At UCSB
(*corresponding/co-corresponding, # equal contribution)
Chacko, A.N., Dhanabalan, K.M., Wan, J., Chien, R., Anderson, N.T., Xu, B., Pham, K., Tiwari, R., Mukherjee, A*. A Programmable Genetic Platform for Engineering Noninvasive Biosensors. Sci. Adv. (2026).
Lau, E., Majerova, M., Hensley, N.M., Mukherjee, A., Vasina, M., Pluskal, D., Damborsky, J., Prokop, Z., Delroise, J., Bayaert, W., Parey, E., Oliveri, P., Marletaz, F., Marek, M., Oakley, T.H. Functional Characterization of Luciferase in a Brittle Star Indicates Parallel Evolution Influenced by Genomic Availability of Haloalkane Dehalogenase. Molecular Biology & Evolution. (2025).
Chacko, A.N.#, Miller, A.D.C.#, Dhanabalan, K.M., Mukherjee, A*. Exploring the potential of water channels for developing MRI reporters and sensors without the need for exogenous contrast agents. J. Magn. Reson. (2024).
Huang, Y., Chen, X., Zhu, Z., Mukherjee, A*. A dual-gene reporter-amplifier architecture for enhancing the sensitivity of MRI by water exchange. ChemBioChem. (2024).
Lau, E.S., Goodheart, J.A., Anderson, N.T., Liu, V.L., Mukherjee, A*., Oakley, T.H*. Similar enzymatic functions in distinct bioluminescence systems: Evolutionary recruitment of sulfotransferases in ostracod light organs. Biol. Letters. (2024).
Anderson, N.T.A, Xie, J., Chacko, A.N., Liu, V.L., Fan, K.C., Mukherjee, A*. Rational design of a circularly permuted flavin-based fluorescent protein. ChemBioChem. (2024). Editorially designated as “Very Important Paper”.
Yun, J., Huang, Y., Miller, A.D.C., Chang, B. L., Baldini, L., Dhanabalan, K.M., Li, E., Li, H., Mukherjee, A*. Destabilized reporters for background-subtracted, chemically-gated, and multiplexed deep-tissue imaging. Chem. Sci. (2024). link
Miller, A.D.C., Chowdhury, S., Hanson, H., Linderman, S.K., Ghasemi, H., Miller, W., Morrissey, M., Richardson, R., Gardner, B., Mukherjee, A*. Genetic engineering of water exchange is a safe and effective approach for magnetic resonance imaging in multiple cell types. J. Biol. Eng. (2024).
Chowdhury, R., Wan, J., Gardier, R., Rafael-Patino, J., Thiran, J., Gibou, F., Mukherjee, A*. Molecular imaging with aquaporin-based reporter genes: quantitative considerations from Monte Carlo diffusion simulations. ACS Synthetic Biology. (2023). link
Borg, R.E.#, Ozbakir, H.F.#, Xu, B., Li E., Fang, X., Peng, H., Chen, I.A*., Mukherjee, A*. Genetically engineered filamentous phage for bacterial detection using magnetic resonance imaging. Sensors & Diagnostics. (2023).
Maity, S., Price, B.D., Wilson, C.B., Mukherjee, A., Starck, M., Parker, D., Wilson, M.Z., Lovett, J.E., Han, S., Sherwin, M*. Triggered Functional Dynamics of AsLOV2 by Time-Resolved Electron Paramagnetic Resonance at High Magnetic Fields. Angewandte Chemie. (2023).
Yun, J., Baldini, L., Chowdhury, R., Mukherjee*, A. Designing Protein-Based Probes for Sensing Biological Analytes with Magnetic Resonance Imaging. Analysis & Sensing. (2022). link
Ozbakir, H.F., Miller, A.D.C., Fishman, K.B., Martins, A.F., Kippin, T.E., Mukherjee, A*. A protein-based biosensor for detecting calcium by magnetic resonance imaging. ACS Sensors. (2021). ACS Editor’s Choice Article, featured in Chemical & Engineering News.
Miller, A.D.C., Ozbakir, H.F., and Mukherjee, A*. Calcium-responsive contrast agents for functional magnetic resonance imaging. Chemical Physics Reviews. 2(2). (2021). Editor's Featured Article, Scilight feature
Anderson, N.T., Weyant, K.B., and Mukherjee, A*. Characterization of flavin binding in oxygen-independent fluorescent proteins. AIChE Journal. 66(12). (2020).
Ozbakir, H.F., Anderson, N.T., Fan, K., Mukherjee, A*. Beyond the green fluorescent protein: biomolecular reporters for anaerobic and deep tissue imaging. Bioconjugate Chemistry. (2019).
Prior to UCSB
Lu, G.J., Farhadi, A., Mukherjee, A., Shapiro, M.G.* Proteins, air, and water: reporter genes for ultrasound and magnetic resonance imaging. Current Opinions in Chemical Biology. 45. 57-63. (2018).
Mukherjee, A., Davis, H., Ramesh, P., Lu, G., Shapiro, M.G.* Biomolecular MRI reporters: evolution of new mechanisms. Progress in NMR Spectroscopy. 102-103. 32-42. (2017).
Mukherjee, A.#, Wu, D.#, Davis, H., Shapiro, M.G.* Non-invasive imaging using reporter genes altering cellular water permeability. Nature Communications. 7. 13891. (2016). PMID: 28008959
Mukherjee, A. and Schroeder, C.M.* Flavin-based Fluorescent Proteins: Emerging Paradigms in Biological Imaging. Current Opinions in Biotechnology. 31. 16-23. (2015).
Mukherjee, A., Weyant, K.B., Agrawal, U., Walker, J., Schroeder, C.M.* Engineering and Characterization of New LOV-based Fluorescent Reporter Proteins from Chlamydomonas reinhardtii and Vaucheria frigida. ACS Synthetic Biology. (2014).
Mukherjee, A., Walker, J., Weyant, K.B., Schroeder, C.M.* Characterization of Flavin-based Fluorescent Proteins: an Emerging Class of Fluorescent Reporters. PLoS ONE. 8:5. (2013).
Mohan, R.#, Mukherjee, A.#, Lee, J., Sevgen, S., Schroeder, C.M., Kenis, P.J.A.* A Multiplexed Microfluidic Platform for Antibiotic Susceptibility Screening. Biosensors and Bioelectronics. 49:15. 118-125 (2013).
Mukherjee, A., Weyant, K.B., Walker, J., Schroeder, C.M.* Directed Evolution of Bright Mutants of a Flavin-binding Fluorescent Protein from Pseudomonas putida. J. Biol. Eng. 6:20. (2012).
Schudel, B.R., Tanyeri, M., Mukherjee, A., Schroeder, C.M., Kenis, P.J.A.* Multiplexed Detection of Nucleic Acids in a Combinatorial Screening Chip. Lab on a Chip. 11. 1916-23. (2011).
Rajagopala, S.V., Goll, J., Gowda, N.D.D., Sunil, K.C., Titz, B., Mukherjee, A., Mary, S.S., Raviswaran, N., et al. MPI-LIT-A Literature-curated Dataset of Microbial Binary Protein-Protein Interactions. Bioinformatics. 24. 2622-27. (2008).
Uetz, P., Mukherjee, A.*, et al. Bioanalytics: analytical methods and concepts in chemistry and biology. In: Lottspeich, F. & Engels, J.W., Wiley-VCH, 2018
Mukherjee, A., Schroeder C.M.* Microfluidic methods in single cell biology. In: Lu, C. & Verbridge, S.S., Microfluidic Methods for Molecular Biology, Springer, 2016