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Publications

Highlighted publications and preprints are those most closely related to my lab’s current projects.

Highlighted Preprints:

  1. Patterson, E.A., Birdwell, A.A., Sabatino, A.M., Williams, C., Walker, A.S.# Utilizing Sequence Similarity Networks for Cross Species Elicitor Identification of Streptomyces Regulatory Proteins. 2026. https://doi.org/10.64898/2026.05.07.723685
  2. Oyedele, A.S., Somnath, J., Jeon, K., Vazrala, N., Stec, D.F., Kim, K., Sulikowski, G., Walker, A.S.# Identification of Siderophores with Unexpected Antibacterial Properties from Actinoplanes teichomyceticus. 2026.   https://doi.org/10.64898/2026.03.19.712980
  3. Kalmer, T.L., Ancajas, C.M.F., Cheng, Z., Oyedele, A.S., Davis, H.L., Walker, A.S.# Assessing the ability of ChatGPT to extract natural product bioactivity and biosynthesis data from publications. https://doi.org/10.1101/2024.08.01.606186

Highlighted Publications, Book Chapters, and News & Views:

  1. Guo, X., Rava, C.M., Walker, A.S.# Learning the chemical language of natural products. Nature Machine Intelligence, 2026. https://doi.org/10.1038/s42256-026-01241-9 
  2. Ancajas, C.M.F*, Shuster, I.E.*, Walker, A.S.# AI-assisted isolation of bioactive Dipyrimicins from Amycolatopsis azurea and identification of its corresponding dip biosynthetic gene cluster. Journal of Natural Products. 2026. 89 (4). 1238-1248. ttps://doi.org/10.1021/acs.jnatprod.6c00057
  3. Oyedele, A.S., Clements, A.E., Cheng, Z., Ancajas, C.M.F., Russ, A., Davis, H.L., Venkat, J., Walker, A.S.# Prediction of natural product bioactivity from BGC sequence to guide genome mining efforts. Computational Approaches to Natural Products Discovery, Methods in Enzymology. https://doi.org/10.1016/bs.mie.2025.09.013
  4. Tydings, C.W., Moretti, R., Meiler, J.,# Walker, A.S.# Lanthipeptide structure prediction and design with Rosetta. Computational Approaches to Natural Products Discovery, Methods in Enzymology. https://doi.org/10.1016/bs.mie.2026.01.001
  5. Clements, A.E., Fieldhouse, M.R., Walker, A.S., Harnessing artificial intelligence for antimicrobial discovery and optimization. Current Opinion in Microbiology, 2026. 91. 102724. https://doi.org/10.1016/j.mib.2026.102724
  6. Butt, C., Walker, A.S.# Reusability Report: evaluating the performance of a meta-learning foundation model on predicting the antibacterial activity of natural products. Nature Machine Intelligence, 2026. 8. 270-275. https://doi.org/10.1038/s42256-026-01187-y
  7. Oyedele, A.S., Walker, A.S.# Benchmarking Methods for Measuring Biosynthetic Gene Cluster Similarity and Determination of Gene Cluster Families. Bioinformatics, 2025. btaf636. https://doi.org/10.1093/bioinformatics/btaf636
  8. Tydings, C.; Meiler, J.#; Walker, A.S.# Computational structure prediction of lanthipeptides with NMR data reveals underappreciated peptide flexibility. Protein Science, 2025. 34 (9). e70252. https://doi.org/10.1002/pro.70252 This work was featured on the American Peptide Society blog: https://americanpeptidesociety.org/research/lanthipeptide-modeling/
  9. Walker, A.S.,# Clardy, J.,# Primed for discovery. Biochemistry, 2024. 63 (21). 2705-2713. https://doi.org/10.1021/acs.biochem.4c00464
