Author

Karim Mrouj

Stanford MedicineORCID 0000-0002-8066-9833Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Research Focus:benchmarking· 2 Research Focus:cell type annotation· 2 Organism:human· 2 Assay:scRNA-seq· 2 Research Focus:batch correction / integration· 1 Approach:benchmark study· 1 Assay:bulk RNA-seq· 1 Approach:contrastive learning· 1

Frequent Co-Authors

Mark A. KrasnowiD· 3 shared Maurizio MorriiD· 3 shared Patrick NeuhöferiD· 3 shared Rebecca Neal CulveriD· 3 shared Robert C. JonesiD· 3 shared Sheela Crasta· 3 shared Shravani MukherjeeiD· 3 shared SoRi JangiD· 3 shared

Activity by Year

2022-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Mark A. KrasnowORCID

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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

Adversarial domain translation networks for fast and accurate integration of large-scale atlas-level single-cell datasets

Jia Zhao, Gefei Wang, Jingsi Ming, Zhixiang Lin, Yang Wang, Snigdha Agarwal, Aditi Agrawal, Ahmad Al‐Moujahed, Alina A. Alam, Megan A. Albertelli, Paul Allegakoen, Thomas H. Ambrosi, Jane Antony, Steven E. Artandi, Fabienne Aujard, , Patricia Kim Phuong Nguyen

Portal integrates large-scale single-cell datasets efficiently and accurately by preserving biological variation across samples, platforms, and species.

Nature Computational Science · May 30, 2022Peer-reviewedBioinformatics

The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans

Robert C. Jones, Jim Karkanias, Mark A. Krasnow, Angela Oliveira Pisco, Stephen R. Quake, Julia Salzman, Nir Yosef, Bryan Bulthaup, Phillip Brown, William Harper, Marisa Hemenez, Ravikumar Ponnusamy, Ahmad Salehi, Bhavani A. Sanagavarapu, Eileen Spallino, , Andrea R. Yung

Nearly 500,000 cells from 24 human tissues, many from one donor, characterize over 400 cell types and enable within-donor study of T-cell clones, B-cell mutation rates and splicing.

Science · May 12, 2022Peer-reviewedCell Biology