ArticleBMC bioinformatics2017
CRISPulator: a discrete simulation tool for pooled genetic screens.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- A massively parallel CRISPR-based screening platform for modifiers of neuronal depolarization.Nature communications · 2026Article
- simCRISPR: Modeling Experimental Complexity in Pooled CRISPR Screens.bioRxiv : the preprint server for biology · 2026Article
- Double-CRISPR Knockout Simulation (DKOsim): A Monte-Carlo randomization system to model cell growth behavior and infer the optimal library design for growth-based double knockout screens.PLoS computational biology · 2026Article
- Scaling perturbations: beyond genome-scale CRISPR screens.bioRxiv : the preprint server for biology · 2026Article
- CRISPR-StAR enables high-resolution genetic screening in complex in vivo models.Nature biotechnology · 2025Article
- Revealing genetic drivers of ovarian cancer and chemoresistance: insights from whole-genome CRISPR-knockout library screens.Cellular oncology (Dordrecht, Netherlands) · 2025Review
- Article
- A model for accurate quantification of CRISPR effects in pooled FACS screens.bioRxiv : the preprint server for biology · 2024Article
- Neutrophils actively swell to potentiate rapid migration.bioRxiv : the preprint server for biology · 2024Article
- A statistical simulation model to guide the choices of analytical methods in arrayed CRISPR screen experiments.PloS one · 2024Article
- Clonal dynamics limits detection of selection in tumour xenograft CRISPR/Cas9 screens.Cancer gene therapy · 2023Article
- NBBt-test: a versatile method for differential analysis of multiple types of RNA-seq data.Scientific reports · 2022Article
- High-content CRISPR screening.Nature reviews. Methods primers · 2022Article
- Covering the Combinatorial Design Space of Multiplex CRISPR/Cas Experiments in Plants.Frontiers in plant science · 2022Article
- Dissecting Molecular Phenotypes Through FACS-Based Pooled CRISPR Screens.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Click chemistry-enabled CRISPR screening reveals GSK3 as a regulator of PLD signaling.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- MAUDE: inferring expression changes in sorting-based CRISPR screens.Genome biology · 2020Article
- gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection.Genome biology · 2020Article
- Article
- Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems.Frontiers in bioengineering and biotechnology · 2020Review
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Authors and funding
2 authors.
Funding
Abstract
backgroundThe rapid adoption of CRISPR technology has enabled biomedical researchers to conduct CRISPR-based genetic screens in a pooled format. The quality of results from such screens is heavily dependent on the selection of optimal screen design parameters, which also affects cost and scalability. However, the cost and effort of implementing pooled screens prohibits experimental testing of a large number of parameters.
resultsWe present CRISPulator, a Monte Carlo method-based computational tool that simulates the impact of screen parameters on the robustness of screen results, thereby enabling users to build intuition and insights that will inform their experimental strategy. CRISPulator enables the simulation of screens relying on either CRISPR interference (CRISPRi) or CRISPR nuclease (CRISPRn). Pooled screens based on cell growth/survival, as well as fluorescence-activated cell sorting according to fluorescent reporter phenotypes are supported. CRISPulator is freely available online ( http://crispulator.ucsf.edu ).
conclusionsCRISPulator facilitates the design of pooled genetic screens by enabling the exploration of a large space of experimental parameters in silico, rather than through costly experimental trial and error. We illustrate its power by deriving non-obvious rules for optimal screen design.
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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.