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Chowdhury, R., Wan, J., Gardier, R., Rafael-Patino, J., Thiran, J-P, Gibou, F., Mukherjee, A. Molecular imaging with aquaporin-based reporter genes: quantitative considerations from Monte Carlo diffusion simulations. (2023) bioRχiv pre-print:


Yun, J., Baldini, L., Huang, Y., Li, E., Li, H., Chacko, A.N., Miller, A.D.C., Wan, J., Mukherjee, A. Engineering ligand stabilized aquaporin reporters for magnetic resonance imaging. (2023) bioRχiv pre-print:

Lau, E.S., Goodheart, J.A., Anderson, N.T., Liu, V.L., Mukherjee, A. (co-corresponding), Oakley, T.H. (co-corresponding) Predictable genetic recruitment for luciferin sulfation in the convergent evolution of bioluminescence. (2023) bioRχiv pre-print:

Maity, S., Price, B.D., Wilson, C.B., Mukherjee, A., Starck, M., Parker, D., Wilson, M.Z., Lovett, J.E., Han, S., Sherwin, M.S.  Triggered Functional Dynamics of AsLOV2 by Time-Resolved Electron Paramagnetic Resonance at High Magnetic Fields. Angewandte Chemie. (2023)

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) bioRχiv pre-print

Yun, J., Baldini, M., Chowdhury, R., Mukherjee, A. Designing Protein-based Probes for Sensing Biological Analytes with Magnetic Resonance Imaging. Analysis & Sensing. 2(5). (2022)

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. 6(9). 3163-3169. (2021) Editor's Choice Article. bioRχiv pre-print:

Ozbakir, H.F., Miller, A.D.C., Mukherjee, A. Calcium-responsive contrast agents for magnetic resonance imaging. Chemical Physics Reviews. 2(2). (2021). Editor's Pick for Featured Article 


Anderson, N.T., Weyant, K.B., Mukherjee, A. Characterization of flavin binding in oxygen-independent fluorescent reportersAIChE J. 66(12). (2020)

Ozbakir, H.F., Anderson, N.T., Fan, K.C., Mukherjee, A. Beyond the Green Fluorescent Protein: Biomolecular Reporters for Anaerobic and Deep-Tissue Imaging. Bioconjugate Chem. 31(2). 293-302. (2020)

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) doi: 10.1016/j.cbpa.2018.02.011

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) doi: 10.1016/j.pnmrs.2017.05.002

Mukherjee, A., Wu, D., Davis, H., Shapiro, M.G. Non-invasive imaging using reporter genes altering cellular water permeability. Nature Communications. 7. 13891. (2016) doi: 10.1038/ncomms13891

Mukherjee, A. and Schroeder, C.M. Flavin-based Fluorescent Proteins: Emerging Paradigms in Biological Imaging. Current Opinions in Biotechnology. 31. 16-23. (2015) doi: 10.1016/j.copbio.2014.07.010

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) doi: 10.1021/sb500237x

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) doi:10.1371/journal.pone.0064753

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) doi:10.1016/j.bios.2013.04.046 (‡ denotes equal contribution)

Mukherjee, A., Weyant, K.B., Walker, J., Schroeder, C.M. Directed Evolution of Bright Mutants of a Flavin-binding Fluorescent Protein from Pseudomonas putida. Journal of Biol. Engineering. 6:20. (2012) doi: 10.1186/1754-1611-6-20

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) doi: 10.1039/C0LC00342E

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) doi: 10.1093/bioinformatics/btn481

Book chapters

Uetz, P., Mukherjee, A., et al. Bioanalytics: analytical methods and concepts in chemistry and biology. In: Lottspeich, F. & Engels, J.W., Wiley-VCH, 2018 (lead author ʺProtein-protein interactions: Förster Resonance Energy Transferʺ)

Mukherjee, A., Schroeder C.M. Microfluidic methods in single cell biology. In: Lu, C. & Verbridge, S.S., Microfluidic Methods for Molecular Biology, Springer, 2016

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