Author

Yuanchao Zhang

Children's Hospital of Philadelphia

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

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Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 3 Research Focus:database / resource· 2 Research Focus:software / tool· 2 Research Focus:dimensionality reduction· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Approach:matrix factorization· 1

Frequent Co-Authors

Asif ChinwallaiD· 3 shared Benjamin J. SteariD· 3 shared Chris NemarichiD· 3 shared Deanne M. TayloriD· 3 shared J. Alan Simmons· 3 shared Jonathan C. SilversteiniD· 3 shared Taha Mohseni AhooyiiD· 3 shared Aditya LahiriiD· 2 shared

Activity by Year

2026-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 44 mutual co-author links

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3 shared papersBioinformatics

Asif ChinwallaORCID

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Author profile →

3 papers

Recent·Most cited

ddkg.skill: A Compositional Agent Skill for Translating Biomedical and Bioinformatics Questions into Cypher for the Data Distillery Knowledge Graph

Deanne M. Taylor, Aditya M. Lahiri, Benjamin J. Stear, Taha Mohseni Ahooyi, Yuanchao Zhang, Asif Chinwalla, Shiping Zhang, Chris Nemarich, J. Alan Simmons, Jonathan C. Silverstein

ddkg.skill translates biomedical questions into Cypher queries for the DDKG, improving accuracy through structured references and validation.

bioRxiv · Oct 7, 2026 · PreprintBioinformatics

MOSAIC: Learning Graph Node Embeddings from Spectrally Isolated Dominant Subspaces of Accumulated Diffusion Operators

Taha Mohseni Ahooyi, Benjamin J. Stear, Yuanchao Zhang, Aditya Lahiri, James Terry, Shiping Zhang, J. Alan Simmons, Ryan Corbett, Patricia Sullivan, Asif Chinwalla, Chris Nemarich, Jo Lynne Rokita, Sharon J. Diskin, Jonathan C. Silverstein, Deanne M. Taylor

MOSAIC learns graph node embeddings by analyzing dominant spectral components of diffusion operators, outperforming existing methods in biomedical graph tasks.

bioRxiv · Oct 6, 2026 · PreprintBioinformatics

BIFO: A Biological Information Flow Ontology for Directed Propagation in Heterogeneous Biomedical Knowledge Graphs

Deanne M. Taylor, Taha Mohseni Ahooyi, Benjamin J. Stear, Yuanchao Zhang, Aditya Lahiri, J. Alan Simmons, Asif Chinwalla, Chris Nemarich, Tiffany J. Callahan, Jonathan C. Silverstein

The paper introduces BIFO, an ontology that specifies biologically admissible directed transformations in biomedical knowledge graphs to enable meaningful signal propagation.

bioRxiv · May 28, 2026 · PreprintBioinformatics