Publications | Huang Lab

Selected · At UCSF

RainBar: Optical Barcoding for Pooled Live-Cell Imaging with Single-Cell Resolution

R. Mosadeghi^#, D. Foyt, L. Sharp, C. Taylor, N.Q. Tay, S. Oberlin, J. Fan, S. Bourke, M. Kattah, B. Huang^#, M.T McManus^#. bioRxiv/2025.11.04.686676 (2025).

De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy

Y. Chen*, K. Yserentant*, K. Hong*, Y. Kuang, A. Bhowmick, A. Charles-Orszag, S.J. Lord, L. Lu, K. Hou, S.I. Mann, J.B. Grimm, L.D. Lavis, R.D. Mullins, W.F. DeGrado^#, B. Huang^#. bioRxiv/2025.06.25.661379 (2025).

Accessible and accurate cytometry analysis of adherent cells using fluorescence microscopes

D. Foyt^#, Y. Kuang, S. Rehem, K. Yserentant, B. Huang^#. Scientific Reports 15, 18691 (2025). Preprint.

CELL-Diff: Unified diffusion modeling for protein sequences and microscopy images

D. Zheng, B. Huang. In: 42th International Conference on Machine Learning (ICML). (2025). Preprint.

CZI Virtual Cell Model Collection

YAP charge patterning mediates signal integration through transcriptional co-condensates

K. Meyer,* K. Yserentant,* R. Cheloor-Kovilakam,* K.M. Ruff, C.I. Chung, X. Shu, B. Huang,^# O.D. Weiner^#. Nat. Commun. 16, 7454 (2025). Preprint.

Mantis: high-throughput 4D imaging and analysis of the molecular and physical architecture of cells.

I.E. Ivanov,*^,# E. Hirata-Miyasaki,* T. Chandler,* R. Cheloor-Kovilakam,* Z. Liu, S. Pradeep, C. Liu, M. Bhave, S. Khadka, C. Arias, M.D. Leonetti, B. Huang,^# S.B. Mehta^#. PNAS Nexus, pgae323 (2024). Preprint.

CELL-E 2: Translating proteins to pictures and back with a bidirectional text-to-image transformer.

E. Khwaja, Y.S. Song, A. Agarunov, B. Huang. In: 37th Neuro Information Procession Systems (NeurIPS). (2023). Preprint.

CELL-E 2 Image Prediction on Hugging Face

HybriSeq: Probe-based device-free single-cell RNA profiling.

D. Foyt, D. Brown, S. Zhou, B. Moser, Q. Zhu, Z.J. Gardner, B. Huang. Commun. Biol. 1250 (2025). Preprint.

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). Preprint.

CELL-E: a text-to-image transformer for protein image prediction.

E. Khwaja, Y.S. Song, B. Huang. In: Research in Computational Molecular Biology (RECOMB) (2024) 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). Preprint.

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). Preprint. 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). Preprint. 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). Preprint. 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). Preprint.

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).

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. Preprint.

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). Preprint.

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). Preprint.

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). Preprint.

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). Preprint.

Multicolor fluorescent imaging by space-constrained computational spectral imaging.

Y. Wang, B. Yang, S. Feng, V. Pessino, B. Huang. Opt. Express 27, 5393 (2019). Preprint.

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). Preprint.

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).

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).

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). Preprint.

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). Preprint. 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). Preprint.

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). Preprint.

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

R. McGorty, D. Xie, B. Huang. Opt. Express, 25, 17798-17810 (2017). Preprint.

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). Preprint. 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).

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). Preprint.

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).

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).

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). Preprint. 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).

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).

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).

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). 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).

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).

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).

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).

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).

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). 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).

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). 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).

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). 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).

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

J. Schnitzbauer, R. McGorty, B. Huang. Opt. Express 21, 19701-19708 (2013). 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). Supporting info.

Active microscope stabilization in three dimensions using image correlation.

R. McGorty, D. Kamiyama, B. Huang. Optical Nanoscopy, 2, 3 (2013).

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). 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). Supporting 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). Supporting 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).

