Publications

Articles under review

1. Krishnan A.*, Anahtar MN.*, Valeri J.*, Jin W.,..., Wong F., and Collins JJ. "A generative deep learning approach to de novo antibiotic design", reviewed, Cell. 

2. Wong F., Omori S., Li A., Krishnan A., ...and Collins JJ. “An explainable deep learning platform for molecular discovery”, reviewed, Nature Protocols.

3. Wong F.*, He D.*, Krishnan A., …, and Collins JJ. “Structure-guided, deep learning-enabled generative design of RNA aptamers”, reviewed, Nature Computational Science.

Articles published

4. Wong F.*, Zheng E.*, Valeri J., ..., Krishnan A., ..., Renner L., & Collins JJ. (2023) "Discovery of a structural class of antibiotics with explainable deep learning." Nature. See publication (Research)

5. Zheng E.*, Valeri J.*, Andrews I.*, Krishnan A., ..., Lourido S., & Collins JJ. (2023) "Discovery of antibiotics that selectively kill metabolically dormant bacteria." Cell Chemical Biology. See publication (Research)

6. Valeri J.*, Krishnan A.* & Collins JJ. (2023) "Gaming bacterial metabolism." Nature Microbiology. See publication (News & Views)

7. Wong F.*, Krishnan A.*, Zheng E., ... & Collins JJ. (2022) "Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery." Molecular Systems Biology. See publication (Research)

8. Ramakrishnan, C., Krishnan, A., Francisco, S., Schmid, M. W., Russo, G., Leitão, A., ... & Hehl, A.B. (2022). "Dissection of Besnoitia besnoiti intermediate host life cycle stages: From morphology to gene expression." PLoS Pathogens. See publication (Research)

9. Nyonda, M. A., Kloehn, J., Sosnowski, P., Krishnan, A., ... & Soldati-Favre, D. (2022). "Ceramide biosynthesis is critical for establishment of the intracellular niche of Toxoplasma gondii." Cell Reports. See publication (Research) 

10. Nyonda, M. A., Boyer, J. B., Belmudes, L., Krishnan A., ... & Giglione, C. (2022). "N-Acetylation of secreted proteins is widespread in Apicomplexa and is independent of acetyl-CoA ER-transporter AT1." Journal of Cell Science. See publication (Research)

11. Bisio, H., Krishnan, A., Marq, J. B., & Soldati-Favre, D. (2022). "Toxoplasma gondii phosphatidylserine flippase complex ATP2B-CDC50.4 critically participates in microneme exocytosis." PLoS Pathogens. See publication (Research)

12. Lunghi, M.*, Kloehn, J.*, Krishnan, A., ..., & Soldati-Favre, D. (2022). "Pantothenate biosynthesis is critical for chronic infection by the neurotropic parasite Toxoplasma gondii." Nature communications. See publication (Research)

13. de Vries, L. E.*, Lunghi, M.*, Krishnan, A., Kooij, T. W., & Soldati-Favre, D., (2021). "Pantothenate and CoA biosynthesis in Apicomplexa and their promise as antiparasitic drug targets." PLoS Pathogens. See publication (Review)

14. Dos Santos Pacheco, N.*, Tosetti, N.*, Krishnan, A., ... & Soldati-Favre, D., (2021). "Revisiting the Role of Toxoplasma gondii ERK7 in the Maintenance and Stability of the Apical Complex." Mbio. See publication (Research)

15. Schastnaya, E., Raguz Nakic, Z., ... , Krishnan, A., ... & Sauer U., (2021) "Extensive regulation of enzyme activity by phosphorylation in Escherichia coli." Nature Communications. See Publication (Research)

16. Krishnan, A.# & Soldati-Favre, D.#, (2021). "Amino acid metabolism in apicomplexan parasites." Metabolites. See publication (Review)

17. Krishnan, A., Kloehn, J., Lunghi, M., Chiappino-Pepe, A., ... , Hehl, A., Lourido, S., Hatzimanikatis, V. & Soldati-Favre, D., (2020). "Functional and computational genomics reveal unprecedented flexibility in stage-specific Toxoplasma metabolism." Cell Host & Microbe. See publication (Research)

18. Krishnan, A., Kloehn, J., Lunghi, M. & Soldati-Favre, D., (2020). "Vitamin and cofactor acquisition in apicomplexans: Synthesis versus salvage." Journal of Biological Chemistry. See publication (Review)

19. Kloehn, J*. and Krishnan, A.*, Tonkin, C.J., McConville, M.J. & Soldati-Favre, D., (2020). "Metabolic networks and metabolomics. In Toxoplasma gondii (p. 451-497)." Academic Press.  See publication (Book chapter)

20. Frénal, K., Krishnan, A. & Soldati-Favre, D., (2020). "The Actomyosin Systems in Apicomplexa." In Myosins (pp. 331-354). Springer. See publication (Book chapter)

21. Krishnan, A.# & Soldati-Favre, D., (2016). "Parasite pathogenesis: Breaching the wall for brain access." Nature microbiology. See publication (News & Views)

Articles in preparation

22. Omori S.*, Li A.*, Krishnan A., Wilson M., Wong F., and Collins JJ. “Large-scale deep learning models of cellular toxicity for drug discovery”, in preparation. (Research)

23. Anahtar MN.*, Valeri J.*, Krishnan A., ..., and Collins JJ. "Deep learning-enabled discovery of antibiotics effective against Neisseria gonorrhoeae", in preparation. (Research)

24. Krishnan A., Marq JB., ..., Soldati-Favre D.#, and Kloehn J.#. "The TCA cycle enzyme aconitase holds essential functions inside the mitochondrion and cytosol of Toxoplasma gondii", in preparation (Research)

* co-authorship
# corresponding author