ArticleBMC genomics2014
Simultaneous analysis of large-scale RNAi screens for pathogen entry.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Artificial Intelligence Methods in Infection Biology Research.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A deep learning dataset for sample preparation artefacts detection in multispectral high-content microscopy.Scientific data · 2024Article
- A fast lasso-based method for inferring higher-order interactions.PLoS computational biology · 2022Article
- Genome-wide siRNA screening reveals several host receptors for the binding of human gut commensal Bifidobacterium bifidum.NPJ biofilms and microbiomes · 2022Article
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- Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation.PLoS computational biology · 2020Article
- Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects.Bioinformatics (Oxford, England) · 2019Article
- A Role for the VPS Retromer inmSphere · 2019Article
- Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration.Nature communications · 2018Article
- Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition.Nucleic acids research · 2018Article
- Improved pathway reconstruction from RNA interference screens by exploiting off-target effects.Bioinformatics (Oxford, England) · 2018Article
- Imaging, Tracking and Computational Analyses of Virus Entry and Egress with the Cytoskeleton.Viruses · 2018Review
- ALPK1 controls TIFA/TRAF6-dependent innate immunity against heptose-1,7-bisphosphate of gram-negative bacteria.PLoS pathogens · 2017Article
- Manipulation of host membranes by the bacterial pathogens Listeria, Francisella, Shigella and Yersinia.Seminars in cell & developmental biology · 2016Review
- Microscopy-based Assays for High-throughput Screening of Host Factors Involved in Brucella Infection of Hela Cells.Journal of visualized experiments : JoVE · 2016Article
- Transfer of DNA from Bacteria to Eukaryotes.mBio · 2016Review
- Viral entry pathways: the example of common cold viruses.Wiener medizinische Wochenschrift (1946) · 2016Review
- A Genome-Wide siRNA Screen Implicates Spire1/2 in SipA-Driven Salmonella Typhimurium Host Cell Invasion.PloS one · 2016Article
- gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens.Genome biology · 2015Article
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Authors and funding
42 authors.
Funding
Abstract
backgroundLarge-scale RNAi screening has become an important technology for identifying genes involved in biological processes of interest. However, the quality of large-scale RNAi screening is often deteriorated by off-targets effects. In order to find statistically significant effector genes for pathogen entry, we systematically analyzed entry pathways in human host cells for eight pathogens using image-based kinome-wide siRNA screens with siRNAs from three vendors. We propose a Parallel Mixed Model (PMM) approach that simultaneously analyzes several non-identical screens performed with the same RNAi libraries.
resultsWe show that PMM gains statistical power for hit detection due to parallel screening. PMM allows incorporating siRNA weights that can be assigned according to available information on RNAi quality. Moreover, PMM is able to estimate a sharedness score that can be used to focus follow-up efforts on generic or specific gene regulators. By fitting a PMM model to our data, we found several novel hit genes for most of the pathogens studied.
conclusionsOur results show parallel RNAi screening can improve the results of individual screens. This is currently particularly interesting when large-scale parallel datasets are becoming more and more publicly available. Our comprehensive siRNA dataset provides a public, freely available resource for further statistical and biological analyses in the high-content, high-throughput siRNA screening field.
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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.