All

D. Foyt, D. Brown, S. Zhou, B. Moser, Q. Zhu, Z.J. Gardner, B. Huang. "HybriSeq: probe-based device-free single-cell RNA profiling". Commun. Biol. 1250 (2025).
Y. Chen*, K. Yserentant*, K. Hong*, Y. Kuang, A. Bhowmick, A. Charles-Orszag, S.J. Lord, L. Lu, K. Hou, S.I. Mann, J.B. Grimm, L.D. Lavis, R.D. Mullins, W.F. DeGrado^#, B. Huang^#, "De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy". bioRxiv/2025.06.25.661379 (2025).
K. Meyer, B. Huang, O.D. Weiner, "Emerging roles of transcriptional condensates as temporal signal integrators". Nat Rev Genetics (2025).
Z. Zhou, K. Hong, B. Huang, G.J. Narlikar, "Understanding how genetically encoded tags and crowding agents affect phase separation by heterochromatin protein HP1a". Cell Reports Methods 5, 101029 (2025).
D. Foyt,^# Y. Kuang, S. Rehem, K. Yserentant, B. Huang^#, "Accessible and accurate cytometry analysis of adherent cells using fluorescence microscopes". Scientific Reports 15, 18691 (2025).
D. Zheng, B. Huang, "Bridging protein sequences and microscopy images with unified diffusion models". In: 42nd International Conference on Machine Learning. ICML (2025).
K. Meyer,* K. Yserentant,* R. Cheloor-Kovilakam,* K.M. Ruff, C.I. Chung, X. Shu, B. Huang,^# O.D. Weiner^#. "YAP charge patterning mediates signal integration through transcriptional co-condensates". Nat. Commun. 16, 7454 (2025).
D. Gonzalez-Martinez, L. Roth, T. Mumford, J. Guan, Bo Huang, A. Tulpule, T. Bivona, A. Le, R. Doebele, M. Niewiadomska-Bugaj, L. Bugaj, "Oncogenic EML4-ALK assemblies suppress growth factor perception and modulate drug tolerance". Nat. Commun. 15, 9473 (2024).
I.E. Ivanov,*^,# E. Hirata-Miyasaki,* T. Chandler,* R. Cheloor-Kovilakam,* Z. Liu, S. Pradeep, C. Liu, M. Bhave, S. Khadka, C. Arias, M.D. Leonetti, B. Huang,^# S.B. Mehta^#, "Mantis: high-throughput 4D imaging and analysis of the molecular and physical architecture of cells," PNAS Nexus, pgae323 (2024).
F. Haderk, Y.-T. Chou, L. Cech, C. Fernandez-Mendez, J. Yu, V. Olivas, I.M. Meraz, D.B. Rabago, D.L. Kerr, C. Gomez, D.V. Allegakoen, J. Guan, K.N. Shah, K.A. Herrington, O.M. Gbenedio, S. Nanjo, M. Majidi, W. Tamaki, Y.K. Pourmoghadam, J.K. Rotow, C.E. McCoach, J.W. Riess, J.S. Gutkind, T.T. Tang, L. Post, B. Huang, P. Santisteban, H. Goodarzi, S. Bandyopadhyay, C.J. Kuo, J.P. Roose, W. Wu, C.M. Blakely, J.A. Roth, T.G. Bivona, "Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer". Nat. Commun. 15, 3741 (2024).
E. Khwaja^#, Y.S. Song, B. Huang^#, "CELL-E: a text-to-image transformer for protein image prediction," In: Research In Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, v14758. Springer, Cham. (2024).
E. Khwaja^#, Y.S. Song, A. Agarunov, B. Huang^#, "CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer," In: 37th Neural Information Processing Systems NeurIPS (2023).
J. Dekker, F. Alber, S. Aufmkolk, B.J. Beliveau, B.G. Bruneau, A.S. Belmont, L. Bintu, A. Boettiger, R. Calandrelli, C.M. Disteche, D.M. Gilbert, T. Gregor, A.S Hansen, B. Huang, D. Huangfu, R. Kalhor, C.S. Leslie, W. Li, Y. Li, J. Ma, W.S. Noble, P.J. Park, J.E. Phillips-Cremins, K.S. Pollard, S.M. Rafelski, B. Ren, Y. Ruan, Y. Shav-Tal, Y. Shen, J. Shendure, X. Shu, C. Strambio-De-Castillia, A. Vertii, H. Zhang, S. Zhong, "Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project," Mol. Cell, 83, 2623 (2023).
