Author

Mallory A. Laboulaye

Harvard University

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· 1 Genetics· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Organism:mouse· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Irene E. Whitney· 2 shared Joshua R. SanesiD· 2 shared A.D. Choudhury· 1 shared Ahmad SalehiiD· 1 shared Alan Gi-Lun ChengiD· 1 shared Ali Reza Rais Sadati· 1 shared Amber Casillas· 1 shared Andres Gottfried‐BlackmoreiD· 1 shared

Activity by Year

2018-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersNeuroscience

Irene E. Whitney

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Author profile →

3 papers

Recent·Most cited

Benchmarking Cell Type and Gene Set Annotation by Large Language Models with AnnDictionary

George Crowley, Robert C. Jones, Mark A. Krasnow, Angela Oliveira Pisco, Julia Salzman, Nir Yosef, Siyu He, Madhav Mantri, Jessie Aguirre, Ron Garner, Sal Guerrero, William Harper, Resham Irfan, Sophia Mahfouz, Ravi Ponnusamy, , David Seong

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

Nature Communications · Oct 28, 2025Peer-reviewedBioinformatics

MOLECULAR IDENTIFICATION OF SIXTY-THREE AMACRINE CELL TYPES COMPLETES A MOUSE RETINAL CELL ATLAS

Wenjun Yan, Mallory A. Laboulaye, Nicholas M. Tran, Irene E. Whitney, Inbal Benhar, Joshua R. Sanes

This paper identifies 63 amacrine cell types in the mouse retina using scRNA-seq and provides molecular markers, neurotransmitter profiles, and transcription factors for each type.

bioRxiv · Mar 10, 2020 · PreprintNeuroscience

Mapping Transgene Insertion Sites Reveals Complex Interactions Between Mouse Transgenes And Neighboring Endogenous Genes

Mallory A. Laboulaye, Xin Duan, Mu Qiao, Irene E. Whitney, Joshua R. Sanes

The paper maps transgene insertion sites in mice and shows that transgene integration affects neighboring endogenous gene expression.

Frontiers in Molecular Neuroscience · Oct 23, 2018Peer-reviewedGenetics