ArticleMolecular systems biology2021
A method for benchmarking genetic screens reveals a predominant mitochondrial bias.
Article in Molecular systems biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 23 citations in OpenAlex.
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- A Chemical-Genetic Interaction Matrix Reveals Drug Mechanism and Genetic Architecture.bioRxiv : the preprint server for biology · 2026Article
- Quantitative analysis of genetic interactions in human cells from genome-wide CRISPR-Cas9 screens.bioRxiv : the preprint server for biology · 2026Article
- mtKO: A dedicated guide RNA library for mitochondria research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A global genetic interaction map of a human cell reveals conserved principles of genetic networks.bioRxiv : the preprint server for biology · 2025Article
- BaCoN (Balanced Correlation Network) improves prediction of gene buffering.Molecular systems biology · 2025Article
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- The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2.bioRxiv : the preprint server for biology · 2024Article
- Functional genomic analysis of genes important for Candida albicans fitness in diverse environmental conditions.Cell reports · 2024Article
- A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds.Scientific reports · 2024Article
- Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens.Molecular systems biology · 2023Article
- Automated assembly of molecular mechanisms at scale from text mining and curated databases.Molecular systems biology · 2023Article
- Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens.bioRxiv : the preprint server for biology · 2023Article
- Recovering false negatives in CRISPR fitness screens with JLOE.Nucleic acids research · 2023Article
- Optimal construction of a functional interaction network from pooled library CRISPR fitness screens.BMC bioinformatics · 2022Article
- A method for benchmarking genetic screens reveals a predominant mitochondrial bias.Molecular systems biology · 2021Article
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Authors and funding
12 authors at 2 institutions in 2 countries.
Funding
Abstract
We present FLEX (Functional evaluation of experimental perturbations), a pipeline that leverages several functional annotation resources to establish reference standards for benchmarking human genome-wide CRISPR screen data and methods for analyzing them. FLEX provides a quantitative measurement of the functional information captured by a given gene-pair dataset and a means to explore the diversity of functions captured by the input dataset. We apply FLEX to analyze data from the diverse cell line screens generated by the DepMap project. We identify a predominant mitochondria-associated signal within co-essentiality networks derived from these data and explore the basis of this signal. Our analysis and time-resolved CRISPR screens in a single cell line suggest that the variable phenotypes associated with mitochondria genes across cells may reflect screen dynamics and protein stability effects rather than genetic dependencies. We characterize this functional bias and demonstrate its relevance for interpreting differential hits in any CRISPR screening context. More generally, we demonstrate the utility of the FLEX pipeline for performing robust comparative evaluations of CRISPR screens or methods for processing them.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.