Biology subjects

Kalinka, A.

Publications and source records attributed to Kalinka, A..

3 recordsLinked to original sources

bioRxiv2026

Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics

Pooled CRISPR screens coupled with single-cell RNA sequencing enable high-throughput functional interrogation of gene regulatory networks, yet systematic comparisons of CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) remain limited. We established a single-cell CRISPRko workflow and benchmarked it against CRISPRi using 87 sgRNAs targeting 29 unfolded protein response genes. CRISPRko generated transcriptional phenotypes are highly concordant with CRISPRi, and induced comparable pathway-level responses. While CRISPRi allows direct assessment of target gene repression, CRISPRko provides an effective complementary approach for complete loss-of-function studies, expanding the toolkit for single-cell functional genomics.

genomics↗

bioRxiv2025

Controlling False Discovery in CRISPR Screens

Excluding false positives is critical for interpreting CRISPR screens. Here, we introduce a new Chronos module for estimating false discovery rates for identifying knockouts that cause loss of viability or have differential viability effects in different conditions. We introduce a rigorous benchmarking framework using real CRISPR data. We show with multiple real datasets that existing methods such as MAGeCK are miscalibrated and can generate uncontrolled numbers of false positives even after multiple hypothesis correction. Only Chronos correctly controls false discovery for all tested tasks. Additionally, Chronoss estimates are well-calibrated, allowing users to accurately specify the acceptable false discovery rate.

bioinformatics↗

bioRxiv2024

A benchmark comparison of CRISPRn guide-RNA design algorithms and generation of small single and dual-targeting libraries to boost screening efficiency

Genome-wide CRISPR sgRNA libraries have emerged as transformative tools to systematically probe gene function. While these libraries have been iterated over time to be more efficient, their large size limits their use in some applications. Here, we benchmarked publicly available genome-wide single-targeting sgRNA libraries and evaluated dual targeting as a strategy for pooled CRISPR loss-of-function screens. We leveraged this data to design two minimal genome-wide human CRISPR-Cas9 libraries that are 50% smaller than other libraries and that preserve specificity and sensitivity, thus enabling broader deployment at scale.

molecular biology↗