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Anthony A. Fung, PhD

Postdoctoral Fellow, NIH NHLBI T32 · Rong Fan Lab, Yale University

I build label-free optical and spatial multi-omic tools that recover the most molecular information from the least tissue, and use them to study how immune aging and senescence reshape our organs. My work spans stimulated Raman imaging, spatial glycomics and computational analysis, from a PhD in Bioengineering at UC San Diego to a postdoc at Yale.

Portrait of Anthony Fung, smiling, arms crossed, wearing glasses and a black quilted vest over a grey sweater.

Research

Spatial context tells us why disease happened, what it touches and where it may return. But precious tissue can run out before the questions do. My work recovers more information from the same piece of anatomy.

Current work

Label-free multimodal imaging

In Lingyan Shi's lab at UC San Diego and with the NIH HuBMAP consortium, I combined stimulated Raman scattering, multiphoton autofluorescence and second-harmonic generation to read tissue chemistry without stains or probes. In human diabetic kidney, five label-free measures of lipid chemistry, redox state and collagen formed one axis of dyslipidemia, oxidative stress and fibrosis. I also wrote the software behind it: hyperspectral lipid unmixing, VISTAmap vignetting correction and A-PoD super-resolution.

Spatial glycomics

In Rong Fan's lab at Yale, I am co-first author on Spatial glyco-codes define human liver pathology and progression (in revision at Cell), which introduces a spatial platform that images glycans alongside proteins and transcripts. Across more than 300 human liver specimens, "glyco-codes" separated cell types, pathologies and immune niches, and stayed informative in archived samples where RNA had degraded. Tumor-like glyco-codes in premalignant regions point to glycans as early biomarkers. The work is patent-pending and funded by a $150,000 Roberts Innovation Fund award, the NIH and agreements with Boehringer Ingelheim.

Immune aging and senescence

With the NIH SenNet consortium I lead the Immune Organ Working Group, mapping senescent immune cells across organs. Tissue context, more than cell lineage, sets a cell's senescence "senotype". I am building ways to score how likely a senescent cell is to be cleared, from a single spatial snapshot.

Future directions

I hope to lead a lab that both builds and applies spatial multi-omic technology, with multimodal integration on the engineering side and immunosenescence on the biomedical side.

  1. Glycan-aware virtual cells

    Combine glycan, protein, transcript and label-free Raman maps, perturb sugar-building genes in tumors, and train models that predict how genetic changes reshape glycans and the immune neighborhood.

  2. Multimodal spatial immunosenescence

    Add glycan motifs and histone marks to spatial profiling across organs and ages, build interpretable AI that estimates clearance hazard, and test whether restoring immune clearance remodels aging tissue.

  3. Raman-enabled, probe-free tissue mapping

    Develop Raman-tagged lectins with narrow vibrational peaks for faster multiplexing, then train models to infer glyco-codes from a tissue's own spectra, with no probes at all.

Projects

Consortia I work with, a company I founded and tools I build on the side.

Publications

24 papers, including first-author work in Nature Communications and Nature Reviews Nephrology. Co-first marks shared first authorship.

Preprints, in revision and accepted

  1. Tian, X., Fung, A. A., Shang, X., et al.

    Spatial glyco-codes define human liver pathology and progression.

    Preprint, 2026 · In revision, Cell Co-first

    doi:10.64898/2026.07.08.737217

  2. Gao, F., Fung, A. A., Zhang, D., et al.

    Decoding and targeting coordinated CDKN1A and CDKN2A senescence programs in ECM-dominant cardiovascular pathologies.

    Preprint, 2026 · In revision, Cell Co-first

    doi:10.64898/2026.06.18.732453

  3. Gwin, M. S., DiPalo, J., Fung, A. A., et al.

    Crystalline silica exposure causes latent biomechanical abnormalities along the cardiopulmonary axis.

    Preprint, 2026 · In revision, Advanced Science Co-first

    doi:10.64898/2026.10.20.760460

  4. Forjaz, A., Queiroga, V., Li, Y., … Fung, A. A., … Kiemen, A. L., Wirtz, D.

    3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors.

    Preprint, 2025 · In revision, Nature

    doi:10.1101/2025.09.21.677628

  5. Younes, S. T., Kint, S., Bao, S., … Fung, A. A., et al.

    Spatial epigenomic niches underlie glioblastoma cell state plasticity.

    Preprint, 2025 · Accepted, Nature Genetics

    doi:10.1101/2025.05.09.653178

Journal articles

  1. Farzad, N., Enninful, A., Lu, Y., Parisi, F., Fung, A. A., et al.

    A spatial multi-omics atlas of immunosenescence reveals germinal-center B cell alteration in human lymph nodes.