  10. Kalmer, T.L.,* Ancajas, C.M.F.,* Cohen, C.I., McDaniel, J.M., Oyedele, A.S., Thirman, H.L., Walker, A.S.# Statistical Coupling Analysis Predicts Correlated Motions in Dihydrofolate Reductase. Journal of Physical Chemistry B, 2024. 128 (42). 10373-10384. https://doi.org/10.1021/acs.jpcb.4c04195
  11. Tydings, C.W., Singh, B., Smith, A.W., Ledwitch, K.V., Lovly, C.M., Brown, B.P., Walker, A.S.,# Meiler, J.# Analysis of EGFR binding hotspots for design of new EGFR inhibitory biologics. Protein Science, 2024. 33. e5141. https://doi.org/10.1002/pro.5141
  12. Ancajas, C.M.F, Oyedele, A., Butt, C., Walker, A.S.,# Advances, Opportunities, and Challenges in the Study of Structure Activity Relationships of Natural Products. Natural Product Reports. 2024. 41. 1543-1578. https://doi.org/10.1039/D4NP00009A
  13. Mabesoone, M.F.J., Leopold-Messer, S., Minas, H.A., Chepkirui, C., Chawengrum, P., Reiter, S., Meoded, R.A., Wolf, S., Genz, F., Magnus, N., Piechulla, B., Walker, A.S., Piel, J. Evolution-Guided Engineering of Trans-Acyltransferase Polyketide Synthases. Science. 2024. 383 (6689). 1312-1317.https://www.science.org/doi/abs/10.1126/science.adj7621
  14. Riedling, O., Walker, A.S., Rokas, A. Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning. Microbiology Spectrum. 2024. 12 (2). e034990-23
    https://journals.asm.org/doi/full/10.1128/spectrum.03400-23
  15. Beck, M.L., Song, S., Shuster, I.E., Miharia, A.,Walker, A.S. Diversity and taxonomic distribution of bacterial biosynthetic gene clusters predicted to produce compounds with therapeutically relevant bioactivities. Journal of Industrial Microbiology and Biotechnology. 2023. 50 (1). kuad024.https://academic.oup.com/jimb/article/50/1/kuad024/7257554
  16. Mullowney, M.W., Duncan, K.R., Elsayed, S.S., Garg, N.,van der Hooft, J.J.J., Martin, M.I., Meijer, D., Terlouw, B.R., Biermann, F., Blin, K.; Durairaj, J., Gorostiola González, M., Helfrich, E.J.N., Huber, F., Leopold-Messer, S., Rajan, K., de Rond, T., van Santen, J.A., Sorokina, M., Balunas, M.J., Beniddir, M., van Bergeijk, D., Carroll, L.M., Clark, C.M., Clevert, D., Dejong, C.A., Du, C., Ferrinho, S., Grisoni, F., Hofstetter, A., Jespers, W., Kalinina, O.V., Kautsar, S.A., Kim, H., Leao, T.F., Masschelein, J., Rees, E.R., Reher, R., Reker, D., Schwaller, P., Segler, M., Skinnider, M.A., Walker, A.S., Willighagen, E.L., Zdrazil, B., Ziemert, N., Goss, R.J.M., Guyomard, P., Volkamer, A., Gerwick, W.H., Kim, H., Müller, R., van Wezel, G.P., van Westen, G., Hirsch, A.K.H., Linington, R.G., Robinson, S.L., Medema, M.H. Artificial Intelligence for Natural Product Drug Discovery. Nature Reviews Drug Discovery. 2023.https://www.nature.com/articles/s41573-023-00774-7
  17. Walker, A.S., Clardy, J. A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters. J. Chem. Inf. Model. 2021. 61 (6). 2560-2571. https://pubs.acs.org/doi/10.1021/acs.jcim.0c01304
    (Featured as a supplemental cover)
  18. Walker, A.S.#, Russ, W.P., Ranganathan, R.,# Schepartz, A.# RNA sectors and allosteric function within the ribosome. Proc. Natl. Acad. Sci. U.S.A, 2020. 177 (33). 19879-19887. https://www.pnas.org/content/117/33/19879.short
  19. Sinclair, J.K.L*., Walker, A.S.*, Doerner, A.E., Schepartz, A. Mechanism of information transfer into and through the plasma membrane by EGFR. Cell Chem. Biol., 2018. 25 (7). 857-870. https://www.sciencedirect.com/science/article/pii/S2451945618301193


