Publications — He Lab

From the He Lab

Redox-activated chemistry for probing and perturbing the proteome: lessons from protein redox switches

Zeng Q., Yang J., He D.^†

Current Opinion in Chemical Biology · 94, 102732 (2026) · ^†corresponding author

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The words of proteins: motif-level language modeling for interpretable protein generation

Low B. H., Goh W. Y., Li B., He D.^†

Proceedings of the 32nd ACM SIGKDD Conference on Knowledge Discovery & Data Mining · Vol. 2, 11564 (2026) · ^†corresponding author

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Grounding structure in language: enriching symbolic representations for molecular reasoning

Liu Z., He D.^†, Chen N. F., Wang W.

Findings of the Association for Computational Linguistics: EMNLP 2026 · 17362–17382 (2026) · ^†corresponding author

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Selected Publications Prior to NTU

RAD23B acquires a copper metalloadapter function during evolution to augment metabolism and regulate genome integrity

Xiao T.^#, He D.^#, Liu D., Jia S., Chen Q., Silverman D., Maitra N., Huang A. Y., Nguyen T. T., Rao G., Tillage R., Deng K., Weinshenker D., Britt R. D., Kelly M. J. S., Dan Y., Chang C. J.

Molecular Cell · 85, 3443–3459 (2025) · ^#co-first authors

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Oxidative cyclization reagents reveal tryptophan cation–π interactions

Xie X.^*, Moon P. J.^*, Crossley S. W. M., Bischoff A. J., He D., Li G., Dao N., Gonzalez-Valero A., Reeves A. G., McKenna J. M., Elledge S. K., Wells J. A., Toste F. D., Chang C. J.

Nature · 627, 680–687 (2024)

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Methionine oxidation activates pyruvate kinase M2 to promote pancreatic cancer metastasis

He D., Feng H., Sundberg B., Yang J., Powers J., Christian A. H., Wilkinson J. E., Monnin C., Avizonis D., Thomas C. J., Friedman R. A., Kluger M. D., Hollingsworth M. A., Grandgenett P. M., Klute K. A., Toste F. D., Chang C. J., Chio I. I. C.

Molecular Cell · 82, 3045–3060 (2022)

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An activity-based oxaziridine platform for identifying and developing covalent ligands for functional allosteric methionine sites: redox-dependent inhibition of cyclin-dependent kinase 4

Gonzalez-Valero A., Reeves A. G., Page A. C. S., Moon P. J., Miller E., Coulonval K., Crossley S. W. M., Xie X., He D., Musacchio P. Z., Christian A. H., McKenna J. M., Lewis R. A., Fang E., Dovala D., Lu Y., McGregor L. M., Schirle M., Tallarico J. A., Roger P. P., Toste F. D., Chang C. J.

Journal of the American Chemical Society · 144, 22890–22901 (2022)

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Distinct RNA N-demethylation pathways catalyzed by nonheme iron ALKBH5 and FTO enzymes enable regulation of formaldehyde release rates

Toh J. D. W., Crossley S. W. M., Bruemmer K. J., Ge E. J., He D., Iovan D. A., Chang C. J.

Proceedings of the National Academy of Sciences USA · 117, 25284–25292 (2020)

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Protease-mediated protein quality control for bacterial acid resistance

He D., Zhang M., Liu S., Xie X., Chen P. R.

Cell Chemical Biology · 26, 144–150 (2019)

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Bioinspired thiophosphorodichloridate reagents for chemoselective histidine bioconjugation

Jia S., He D., Chang C. J.

Journal of the American Chemical Society · 141, 7294–7301 (2019)

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Quantitative and comparative profiling of protease substrates through a genetically encoded multifunctional photocrosslinker

He D., Xie X., Yang F., Zhang H., Su H., Ge Y., Song H., Chen P. R.

Angewandte Chemie International Edition · 56, 14521–14525 (2017)

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Genetically encoded releasable photo-cross-linking strategies for studying protein–protein interactions in living cells

Yang Y., Song H., He D., Zhang S., Dai S., Xie X., Lin S., Hao Z., Zheng H., Chen P. R.

Nature Protocols · 12, 2147–2168 (2017)

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Conditional chaperone–client interactions revealed by genetically encoded photo-cross-linkers

Zhang S., He D., Lin Z., Yang Y., Song H., Chen P. R.

Accounts of Chemical Research · 50, 1184–1192 (2017)

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Comparative proteomics reveal distinct chaperone-client interactions in supporting bacterial acid resistance

Zhang S.^*, He D.^*, Yang Y., Lin S., Zhang M., Dai S., Chen P. R.

Proceedings of the National Academy of Sciences USA · 113, 10872–10877 (2016) · ^*co-first authors

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Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label

Yang Y., Song H., He D., Zhang S., Dai S., Lin S., Meng R., Wang C., Chen P. R.

Nature Communications · 7, 12299 (2016)

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Genetically encoded cleavable protein photo-cross-linker

Lin S., He D., Long T., Zhang S., Meng R., Chen P. R.

Journal of the American Chemical Society · 136, 11860–11863 (2014)

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