Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data. - Shuonan Chen; Jessica Cara Mar (BMC Bioinform., 2018)

BARcode DEmixing through Non-negative Spatial Regression (BarDensr). - Shuonan Chen; Jackson Loper; Xiaoyin Chen; Alex Vaughan; Anthony M. Zador; Liam Paninski (PLoS Comput. Biol., 2021)

Blind demixing methods for recovering dense neuronal morphology from barcode imaging data. - Shuonan Chen; Jackson Loper; Pengcheng Zhou; Liam Paninski (PLoS Comput. Biol., 2022)

Multimodal Microscopy Image Alignment Using Spatial and Shape Information and a Branch-and-Bound Algorithm. - Shuonan Chen; Bovey Y. Rao; Stephanie Herrlinger; Attila Losonczy; Liam Paninski; Erdem Varol (ICASSP, 2023)