinig, D. Kamiyama, X. Tao, B. Huang, J. Kubby

Photonics Res., 5, 329-334 (2017) [link]


Covalent protein labeling by SpyTag-SpyCatcher in fixed cells for super-resolution microscopy

V. Pessino, Y.R. Citron, S. Feng, B. Huang

ChemBioChem, 18, 1942-1945 (2017) [link] [Preprint: bioRxiv/2017/125013]


Functional selectivity of GPCR-directed drug action through location bias

R. Irannejad, V. Pessino, D. Mika, B. Huang, P.B. Wedegaertner, M. Conti, M. von Zastrow

Nat. Chem. Biol., 13, 799-806 (2017) [link]

EGF and NRG induce phosphorylation of HER3/ERBB3 by EGFR using distinct oligomeric mechanisms

B. van Lengerich, E. M. Puchner, C. Angew, B. Huang, N. Jura

Proc. Nat. Acad. Sci. USA,114, E2836-E2845 (2017) [link]


Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH

J. Guan, H. Liu, X. Shi, S. Feng, B. Huang

Biophys. J., 112, 1077-1084 (2017) [link] [Preprint: bioRxiv]
--- New and Notable


Live cell imaging of endogenous mRNA using RNA-based fluorescence "turn-on" probe"

W.Q. Ong, Y.R. Citron, S. Sekine, B. Huang

ACS Chem. Biol., 12, 200-205 (2017) [link]


A high-content larval zebrafish brain imaging method for small molecule drug discovery

H. Liu, S. Chen, K. Huang, J. Jim, H. Mo, R. Iovine, J. Gendre, P. Pascal, Q. Li, Z. Dong, M. Arkin, S. Guo, B. Huang

PLoS One, 11, e0164645 (2016) [link]


Identification of environmental stressors and validation of light preference as a measure of anxiety in larval zebrafish

Y. Bai, H. Liu, B. Huang, M. Wagle, S. Guo

BMC Neurosci., 17, 63 (2016) [link]


A scalable strategy for high-throughput GFP tagging of endogenous human proteins

M.D. Leonetti*, S. Sekine*, D. Kamiyama#, J.S. Weissman#, B. Huang#

Proc. Nat. Acad. Sci. USA, 113, E3501-E3508 (2016) [link] [bioRxiv]
--- Highlight in Nature Methods

Selective-plane illumination microscopy for high-content volumetric biological imaging

R. McGorty, B. Huang

Proc. SPIE, 9720, 97200P, doi:10.1117/12.2212889 (2016) [link]


Versatile protein tagging in cells with split fluorescent protein

D. Kamiyama*, S. Sekine*, B. Barsi-Rhyne, J. Hu, B. Chen, L.A. Gilbert, H. Ishikawa, M.D. Leonetti, W.F. Marshall, J.S. Weissman, B. Huang

Nat. Comm., 7, 11046 (2016) [link]


Force feedback controls motor activity and mechanical properties of self-assembling branched actin networks

P. Bieling, T.D. Li, J. Weichsel, R. McGorty, P. Jreij, B. Huang, D.A. Fletcher, R.D. Mullins

Cell, 164, 115-127 (2016) [link]


Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci

B. Chen, J. Hu, R. Almeida, H. Liu, S. Balakrishnan, C. Covill-Cooke, W.A. Lim, B. Huang

Nucleic Acids Res., 44, e75 (2016) [link]


Specification of dendritogenesis site in Drosophila aCC motoneuron by membrane-enrichment of Pak1 through Dscam1

D. Kamiyama, R. McGorty, R. Kamiyama, M.D. Kim, A. Chiba, B. Huang

Dev. Cell, 35, 93-106 (2015) [link]


Heavy water: a simple solution to increasing brightness of fluorescence protein in super-resolution imaging

W.Q. Ong, Y.R. Citron, J. Schnitzbauer, D. Kamiyama, B. Huang

Chem. Comm., 51, 13451 - 13453 (2015) [link]
Cover image

Open-top selective plane illumination microscope for conventionally mounted specimens

R. McGorty, H. Liu, D. Kamiyama. Z. Dong, S. Guo, B. Huang

Opt. Express, 23, 16142-16153 (2015) [link]


Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm

Y. Wang, J. Schnitzbauer, Z. Hu, X. Li, Y. Cheng, Z.L. Huang, B. Huang

Opt. Express, 22, 15982-15991 (2014) [link] [software]


Correction of depth-dependent aberrations in 3D single molecule localization and super-resolution microscopy

R. McGorty, J. Schnitzbauer, W. Zhang, B. Huang

Opt. Lett., 39, 275-278 (2014) [link]


Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system

B. Chen, L.A. Gilbert, B.A. Cimini, J. Schnitzbauer, W. Zhang, G.W. Li, J. Park. E.H. Blackburn, J.S. Weissman, L.S. Qi#, B. Huang#

Cell, 155, 1479-1491(2013) [link]
--- Featured in BioTechnique.


