2026
A Multimodal Foundation Model of Spatial Transcriptomics and Histology for Biological Discovery and Clinical Prediction
J Xiang*, S Hou*, Y Li*, ..., M Diehn, X Zhou#, R Li# (* equal contribution, # corresponding author)
arXiv preprint. 2026
STORM is a multimodal foundation model that integrates spatial transcriptomics and histology for biological discovery, spatial gene expression prediction, and clinical outcome modeling.
A Multimodal Foundation Model of Spatial Transcriptomics and Histology for Biological Discovery and Clinical Prediction
J Xiang*, S Hou*, Y Li*, ..., M Diehn, X Zhou#, R Li# (* equal contribution, # corresponding author)
arXiv preprint. 2026
STORM is a multimodal foundation model that integrates spatial transcriptomics and histology for biological discovery, spatial gene expression prediction, and clinical outcome modeling.
A Generative Foundation Model for Multimodal Histopathology
J Xiang, M Li, S Hou, Y Chen, X Luo, Y Ji, X Zhou, E Adeli, A Chaudhari, CP Langlotz, KM Pohl, R Li
arXiv preprint. 2026
MuPD is a generative foundation model for multimodal histopathology that unifies histology, RNA, and clinical text for cross-modal synthesis, virtual staining, and data augmentation.
A Generative Foundation Model for Multimodal Histopathology
J Xiang, M Li, S Hou, Y Chen, X Luo, Y Ji, X Zhou, E Adeli, A Chaudhari, CP Langlotz, KM Pohl, R Li
arXiv preprint. 2026
MuPD is a generative foundation model for multimodal histopathology that unifies histology, RNA, and clinical text for cross-modal synthesis, virtual staining, and data augmentation.
Large language models for predicting one-year major adverse cardiovascular events in acute coronary syndrome
X Zhang, L Shang, S Hou, J Li, K Yang, F Lai, P Tian, Y Zheng, G Su, T Xu, K Hu, R Huang
iScience 2026
A study on using large language models to predict one-year major adverse cardiovascular events in acute coronary syndrome.
Large language models for predicting one-year major adverse cardiovascular events in acute coronary syndrome
X Zhang, L Shang, S Hou, J Li, K Yang, F Lai, P Tian, Y Zheng, G Su, T Xu, K Hu, R Huang
iScience 2026
A study on using large language models to predict one-year major adverse cardiovascular events in acute coronary syndrome.
A unified framework enables accessible deployment and comprehensive benchmarking of single-cell foundation models
S Hou, P Yang, W Ma, JX Wang, X Zhou
bioRxiv preprint. 2026
A unified framework for deploying and benchmarking single-cell foundation models in a more accessible and reproducible way.
A unified framework enables accessible deployment and comprehensive benchmarking of single-cell foundation models
S Hou, P Yang, W Ma, JX Wang, X Zhou
bioRxiv preprint. 2026
A unified framework for deploying and benchmarking single-cell foundation models in a more accessible and reproducible way.
2025
FastCCC: a permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single-cell transcriptomics studies
S Hou, W Ma, X Zhou
Nature Communications 2025
A scalable framework for robust cell-cell communication analysis in single-cell transcriptomics without costly permutation procedures.
FastCCC: a permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single-cell transcriptomics studies
S Hou, W Ma, X Zhou
Nature Communications 2025
A scalable framework for robust cell-cell communication analysis in single-cell transcriptomics without costly permutation procedures.
Meteorin-like protein inhibits vascular smooth muscle cell-derived foam cell formation and atherosclerosis via KIT-endoplasmic reticulum stress signaling
X Chen*, X Jiang*, S Hou*, ..., T Xu, G Su, R Huang (* equal contribution)
Metabolism 2025
A study on the role of meteorin-like protein in foam cell formation and atherosclerosis through KIT-endoplasmic reticulum stress signaling.
Meteorin-like protein inhibits vascular smooth muscle cell-derived foam cell formation and atherosclerosis via KIT-endoplasmic reticulum stress signaling
X Chen*, X Jiang*, S Hou*, ..., T Xu, G Su, R Huang (* equal contribution)
Metabolism 2025
A study on the role of meteorin-like protein in foam cell formation and atherosclerosis through KIT-endoplasmic reticulum stress signaling.
Optimal transport modeling uncovers spatial domain dynamics in spatiotemporal transcriptomics studies
W Ma, S Hou, L Shang, J Lu, X Zhou
bioRxiv preprint. 2025
A preprint using optimal transport modeling to characterize spatial domain dynamics in spatiotemporal transcriptomics.
Optimal transport modeling uncovers spatial domain dynamics in spatiotemporal transcriptomics studies
W Ma, S Hou, L Shang, J Lu, X Zhou
bioRxiv preprint. 2025
A preprint using optimal transport modeling to characterize spatial domain dynamics in spatiotemporal transcriptomics.
2024
Phenylacetylglutamine accelerated endothelial senescence and early-stage atherosclerosis formation by modulating cholesterol synthesis
R Huang, X Jiang, S Hou, J Li
Circulation 2024
A conference abstract on phenylacetylglutamine, endothelial senescence, and early-stage atherosclerosis.
Phenylacetylglutamine accelerated endothelial senescence and early-stage atherosclerosis formation by modulating cholesterol synthesis
R Huang, X Jiang, S Hou, J Li
Circulation 2024
A conference abstract on phenylacetylglutamine, endothelial senescence, and early-stage atherosclerosis.
Targeting the mSWI/SNF complex in POU2F-POU2AF transcription factor-driven malignancies
T He, L Xiao, Y Qiao, O Klingbeil, E Young, XS Wu, R Mannan, S Hou, et al.
