publications

Journals

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

        • The article was picked up by 3 news outlets: Science Newline, Medical Xpress and Science blog.

  • Singla J., White K. L., Stevens R. C. and Alber F. Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography.bioRxiv 2020.06.23.125823 (Conditionally accepted at Journal of Structural Biology) Paper

  • Singla J. and White K. L. “A community approach to whole-cell modeling” (Invited review in Current Opinion in Systems Biology, Under Review)

  • 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.Structure, 27(4), 679-691 (2019) Paper

        • Highlighted by Nature Methods under title “Template-free visual proteomics.

  • 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. and Stevens R. C. “Visualizing subcellular rearrangements in intact β-cells using soft X-ray tomography ." Science Advances 6, eabc8262 (2020) Paper

        • Highlighted by Science under title “Subcellular map of vesicle maturation.”

        • The article was picked up by 4 news outlets: Phys.org, Mirage News, Medical Xpress and EurekAlert.

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

  • Srihari S., Singla J., Wong L., and Ragan M. A. Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer.” Biology direct, 10(1), 57 (2015) Paper

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

Conference Posters

  • 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. Abstract

  • 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. Abstract

  • 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 Abstract

Talks / Panels / Seminars

  • Invited talk at the Department of Biotechnology, IIT Roorkee, Jan 23, 2020, "Unsupervised Pattern Mining for building whole cell models".

  • 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".