WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. - Anthony Santella; Raúl Catena; Ismar Kovacevic; Pavak K. Shah; Zidong Yu; Javier Marquina-Solis; Abhishek Kumar; Yicong Wu; James C. Schaff; Daniel Colón-Ramos; Hari Shroff; William Mohler; et al. (BMC Bioinform., 2015)

An Exact Hypergraph Matching Algorithm for Nuclear Identification in Embryonic Caenorhabditis elegans. - Andrew Lauziere; Ryan Christensen; Hari Shroff; Radu Balan (CoRR, 2021)

Multiple Hypothesis Hypergraph Tracking for Posture Identification in Embryonic Caenorhabditis elegans. - Andrew Lauziere; Evan Ardiel; Stephen Xu; Hari Shroff (CoRR, 2021)

Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10. - Leonard Campanello; Maria K. Traver; Hari Shroff; Brian C. Schaefer; Wolfgang Losert (PLoS Comput. Biol., 2021)

A Semi-automatic Cell Tracking Process Towards Completing the 4D Atlas of C. elegans Development. - Andrew Lauziere; Ryan Christensen; Hari Shroff (CoRR, 2022)

Prediction of Cellular Identities from Trajectory and Cell Fate Information. - Baiyang Dai; Jiamin Yang; Hari Shroff; Patrick La Riviere (ISBI, 2024)

DeepPD: Joint Phase and Object Estimation from Phase Diversity with Neural Calibration of a Deformable Mirror. - Magdalena C. Schneider; Courtney Johnson; Cédric Allier; Larissa Heinrich; Diane Adjavon; Joren Husic; Patrick La Riviere; Stephan Saalfeld; Hari Shroff (CoRR, 2025)