Nanda, P., McCaffrey, E.F., Michael, C.T., Delmastro, A.C., Michael, G., Mattila, J.T., Flynn, J.L., Angelo, R.M., & Kirschner, D. (2026). A tissue time machine to forward-predict single-timepoint data applied to tuberculosis granulomas. In openRxiv. doi: 10.64898/2026.10.09.758083.
Budak, M., Nanda, P., & Kirschner, D. (2025). A novel machine-learning based optimization: identifying new treatment regimens for tuberculosis. Numer Algebr Control Optim, 18(0), 116-145.American Institute of Mathematical Sciences (AIMS). doi: 10.3934/naco.2025025.
Krupinsky, K.C., Michael, C.T., Nanda, P., Mattila, J.T., & Kirschner, D. (2025). Distinguishing multiple roles of T cell and macrophage involvement in determining lymph node fates during Mycobacterium tuberculosis infection. In Smith, A.M. (Ed.). PLoS Comput Biol, 21(5), e1013033.Public Library of Science (PLoS). doi: 10.1371/journal.pcbi.1013033.
Budak, M., Via, L.E., Weiner, D.M., Barry, C.E., Nanda, P., Michael, G., Mdluli, K., & Kirschner, D. (2024). A systematic efficacy analysis of tuberculosis treatment with BPaL-containing regimens using a multiscale modeling approach. CPT Pharmacometrics Syst Pharmacol, 13(4), 673-685.Wiley. doi: 10.1002/psp4.13117.
Nanda, P., Budak, M., Michael, C.T., Krupinsky, K., & Kirschner, D.E. (2024). Development and Analysis of Multiscale Models for Tuberculosis: From Molecules to Populations. In Predicting Pandemics in a Globally Connected World, Volume 2. (pp. 11-43).Springer Nature. doi: 10.1007/978-3-031-56794-0_2.
Janakiraman, S., Engels, S., Nanda, P., Budak, M., Greenstein, T., Moraes, M.P., Aldridge, B.B., & Kirschner, D.E. (2023). Semi-automated colony-forming unit counting for biosafety level 3 laboratories. STAR Protoc, 4(3), 102442.Elsevier. doi: 10.1016/j.xpro.2023.102442.
Nanda, P., & Kirschner, D.E. (2023). Calibration methods to fit parameters within complex biological models. Front Appl Math Stat, 9.Frontiers. doi: 10.3389/fams.2023.1256443.
Nanda, P., Budak, M., Michael, C.T., Krupinsky, K., & Kirschner, D.E. (2023). Development and Analysis of Multiscale Models for Tuberculosis: From Molecules to Populations. bioRxiv, 2023.11.13.566861.Cold Spring Harbor Laboratory. doi: 10.1101/2023.11.13.566861.
Wojenski, L.A., Wainman, L., Villafano, G.J., Kuhlberg, C., Nanda, P., & Core, L. (2021). Multiple Modes of Regulation Control Dynamic Transcription Patterns During the Mitosis-G1 Transition. SSRN Electronic Journal.Elsevier. doi: 10.2139/ssrn.3867721.
Wojenski, L.A., Wainman, L.M., Villafano, G., Kuhlberg, C., Nanda, P., & Core, L. (2021). Multiple modes of regulation control dynamic transcription patterns during the mitosis-G1 transition. In bioRxiv. doi: 10.1101/2021.06.22.449286.
Pardakhti, M., Nanda, P., & Srivastava, R. (2020). Impact of Chemical Features on Methane Adsorption by Porous Materials at Varying Pressures. JOURNAL OF PHYSICAL CHEMISTRY C, 124(8), 4534-4544.American Chemical Society (ACS). doi: 10.1021/acs.jpcc.9b09319.
Dong, S., Nanda, P., Guo, K., Liao, J., & Zheng, G. (2015). Incoherent Fourier ptychographic photography using structured light. PHOTONICS RESEARCH, 3(1), 19-23.Optica Publishing Group. doi: 10.1364/PRJ.3.000019.
Guo, K., Bian, Z., Dong, S., Nanda, P., Wang, Y.M., & Zheng, G. (2015). Microscopy illumination engineering using a low-cost liquid crystal display. Biomed Opt Express, 6(2), 574-579.Optica Publishing Group. doi: 10.1364/BOE.6.000574.
Guo, K., Dong, S., Nanda, P., & Zheng, G. (2015). Optimization of sampling pattern and the design of Fourier ptychographic illuminator. Opt Express, 23(5), 6171-6180.Optica Publishing Group. doi: 10.1364/OE.23.006171.
Dong, S., Guo, K., Nanda, P., Shiradkar, R., & Zheng, G. (2014). FPscope: a field-portable high-resolution microscope using a cellphone lens. Biomed Opt Express, 5(10), 3305-3310.Optica Publishing Group. doi: 10.1364/BOE.5.003305.
Dong, S., Nanda, P., Shiradkar, R., Guo, K., & Zheng, G. (2014). High-resolution fluorescence imaging via pattern-illuminated Fourier ptychography. Opt Express, 22(17), 20856-20870.Optica Publishing Group. doi: 10.1364/OE.22.020856.
Dong, S., Shiradkar, R., Nanda, P., & Zheng, G. (2014). Spectral multiplexing and coherent-state decomposition in Fourier ptychographic imaging. Biomed Opt Express, 5(6), 1757-1767.Optica Publishing Group. doi: 10.1364/BOE.5.001757.
