Author

Ari J. Firestone

Calico Life SciencesORCID 0000-0001-9902-443XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Assay:CRISPR screen· 1 Approach:deep learning· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Caitlin Baxter· 1 shared Charles L. SawyersiD· 1 shared Chen Khuan WongiD· 1 shared D. Henry Kates· 1 shared Diana Zakharova· 1 shared Hojin Lee· 1 shared Jungmin ChoiiD· 1 shared Maren BüttneriD· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

1 shared paperCancer Biology

Caitlin Baxter

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

MAJEC: unified gene, isoform, and locus-level transposable element quantification from RNA-seq

Tian-Yeh Lim, Ari J. Firestone

MAJEC improves TE quantification by jointly estimating gene, isoform, and locus-level TE counts from RNA-seq, reducing exon-overlap contamination and increasing accuracy.

Bioinformatics · Oct 1, 2026Peer-reviewedBioinformatics

Dependencies in heterogeneous, lineage plastic patient-derived prostate cancer organoids revealed through integrated single-cell multiomics and CRISPR screening

Samir Zaidi, Maren Büttner, Weiran Feng, Caitlin Baxter, D. Henry Kates, Tiago Paiva Prudente, Diana Zakharova, Sanjoy Mehta, Subhiksha Nandakumar, Chen Khuan Wong, Hojin Lee, Pierre-Jacques Hamard, Wenfei Kang, Jungmin Choi, Ronan Chaligne, , Charles L. Sawyers

The paper integrates single-cell multiomics and CRISPR screening in prostate cancer organoids to reveal lineage-specific dependencies and heterogeneity effects on gene essentiality.

bioRxiv · May 8, 2026 · PreprintCancer Biology