Author

James Boylan

Novartis (Switzerland)

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

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Approach:benchmark study· 2 Research Focus:benchmarking· 2 Research Focus:perturbation response prediction· 2 Assay:bulk RNA-seq· 1 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Bulent Ataman· 2 shared Elizaveta M. SolovyevaiD· 2 shared Jeremy L. JenkinsiD· 2 shared Murthy V DevarakondaiD· 2 shared Sebastian Hoersch· 2 shared Theophile Bouiller· 2 shared Xiong LiuiD· 2 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

7 top collaborators · 21 mutual co-author links

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2 shared papersBioinformatics

Bulent Ataman

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Author profile →

2 papers

Recent·Most cited

Single Cell Foundation Models Evaluation (scFME) for In-Silico Perturbation

James Boylan, Elizaveta M. Solovyeva, Theophile Bouiller, Xiong Liu, Sebastian Hoersch, Bulent Ataman, Jeremy L. Jenkins, Murthy V Devarakonda

The paper introduces scFME, a framework to evaluate fine-tuned foundation models for in-silico perturbation, showing its effectiveness in characterizing model performance.

bioRxiv · Sep 22, 2025 · PreprintBioinformatics

Evaluating Foundation Models for In-Silico Perturbation

Xiong Liu, James Boylan, Theophile Bouiller, Elizaveta M. Solovyeva, Bulent Ataman, Sebastian Hoersch, Jeremy L. Jenkins, Murthy V Devarakonda

This paper evaluates foundation models for in-silico perturbation using a novel framework, revealing differences in their performance across biological contexts and gene categories.

bioRxiv · May 11, 2025 · PreprintBioinformatics