Author

Muhammad Haroon Shakeel

Adelaide UniversityORCID 0000-0001-6237-3388Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:dimensionality reduction· 2 Assay:scRNA-seq· 2 Research Focus:batch correction / integration· 1 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Mengyuan SheniD· 2 shared Stefano MangiolaiD· 2 shared Anthony T. PapenfussiD· 1 shared Chen Zhan· 1 shared Dharmesh Dinesh BhuvaiD· 1 shared Edward YangiD· 1 shared Jared M. AndrewsiD· 1 shared Jose Maria PoloiD· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Mengyuan ShenORCID

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2 papers

Recent·Most cited

Re-evaluating the benefit of training scale in cell foundation models

Muhammad Haroon Shakeel, Mengyuan Shen, Stefano Mangiola

This study evaluates how training scale affects cell foundation models by comparing performance with frozen representations and finds that larger pretraining data improves model performance.

bioRxiv · Jun 6, 2026 · PreprintBioinformatics

cellNexus: Quality control, annotation, aggregation and analytical layers for the Human Cell Atlas data

Mengyuan Shen, Yingnan Gao, Ning Liu, Dharmesh Dinesh Bhuva, Michael Milton, Juan Henao, Jared M. Andrews, Edward Yang, Chen Zhan, Nora Liu, Susan Si, William J. Hutchison, Muhammad Haroon Shakeel, Martin T. Morgan, Anthony T. Papenfuss, , Stefano Mangiola

cellNexus enhances Human Cell Atlas data by adding quality control, metadata, normalization, and analysis layers to enable multi-study analyses and large-scale biological discovery.

bioRxiv · May 5, 2026 · PreprintBioinformatics