J. Zhao*, S. Makhija*, C. Zhou, H. Zhang, Y.Q. Wang, M. Muralidharan, B. Huang#, Y. Cheng#, "Structural insights into the human PA28–20S proteasome enabled by efficient tagging and purification of endogenous proteins," Proc. Nat. Acad. Sci. U.S.A., 119, e2207200119 (2022).
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, "OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization," Science, 375, eabi6983 (2022).
M. Zarei, D. Xie, F. Jiang, A. Bagirov, B. Huang, A. Raj, S. Nagarajan, S. Guo, "High activity and high functional connectivity are mutually exclusive in resting state zebrafish and human brains," BMC Biology, 20, 84 (2022).
W. Liu, W. Zhong, J. Chen, B. Huang, M. Hu, Y. Li, "Understanding regulatory mechanisms of brain function and disease through 3D genome organization," Genes, 13, 586 (2022).
Y. Wang, H. Pinkard, E. Khwaja, S. Zhou, L. Waller, B. Huang, Image denoising for fluorescence microscopy by supervised to self-supervised transfer learning, Opt. Express 29, 41303-41312 (2021).
G.J. Kim, H. Mo, H. Liu, Z. Wu, S. Chen, J. Zheng, X. Zhao, D. Nucum, J. Shortland, L. Peng, M. Elepano, B. Tang, S. Olson, N. Paras, H. Li, A.R. Renslo, M.R. Arkin, B. Huang, B. Lu, M. Sirota, S. Guo, A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial restoration in dopamine neurons, eLife 10, e69795 (2021).
D. Kumar, A. Rains, V. Herranz-Pérez, Q. Lu, X. Shi, D.L. Swaney, E. Stevenson, N.J. Krogan, B. Huang, C. Westlake, J.M. Garcia-Verdugo, B.K. Yoder, J.F. Reiter, A ciliopathy complex builds distal appendages to initiate ciliogenesis, J. Cell Biol., 220, e202011133 (2021).
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, Label-retention expansion microscopy, J. Cell Biol., 220, e202105067 (2021).
X. Zhao, J.Q. Garcia, K. Tong, X. Chen, B. Yang, Q. Li, Z. Dai, X. Shi, I.B. Seiple, B. Huang, S. Guo, Polarized endosome dynamics engage cytoplasmic Par-3 that recruits dynein during asymmetric cell division, Sci. Adv., 7, eabg1244 (2021).
B. Tenner, J.Z. Zhang, Y. Kwon, V. Pessino, S. Feng, B. Huang, S. Mehta, J. Zhang, FluoSTEPs: Fluorescent biosensors for monitoring compartmentalized signaling within endogenous microdomains, eLife, 7, eabe4091 (2021).
A. Tulpule, J. Guan, D.S. Neel, H.R. Allegakoen, Y.P. Lin, D. Brown, Y. 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, B. Huang, T.G. Bivona, Kinase-mediated RAS signaling via membraneless cytoplasmic protein, Cell 184, 2649-2664.e18 (2021).
S. Makhija, D. Brown, R.M. Rudlaff, J. Doh, S. Bourke, Y. Wang, S. Zhou, R. Cheloor-Kovilakam, B. Huang, Versatile labeling and detection of endogenous proteins using tag-assisted split enzyme complementation, ACS Chem. Biol. 16, 671-681 (2021).
G.E. Peng, V. Pessino, B. Huang, M. von Zastrow, Spatial decoding of endosomal cAMP signals by a metastable cytoplasmic PKA network, Nat. Chem. Biol. 17, 558-566 (2021).
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, HP1 proteins compact DNA into mechanically and positionally stable phase separated domains, eLife 10, e64563 (2021).
S. Zhou, S. Feng, D. Brown, B. Huang, Improved yellow-green split fluorescent proteins for protein labeling and signal amplification, PLoS ONE 15, e0242592 (2020).
J. Zhang, D. Velmeshev, K. Hashimoto, Y. Huang, J.W. Hofmann, X. Shi, J. Chen, A.M. Leidal, J.G. Dishart, M.K. Cahill, K.W. Kelley, S.A. Liddelow, W.W. Seeley, B.L. Miller, T.C. Walther, R.V. Farase Jr., J.P. Taylor, E.M. Ullian, B. Huang, J. Debnath, T. Wittmann, A.R. Kreigstein, E.J. Huang, Neurotoxic microglia promote TDP-43 proteinopathy in progranulin deficiency, Nature 588, 459-465 (2020).