    Cell Press Blue 1(4), 2026 · Co-first

    doi:10.1016/j.cpblue.2026.100053

  2. Li, Y., Zhang, Z., Enninful, A., … Fung, A. A., et al.

    All-optical multimodal mapping of single cell type-specific metabolic activities via REDCAT.

    Nature Methods 23(9), 1840–1853, 2026

    doi:10.1038/s41592-026-03180-0

  3. Chen, X., Fung, A. H., Luka, G., Fung, A. A.

    Interdisciplinary nanomaterials for biomedical imaging and sensing applications.

    Nanomaterials 16(1), 21, 2026

    doi:10.3390/nano16010021

  4. Fung, A. A., Shi, L.

    A label-free optical analysis for molecular nephrology.

    Nature Reviews Nephrology (Tools of the Trade), 2025

    doi:10.1038/s41581-025-01023-3

  5. Fung, A. A., Li, Z., Boote, C., Markov, P., Jain, S., Shi, L.

    Label-free multimodal optical biopsy reveals biomolecular and morphological features of diabetic kidney tissue in 2D and 3D.

    Nature Communications 16, 4509, 2025

    doi:10.1038/s41467-025-59163-w

  6. Fung, A. A., Fung, A. H., Li, Z., Shi, L.

    Single-frame vignetting correction for post-stitched-tile imaging using VISTAmap.

    Nanomaterials 15(7), 563, 2025

    doi:10.3390/nano15070563

  7. Li, H., Bao, S., Farzad, N., Qin, X., Fung, A., Zhang, D., Bai, Z., Tao, B., Fan, R.

    Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq.

    Nature Protocols, 1–35, 2025

    doi:10.1038/s41596-025-01145-9

  8. Zhang, W., Li, Y., Fung, A. A., Li, Z., Jang, H., Zha, H., Chen, X., et al.

    Multi-molecular hyperspectral PRM-SRS microscopy.

    Nature Communications 15, 1599, 2024 · Co-first

    doi:10.1038/s41467-024-45576-6

  9. Jang, H., Li, Y., Fung, A. A., Bagheri, P., Hoang, K., Skowronska-Krawczyk, D., Chen, X., Wu, J. Y., Bintu, B., Shi, L.

    Super-resolution SRS microscopy with A-PoD.

    Nature Methods 20(3), 448–458, 2023

    doi:10.1038/s41592-023-01779-1

  10. Jain, S., Pei, L., Spraggins, J. M., Angelo, M., Carson, J. P., Gehlenborg, N., Ginty, F., et al.

    Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP).

    Nature Cell Biology 25(8), 1089–1100, 2023

    doi:10.1038/s41556-023-01194-w

  11. Zhang, Z., Tang, R., Chen, X., Waller, L., Kau, A., Fung, A. A., Gutierrez, B., et al.

    A high-throughput technique to map cell images to cell positions using a 3D imaging flow cytometer.

    Proceedings of the National Academy of Sciences 119(8), e2118068119, 2022

    doi:10.1073/pnas.2118068119

  12. Li, Y., Zhang, W., Fung, A. A., Shi, L.

    DO-SRS imaging of diet regulated metabolic activities in Drosophila during aging processes.

    Aging Cell 21(4), e13586, 2022

    doi:10.1111/acel.13586

  13. Li, Y., Bagheri, P., Chang, P., Zeng, A., Hao, J., Fung, A., Wu, J. Y., Shi, L.

    Direct imaging of lipid metabolic changes in Drosophila ovary during aging using DO-SRS microscopy.

    Frontiers in Aging 2, 819903, 2022

    doi:10.3389/fragi.2021.819903

  14. Fung, A. A., Hoang, K., Zha, H., Chen, D., Zhang, W., Shi, L.

    Imaging sub-cellular methionine and insulin interplay in triple negative breast cancer lipid droplet metabolism.

    Frontiers in Oncology 12, 858017, 2022

    doi:10.3389/fonc.2022.858017

  15. Shi, L., Fung, A. A., Zhou, A.

    Advances in stimulated Raman scattering imaging for tissues and animals.

    Quantitative Imaging in Medicine and Surgery 11(3), 1078, 2021 · Co-first

    doi:10.21037/qims-20-712

  16. Li, Y., Zhang, W., Fung, A. A., Shi, L.

    DO-SRS imaging of metabolic dynamics in aging Drosophila.

    Analyst 146(24), 7510–7519, 2021

    doi:10.1039/d1an01638e

  17. Fung, A. A., Zhou, A., Vanos, J. K., Schmid-Schönbein, G. W.

    Enhanced intestinal permeability and intestinal co-morbidities in heat strain: a review and case for autodigestion.

