Author

Asaf Rotem

Broad InstituteORCID 0000-0002-6859-7435Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 4 Research Focus:cell type annotation· 3 Approach:experimental assay· 3 Assay:scRNA-seq· 3 Research Focus:benchmarking· 2 Research Focus:differential expression· 2 Assay:snRNA-seq· 2 Approach:statistical model· 2

Frequent Co-Authors

Aviv RegeviD· 3 shared Benjamin IzariD· 3 shared Orit Rozenblatt–RoseniD· 3 shared Bruce Evan JohnsoniD· 2 shared Livnat Jerby‐ArnoniD· 2 shared Mei-Ju Su· 2 shared Michael S. CuocoiD· 2 shared Sébastien VigneauiD· 2 shared

Activity by Year

2020-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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3 shared papersGenomics

Aviv RegevORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples

Ojasvi Chaudhary, Mia K. Steinberg, Grant E. Duclos, Peter Gathungu, Manisha Rao, Rogelio Aguilar, Varsha Shankarappa, Chris M. Rands, Xi Chen, Rebecca Halpin, Elizabeth Galery, Joseph F. Boland, Maurizio Scaltriti, Brian Andrew Dougherty, Asaf Rotem

The paper develops a method for single-nucleus RNA-seq of archived PAXgene whole blood samples, achieving high nuclei yields and unbiased cell-type representation through optimized isolation and globin depletion.

Cell Reports Methods · Mar 1, 2026Peer-reviewedGenomics

Transcriptional mediators of treatment resistance in lethal prostate cancer

Meng Xiao He, Michael S. Cuoco, Jett P. Crowdis, Alice Bosma-Moody, Zhenwei Zhang, Kevin Bi, Abhay Kanodia, Mei-Ju Su, Sheng‐Yu Ku, Maria Mica Garcia, Amalia R. Sweet, Christopher Rodman, Laura K. DelloStritto, Rebecca Silver, John A. Steinharter, , Eliezer M. Van Allen

This study identifies transcriptional states in mCRPC that mediate treatment resistance, including AR splicing heterogeneity, TGF-β signaling, and immune infiltration patterns.

Nature Medicine · Mar 1, 2021Peer-reviewedGenomics

Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion

Chris J. Frangieh, Johannes C. Melms, Pratiksha I. Thakore, Kathryn R. Geiger-Schuller, Patricia Ho, Adrienne Luoma, Brian Cleary, Livnat Jerby‐Arnon, Shruti Malu, Michael S. Cuoco, Maryann Zhao, Casey R. Ager, Meri Rogava, Lila Hovey, Asaf Rotem, , Benjamin Izar

The paper uses Perturb-CITE-Seq to identify novel immune evasion mechanisms in cancer by analyzing multi-modal single-cell data from patient-derived models.

Nature Genetics · Mar 1, 2021Peer-reviewedGenomics

A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors

Michal Slyper, Caroline B. M. Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Christopher S. Smillie, Gabriela Smith-Rosario, Jingyi Wu, Danielle Ashley Dionne, Sébastien Vigneau, Judit Jané‐Valbuena, Timothy L. Tickle, Sara Napolitano, Mei-Ju Su, , Aviv Regev

The paper develops a toolbox for scRNA-Seq and snRNA-Seq of fresh and frozen human tumors, testing it across eight tumor types and optimizing protocols for different tissue characteristics.

Nature Medicine · May 1, 2020Peer-reviewedGenomics