Author

Pengyue Zhang

Indiana University IndianapolisORCID 0000-0002-9148-5589Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Systems Biology· 2 Neuroscience· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 3 Research Focus:drug response / drug discovery· 3 Organism:human· 2 Assay:DNA methylation· 1 Assay:electronic health records· 1 Research Focus:gene regulatory network inference· 1 Approach:graph neural network· 1 Assay:GWAS summary statistics· 1

Frequent Co-Authors

Mohammadsadeq MottaqiiD· 2 shared Andrew A. PieperiD· 1 shared Chien‐Wei ChiangiD· 1 shared Feixiong ChengiD· 1 shared Ian Adoremos· 1 shared James B. LeverenziD· 1 shared Jeffrey L. CummingsiD· 1 shared Jielin Xu· 1 shared

Activity by Year

2021-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersSystems Biology

Mohammadsadeq MottaqiORCID

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3 papers

Recent·Most cited

A Scalable Sign-Aware Multi-Omics Knowledge Graph Foundation Model for Mechanistic Drug Action and Clinical Response Predictions

Mohammadsadeq Mottaqi, Shuo Zhang, Ian Adoremos, Pengyue Zhang, Lei Xie

This paper introduces a signed multi-omics knowledge graph foundation model for drug action and clinical response predictions, achieving high accuracy and efficiency.

bioRxiv · May 11, 2026 · PreprintSystems Biology

Integrating explainable AI with multiomics systems biology and EHR data mining for personalized drug repurposing in Alzheimer's disease

Mohammadsadeq Mottaqi, Pengyue Zhang, Lei Xie

PRISM-ML integrates multi-omics and EHR data to identify drug repurposing opportunities in Alzheimer's disease by analyzing molecular heterogeneity and predicting therapeutic targets.

Briefings in Bioinformatics · Nov 1, 2025Peer-reviewedSystems Biology

Multimodal single-cell/nucleus RNA-sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer's disease

Jielin Xu, Pengyue Zhang, Yin Huang, Yadi Zhou, Yuan Hou, Lynn M. Bekris, Justin Durla Lathia, Chien‐Wei Chiang, Lang Li, Andrew A. Pieper, James B. Leverenz, Jeffrey L. Cummings, Feixiong Cheng

Genome Research · Feb 24, 2021Peer-reviewedNeuroscience