iScience: Predicting and interpreting protein and phosphoprotein abundance from pan-cancer and single-cell transcriptomes (Chen Lab)

March 12, 2026

 Hui-Mei Tsai1,2,3,12 ∙ Tzu-Hung Hsiao2,4,5,12 ∙ Yu-Chiao Chiu6,7 ∙ Yufei Huang6,7 ∙ Eric Y. Chuang1,8,9,10 chuangey@ntu.edu.tw ∙ Yidong Chen3,11,13 cheny8@uthscsa.edu Highlights • DeepGxP provides a framework to translate transcriptomes into proteomic insight • DeepEnrich links RNA predictors to functional protein pathways and activities • DeepEnrich reveals cancer type-specific EGFR and HER2 phosphorylation patterns • Mutation effects are captured even without mutation data in model training Summary Proteins that impact phenotype and disease are [...]

Star Protocols: Transformer and graph variational autoencoder to identify microenvironments: A deep learning protocol for spatial transcriptomics (Chen)

January 6, 2026

 Karla Paniagua 1 8, Yufei Huang 2 3 4, Shou-jiang Gao 2 5, Yidong Chen 6 7, Yu-Fang Jin 1, Mario Flores 1 9 Highlights Workflow to build spatial objects linking stitched images with transcriptomics data Steps to apply the transformer and GraphVAE for spatial and contextual tissue modeling Guide to merge gene expression and histology data into one spatial framework. Instructions for clustering and deconvolution to map tumor niches at the single-cell level Summary We present a [...]

Cancer Research: Antibody-Mediated Targeting of Secretory Protein SCUBE3 Suppresses Cancer Progression by Inhibiting Oncogenic Signaling and Inducing Anti-tumor Immunity (Rao, Zhou, Hromas, Sung, Chen, et al)

December 3, 2025

 Deepika Singh Benjamin C. Onyeagucha Daisy Medina Panneerdoss Subbarayalu Rahul Mojidra Dongwen Lv Mukund Bhandari Santosh Timilsina Prabhakar Pitta Venkata Jian Yu. Huang Saif Nirzhor Shahad Abdulsahib Jack Yancy. Prochnau Chris TP. Do Subapriya Rajamanickam Yidong Chen Alexander B. Taylor Suryavathi Viswanadhapalli Maria E. Falzone Jean Jiang Patrick Sung Daohong Zhou Abstract Approaches targeting factors [...]

Cancer Research: Antibody-Mediated Targeting of Secretory Protein SCUBE3 Suppresses Cancer Progression by Inhibiting Oncogenic Signaling and Inducing Anti-tumor Immunity (Rao, Zhou, Hromas, Sung, Chen

December 3, 2025

 Deepika Singh Benjamin C. Onyeagucha Daisy Medina Panneerdoss Subbarayalu Rahul Mojidra Dongwen Lv Mukund Bhandari Santosh Timilsina Prabhakar Pitta Venkata Jian Yu. Huang Saif Nirzhor Shahad Abdulsahib Jack Yancy. Prochnau Chris TP. Do Subapriya Rajamanickam Yidong Chen Alexander B. Taylor Suryavathi Viswanadhapalli Maria E. Falzone Jean Jiang Patrick Sung Daohong Zhou Abstract Approaches targeting factors [...]

Journal of the National Cancer Institute: Integrative multi-omics characterization of hepatocellular carcinoma in Hispanic patients (Zheng, Chen & Lai Labs)

September 4, 2024

 Debodipta Das, PhD, Xiaojing Wang, PhD, Yu-Chiao Chiu, PhD, Hakim Bouamar, PhD, Francis E Sharkey, MD, Jorge E Lopera, MD, Zhao Lai, PhD, Susan T Weintraub, PhD, Xianlin Han, PhD, Yi Zou, MS, Hung-I H Chen, PhD, Carla R Zeballos Torrez, MD, PhD, Xiang Gu, PhD, Matyas Cserhati, PhD, Joel E Michalek, PhD, Glenn A Halff, MD, Yidong Chen, PhD, Siyuan Zheng, PhD, Francisco G Cigarroa, MD, Lu-Zhe Sun, Ph Abstract Background The [...]

Precision Oncology: Pharmacological inhibition of the LIF/LIFR autocrine loop reveals vulnerability of ovarian cancer cells to ferroptosis (Chen, Lai, Rao, et al)

June 17, 2024

       Behnam Ebrahimi, Suryavathi Viswanadhapalli, Uday P. Pratap, Gopalam Rahul, Xue Yang, Prabhakar Pitta Venkata, Viktor Drel, Bindu Santhamma, Swapna Konda, Xiaonan Li, Alondra Lee Rodriguez Sanchez, Hui Yan, Gangadhara R. Sareddy, Zhenming Xu, Brij B. Singh, Philip T. Valente, Yidong Chen, Zhao Lai, Manjeet Rao, Edward R. Kost, Tyler Curiel, Rajeshwar R. [...]

Patterns: Predicting drug response through tumor deconvolution by cancer cell lines (Chen Lab)

April 23, 2024

 Yu-Ching Hsu 1 2 3 4, Yu-Chiao Chiu 5 6, Tzu-Pin Lu 3, Tzu-Hung Hsiao 7, Yidong Chen 4 8 9 Highlights •Scaden-CA is a deep-learning model for tumor deconvolution •Tumor deconvolution facilitates the use of a drug response prediction algorithm •The model explores drug response mechanisms via DNA mutations and/or expression changes The bigger picture Drug repurposing involves utilizing approved or investigational drugs beyond the scope of the original medical application. This approach offers [...]

Science Reports: Sex-dependent differences in the genomic profile of lingual sensory neurons in naïve and tongue-tumor bearing mice (Chen, Lai)

August 14, 2023

 Tarek Ibrahim, Ping Wu, Li-Ju Wang, Chang Fang-Mei, Josue Murillo, Jaclyn Merlo, Sergey S. Shein, Alexei V. Tumanov, Zhao Lai, Korri Weldon, Yidong Chen & Shivani Ruparel Abstract Mechanisms of sex-dependent orofacial pain are widely understudied. A significant gap in knowledge exists about the comprehensive regulation of tissue-specific trigeminal sensory neurons in diseased states of both [...]

PLOS GENETICS: Hepatic ribosomal protein S6 (Rps6) insufficiency results in failed bile duct development and loss of hepatocyte viability; a ribosomopathy-like phenotype that is partially p53-dependent (Chen)

April 6, 2023

 Sarah A. Comerford, Elizabeth A. Hinnant, Yidong Chen, Robert E. Hammer Sarah A. Comerford, Elizabeth A. Hinnant, Yidong Chen, Robert E. Hammer Abstract Defective ribosome biogenesis (RiBi) underlies a group of clinically diverse human diseases collectively known as ribosomopathies, core manifestations of which include cytopenias and developmental abnormalities that are believed to stem primarily from [...]