Cancer Cell 2024
A study on targeting the mSWI/SNF complex in transcription factor-driven malignancies.
Targeting the mSWI/SNF complex in POU2F-POU2AF transcription factor-driven malignancies
T He, L Xiao, Y Qiao, O Klingbeil, E Young, XS Wu, R Mannan, S Hou, et al.
Cancer Cell 2024
A study on targeting the mSWI/SNF complex in transcription factor-driven malignancies.
Cohort profile: A longitudinal multi-omics cohort of patients with acute coronary syndrome
R Huang, J Li, K Hu, R Xu, H Yuan, J Wang, M Gao, Q Xiao, B Dong, S Hou, et al.
iMetaOmics 2024
A cohort profile describing a longitudinal multi-omics study of patients with acute coronary syndrome.
Cohort profile: A longitudinal multi-omics cohort of patients with acute coronary syndrome
R Huang, J Li, K Hu, R Xu, H Yuan, J Wang, M Gao, Q Xiao, B Dong, S Hou, et al.
iMetaOmics 2024
A cohort profile describing a longitudinal multi-omics study of patients with acute coronary syndrome.
Development of an orally bioavailable mSWI/SNF ATPase degrader and acquired mechanisms of resistance in prostate cancer
T He, C Cheng, Y Qiao, H Cho, E Young, R Mannan, S Mahapatra, S Hou, et al.
Proceedings of the National Academy of Sciences 2024
A study on an orally bioavailable mSWI/SNF ATPase degrader and resistance mechanisms in prostate cancer.
Development of an orally bioavailable mSWI/SNF ATPase degrader and acquired mechanisms of resistance in prostate cancer
T He, C Cheng, Y Qiao, H Cho, E Young, R Mannan, S Mahapatra, S Hou, et al.
Proceedings of the National Academy of Sciences 2024
A study on an orally bioavailable mSWI/SNF ATPase degrader and resistance mechanisms in prostate cancer.
2023
Metrnl Deficiency Destabilized the Atherosclerotic Plaque and Increased the Risk of Acute Coronary Syndrome
R Huang, F Lai, S Hou
Circulation 2023
A conference abstract on the role of Metrnl deficiency in plaque destabilization and acute coronary syndrome risk.
Metrnl Deficiency Destabilized the Atherosclerotic Plaque and Increased the Risk of Acute Coronary Syndrome
R Huang, F Lai, S Hou
Circulation 2023
A conference abstract on the role of Metrnl deficiency in plaque destabilization and acute coronary syndrome risk.
Development of attention-based robust deep learning model for tongue diagnosis by smartphone
C Ma, C Gao, S Hou, S Li
bioRxiv preprint. 2023
A robust attention-based deep learning model for smartphone-based tongue diagnosis.
Development of attention-based robust deep learning model for tongue diagnosis by smartphone
C Ma, C Gao, S Hou, S Li
bioRxiv preprint. 2023
A robust attention-based deep learning model for smartphone-based tongue diagnosis.
2022
St2cell: Reconstruction of in situ single-cell spatial transcriptomics by integrating high-resolution histological image
S Hou, K Tian, S Yang, J Xiang, W Yang, J Zhang, X Han
bioRxiv preprint. 2022
A preprint on reconstructing in situ single-cell spatial transcriptomics by integrating high-resolution histology images.
St2cell: Reconstruction of in situ single-cell spatial transcriptomics by integrating high-resolution histological image
S Hou, K Tian, S Yang, J Xiang, W Yang, J Zhang, X Han
bioRxiv preprint. 2022
A preprint on reconstructing in situ single-cell spatial transcriptomics by integrating high-resolution histology images.
Decoding multilevel relationships with the human tissue-cell-molecule network
S Hou*, P Zhang*, K Yang*, L Wang, C Ma, Y Li, S Li (* equal contribution)
Briefings in Bioinformatics 2022
A systems-level study that models multilevel relationships across tissues, cell types, and molecules in the human body.
Decoding multilevel relationships with the human tissue-cell-molecule network
S Hou*, P Zhang*, K Yang*, L Wang, C Ma, Y Li, S Li (* equal contribution)
Briefings in Bioinformatics 2022
A systems-level study that models multilevel relationships across tissues, cell types, and molecules in the human body.
Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients
J Cui, S Hou, B Liu, M Yang, L Wei, S Du, S Li
BMC Medical Genomics 2022
A study connecting tongue coating and gastric fluid microbiomes in gastritis patients through species composition and diversity analysis.
Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients
J Cui, S Hou, B Liu, M Yang, L Wei, S Du, S Li
BMC Medical Genomics 2022
A study connecting tongue coating and gastric fluid microbiomes in gastritis patients through species composition and diversity analysis.
2021
iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks
D Wang*, S Hou*, L Zhang, X Wang, B Liu, Z Zhang (* equal contribution)
Genome Biology 2021
A transfer-learning framework for integrating multiple single-cell datasets through adversarial paired networks.
iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks
D Wang*, S Hou*, L Zhang, X Wang, B Liu, Z Zhang (* equal contribution)
Genome Biology 2021
A transfer-learning framework for integrating multiple single-cell datasets through adversarial paired networks.
2020
VISAR: an interactive tool for dissecting chemical features learned by deep neural network QSAR models
Q Ding, S Hou, S Zu, Y Zhang, S Li
Bioinformatics 2020
An interactive analysis tool for interpreting chemical features captured by deep neural network QSAR models.
VISAR: an interactive tool for dissecting chemical features learned by deep neural network QSAR models
Q Ding, S Hou, S Zu, Y Zhang, S Li
Bioinformatics 2020
An interactive analysis tool for interpreting chemical features captured by deep neural network QSAR models.