Counting molecules in single organelles with super-resolution microscopy allows tracking of the endosome maturation trajectory

E.M. Puchner, J.M. Walter, R. Kasper, B. Huang#, W.A. Lim#

Proc. Nat. Acad. Soc. USA, 110, 16015-16020 (2013) [link]


4Pi fluorescence detection and 3D particle localization with a single objective

J. Schnitzbauer, R. McGorty, B. Huang
Opt. Express 21, 19701-19708 (2013) [link]
--- Featured in Laser Focus World.

TMEM16C facilitates Na(+)-activated K(+) currents in rat sensory neurons and regulates pain processing

F. Huang, X. Wang, E.M. Ostertag, T. Nuwal, B. Huang, Y.N. Jan, A.I. Basbaum and L.Y. Jan

Nat. Neurosci., 16, 1284-1290 (2013) [link] [supp info]


Active microscope stabilization in three dimensions using image correlation

R. McGorty, D. Kamiyama, B. Huang

Optical Nanoscopy, 2, 3 (2013) [link]


Conformational biosensors reveal adrenoceptor signaling from endosomes

R. Irannejad, J.C. Tomshine, J.R. Tomshine, M. Chevalier, J. Steyaert, S.G.F. Rasmussen, H. El-Samad, B. Huang, M. von Zastrow

Nature, 495, 534-538 (2013) [link] [Supporting info]
--- News and Views in Nature
--- 2013 Methods to Watch by Nature Methods


Sub-diffraction-resolution fluorescence microscopy reveals a novel domain of the centrosome critical for pericentriolar material organization

V. Mennella, B. Keszthelyi, K.L. McDonald, B. Chhun, F. Kan, G.C. Rogers, B. Huang, D.A. Agard
Nat. Cell Biol, 14, 1159-1168 (2012) [link] [supp info]
--- News and Views in Nat. Cell Biol.


Faster STORM using compressed sensing

L. Zhu#, W. Zhang, D. Elnatan, B. Huang#
Nat Methods, 9, 721-723 (2012) [link] [supp info]

--- News and Views in Nat. Methods


Afadin, a Ras/Rap effector that controls cadherin function, promotes spine and excitatory synapse density in the hippocampus

G.M.J. Beaudoin, III, G.M. Schofield, T. Nuwal, K. Zang, E.M. Ullian, B. Huang, L.F. Reichard

J Neurosci., 32, 99-110 (2012) [link]

