Publications

25) Many circulating indole and phenol metabolites are host derived. Nature Metabolism, 2026.

AbuSalim J. E., Olszewski, K., Youssef, S., Mitchell, S., Hunter C. J., Little, J., Sidebottom, A., Boyer, J. A., Knutson, S. D., Samarah, L. Z., MacArthur, M. R., Henneberg, A., Ryseck, R., Opitz, C., MacMillan, D. W. C., Donia, M. S., Imam, S., Lehmann, C. J., Rabinowitz, J. D.

24) Micromap (µMap) photoproximity labeling for integrated phenotypic screening and accelerated prioritization of targeted protein degrader compounds. ChemRxiv, 2025.

Knutson, S. D.*, Morgan, D. C.*, Sloan, J. L., Olsen, J. B., Levine, S., Mintier, G., Sheth, P. R., Kwok, M., MacMillan, D. W. C.

23) Micromapping (μMap) of HER2 across human breast cancers: photocatalytic proximity labeling identifies primary resistance mechanisms and functional interactors. bioRxiv, 2025.

Knutson, S. D.*, Boyer, J. A.*, Morgan, D. C., Großkopf, J., Rabinowitz, J. D., MacMillan, D. W. C.

22) A high-resolution protein proximity labeling platform for formalin-fixed paraffin-embedded tissue samples. Journal of the American Chemical Society, 2025. 147(27), 23387–23394.

Bissonette, N., Zamanis, M. E., Knutson, S. D., Boyer, Z., Harris, A., Martin, D., Geri, J. B., Couto, S., Ahmadi, T., Muthuswamy, A., Fereshteh, M., MacMillan, D. W. C.

21) Temporal Microenviroment mapping (µMap) of intracellular trafficking pathways of cell-penetrating peptides across the blood-brain barrier. bioRxiv, 2025.

Morgan, D. C., Knutson, S. D., Pan, R., MacMillan, D. W. C.

20) EndoVIA for quantifying A-to-I editing and mapping the subcellular localization of edited transcripts. Methods in Enzymology, 2024. 710, 99-130.

Quillin, A. L., Arnould, B., Knutson, S. D., Flores, T. F., Heemstra. J. M. 

19) Parallel proteomic and transcriptomic microenvironment mapping (µMap) of nuclear condensates in living cells. Journal of the American Chemical Society, 2024. 147(27), 23387–23394.

Knutson, S. D., Pan, R., Bisballe, N., Bloomer, B. J., Raftopolous, P., Saridakis, I., MacMillan, D. W. C.

18) Glyoxal caging of nucleoside antivirals toward self-activating, extended-release prodrugs. Journal of the American Chemical Society, 2024. 146(43), 29402-29406.

Karloff, D. B., Stubbs, R. T., Ibukun, O., Knutson, S. D., James, S., Heemstra, J. M.

17) µMap proximity labeling in living cells reveals stress granule disassembly mechanisms. Nature Chemical Biology, 2024, 21, 490–500.

Pan, R., Knutson, S. D., Huth, S., MacMillan, D. W. C.

16) Spatial visualization of A-to-I editing in cells using Endonuclease V immunostaining assay (EndoVIA). ACS Central Science, 2024. 10(7), 1396-1405.

Quillin, A. L., Arnould, B., Knutson, S. D., Heemstra, J.M. 

15) Current advances in photocatalytic proximity labeling. Cell Chemical Biology, 2024. 31(6), 1145-1161.

Knutson, S. D., Buksh, B. F., Huth, S., Morgan, D. C., MacMillan, D. W. C. 

14) Forced intercalation peptide nucleic acid probes for the detection of an Adenosine-to-Inosine modification. ACS Omega, 2023. 8(1), 238-248.

Swenson, C. S., Argueta-Gonzalez, H., Sterling, S., Robichaux, R., Knutson, S. D., Heemstra, J. M.

13) Photoproximity Labeling of Sialylated Glycoproteins (GlycoMap) Reveals Sialylation-Dependent Regulation of Ion Transport. Journal of the American Chemical Society, 2022. 144(51), 23633-23641.

Meyer, C. F., Seath, C. P., Knutson, S. D., Lu, W., Rabinowitz, J. D., MacMillan, D. W. C. 

12) Photochemical identification of auxilliary SARS-CoV-2 host-entry factors using µMap. Journal of the American Chemical Society, 2022. 144(36), 16604-16611.

Suzuki, S. *, Geri, J. B. *, Knutson, S. D. *, Tomokazu, T., Bell-Temin, H., Fernandez, D., Lovett, G., Dong, Z., Till, N. A., MacMillan, D. W. C., Ploss, A.

11) µMap-Red: Proximity labeling by red light photocatalysis. Journal of the American Chemical Society, 2022. 144(14), 6154-6162.

Buksh, B. F., Knutson, S. D., Oakley, J. V., Bissonette, N., Oblinsky, D. G., Schwoerer, M., Seath, C. P., Geri, J. B., Scholes, G., Ploss, A., MacMillan, D. W. C. 

10) Direct immunodetection of global A-to-I RNA editing signatures with a chemiluminescent bioassay. Angewandte Chemie, 2021. 60(31), 17009-17017.

Knutson, S. D., Arthur, R.A., Johnston, H. R., Heemstra, J. M.  

9) Protein-based molecular recognition tools for detecting and profiling RNA modifications. Current Opinion in Structural Biology, 2021. 69, 1-10.

Knutson, S. D., Heemstra, J. M.  

8) Thermoreversible Control of Nucleic Acid Function with Glyoxal Caging. Journal of the American Chemical Society, 2020. 142(41), 17766–17781.

Knutson, S. D.*, Sanford, A. A.*, Swenson, C. S., Korn, M.†, Manuel, B., Heemstra, J. M.

7) EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA. Current Protocols in Chemical Biology, 2020. 12(2), e82.

Knutson, S. D.*, Heemstra, J. M.

6) Chemical profiling of A-to-I RNA editing using a click-compatible acrylamide derivative. Chemistry: A European Journal, 2020. 26(44), 9874-9878.

Knutson, S. D., Korn, M.†, Johnson, R.†, Monteleone, L. R., Dailey, D.†, Swenson, C., Beal, P. A., Heemstra, J. M.

5) Covalent live-cell labeling of proteins using a photoreactive fluorogen. Methods in Enzymology, 2020. 639(16), 355-377.

Ayele, T. M.*, Knutson, S. D.*, Heemstra, J.M.

4) Selective enrichment of A-to-I edited transcripts from cellular RNA using Endonuclease V. Journal of the American Chemical Society, 2020. 142(11), 5241-5251.9(16), 355-377.

Knutson, S. D., Arthur, R.A., Johnston, H. R., Heemstra, J. M.

3) Fluorogenic photoaffinity labeling of proteins in living cells. Bioconjugate Chemistry, 2019, 30(5), 1309-1313.

Ayele, T. M., Knutson, S. D., Ellipilli, S., Hwang, H., Heemstra, J.M.

2) Chemical labeling and affinity capture of inosine-containing RNAs using acrylamidofluorescein. Bioconjugate Chemistry, 2018, 29(9), 2899-2903.

Knutson, S. D., Ayele, T. M., Heemstra, J. M. 

1) Development and evaluation of a fluorescent Antibody-Drug Conjugate for molecular imaging and targeted therapy of pancreatic cancer. PLoS One, 2016, 11.6, e0157762.

Knutson, S. D., Raja, E., Bomgarden, R., Chen, A., Kalyanasundaram, R., Desai, S.