ArticleBMC genomics2021
CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens.
Article in BMC genomics, 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, 33 citations in OpenAlex.
- Article
- CRISPR screening redefines therapeutic target identification and drug discovery with precision and scalability.Journal of pharmaceutical analysis · 2026Review
- PRODE recovers essential and context-essential genes through neighborhood-informed scores.Genome biology · 2025Article
- Morphoregulatory ADD3 underlies glioblastoma growth and formation of tumor-tumor connections.Life science alliance · 2025Article
- PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals.Cell reports methods · 2024Article
- HELP: A computational framework for labelling and predicting human common and context-specific essential genes.PLoS computational biology · 2024Article
- A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data.Genome biology · 2024Article
- Exome-wide evidence of compound heterozygous effects across common phenotypes in the UK Biobank.Cell genomics · 2024Article
- CRISPR-Cas9 screens reveal common essential miRNAs in human cancer cell lines.Genome medicine · 2024Article
- Inferring compound heterozygosity from large-scale exome sequencing data.Nature genetics · 2024Article
- Untangling the Context-Specificity of Essential Genes by Means of Machine Learning: A Constructive Experience.Biomolecules · 2023Article
- Gene essentiality in cancer is better predicted by mRNA abundance than by gene regulatory network-inferred activity.NAR cancer · 2023Article
- Inferring compound heterozygosity from large-scale exome sequencing data.bioRxiv : the preprint server for biology · 2023Article
- Exome-wide evidence of compound heterozygous effects across common phenotypes in the UK Biobank.medRxiv : the preprint server for health sciences · 2023Article
- Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank.Nature genetics · 2023Article
- Recovering false negatives in CRISPR fitness screens with JLOE.Nucleic acids research · 2023Article
- High-content CRISPR screening.Nature reviews. Methods primers · 2022Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCRISPR-Cas9 genome-wide screens are being increasingly performed, allowing systematic explorations of cancer dependencies at unprecedented accuracy and scale. One of the major computational challenges when analysing data derived from such screens is to identify genes that are essential for cell survival invariantly across tissues, conditions, and genomic-contexts (core-fitness genes), and to distinguish them from context-specific essential genes. This is of paramount importance to assess the safety profile of candidate therapeutic targets and for elucidating mechanisms involved in tissue-specific genetic diseases.
resultsWe have developed CoRe: an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens. We demonstrate, through a fully reproducible benchmarking pipeline, that CoRe outperforms state-of-the-art tools, yielding more reliable and biologically relevant sets of core-fitness genes.
conclusionsCoRe offers a flexible pipeline, compatible with many pre-processing methods for the analysis of CRISPR data, which can be tailored onto different use-cases. The CoRe package can be used for the identification of high-confidence novel core-fitness genes, as well as a means to filter out potentially cytotoxic hits while analysing cancer dependency datasets for identifying and prioritising novel selective therapeutic targets.
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