X. Huang, X. Shi, M. Hansen, I. Setiady, C. Nemeth, A. Celli, B. Huang, T. Mauro, M. Koval, T. Desai, Nanotopography enhances dynamic remodeling of tight junction proteins through cytosolic liquid complexes, ACS Nano 14, 13192–13202 (2020).
S. Chaturvedi, J. Klein, N. Vardi, C. Bolovan-Fritts, M. Wolf, K. Du, L. Mlera, M. Calvert, N.J. Moorman, F. Goodrum, B. Huang, L.S. Weinberger, A molecular mechanism for probabilistic bet-hedging and its role in viral latency, Proc. Nat. Acad. Sci. USA 117, 17240-17248 (2020).
S. Feng, A. Varshney, D. Coto Villa, C. Modavi, J. Kohler, F. Farah, S. Zhou, N. Ali, J.D. Müller, M. VanHoven, B. Huang, Bright split red fluorescent proteins for the visualization of endogenous proteins and synapses, Commun. Biol. 2, 344 (2019).
J.M. Alexander, J. Guan, B. Li, L. Maliskova, M. Song, Y. Shen, B. Huang, S. Lomvardas, O.D. Weiner, Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity, eLife 8, e41769 (2019).
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, Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution, Nat. Methods 16, 501-504 (2019).
S. Das, The Extracellular RNA Communication Consortium, K.M. Ansel, M. Bitzer, X.O. Breakefield, A. Charest, D.J. Galas, M.B. Gerstein, M. Gupta, A. Milosavljevic, M.T. McManus, T. Patel, R.L. Raffai, J. Rozowsky, M.E. Roth, J.A. Saugstad, K. Van Keuren-Jensen, A.M. Weaver, L.C. Laurent, The Extracellular RNA Communication Consortium: Establishing foundational knowledge and technologies for extracellular RNA research, Cell, 177, 231-242 (2019).
X. Shi, G. Garcia III, Y. Wang, J.F. Reiter, B. Huang, Deformed alignment of super-resolution images for semi-flexible structures in 3D, PLoS One 0212735 (2019).
Y. Wang, B. Yang, S. Feng, V. Pessino, B. Huang, Multicolor fluorescent imaging by space-constrained computational spectral imaging, Opt. Express 27, 5393 (2019).
B. Chen, W. Zou, H. Xu, Y. Liang, B. Huang, Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-Tag, Nat. Commun. 9, 5065 (2018).
T.T. Chow, X. Shi, J.H. Wei, J. Guan, G. Stadler, B. Huang, E. Blackburn, Local enrichment of HP1alpha at telomeres alters their structure and regulation of telomere protection, Nat. Commun. 9, 3583 (2018).
M. Percharde, C. Lin, Y. Yin, J. Guan, G.A. Peixoto, A. Bulut-Karslioglu, S. Biechele, B. Huang, X. Shen, M. Ramalho-Santos, A LINE1-Nucleolin partnership regulates embryonic stem cell identity, Cell 174, 391-405 (2018).
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, Co-translational protein targeting facilitates centrosomal recruitment of PCNT during centrosome maturation, eLife 7, e34959 (2018).
M.T. Kelliher, Y. Yue, A. Ng, D. Kamiyama, B. Huang, K.J. Verhey, J. Wildonger, Autoinhibition of kinesin-1 is essential to the dendrite-specific localization of Golgi outposts, J. Cell Biol. 217, 2531-2547 (2018).
J. Schnitzbauer, Y. Wang, M. Bakalar, B. Chen, T. Nuwal, S. Zhao, B. Huang, Correlation analysis framework for localization-based superresolution microscopy, Proc. Nat. Acad. Sci. USA 115, 3219-3224 (2018).
P. Viswanath, M. Radoul, J.L. Izquierdo-Garcia, W.Q. Ong, H.A. Luchman, J.G. Cairncross, B. Huang, R.O. Pieper, J.J. Phillips, S.M. Ronen, 2-hydroxyglutarate-mediated autophagy of the endoplasmic reticulum leads to an unusual downregulation of phospholipid biosynthesis in mutant IDH1 gliomas, Cancer Res. 78, 2290-2304 (2018).
Y.R. Citron, Y.R. Citron, C.J. Fagerstrom, B. Keszthelyi, B. Huang, N.M. Rusan, M.J.S. Kelly, D.A. Agard, The centrosomin CM2 domain is a multi-functional binding domain with distinct cell cycle roles, PLoS One 13, e0190530 (2018).
