Vipul Singhal

Vipul Singhal

I am interested in developing AI and ML algorithms for spatial multi-omics data analysis.

Mentorship (undergraduate and masters students)

Mentorship, Caltech and GIS, 2020

Over the years, I have had the opportunity to mentor and work with various students. Here is a list of their projects.

GIS

  • Jeena Kataria (NJIT, 2024)
    • Working on developing an exon-intron split analysis (EISA) workflow for spatial omics.
  • Zhang Xiaoyu (NUS, 2020)
    • Worked on improving the stability and documentation of a code base for fast spot assignment to segmentation masks, which implicitly impements a generalized Voronoi segmentation scheme on DAPI stains.
  • Joseph Lee (NUS, 2021-2023)
    • Became a core developer for the BANKSY project, going from refactoring and greatly improving the code base to analyzing datasets, and helping develop ideas conceptually.
  • Yew Shu Ning (NUS, 2020)
    • Integrated registration and stitching code for the MERFISH project into the existing framework of the decoding pipeline. Developed methods for smFISH spot callout by devising methods to discriminate between off-target and on-target signal.

Caltech

  • Xianglin (Flora) Meng (Oxford, UK, 2015). Flora managed to publish a paper from the work she did during the three months she was in our lab in Caltech. Her work was on finding stationary solutions to the chemical master equation (CME) by gluing graphs representing CME state spaces.
  • Cody Dunn (Cal State University, Long Beach, USA, 2015). Cody worked on methods for identifying bimodality in distributions arising from solutions of the CME (via the stochastic simulation algorithm, for example) chemical reaction networks.
  • Ronnie Rodrigues Pereira (KTH Royal Institute of Technology, Sweden), 2015. Identifiability analysis (using the GenSSI toolbox) and MCMC based parameter estimation for mass action models of synthetic genetic circuits.
  • Anushka Rau (Caltech, USA), Enrique Amaya (Mexico), 2015; Anton Frisk (Lund University, Sweden), Pulkit Malik (University of Maryland, USA), Tiffany Zhou (Caltech, USA), 2014. These interns worked on wet lab and dry lab characterization of genetic circuits (IFFL, bistable switch, and the characterization of various combinatorial promoters) in cell-free systems over 2014-2015.