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Walker Lab

Publications

 
Highlighted Publications:

  1. 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. 2024. Natural Product Reports. https://doi.org/10.1039/D4NP00009A

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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)

    7. Preprints:

  7. 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.https://doi.org/10.1101/2024.06.18.599103

  8. 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.https://www.biorxiv.org/content/10.1101/2023.11.03.565440v1

    9. Other Independent Career Publications:

  9. 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

    10. Other Publications Prior to Vanderbilt:

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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)

  15. 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

  16. 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

  17. 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

  18. 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