X. Shi, G. Garcia, J.C. Van De Weghe, R. McGorty, G.J. Pazour, D. Doherty, B. Huang, J.F. Reiter, Super-resolution microscopy reveals that disruption of ciliary transition-zone architecture causes Joubert syndrome, Nat. Cell Biol. 19, 1178-1188 (2017).
R. McGorty, D. Xie, B. Huang, High-NA open-top selective-plane illumination microscopy for biological imaging, Opt. Express, 25, 17798-17810 (2017).
S. Feng, S. Sekine, V. Pessino, H. Li, M.D. Leonetti, B. Huang, Improved split fluorescent proteins for endogenous protein labeling, Nat. Commun., 8, 370 (2017).
Q. Li, M. Reinig, D. Kamiyama, X. Tao, B. Huang, J. Kubby, Woofer-tweeter adaptive optical structured illumination microscopy, Photonics Res., 5, 329-334 (2017).
V. Pessino, Y.R. Citron, S. Feng, B. Huang, Covalent protein labeling by SpyTag-SpyCatcher in fixed cells for super-resolution microscopy, ChemBioChem, 18, 1942-1945 (2017).
R. Irannejad, V. Pessino, D. Mika, B. Huang, P.B. Wedegaertner, M. Conti, M. von Zastrow, Functional selectivity of GPCR-directed drug action through location bias, Nat. Chem. Biol. 13, 799-806 (2017).
B. van Lengerich, E.M. Puchner, C. Angew, B. Huang, N. Jura, EGF and NRG induce phosphorylation of HER3/ERBB3 by EGFR using distinct oligomeric mechanisms, Proc. Nat. Acad. Sci. USA 114, E2836-3845 (2017).
J. Guan, H. Liu, X. Shi, S. Feng, B. Huang, Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH, Biophys. J., 112, 1077-1084 (2017).
W.Q. Ong, Y.R. Citron, S. Sekine, B. Huang, Live cell imaging of endogenous mRNA using RNA-based fluorescence “turn-on” probe, ACS Chem. Biol., 12, 200-205 (2017).
B. Huang, A microscopic view of the cell, Mol. Biol. Cell, 27, 3183-3184 (2016).
L. Zhu, B. Huang, STORM using compressed sensing, in Adrian Stern, editor: Optical Compressive Sensing, CRC Press, pp. 225-238 (2016).
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, A high-content larval zebrafish brain imaging method for small molecule drug discovery, PLoS One, 11, e0164645 (2016).
Y. Bai, H. Liu, B. Huang, M. Wagle, S. Guo, Identification of environmental stressors and validation of light preference as a measure of anxiety in larval zebrafish, BMC Neurosci., 17, 63 (2016).
M.D. Leonetti, S. Sekine, D. Kamiyama, J.S. Weissman, B. Huang, A scalable strategy for high-throughput GFP tagging of endogenous human proteins, Proc. Nat. Acad. Sci. USA, 113, E3501-E3508 (2016).
B. Chen, J. Guan, B. Huang, Imaging specific genomic DNA in living cells, Ann. Rev. Biophys., 45, 1-23 (2016).
R. McGorty, B. Huang, Selective-plane illumination microscopy for high-content volumetric biological imaging , Proc. SPIE, 9720, 97200P, doi:10.1117/12.2212889 (2016).
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, Versatile protein tagging in cells with split fluorescent protein, Nat. Commun., 7, 11046 (2016).
P. Bieling, T.D. Li, J. Weichsel, R. McGorty, P. Jreij, B. Huang, D.A. Fletcher, R.D. Mullins, Force feedback controls motor activity and mechanical properties of self-assembling branched actin networks, Cell, 164, 115-127 (2016).
B. Chen, J. Hu, R. Almeida, H. Liu, S. Balakrishnan, C. Covill-Cooke, W.A. Lim, B. Huang, Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci, Nucleic Acids Res., 44, e75 (2016).
D. Kamiyama, R. McGorty, R. Kamiyama, M.D. Kim, A. Chiba, B. Huang, Specification of dendritogenesis site in Drosophila aCC motoneuron by membrane-enrichment of Pak1 through Dscam1, Dev. Cell, 35, 93-106 (2015).
