Analytical first derivatives of the RE-squared interaction potential. - Mehrtash Babadi; Mohammad Reza Ejtehadi; Ralf Everaers (J. Comput. Phys., 2006)

A Coding Theory Perspective on Multiplexed Molecular Profiling of Biological Tissues. - Luca D'Alessio; Litian Liu; Ken Duffy; Yonina C. Eldar; Muriel Médard; Mehrtash Babadi (ISITA, 2020)

CellSegmenter: unsupervised representation learning and instance segmentation of modular images. - Luca D'Alessio; Mehrtash Babadi (CoRR, 2020)

A Coding Theory Perspective on MultiplexedMolecular Profiling of Biological Tissues. - Luca D'Alessio; Litian Liu; Ken Duffy; Yonina C. Eldar; Muriel Médard; Mehrtash Babadi (CoRR, 2021)

SynapseCLR: Uncovering features of synapses in primary visual cortex through contrastive representation learning. - Alyssa Wilson; Mehrtash Babadi (Patterns, 2023)

Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning. - Robert van Dijk; John Arevalo; Mehrtash Babadi; Anne E. Carpenter; Shantanu Singh (PLoS Comput. Biol., 2024)

TissueMosaic Enables Cross-Sample Differential Analysis of Spatial Transcriptomics Datasets Through Self-supervised Representation Learning. - Sandeep Kambhampati; Luca D'Alessio; Fedor Grab; Stephen Fleming; Fei Chen; Mehrtash Babadi (RECOMB, 2025)

Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching. - Tinglin Huang; Tianyu Liu 005; Mehrtash Babadi; Wengong Jin; Rex Ying (CoRR, 2025)