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Huang, Y., Chen, X., Zhu, Z., Mukherjee, A.* A dual-gene reporter-amplifier architecture for enhancing the sensitivity of MRI by water exchange. (submitted, Jan. 2024) bioRxiv preprint:

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. (submitted, Jan. 2024) bioRxiv preprint: doi:10.1101/2023.06.02.543364v1

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 (submitted, Dec. 2023) bioRxiv preprint:

Lau, E.S., Goodheart, J.A., Anderson, N.T., Liu, V.L., Mukherjee, A.* (co-corresponding), Oakley, T.H. (co-corresponding) Similar enzymatic functions in distinct bioluminescence systems: Evolutionary recruitment of sulfotransferases in ostracod light organs (submitted, Dec. 2023) bioRxiv preprint:


Anderson, N.T.A, Xie, J., Chacko, A.N., Liu, V.L., Fan, K.C., Taylor, R., Imansjah, Z., Mukherjee, A.* Rational design of a circularly permuted flavin-based fluorescent protein. (in revision, ChemBioChem)

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. (in revision, J. Biological Engineering) bioRxiv preprint:


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). doi:10.1021/acssynbio.3c00372, bioRxiv preprint:


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). doi:10.1039/D3SD00026E, bioRxiv preprint:  


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). doi: 10.1002/ange.202212832bioRxiv preprint:


Yun, J., Baldini, L., Chowdhury, R., Mukherjee, A.* Designing Protein-Based Probes for Sensing Biological Analytes with Magnetic Resonance Imaging. Analysis & Sensing. (2022). doi:10.1002/anse.202200019


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). doi:10.1021/acssensors.1c01085. ACS Editor’s Choice Article, bioRxiv preprint:


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). doi:10.1063/5.0041394. Editor's Featured Article


Anderson, N.T., Weyant, K.B., and Mukherjee, A.* Characterization of flavin binding in oxygen-independent fluorescent proteins. AIChE Journal. 66(12). (2020) doi:10.1002/aic.17083


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). doi:10.1021/acs.bioconjchem.9b006

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 ImagingCurrent 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. J. Biol. Eng. 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


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

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