J.G. Patton, J.L. Franklin, A.M. Weaver, K. Vickers, B. Zhang, R.J. Coffey, K.M. Ansel, R. Blelloch, A. Goga, B. Huang, N. L'Etoille, R. Raffai, C.P. Lai, A.M. Krichevsky, B. Mateescu, V.J. Greiner, C. Hunter, O. Voinnet, M.T. McManus, Biogenesis, delivery and function of extracellular RNA, J. Extracellular Vesicles, 4, 27494 (2015).
W.Q. Ong, Y.R. Citron, J. Schnitzbauer, D. Kamiyama, B. Huang, Heavy water: a simple solution to increasing brightness of fluorescence protein in super-resolution imaging, Chem. Commun., 51, 13451 - 13453 (2015).
R. McGorty, H. Liu, D. Kamiyama.Z. Dong, S. Guo, B. Huang, Open-top selective plane illumination microscope for conventionally mounted specimens, Opt. Express, 23, 16142-16153 (2015).
B. Chen, B. Huang, Imaging genomic elements in living cells using CRISPR/Cas9. In J.A. Doudna, E.J. Sontheimer, editors: The use of CRISPR/cas9, ZFNs, TALENs in generating site specific genome alterations, Vol 546, MIE, UK: Academic Press, pp. 337-354 (2014).
E. Puchner, B. Huang, H. Gaub, Single molecule techniques - applications in biology, FEBS Lett., 588, 3519 (2014).
Y. Wang, J. Schnitzbauer, Z. Hu, X. Li, Y. Cheng, Z.L. Huang, B. Huang, Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm, Opt. Express, 22, 15982-15991 (2014).
S. Sun, C. Zhou, S. Chen, J. Liu, J. Yu, J. Chilek, L. Zhao, M. Y, R. Vinluan, B. Huang, J. Zheng, Surface-chemistry effect on cellular response of luminescent plasmonic silver nanoparticles, Bioconjugate Chem., 25, 453-458 (2014).
R. McGorty, J. Schnitzbauer, W. Zhang, B. Huang, Correction of depth-dependent aberrations in 3D single molecule localization and super-resolution microscopy. Opt. Lett., 39, 275-278 (2014).
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, Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell, 155, 1479-1491 (2013).
V. Mennella, D.A. Agard, B. Huang, L. Pelletier, Amorphous no more: subdiffraction view of the pericentriolar material architecture. Trends Cell Biol. 24, 188-197. (2014).
E.M. Puchner, J.M. Walter, R. Kasper, B. Huang, W.A. Lim, Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory. Proc. Nat. Acad. Soc. USA, 110, 16015-16020 (2013).
J. Schnitzbauer, R. McGorty, B. Huang, 4Pi fluorescence detection and 3D particle localization with a single objective. Opt. Express, 21, 19701-19708 (2013).
F. Huang, X. Wang, E.M. Ostertag, T. Nuwal, B. Huang, Y.N. Jan, A.I. Basbaum and L.Y. Jan, TMEM16C facilitates Na(+)-activated K(+) currents in rat sensory neurons and regulates pain processing. Nat. Neurosci., 16, 1284-1290 (2013).
R. McGorty, D. Kamiyama, B. Huang, Active microscope stabilization in three dimensions using image correlation. Optical Nanoscopy, 2, 3 (2013).
R. Irannejad, J.C. Tomshine, J.R. Tomshine, M. Chevalier, J. Steyaert, S.G.F. Rasmussen, H. El-Samad, B. Huang, M. von Zastrow, Conformational biosensors reveal adrenoceptor signaling from endosomes. Nature, 459, 534-538 (2013).
A.S. Stender, K. Marchuk, C. Liu, S. Sander, M.W. Meyer, E.A. Smith, B. Neupane, G. Wang, J. Li, J.X. Cheng, B. Huang, N. Fang, Single cell optical imaging and spectroscopy, Chem. Rev., 113, 2469-2527 (2013).
D. Kamiyama B. Huang, Development in the STORM. Developmental Cell, 23, 1103 (2012)
V. Mennella, B. Keszthelyi, K.L. McDonald, B. Chhun, F. Kan, G.C. Rogers, B. Huang, D.A. Agard, Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization. Nat. Cell Biol., 14, 1159-1168 (2012).
