Recent papers
T Barry, Z Niu, E Katsevich, X Lin. “The permuted score test for robust differential expression analysis,” 2025. [arXiv]
L Fischer, T Barry, A Ramdas. “Multiple testing with anytime-valid Monte-Carlo p-values,” 2024. [arXiv]
T Barry, K Mason, K Roeder, E Katsevich. “Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection,” Genome Biology, 2024. [Journal] [bioRxiv] [Replication code]. (Mihaela Serban Memorial Award, American Statistical Association, Pittsburgh chapter)
T Barry, K Roeder, E Katsevich. “Exponential family measurement error models for single-cell CRISPR screens.” Biostatistics, 2024. [Journal] [arXiv] [Replication code].
J Morris, C Caragine, Z Daniloski, J Domingo, T Barry, L Lu, K Davis, M Ziosi, D Glinos, S Hao, E Mimitou, P Smibert, K Roeder, E Katsevich, T Lappalainen, N Sanjana. “Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens.” Science, 2023. [Journal].
T Barry, X Wang, J Morris, K Roeder, E Katsevich. “SCEPTRE improves calibration and sensitivity in single-cell CRISPR screen analysis.” Genome Biology, 2021. [Journal] [Replication code]. (Reviewers’ choice, American Society of Human Genetics conference)
Book
T Barry, J Deutsch, E Katsevich. “Hands-on single-cell CRISPR screen analysis,” updated April 2024. [ebook preprint]
Software
- sceptre: statistically rigorous, massively scalable single-cell CRISPR screen analysis
- ondisc: out-of-core and cluster-scale computing on single-cell data
Broader use of these tools
Industry: 10x Genomics (main commercial supplier of single-cell CRISPR screen kits)
Example research: Chardon et al., Nat. Com. 2024; Morris et al., Science 2023