publications

Journals

• Jothishwaran, C. A., Srivastava, B., Singla, J., & Gangopadhyay, S. (2023). On Learning with LAD. arXiv preprint arXiv:2309.16630.

• Li, A., Zhang, S., Loconte, V., Liu, Y., Ekman, A., Thompson, G.J., Sali, A., Stevens, R.C., White, K., Singla, J., Sun, L. (2022). An intensity-based post-processing tool for 3D instance segmentation of organelles in Soft X-ray tomograms. PLOS One, 17(9), e0269887.

• Singla, J., Burdsall, K., Cantrell, B., Halsey, J. R., McDowell, A., McGregor, C., ... & Berman, H. M. (2022). A New Visual Design Language for Biological Structures in a Cell. Structure, 30(4), 485-497.E3.

• Loconte, V., Singla, J., Li, A., Chen, J.H., Ekman, A., McDermott, G., Sali, A., White, K.L. & Larabell, C.A. (2022). Soft X-ray tomography to map and quantify organelle interactions at the mesoscale. Structure, 30(4), 510-521.E3.

  • • • Highlighted in Nature: Soft X-rays capture the dance of the organelles

• Li, A., Zhang, X., Singla, J., White, K.L., Loconte, V., Hu, C., Zhang, C., Li, S., Li, W., Francis, J.P., Sali, A., Wang, C., Sun, L., He, X. & Stevens, R.C. (2022). Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in β-cells during insulin secretion. PLOS One, 17(3), e0265567.

• Raveh, B., Sun, L., White, K. L., Sanyal, T., Tempkin, J., Zheng, D., Bharat, K., Singla, J., Wang, C., Zhao, J., Li, A., Graham, N. A., Kesselman, C., Stevens, R. C., & Sali, A. (2021). Bayesian metamodeling of complex biological systems across varying representations. PNAS, 118(35), e2104559118.

• Singla, J., White, K. L., Stevens, R. C., & Alber, F. (2021). Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography. Journal of Structural Biology, 213(2), 107727.

• Singla, J., & White, K. L. (2021). A community approach to whole-cell modeling. Current Opinion in Systems Biology, 26, 33-38.

• White, K. L., Singla, J., Loconte, V., Chen, J. H., Ekman, A., Sun, L., Zhang, X., Francis, J. P., Li, A., Lin, W., Tseng, K., McDermott, G., Alber, F., Sali, A., Larabell, C., & Stevens, R. C. (2020). Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography. Science advances, 6(50), eabc8262.

  • • • Highlighted in Science: Subcellular map of vesicle maturation

• Zhang, X., Carter, S. D., Singla, J., White, K. L., Butler, P. C., Stevens, R. C., & Jensen, G. J. (2020). Visualizing insulin vesicle neighborhoods in β cells by cryo–electron tomography. Science Advances, 6(50), eabc8258.

• Xu, M., Singla, J., Tocheva, E. I., Chang, Y. W., Stevens, R. C., Jensen, G. J., & Alber, F. (2019). De novo structural pattern mining in cellular electron cryotomograms. Structure, 27(4), 679-691.

  • • • Highlighted in Nature Methods: Template-free visual proteomics

• Singla, J., McClary, K. M., White, K. L., Alber, F., Sali, A., & Stevens, R. C. (2018). Opportunities and challenges in building a spatiotemporal multi-scale model of the human pancreatic β cell. Cell, 173(1), 11-19.

• Srihari, S., Kalimutho, M., Lal, S., Singla, J., Patel, D., Simpson, P. T., Khanna, K. K., & Ragan, M. A. (2016). Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach. Molecular BioSystems, 12(3), 963-972.

• Srihari, S., Singla, J., Wong, L., & Ragan, M. A. (2015). Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Biology direct, 10(1), 1-18.

Conference Papers

• Schuler, R. E., Singla, J., Vallat, B., White, K. L., Berman, H. M., & Kesselman, C. (2023, October). Database Evolution, by Scientists, for Scientists: A Case Study. In 2023 IEEE 19th International Conference on e-Science (e-Science) (pp. 1-10). IEEE

Conference Posters

• Loconte, V., Singla, J., Li, A., Chen, J. H., Ekman, A., McDermott, G., ... & Larabell, C. A. (2023). Soft X-ray Tomography for Mapping and Quantifying Intracellular Organelle Interactions. Microscopy and Microanalysis, Volume 29, Issue Supplement_1, 1 August 2023, Page 1181

• White K. L., Singla J., Francis J. P., Chen J. H., Ekman A., Xu M., Alber F., Larabell C. and Stevens R. C. “Multi-scale architecture of β-cells using Soft X-ray and Cryo-Electron Tomography.” 63rd Annual Meeting of the Biophysical Society, March 2-6, 2019, Baltimore, Maryland.

• Xu M., Singla J., Tocheva E. I., Chang Y.W., Stevens R. C., Jensen G. J. and Alber F. “De novo structural pattern mining in cellular electron cryo-tomograms.” 4th Annual QCBio Retreat, 25th September, 2018, Malibu, California.

• White K. L., McClary K. M., Singla J., and Stevens R. C. “Towards Generating Spatiotemporal Multiscale Models of Human Pancreatic Beta Cells” American Diabetes Association’s 78th Scientific Sessions, June 22-26, 2018, Orlando, Florida, USA.

• Xu M., Singla J., Tocheva E. I., Chang Y.W., Stevens R. C., Jensen G. J. and Alber F. “De novo structural pattern mining in cellular electron cryo-tomograms.” 5th Annual Shanghai iHuman Forum, November 5-10, 2017, Shanghai, China.

• Elizabeth V., Watanabe R., Buschauer R., Khanna K., Lam V., Singla J. and Alber F. “Revealing the Native Molecular Architecture of the Nuclear Periphery using Cryo-Focused-Ion-Beam Milling, Light Microscopy and Electron Tomography” Microscopy and Microanalysis 23, no. S1 (2017): 1248-1249.

• Srihari S., Singla J., Wong L., Simpson P. T., Khanna K. K. and Ragan M. A. “Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response”, accepted for Poster presentation in San Antonio Breast Cancer Symposium (SABCS 2015) and abstract appeared in AACR Cancer Research - Abstract PD6-05. Poster

Book Chapters

• Singh, A., Dhaka, P., Kumar, P., Tomar, S., & Singla, J. (2024). Bioinformatics Databases and Tools Available for the Development of Antiviral Drugs. In Advances in Antiviral Research (pp. 41-71). Singapore: Springer Nature Singapore.

Talks / Panels / Seminars

• Invited talk, "Algorithms to Architecture: Navigating the Molecular and Mesoscale Landscape of Cells" at Department of Biological Sciences and Engineering, IIT Gandhinagar, 22 Jan 2024.

• Invited Speaker for Panel Discussion on "New Technologies" at IndicTeenFest19, organized by IGenPlus, June 5-9, 2019, Sonipat, India.

• Lead a panel discussion on “Where are we going?” at Pancreatic Beta Cell Consortium Retreat, November 9-11, 2018, Catalina Island, California.

• Talk at the Dynamo Workshop, University of Basel, Switzerland, August 23-25, 2017. "From Visual Proteomics to Whole cell modeling".

• Invited talk at the 2nd Annual da Vinci Convergence Symposium: A Scientific Summit on Computational Modeling across the Scales, Santa Monica, CA, Mar 9, 2017. "From Visual Proteomics to Whole cell modeling".