Pamuditha Somarathne, Tharindu Wickremasinghe, Amashi Niwarthana, A. Thieshanthan, Chamira U.S. Edussooriya, Dushan N. Wadduwage*, 2023. MOSAIC: Masked Optimisation with Selective Attention for Image Reconstruction. arXiv preprint arxiv:2306.00906.

Das, S., Saxena, K., Tinguely, J.C., Pal, A., Wickramasinghe, N.L., Khezri, A., Dubey, V., Ahmad, A., Perumal, V., Ahmad, R. Wadduwage, D.N., Ahluwalia, B.S.*, and Mehta, D.S.*, 2023. SERS Nanowire Chip and Machine Learning-Enabled Classification of Wild-Type and Antibiotic-Resistant Bacteria at Species and Strain Levels. ACS Applied Materials & Interfaces.

Ahmad, A., Hettiarachchi, R., Khezri, A., Singh Ahluwalia, B., Wadduwage, D.N. and Ahmad, R., 2023. Highly sensitive quantitative phase microscopy and deep learning aided with whole genome sequencing for rapid detection of infection and antimicrobial resistance. Frontiers in Microbiology, 14, p.1006.

Wijethilake N., Anandakumar M., Zheng C., So P.T., Yildirim M., Wadduwage D.N.*, 2022. DEEP2: Deep Learning Powered De-scattering with Excitation Patterning. arXiv preprint arXiv:221010892.

Herath, K., Haputhanthri, U., Hettiarachchi, R., Kariyawasam, H., Ahmad, A., Ahluwalia, B.S., Edussooriya, C.U. and Wadduwage, D., 2022. Differentiable Microscopy Designs an All Optical Quantitative Phase Microscope. arXiv preprint arXiv:2203.14944.

Haputhanthri, U., Herath, K., Hettiarachchi, R., Kariyawasam, H., Ahmad, A., Ahluwalia, B.S., Edussooriya, C.U.* and Wadduwage, D.N.*, 2022. From Hours to Seconds: Towards 100x Faster Quantitative Phase Imaging via Differentiable Microscopy. arXiv preprint arXiv:2205.11521.

Haputhanthri, U., Seeber, A. and Wadduwage, D.N.*, 2022. Differentiable Microscopy for Content and Task Aware Compressive Fluorescence Imaging. arXiv preprint arXiv:2203.14945.

Arguello, H., Bacca, J., Kariyawasam, H., Vargas, E., Marquez, M., Hettiarachchi, R., Garcia, H., Herath, K., Haputhanthri, U., Ahluwalia, B.S., So, P.T.C., Wadduwage, D.N., Edussooriya, C.U.S.*, 2022. Deep Optical Coding Design in Computational Imaging, IEEE Signal Processing Magazine (in press).

Zheng, C., Park, J.K., Yildirim, M., Boivin, J.R., Xue, Y., Sur, M., So, P.T. and Wadduwage, D.N.*, 2021. De-scattering with Excitation Patterning enables rapid wide-field imaging through scattering media. Science Advances, 7(28), p.eaay5496.

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Kay, J.E., Mirabal, S., Briley, W.E., Kimoto, T., Poutahidis, T., Ragan, T., So, P.T., Wadduwage, D.N., Erdman, S.E. and Engelward, B.P., 2021. Analysis of mutations in tumor and normal adjacent tissue via fluorescence detection. Environmental and molecular mutagenesis, 62(2), pp.108-123.

Pradeepkumar, J., Anandakumar, M., Kugathasan, V., Seeber, A., & Wadduwage, D.N.*, 2021. Physics Augmented U-Net: A High-Frequency Aware Generative Prior for Microscopy. bioRxiv 2021.12.01.470743.

Kay, J.E., Corrigan, J.J., Armijo, A.L., Nazari, I.S., Kohale, I.N., Torous, D.K., Avlasevich, S.L., Croy, R.G., Wadduwage, D.N., Carrasco, S.E. and Dertinger, S.D., 2021. Excision of mutagenic replication- blocking lesions suppresses cancer but promotes cytotoxicity and lethality in nitrosamine-exposed mice. Cell Reports, 34(11), p.108864.

Agbleke, A.A., Amitai, A., Buenrostro, J.D., Chakrabarti, A., Chu, L., Hansen, A.S., Koenig, K.M., Labade, A.S., Liu, S., Nozaki, T. and Ovchinnikov, S., Seeber, A., Shaban, H. A., Spille, J., Stephens, A. D., Su, J., Wadduwage, D.N., 2020. Advances in chromatin and chromosome research: perspectives from multiple fields. Molecular Cell, 79(6), pp.881-901.

Coucheron, D.A., Wadduwage, D.N., Murugan, G.S., So, P.T. & Ahluwalia, B.S.*, 2019. Chip-based resonance Raman spectroscopy using tantalum pentoxide waveguides. IEEE Photonics Technology Letters, 31(14), pp.1127-1130.

Wei, Z., Boivin, J.R., Xue, Y., Chen, X., So, P.T., Nedivi, E. & Wadduwage, D.N.*, 2019. 3D Deep Learning Enables Fast Imaging of Spines through Scattering Media by Temporal Focusing Microscopy. arXiv preprint arXiv:2001.00520.

Wadduwage, D.N.*, Kay, J., Singh, V.R., Kiraly, O., Sukup-Jackson, M.R., Rajapakse, J., Engelward, B.P. & So, P.T., 2018. Automated fluorescence intensity and gradient analysis enables detection of rare fluorescent mutant cells deep within the tissue of RaDR mice. Scientific reports, 8(1), p.12108.

Xue, Y., Berry, K.P., Boivin, J.R., Wadduwage, D. N., Nedivi, E. & So, P.T.*, 2018. Scattering reduction by structured light illumination in line-scanning temporal focusing microscopy. Biomedical optics express, 9(11), p.5654.

Wadduwage, D.N., Singh, V.R., Choi, H., Yaqoob, Z., Heemskerk, H., Matsudaira, P. and So, P.T., 2017. Near-common-path interferometer for imaging Fourier-transform spectroscopy in wide-field microscopy. Optica, 4(5), pp.546-556.

Choi, H., Wadduwage, D.N., Tu, T.Y., Matsudaira, P. and So, P.T.*, 2015. Three-dimensional image cytometer based on widefield structured light microscopy and high-speed remote depth scanning. Cytometry Part A, 87(1), pp.49-60. (Best Paper Award, Cytometry Part A)

Choi, H., Wadduwage, D.N., Matsudaira, P.T. and So, P.T.*, 2014. Depth resolved hyperspectral imag- ing spectrometer based on structured light illumination and Fourier transform interferometry. Biomedical optics express, 5(10), pp.3494-3507.

Sukup-Jackson, M.R., Kiraly, O., Kay, J.E., Na, L., Rowland, E.A., Winther, K.E., Chow, D.N., Kimoto, T., Matsuguchi, T., Jonnalagadda, V.S., Maklakova, V.I., Singh V.R., Wadduwage D.N., Rajapakse J., So P.T., Collier L.S., & Engelward* B.P., 2014. Rosa26-GFP direct repeat (RaDR-GFP) mice reveal tissue- and age-dependence of homologous recombination in mammals in vivo. PLoS genetics, 10(6), p.e1004299.