    20. Other publications:

  20. Talbert, J.A., Kalmer, T.L., Cantrell, L.S., Bandara, M.D., Demchenko, A.V., Walker, A.S., Gaddy, J.A., Townsend, S.D. Human Milk Oligosaccharides Inhibit Group B Streptococcal Growth by Binding PcsB, an Essential Cell Wall Separation Protein. JACS Au, 2026. 6 (4). 2355-2366.  https://doi.org/10.1021/jacsau.5c01741
  21. Harmych, S.J., Joshi, N., Tanaka, H., Bogatcheva, G., Ramirez, M.A., Graves-Deal, R., Tydings, C.W., Elia, M.T., Mueller, H.R.L., Silvestri, I.M., Ti Ning, K., Wahoski, C.C., Sievers, C.K., Higginbotham, J.N., Irudayam, M.J., Revetta, F.L., Zhao, Z., Franklin, J.L., Yilma, B., O’Grady, T.M., Fragkogianni, S., Ciampricotti, M., Washington, M.K., Guo, X., Lovly, C.M., Walker, A.S., Meiler, J., Mudumbi, K.C., Liu, Q., Coffey, R.J., Rosenthal, E., Singh B. EGFR S442 ectodomain mutation confers cetuximab resistance that can be overcome by ERBB2 blockade with trastuzumab-deruxtecan. Cancer Lett, 2026. 654. 218607. https://doi.org/10.1016/j.canlet.2026.218607
  22. Boutwell, D., Cao, A., Walker, A.S., Buchanan, L. Refining Structural Analysis of Proteins: Automated Methods to Measure Transition Dipole Strength of Single Residues. Journal of Physical Chemistry B, 2025. 129 (33). 8360-8367. https://doi.org/10.1021/acs.jpcb.5c03566
  23. Dorival, J., Hua, Y., Walker, A.S., Gongli, T., Eichman, B. Yatakemycin biosynthesis requires two deoxyribonucleases for toxin self-resistance. RSC Chemical Biology, 2024. 6. 94-105. https://doi.org/10.1039/d4cb00203b
  24. Chaudhri, A.A., Kakumu, Y., Thiengmag, S., Liu, J., Lin, G., Durusu, S., Biermann, F., Boeck, M., Voigt, C., Clardy, J., Ueoka, R., Walker, A.S., Helfrich, E.J.N. Functional redundancy and dual function of a hypothetical protein the biosynthesis of eunicellane-type diterpenoids. ACS Chemical Biology, 2024. 19. 2314-2322. https://doi.org/10.1021/acschembio.4c00413
  25. Biermann, F., Tan, B., Breitenbach, M., Nanudorn, P., Kakumu, Y., Dimitrova, Y., Walker, A.S., Ueoka, R., Helfrich, E.J.N. Machine-learning based exploration, expansion and definition of the atropopeptide family of ribosomally synthesized and posttranslationally modified peptides. Chemical Science, 2024. 15 (42). 17506-17523. https://doi.org/10.1039/d4sc03469d
  26. You, C., Lee, S., Lee, J., Vuong, T., Lee, H. Jeong, S., Alishir, A., Walker, A.S., Bae, G., Kim, K., Kang, J. Inonotus obliquus upregulates muscle regeneration and augments function through muscle oxidative metabolism. International Journal of Biological Sciences. 2023. 19 (15). 4898-4914.https://www.ijbs.com/v19p4898.htm
  27. Walker, A.S., Pishchany, G., Clardy, J. Parsing Molecules for Drug Discovery. Biochemistry, 2020. 59 (17). 1645-1646. https://pubs.acs.org/doi/full/10.1021/acs.biochem.0c00278
  28. Reisberg, S.H., Gao, Y., Walker, A.S., Helfrich, E.J.N., Clardy, J., Baran, P.S. Total synthesis reveals atypical atropisomerism in a small molecule Tryptorubin A. Science, 2020. 367 (6476). 458-463. https://science.sciencemag.org/content/367/6476/458.abstract
  29. Walker, A.S., Rablen, P.R., Schepartz, A., Rotamer-restricted fluorogenicity of the bis-arsenical ReAsH. J. Am. Chem. Soc., 2016. 138 (22). 7143-7150. https://pubs.acs.org/doi/abs/10.1021/jacs.6b03422
    (Featured in spotlights on recent JACS publications and the cover of the June 8, 2016 JACS issue)
  30. Melo Czekster, C., Robertson, W.E., Walker, A.S., Söll, D., Schepartz, A. In vivo biosynthesis of a β-amino acid-containing protein. J. Am. Chem. Soc., 2016. 138 (16). 5194-5197. https://pubs.acs.org/doi/full/10.1021/jacs.6b01023
  31. Melicher, M.S., Walker, A. S., Shen, J. Miller, S.J., Schepartz, A. Improved carbohydrate recognition in water with an electrostatically enhanced β-peptide bundle. Org. Lett., 2015. 17 (19). 4718-4721. https://pubs.acs.org/doi/abs/10.1021/acs.orglett.5b02187
  32. Melicher, M.S., Chu, J., Walker, A.S., Miller, S.J., Baxter, R.H., Schepartz, A. A β-boronopeptide bundle of known structure as a vehicle for polyol recognition. Org. Lett., 2013. 15 (19). 5048-5051. https://pubs.acs.org/doi/abs/10.1021/ol402381n
  33. Hobert, E.M., Doerner, A.E., Walker A.S., Schepartz, A. Effective molarity redux: proximity as a guiding force in chemistry and biology. Isr. J. Chem. 2013. 53 (8). 567-576. https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.201300063

* = authors contributed equally

# = I am corresponding or co-corresponding author