All Publications

The complete and automatically updated list of my publications is available on Google Scholar. Below is a manually curated list cross-checked against Google Scholar and my CV, most recent first. Names in bold indicate me; an asterisk (*) denotes co-first authorship.

View complete list on Google Scholar



Evidence of off-target probe binding affecting 10x Genomics Xenium gene panels compromise accuracy of spatial transcriptomic profiling

Hallinan C, Ji HJ, Tsou E, Salzberg SL, Fan J

eLife, 2026 Journal

eLife DOI Code

Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity

Velazquez D, Hallinan C, An R, Clifton K, Fan J

bioRxiv, 2025 Preprint

Preprint PDF Code

Impact of Data Quality on Deep Learning Prediction of Spatial Transcriptomics from Histology Images

Hallinan C, Lucas C-HG, Fan J

bioRxiv, 2025 Preprint

Preprint PDF DOI

Spatial mutual nearest neighbors for spatial transcriptomics data

Zhou H, Panwar P, Guo B, Hallinan C, Ghazanfar S, Hicks SC

Bioinformatics, 2025 Journal

Article DOI Code

Heterogeneity-preserving discriminative feature selection for disease-specific subtype discovery (PHet)

M A Basher AR*, Hallinan C*, Lee K

Nature Communications, 2025 Journal

Article DOI Code

Breast Cancer-Derived Extracellular Vesicles Modulate the Cytoplasmic and Cytoskeletal Dynamics of Blood-Brain Barrier Endothelial Cells

Busatto S, Song T-H, Kim HJ, Hallinan C, Lombardo MN, Stemmer-Rachamimov AO, Lee K, Moses MA

Journal of Extracellular Vesicles, 2025 Journal

Article DOI

Crosstalk with postmenopausal obese mammary adipocytes impacts breast cancer cell metabolism and promotes tumorigenesis

Roy R, Aldakhlallah R, Cobbs S, Man E, Hallinan C, Lee K, Lotz-Bousvaros M, Pories S, Moses MA

Cancer Research, 2024 Conference

Integrating Motility and Morphology for Unraveling Cellular Phenotypic Heterogeneity in Breast Cancer Stem Cells

Lee K, Hallinan C, Kim H, Basher A, Abul M, Sui L, Watnick R

Molecular Biology of the Cell, 2024 Conference

Screening adequacy of unstained thyroid fine needle aspiration samples using a deep learning-based classifier (FNA-Net)

Jang J, Kim YH, Westgate B, Zong Y, Hallinan C, Akalin A, Lee K

Scientific Reports, 2023 Journal

Article DOI

Protocol for live cell image segmentation to profile cellular morphodynamics using MARS-Net

Jang J, Hallinan C, Lee K

STAR Protocols, 2022 Journal

Article DOI