(*-equal contribution, †-Corresponding Author)
1. Kumar K.C.A., Nair A., Sharma S., Singh D., Yadav S., Bhimsaria D., Gupta S., and Hazra S. Strategic design of a multi-tier database for class A β-lactamase BlaC variants of M. tuberculosis: advancing the fight against antibacterial resistance. The Journal of Antibiotics (2025). https://doi.org/10.1038/s41429-025-00862-3. (Impact factor: 2.1)
2. Arabzade A., Shirnekhi H.K., Varadharajan S. et al. Synthetic ZFTA fusions pinpoint disordered protein domain acquisition as a mechanism of brain tumorigenesis. Nature Cell Biology (2025) 27, 1496–1509 (2025). https://doi.org/10.1038/s41556-025-01745-3. (Impact factor: 21.3)
3. Bhimsaria D.*†, Rodríguez-Martínez J.A.*, Méndez J., Ghoshdastidar D., Varadarajan A., Bansal M., Daniels D.L., Ramanathan P., and Ansari A.Z. (2023) Hidden Modes of DNA Binding by Human Nuclear Receptors. Nature Communications 14, 4179. (Impact factor: 17.69)
4. Jana I.D., Bhattacharya P., Mayilsamy K., Banerjee S., Bhattacharje G., Das S., Aditya S., Ghosh A., McGill A.R., Srikrishnan S., Das A.K., Basak A., Mohapatra S.S., Chandran B., Bhimsaria D., Mohapatra S., Roy A., Mondal A. (2022) Targeting an evolutionarily conserved “ELL” motif in spike protein to identify a small molecule fusion inhibitor against SARS-CoV-2. PNAS nexus, Volume 1, Issue 5, November 2022, pgac198.
5. Finn P.B.*, Bhimsaria D.*, Ali A., Eguchi A., Ansari A.Z., and Dervan P.B. (2020) Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome. PLoS ONE 15(12): e0243905. (Impact factor: 3.75)
6. Liu X., Gupta S.T.P., Bhimsaria D., Reed J.L., Rodríguez-Martínez J.A., Ansari A.Z., and Raman S. (2019) De novo design of programmable inducible promoters. Nucleic Acids Research, 47, 10452–10463. (Impact factor: 19.16)
7. Yella V.R.*, Bhimsaria D.*, Ghoshdastidar D., Rodríguez-Martínez J.A., Ansari A.Z., and Bansal M. (2018) Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif. Nucleic Acids Research, 46, 11883–11897. (Impact factor: 19.16)
8. Bhimsaria D., Rodríguez-Martínez J.A., Pan J., Roston D., Korkmaz E.N., Cui Q., Ramanathan P., and Ansari A.Z. (2018) Specificity landscapes unmask submaximal binding site preferences of transcription factors. Proceedings of the National Academy of Sciences of the United States of America, 115, E10586–E10595. (Impact factor: 12.78)
9. Rodríguez-Martínez J.A.*, Reinke A.W.*, Bhimsaria D.*, Keating A.E., and Ansari A.Z. (2017) Combinatorial bZIP dimers define complex DNA-binding specificity landscapes. eLife 6, e19272. (Impact factor: 8.71)
10. Eguchi A., Wleklinski M.J., Spurgat M.C., Heiderscheit E.A., Kropornicka A.S., Vu C.K., Bhimsaria D., Swanson S.A., Stewart R.M., Ramanathan P., Kamp T.J., Slukvin I.I., Thomson J.A., Dutton J.R., and Ansari A.Z. (2016) Reprogramming cell fate with a genome-scale library of artificial transcription factors. Proceedings of the National Academy of Sciences of the United States of America, 113 (51) E8257-E8266. (Impact factor: 12.78)
11. Erwin G.S., Grieshop M.P.*, Bhimsaria D.*, Do T.J., Rodríguez-Martínez J.A., Mehta C., Khanna K., Swanson S.A., Stewart R., Thomson J.A., Ramanathan P., and Ansari A.Z. (2016) Synthetic genome readers target clustered binding sites across diverse chromatin states. Proceedings of the National Academy of Sciences of the United States of America, 113 (47) E7418-E7427. (Impact factor: 12.78)
12. Erwin G.S., Grieshop M.P., Bhimsaria D., Eguchi A., Rodríguez-Martínez J.A., and Ansari A.Z. (2016) Genome-wide mapping of drug-DNA interactions in cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin). Journal of Visualized Experiments, (107), e53510. (Impact factor: 1.4)
13. Erwin G.S., Bhimsaria D., Eguchi A., and Ansari A.Z. (2014) Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites. Angewandte Chemie (International Ed. in English), 53(38), 1–6. (Impact factor: 16.82)
14. Meyer P., Cokelaer T., Chandran D., Kim K.H., Loh P.R., Tucker G., Lipson M., Berger B., Kreutz C., Raue A., Steiert B., Timmer J., Bilal E., DREAM 6&7 Parameter Estimation consortium, Sauro H.M., Stolovitzky G., and Saez-Rodriguez J. (2014) Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BioMed Central Systems Biology 8(1), 13. (Impact factor: 2.05)
15. Campbell Z.T., Bhimsaria D., Valley C.T., Rodriguez-Martinez J.A., Menichelli E., Williamson J.R., Ansari A.Z., and Wickens M. (2012) Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity. Cell Reports, 1(5), 570–581. (Impact factor: 9.99)
16. Tietjen J.R., Donato L.J., Bhimsaria D., and Ansari A.Z. (2011) Sequence-specificity and energy landscapes of DNA-binding molecules. Methods in Enzymology, 497, 3–30. (Impact factor: 1.68)
17. Carlson C.D., Warren C.L., Hauschild K.E., Ozers M.S., Qadir N., Bhimsaria D., Lee Y, Cerrina F, and Ansari A.Z. (2010) Specificity landscapes of DNA binding molecules elucidate biological function. Proceedings of the National Academy of Sciences of the United States of America, 107(10), 4544–9. (Impact factor: 12.78)
18. Singh D., Srivastava V., Pandey B., and Bhimsaria D. (2009) Application of neural network with error correlation and time evolution for retrieval of soil moisture and other vegetation variables. Progress In Electromagnetics Research, 15(15), 245–465. (Impact factor: 2.95)