    Temperature 8(3), 223–244, 2021

    doi:10.1080/23328940.2021.1922261

  18. Bagheri, P., Hoang, K., Fung, A. A., Hussain, S., Shi, L.

    Visualizing cancer cell metabolic dynamics regulated with aromatic amino acids using DO-SRS and 2PEF microscopy.

    Frontiers in Molecular Biosciences 8, 779702, 2021

    doi:10.3389/fmolb.2021.779702

  19. Fung, A. A., Shi, L.

    Mammalian cell and tissue imaging using Raman and coherent Raman microscopy.

    WIREs Systems Biology and Medicine 12(6), e1501, 2020

    doi:10.1002/wsbm.1501

Book chapters

  1. Fung, A. A., Parisi, F., Fan, R.

    Characterizing senescent cell niches by quantitative cartography.

    In Senescent Cells: Methods and Protocols. Springer, 2027 · In preparation

  2. Fung, A. A., Hoang, K., Zha, H., Chen, D., Zhang, W., Shi, L.

    Imaging sub-cellular methionine and insulin interplay in triple negative breast cancer lipid droplet metabolism.

    In Jia, D., Li, X., Su, Y. (Eds.), Systems Biology and Single-cell Analysis of Cancer Metabolism and its Role in Cancer Emergent Properties. Frontiers Media, 2022

    doi:10.3389/fonc.2022.858017

  3. Wei, W., Wang, X., Li, Y., Cheng, Y., Fung, A. A., Yang, X., Shi, L.

    Advances in optical imaging of drug delivery across the blood-brain barrier.

    In Progress in Optics 66, 171–253. Elsevier, 2021

    doi:10.1016/bs.po.2021.01.002

Patent: US Patent Application 64/088,572, methods and compositions for spatial multimodal omics profiling of glycans, proteins and transcriptomes in tissue. Full citation metrics on Google Scholar.

Teaching & mentoring

Bioengineering has always felt like a passport to me: allowing travel among mechanics, biology, chemistry, imaging and computation. I want students to experience that same freedom.

I've taught and learned in classes of six to six hundred students. I want students to understand what assumptions justify a mechanistic model and what an image actually measures, to use AI thoughtfully rather than depend on it, and to leave with the confidence to travel farther than I have.

Courses

  • Single-Cell Biology, Technologies, and Analysis (ENAS 569), Yale, 2025. Guest lecture on metabolomic spectroscopy and spectrometry.
  • Biomechanics Series 1 (BENG 110), UC San Diego, 2020. Teaching assistant; designed and led discussion sections.
  • Chemical and Molecular Bioengineering Techniques (BENG 160), UC San Diego, 2019. Teaching assistant; designed lab experiments.
  • Introduction to Bioengineering (BENG 1), UC San Diego, 2018–2020. Teaching assistant; designed labs and kept the equipment running.

Mentoring

  • 9undergraduate researchers
  • 6graduate students advised on projects
  • 3high school interns

Undergraduate mentees have gone on to PhD programs at Duke, Georgia Tech–Emory and UC San Diego, and two ENLACE exchange students have since earned their MDs. My three high school interns presented posters at BMES and CMBE. Graduate students I've advised have co-authored work on thymic aging, lymph node senescence, lymphoma analysis and label-free kidney imaging.

Awards & news

Recent news

  • 2026Awarded the Roberts Innovation Fund ($150,000, Yale Ventures) to build on spatial glyco-codes.
  • 2026REDCAT all-optical metabolic mapping published in Nature Methods.
  • 2026Lymph node immunosenescence atlas published in Cell Press Blue.
  • 2026Session chair, WACBE 2026 (AI, Data Sciences and Systems Biomedicine), and invited talk on spatial glycomics, Changzhou.
  • 2026Plenary talk on pan-organ immune cell senescence at Winter QBio, Maui; travel award at CMBE.
  • 2025Diabetic kidney optical biopsy published in Nature Communications; Tools of the Trade in Nature Reviews Nephrology.
  • 2025Guest editor, Nanomaterials special issue on nanoscale detection for biomedical imaging.

Awards

  • 2026Roberts Innovation Fund Award
  • 2025ICANX Young Scientist Award, finalist
  • 2025Thermo Fisher QP Grant Award (one of two annually)
  • 2023Triton Innovation Challenge, 3rd prize
  • 2022California Organoid Research Award
  • 2022Baxter Young Investigator Award, 2nd prize
  • 2022American Society for Laser Medicine and Surgery Scholarship
  • 2018Big Ideas Pitch Competition
  • 2018Hult Prize, honorable mention

Contact

For collaborations, talks or questions about label-free and spatial imaging.