ArticlePacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2009
Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies.
Article in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 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.
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Who cites it
82 citing papers in PubMed.
- Polygenic inheritance of paclitaxel-induced sensory peripheral neuropathy driven by axon outgrowth gene sets in CALGB 40101 (Alliance).The pharmacogenomics journal · 2014Trial
- Use of biological knowledge to inform the analysis of gene-gene interactions involved in modulating virologic failure with efavirenz-containing treatment regimens in ART-naïve ACTG clinical trials participants.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2011Trial
- Article
- Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets.American journal of human genetics · 2023Article
- Development and Trends in Artificial Intelligence in Critical Care Medicine: A Bibliometric Analysis of Related Research over the Period of 2010-2021.Journal of personalized medicine · 2022Article
- Leveraging phenotypic variability to identify genetic interactions in human phenotypes.American journal of human genetics · 2021Article
- A framework for pathway knowledge driven prioritization in genome-wide association studies.Genetic epidemiology · 2020Article
- Application of data mining for predicting hemodynamics instability during pheochromocytoma surgery.BMC medical informatics and decision making · 2020Article
- Investigation of gene-gene interactions in cardiac traits and serum fatty acid levels in the LURIC Health Study.PloS one · 2020Article
- Discovering genetic interactions bridging pathways in genome-wide association studies.Nature communications · 2019Article
- Integration of genetic and functional genomics data to uncover chemotherapeutic induced cytotoxicity.The pharmacogenomics journal · 2019Article
- Innovative strategies for annotating the "relationSNP" between variants and molecular phenotypes.BioData mining · 2019Review
- Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies.BioData mining · 2019Article
- Leveraging epigenomics and contactomics data to investigate SNP pairs in GWAS.Human genetics · 2018Article
- Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWAS.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- Improving machine learning reproducibility in genetic association studies with proportional instance cross validation (PICV).BioData mining · 2018Article
- Evaluation of PrediXcan for prioritizing GWAS associations and predicting gene expression.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures?Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- Identification of epistatic interactions between the human RNA demethylases FTO and ALKBH5 with gene set enrichment analysis informed by differential methylation.BMC proceedings · 2018Article
- Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases.American journal of epidemiology · 2017Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Genome-wide association studies provide an unprecedented opportunity to identify combinations of genetic variants that contribute to disease susceptibility. The combinatorial problem of jointly analyzing the millions of genetic variations accessible by high-throughput genotyping technologies is a difficult challenge. One approach to reducing the search space of this variable selection problem is to assess specific combinations of genetic variations based on prior statistical and biological knowledge. In this work, we provide a systematic approach to integrate multiple public databases of gene groupings and sets of disease-related genes to produce multi-SNP models that have an established biological foundation. This approach yields a collection of models which can be tested statistically in genome-wide data, along with an ordinal quantity describing the number of data sources that support any given model. Using this knowledge-driven approach reduces the computational and statistical burden of large-scale interaction analysis while simultaneously providing a biological foundation for the relevance of any significant statistical result that is found.
Indexed as
Identifiers
19209715PMC2859610What OpenQuestion holds
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.