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, 13978-3983 (2012).
L. Zhu, W. Zhang, D. Elnatan, B. Huang, Faster STORM with compressed sensing. Nat. Methods, 9, 721-723 (2012).
R. Kasper, B. Huang, SnapShot: Light Microscopy. Cell, 147, 1198 (2011).
G.M.J. Beaudoin, III, G.M. Schofield, T. Nuwal, K. Zang, E.M. Ullian, B. Huang, L.F. Reichardt, Afadin, a Ras/Rap effector that controls cadherin function, promotes spine and excitatory synapse density in the hippocampus. J Neurosci., 32, 99-110 (2012).
B. Huang, An in-depth view. Nat Methods, 8, 304-305 (2011).
B. Huang, H. Babcock, X. Zhuang, Breaking the diffraction barrier: super-resolution imaging of cells. Cell, 143, 1047-1058 (2010).
A. Dani, B. Huang, J. Bergan, C. Dulac, X. Zhuang, Superresolution imaging of chemical synapses in the brain. Neuron, 68, 843-856 (2010).
A. Dani, B. Huang, New resolving power for light microscopy: applications to neurobiology. Curr. Opin. Neurobiol., 20, 648-652 (2010).
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).
B. Huang, Super resolution optical microscopy: multiple choices. Curr. Opin. Chem. Biol., 14, 10-14 (2010).
B. Huang, M. Bates, X. Zhuang, Super resolution fluorescence microscopy. Ann. Rev. Biochem., 78, 993-1016 (2009).
M. Bates, B. Huang, X. Zhuang, Super-resolution imaging by nanoscale localization of photo-switching fluorescent probes. Curr. Opin. Chem. Biol., 12, 505-514 (2008).
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).
B. Huang, W. Wang, M. Bates, X. Zhuang, Three-dimension super-resolution imaging by stochastic optical reconstruction microscopy. Science, 319, 810-813 (2008).
M. Bates, B. Huang, G.T. Dempsey, X. Zhuang, Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science, 317, 1749-1753 (2007).
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).
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).
B. Huang, S. Kim, R.N. Zare, Use of a mixture of n-dodecyl-β-D-maltoside and sodium dodecyl sulfate in poly (dimethylsiloxane) microchips to suppress adhesion and promote separation of proteins. Anal. Chem., 79, 9145-9149 (2007).
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).
B. Huang, F. Yu, R.N. Zare, Surface plasmon resonance imaging using a high numerical aperture microscope objective. Anal. Chem., 79, 2979-2983 (2007).
H. Wu, B. Huang, R.N. Zare, Generation of complex, static solution gradients in microfluidic channels. J. Am. Chem. Soc., 128, 4194-4195 (2006).
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).
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).
H. Wu, B. Huang, R.N. Zare, Construction of microfluidic chips using polydimethylsiloxane for adhesive bonding. Lab Chip, 5, 1393-1398 (2005).
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).
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).
B. Huang, T.D. Perroud, R.N. Zare, Photon counting histogram: one-photon excitation. ChemPhysChem, 5, 1523-1531 (2004).
T.D. Perroud, B. Huang, M.I. Wallace, R.N. Zare, Photon counting histogram for one-photon excitation. ChemPhysChem, 4, 1121-1123 (2003).
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).
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).
L. Ying, X. Huang, B. Huang, J. Zhao, X. Zhao, Spectra of single cyanobacterial cells. Acta Physico-Chimica Sinica, 18, 673-675 (2002).
B. Huang, Y. Yang, Treatment of experimental data of surface adsorption in solution by computer linear fitting method. University Chemistry, 17, 51 (2002).