ArticlePLoS computational biology2016
Pathway-Based Genomics Prediction using Generalized Elastic Net.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- A Pharmacogenetic Prediction Model of Progression-Free Survival in Breast Cancer using Genome-Wide Genotyping Data from CALGB 40502 (Alliance).Clinical pharmacology and therapeutics · 2019Trial
- An airway epithelial IL-17A response signature identifies a steroid-unresponsive COPD patient subgroup.The Journal of clinical investigation · 2019Trial
- A systems microbiology framework for reproducible multi-dataset omics integration with application to long COVID.Frontiers in systems biology · 2026Article
- MCLRP: enhanced prediction of anticancer drug response through low-rank matrix completion and transcriptomic profiling.BMC biology · 2025Article
- Single-cell multi-omics analysis reveals drivers of intrahepatic cholangiocarcinoma metastasis.BMC cancer · 2025Article
- Statistical Methods for Multi-Omics Analysis in Neurodevelopmental Disorders: From High Dimensionality to Mechanistic Insight.Biomolecules · 2025Review
- Weight-loss associated DNA methylation patterns: targetable biomarkers and pathway insights.BMC research notes · 2025Article
- Genomic Prediction of Semen Traits in Boars Incorporating Biological Interactions.International journal of molecular sciences · 2024Article
- Integration of single-cell sequencing and bulk transcriptome data develops prognostic markers based on PCLAFHeliyon · 2024Article
- Multi-output prediction of dose-response curves enables drug repositioning and biomarker discovery.NPJ precision oncology · 2024Article
- Machine Learning-based Development and Validation of a Cell Senescence Predictive and Prognostic Signature in Intrahepatic Cholangiocarcinoma.Journal of Cancer · 2024Article
- PBK correlates with prognosis, immune escape and drug response in LUAD.Scientific reports · 2023Article
- Machine learning-identified stemness features and constructed stemness-related subtype with prognosis, chemotherapy, and immunotherapy responses for non-small cell lung cancer patients.Stem cell research & therapy · 2023Article
- Automated assembly of molecular mechanisms at scale from text mining and curated databases.Molecular systems biology · 2023Article
- LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients.BMC bioinformatics · 2023Article
- Network-based integration of multi-omics data for clinical outcome prediction in neuroblastoma.Scientific reports · 2022Article
- An overview of machine learning methods for monotherapy drug response prediction.Briefings in bioinformatics · 2022Article
- CDKN2A-mediated molecular subtypes characterize the hallmarks of tumor microenvironment and guide precision medicine in triple-negative breast cancer.Frontiers in immunology · 2022Article
- Stemness Analysis Uncovers That The Peroxisome Proliferator-Activated Receptor Signaling Pathway Can Mediate Fatty Acid Homeostasis In Sorafenib-Resistant Hepatocellular Carcinoma Cells.Frontiers in oncology · 2022Article
- Xprediction: Explainable EGFR-TKIs response prediction based on drug sensitivity specific gene networks.PloS one · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We present a novel regularization scheme called The Generalized Elastic Net (GELnet) that incorporates gene pathway information into feature selection. The proposed formulation is applicable to a wide variety of problems in which the interpretation of predictive features using known molecular interactions is desired. The method naturally steers solutions toward sets of mechanistically interlinked genes. Using experiments on synthetic data, we demonstrate that pathway-guided results maintain, and often improve, the accuracy of predictors even in cases where the full gene network is unknown. We apply the method to predict the drug response of breast cancer cell lines. GELnet is able to reveal genetic determinants of sensitivity and resistance for several compounds. In particular, for an EGFR/HER2 inhibitor, it finds a possible trans-differentiation resistance mechanism missed by the corresponding pathway agnostic approach.
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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.