ArticleGenome biology2015
Network analysis of gene essentiality in functional genomics experiments.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- CNN4Essential: a convolutional neural network model for predicting bacterial gene essentiality based on multi-feature fusion.BMC genomics · 2026Article
- NetCrafter: ontology-derived gene network modeling and functional interpretation.Briefings in bioinformatics · 2026Article
- Epitope Generation Gateway: A biological context-dependent approach to cancer vaccine development.GigaScience · 2026Article
- PEANUT: Pathway Enrichment Analysis through Network UTilization.Bioinformatics (Oxford, England) · 2025Article
- PRODE recovers essential and context-essential genes through neighborhood-informed scores.Genome biology · 2025Article
- Machine learning identifies key metabolic reactions in bacterial growth on different carbon sources.Molecular systems biology · 2024Article
- Artificial intelligence in cancer target identification and drug discovery.Signal transduction and targeted therapy · 2022Review
- Review
- An integrated pipeline for mammalian genetic screening.Cell reports methods · 2021Article
- PathCNN: interpretable convolutional neural networks for survival prediction and pathway analysis applied to glioblastoma.Bioinformatics (Oxford, England) · 2021Article
- Dual Inhibition of DKC1 and MEK1/2 Synergistically Restrains the Growth of Colorectal Cancer Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- Systems biology analysis identifiesComputational and structural biotechnology journal · 2021Article
- Coinhibition of activated p38 MAPKα and mTORC1 potentiates stemness maintenance of HSCs from SR1-expanded human cord blood CD34Stem cells translational medicine · 2020Article
- Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling.Cancers · 2020Article
- MasterPATH: network analysis of functional genomics screening data.BMC genomics · 2020Article
- Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources.Metabolites · 2020Review
- SCNrank: spectral clustering for network-based ranking to reveal potential drug targets and its application in pancreatic ductal adenocarcinoma.BMC medical genomics · 2020Article
- WIPER: Weighted in-Path Edge Ranking for biomolecular association networks.Quantitative biology (Beijing, China) · 2019Article
- NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets.Molecules and cells · 2019Article
- HumanNet v2: human gene networks for disease research.Nucleic acids research · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
Many genomic techniques have been developed to study gene essentiality genome-wide, such as CRISPR and shRNA screens. Our analyses of public CRISPR screens suggest protein interaction networks, when integrated with gene expression or histone marks, are highly predictive of gene essentiality. Meanwhile, the quality of CRISPR and shRNA screen results can be significantly enhanced through network neighbor information. We also found network neighbor information to be very informative on prioritizing ChIP-seq target genes and survival indicator genes from tumor profiling. Thus, our study provides a general method for gene essentiality analysis in functional genomic experiments ( http://nest.dfci.harvard.edu ).
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Registered trials
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.