publications

Journals and Conferences

2024

Singh, V., Bhutkar, M., Choudhary, S., Nehul, S., Kumar, R., Singla, J., ... & Tomar, S. (2024). Enhancing affinity of neutralizing SARS-CoV-2 nanobody through facile structure-guided mutations in CDRs. bioRxiv, 2024-05.
Kaur, H., Rode, S., Sandra, K. P., Mahto, J. K., Alam, M. S., Gupta, D. N., ... & Sharma, A. K. (2024). Characterization of haloacid dehalogenase superfamily acid phosphatase from Staphylococcus lugdunensis. Archives of Biochemistry and Biophysics, 753, 109888.

2023

Jothishwaran, C. A., Srivastava, B., Singla, J., & Gangopadhyay, S. (2023). On Learning with LAD. arXiv preprint arXiv:2309.16630.
Maheshwari, A., Gupta, A., Krishna, A., Singh, A. K., Ramakrishnan, G., Kumar, G. A., & Singla, J. (2023). Sāmayik: A Benchmark and Dataset for English-Sanskrit Translation. arXiv preprint arXiv:2305.14004.
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

2022

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.

2021

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.

2015-2020

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 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

Interacted with Indian PhD students at USC Viterbi School of Engineering on "Career oppotunities in Indian Academic", focusing on opportunities at IIT Roorkee.
Invited talk, "Algorithms to Architecture: Navigating the Molecular and Mesoscale Landscape of Cells" at Bridge Institute, Universoty of Southern California, Los Angeles, USA, 19 Jun 2024.
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".