Prior to UCSF

  • 32. S.H. Shim, C. Xia, G. Zhong, H.P. Babcock, J.C. Vaughan, B. Huang, X. Wang, C. Xu, G.Q. Bi, X. Zhuang, "Super-resolution fluorescence imaging of organelles in live cells with photoswitchable membrane probes", Proc. Nat. Acad. Sci. USA, 109, 13978-13983 (2012) [link][supp info]
  • 26. A. Dani*, B. Huang*, J. Bergan, C. Dulac, X. Zhuang, “Super-resolution imaging of chemical synapses in the brain”, Neuron, 68, 843-856 (2010) [link] [supp info]
    --- 2010 European Microscopy Society Outstanding Paper Award - Life Sciences.
  • 24. M. Wu, B. Huang, M. Graham, A. Raimondi, J.E. Heuser, X. Zhuang, P. De Camilli, “Coupling between clathrin-dependent budding and F-BAR-dependent membrane tubulation in a cell-free system of endocytosis”, Nat. Cell. Biol., 12, 902-908 (2010) [link] [supp info].
    --- Featured in Science.
  • 20. B. Huang*, S. A. Jones*, B. Brandenburg, X. Zhuang, “Whole cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution”, Nat. Methods, 5, 1047-1052 (2008) [link] [supp info].
  • 19. B. Huang , W. Wang, M. Bates, X. Zhuang, “Three-dimension super-resolution imaging by stochastic optical reconstruction microscopy”, Science, 319, 810-813 (2008) [link] [supp info].
  • 18. M. Bates, B. Huang, G. T. Dempsey, X. Zhuang, “Multicolor super-resolution imaging with photo-switchable fluorescent probes”, Science, 317, 1749-1753 (2007) [link] [supp info].
  • 17. B. Huang , H. Wu, D. Bhaya, A. R. Grossman, S. Granier, B. K. Kobilka, R. N. Zare, “Counting low-copy-number proteins in a single cell”, Science, 315, 81-84 (2007) [link] [supp info].
  • 16. S. Kim, B. Huang, H. Wu, R. N. Zare, “Microfluidic separation and capture of analytes for single-molecule spectroscopy”, Lab Chip, 7, 1663-1665 (2007) [link] [supp info].
  • 15. B. Huang , S. Kim, R. N. Zare, “Use of a mixture of n-dodecyl-beta-D-maltoside and sodium dodecyl sulfate in poly(dimethylsiloxane) microchips to suppress adhesion and promote separation of proteins”, Anal. Chem., 79, 9145-9149 (2007) [link].
  • 14. M. R. Whorton, M. P. Bokoch, S. G. F. Rasmussen, A. Kuszak, B. Huang, R. N. Zare, B. K. Kobilka, R. K. Sunahara, “A monomeric G protein-coupled receptor isolated in a high-density lipoprotein particle efficiently activates its G protein”, Proc. Nat. Acad. Sci. U.S.A., 104, 7682-7687 (2007) [link] [supp info].
  • 13. B. Huang , F. Yu, R. N. Zare, “Surface plasmon resonance imaging using a high numerical aperture microscope objective”, Anal. Chem., 79, 2979-2983 (2007) [link].
  • 12. H. Wu, B. Huang, R. N. Zare, “Generation of complex, static solution gradients in microfluidic channels”, J. Am. Chem. Soc., 128, 4194-4195 (2006) [link] [supp info].
  • 11. Y. Luo, B. Huang, H. Wu, R. N. Zare, “Controlling electroosmotic flow in polydimethylsiloxane (PDMS) separation channels by means of prepolymer additives”, Anal. Chem., 78, 4588-4592 (2006) [link].
  • 10. B. Huang , H. Wu, S. Kim, B. K. Kobilka, R. N. Zare, “Phospholipid biotinylation of polydimethylsiloxane (PDMS) for protein immobilization”, Lab Chip, 6, 369-373 (2006) [link].
  • 9. H. Wu, B. Huang, R. N. Zare, “Construction of microfluidic chips using polydimethylsiloxane for adhesive bonding”, Lab Chip, 5, 1393-1398 (2005) [link] [supp info].
  • 8. B. Huang , H. Wu, S. Kim, R. N. Zare, “Coating of poly(dimethylsiloxane) with n-dodecyl-beta-D-maltoside to minimize nonspecific protein adsorption”, Lab Chip, 5, 1005-1007 (2005) [link].
  • 7. T. D. Perroud, B. Huang, R. N. Zare, “Effect of bin time on the photon counting histogram for one-photon excitation”, ChemPhysChem, 6, 905-912 (2005) [link].
  • 6. B. Huang , T. D. Perroud, R. N. Zare, “Photon counting histogram: one-photon excitation”, ChemPhysChem, 5, 1523-1531 (2004) [link] [supp info].
  • 5. T. D. Perroud, B. Huang, M. I. Wallace, R. N. Zare, “Photon counting histogram for one-photon excitation”, ChemPhysChem, 4, 1121-1123 (2003) [link].
  • 4. R. J. Whelan, T. Wohland, L. Neumann, B. Huang, B. K Kobilka, R. N Zare, “Analysis of bimolecular interactions using a miniaturized surface plasmon resonance sensor”, Anal. Chem., 74, 4570-4576 (2002) [link] [supp info].
  • 3. L. Ying, X. Huang, B. Huang, J. Xie, J. Zhao, X. Zhao, “Fluorescence emission and absorption spectra of single Anabaena sp strain PCC7120 cells”, Photochem. Photobio., 76, 310-313 (2002).
  • 2. L. Ying, X. Huang, B. Huang, J. Zhao, X. Zhao, “Spectra of single cyanobacterial cells”, Acta Physico-Chimica Sinica, 18, 673-675 (2002).
  • 1. B. Huang , Y. Yang, “Treatment of experimental data of surface adsorption in solution by computer linear fitting method”, University Chemistry, 17, 51 (2002).

Huang Lab | UCSF Mission Bay Campus | Byers Hall 304 | 1700 4th St, MC 2532, San Francisco, CA 94143 | Fax: (415) 514-1028

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