论文 — AIDDPM 实验室

2026 Nature Medicine

Generalizable AI predicts immunotherapy outcomes across cancers and treatments

Shen W., Moon I., Nguyen T. H., Li M. M., Huang Y., Nair N., Marbach D.*, and Zitnik M.*

Nat. Med., 32, 3010–3022, 2026
2026 Nature Communications

Activity-cliff awareness enables robust graph learning for molecular property prediction

Cui C., Shi X. C., Su X., Zhang Z., Arce A. V., Wang J., Zhang Y., Wu J., Chen Y. Z.*, Zitnik M.*, and Shen W.*

Nat. Commun., 17, 9376, 2026
2026 ChemRxiv

MusicMol: Bidirectional Molecule–Music Translation via Neighborhood-Aligned Generation and Transformer Decoding

Tang J., Zhu Z., Cui C., Ke N., Song C., Li Y., Zhou Y., Yu C., Jing P., Zhu C., Yang Z., Shen W.*

ChemRxiv, 2026
2026 ChemRxiv

Bridging Molecular Fingerprints and Graph Neural Networks through Knowledge-Guided Pooling (FPPool)

Cui C., Feng S., Song C., Yu S., Lu S., Chen Y. Z.*, Shen W.*

ChemRxiv, 2026
2026 bioRxiv

Medea: An Omics AI Agent for Therapeutic Discovery

Sui P., Li M. M., Gao S., Shen W., Giunchiglia V., Shen A., Huang Y., Kong Z., Zitnik M.*

bioRxiv, 2026
2026 Journal of Chemical Information and Modeling

TradePool: A Novel Interpretable Framework for Quantifying Atomic Attribution Values in Molecular Property Prediction

Ni B, Shen W., Ye Z*

J. Chem. Inf. Model., 66 (2), 881–893, 2026
2024 Nature Machine Intelligence

Efficient Generation of Protein Pockets with PocketGen

Zhang Z., Shen W., Liu Q.*, Zitnik M.*

Nat. Mach. Intell., 6(11), 1382–1395, 2024
2024 PNAS Nexus

Raman Spectroscopic Deep Learning with Signal Aggregated Representations for Enhanced Cell Phenotype and Signature Identification

Lu S., Huang Y., Shen W., Cao Y. L., Cai M., Chen Y., Tan Y., Jiang Y. Y.*, Chen Y. Z.*

PNAS Nexus, 3(8), pgae268, 2024
2024 Nature Biomedical Engineering

Bidirectional Linkage of DNA Barcodes for the Multiplexed Mapping of Higher-Order Protein Interactions in Cells

Liu Y.*, Sundah N. R.*, Ho N. R. Y., Shen W., Xu Y., Natalia A., Yu Z., Seet J. E., Chan C. W., Loh T. P., Lim B. Y.*, Shao H.*

Nat. Biomed. Eng., 8(7), 909–923, 2024
2023 Cell Press Patterns

Enhanced Metagenomic Deep Learning for Disease Prediction and Consistent Signature Recognition by Restructured Microbiome 2D Representations

Shen W., Liang S. R., Jiang Y. Y.*, Chen Y. Z*.

Patterns, 4(1), 100658, 2023
2023 Cell Press Patterns 🏆 People of Data Feature

Toward Ordered-Omics Data Science: Researchers on the Magic of Turning Metagenomic Chaos into Image-Like Patterns

Shen W.*, Chen Y. Z.*

Patterns, People of Data Special Issue, 4(1), 100673, 2023
2023 Computers in Biology and Medicine

Deep Learning of 2D-Restructured Gene Expression Representations for Improved Low-Sample Therapeutic Response Prediction

Cheng K.#, Shen W.#, Jiang Y., Chen Y., Chen Y. Z.*, Tan Y.*

Comput. Biol. Med., 164, 107245, 2023
2023 Brain, Behavior, & Immunity – Health

Chronic Treatment with Baicalein Alleviates Behavioural Disorders and Improves Cerebral Blood Flow via Reverting Metabolic Abnormalities in a J20 Transgenic Mouse Model of Alzheimer's Disease

Zhang L., Wong L. R., Wong P., Shen W., Yang S., Huang L., Lim Y. A., Ho P. C. L.*

Brain Behav. Immun. Health, 28, 100599, 2023
2022 Nucleic Acids Research

AggMapNet: Enhanced and Explainable Low-Sample Omics Deep Learning with Feature-Aggregated Multi-Channel Networks

Shen W., Liu Y., Chen Y., Zeng X., Tan Y., Jiang Y. Y.*, Chen Y. Z.*

Nucleic Acids Res., 50(8), e45, 2022
2022 ACS Sensors

Fluorescence Analysis of Circulating Exosomes for Breast Cancer Diagnosis Using a Sensor Array and Deep Learning

Jin Y., Du N., Huang Y., Shen W., Tan Y., Chen Y. Z., Dou W.-T., He X.-P., Yang Z., Xu N., Tan C.*

ACS Sens., 7(5), 1524–1532, 2022
2021 Nature Machine Intelligence

Out-of-the-Box Deep Learning Prediction of Pharmaceutical Properties by Broadly Learned Knowledge-Based Molecular Representations (MolMap)

Shen W., Zeng X., Zhu F., Wang Y., Qin C., Tan Y., Jiang Y. Y.*, Chen Y. Z.*

Nat. Mach. Intell., 3(4), 334–343, 2021
2021 ACS Chemical Biology

High-Content Phenotypic Screen of a Focused TCAMS Drug Library Identifies Novel Disruptors of the Malaria Parasite Calcium Dynamics

Chia W., Gomez-Lorenzo M. G., Castellote I., Tong J. X., Chandramohanadas R., Thu Chu T. T., Shen W., … Tan K. S.*

ACS Chem. Biol., 16(11), 2348–2372, 2021
2021 Life Sciences

Functional Effects of Berberine in Modulating Mitochondrial Dysfunction and Inflammatory Response in the Respective Amyloidogenic Cells and Activated Microglial Cells – In Vitro Models Simulating Alzheimer's Disease Pathology

Wong L. R., Tan E. A., Lim M. E. J., Shen W., Lian X. L., Wang Y., Chen L., Ho P. C. L.*

Life Sci., 282, 119824, 2021
2021 Nucleic Acids Research

MASI: Microbiota–Active Substance Interactions Database

Zeng X., Yang X., Fan J., Tan Y., Ju L., Shen W., Cui C., Zhu F., Chen Y. Z.*

Nucleic Acids Res., 49(D1), D776–D782, 2021
2017 Molecular Informatics

Predicting the Enzymatic Hydrolysis Half-Lives of New Chemicals Using Support Vector Regression Models Based on Stepwise Feature Elimination

Shen W., Xiao T., Chen S., Liu F., Chen Y. Z.*, Jiang Y.*

Mol. Inform., 36(11), 2017
2017 Oncotarget

Arctigenin Inhibits STAT3 and Exhibits Anticancer Potential in Human Triple-Negative Breast Cancer Therapy

Feng T. T.#, Cao W.#, Shen W., … [et al.]

Oncotarget, 8(1), 329–344, 2017
2015 Open Life Sciences

Mutation of the Conserved GRG Motif and Decreasing Activity of Human RNase H2

Li L., Shen W., Zheng J., [et al.]

Open Life Sci., 10(1), 2015