ArticleNucleic acids research2011
Génie: literature-based gene prioritization at multi genomic scale.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 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.
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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.
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Who cites it
46 citing papers in PubMed.
- Literature-informed gene extraction and ranking for multimodal data fusion.Briefings in bioinformatics · 2026Article
- Immediate implant placement in infected sites using the "Roll BMP" technique: a 3-year case report with bioinformatic analysis.Frontiers in dental medicine · 2026Article
- Automating candidate gene prioritization with large language models: from naive scoring to literature-grounded validation.Bioinformatics (Oxford, England) · 2025Article
- Etiology of pulp necrosis as a predictor of success in regenerative endodontics: a case report and bioinformatic analysis.Frontiers in dental medicine · 2025Article
- Aphthous stomatitis - computational biology suggests external biotic stimulus and immunogenic cell death involved.BMC oral health · 2024Article
- A multi-platform analysis of human gingival crevicular fluid reveals ferroptosis as a relevant regulated cell death mechanism during the clinical progression of periodontitis.International journal of oral science · 2024Article
- Text-mining-based feature selection for anticancer drug response prediction.Bioinformatics advances · 2024Article
- A Systematic Review of Lipid-Focused Cardiovascular Disease Research: Trends and Opportunities.Current issues in molecular biology · 2023Review
- Adverse Crosstalk between Extracellular Matrix Remodeling and Ferroptosis in Basal Breast Cancer.Cells · 2023Article
- Creating an ignorance-base: Exploring known unknowns in the scientific literature.Journal of biomedical informatics · 2023Article
- Genetics in non-alcoholic fatty liver disease: The role of risk alleles through the lens of immune response.Clinical and molecular hepatology · 2023Review
- Early Deregulation of Cholangiocyte NR0B2 During Primary Sclerosing Cholangitis.Gastro hep advances · 2023Article
- A novel candidate disease gene prioritization method using deep graph convolutional networks and semi-supervised learning.BMC bioinformatics · 2022Article
- Performance Assessment of the Network Reconstruction Approaches on Various Interactomes.Frontiers in molecular biosciences · 2021Article
- Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways.Briefings in bioinformatics · 2020Article
- Dynamics of a Protein Interaction Network Associated to the Aggregation of polyQ-Expanded Ataxin-1.Genes · 2020Article
- Oral lichen planus interactome reveals CXCR4 and CXCL12 as candidate therapeutic targets.Scientific reports · 2020Article
- Gene Prioritization through Consensus Strategy, Enrichment Methodologies Analysis, and Networking for Osteosarcoma Pathogenesis.International journal of molecular sciences · 2020Article
- A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases.Journal of integrative bioinformatics · 2019Review
- 'Omics Approaches to Explore the Breast Cancer Landscape.Frontiers in cell and developmental biology · 2019Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledBiomedical literature is traditionally used as a way to inform scientists of the relevance of genes in relation to a research topic. However many genes, especially from poorly studied organisms, are not discussed in the literature. Moreover, a manual and comprehensive summarization of the literature attached to the genes of an organism is in general impossible due to the high number of genes and abstracts involved. We introduce the novel Génie algorithm that overcomes these problems by evaluating the literature attached to all genes in a genome and to their orthologs according to a selected topic. Génie showed high precision (up to 100%) and the best performance in comparison to other algorithms in most of the benchmarks, especially when high sensitivity was required. Moreover, the prioritization of zebrafish genes involved in heart development, using human and mouse orthologs, showed high enrichment in differentially expressed genes from microarray experiments. The Génie web server supports hundreds of species, millions of genes and offers novel functionalities. Common run times below a minute, even when analyzing the human genome with hundreds of thousands of literature records, allows the use of Génie in routine lab work. AVAILABILITY: http://cbdm.mdc-berlin.de/tools/genie/.
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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.