ArticlePLoS computational biology2015
Integrative multi-omics module network inference with Lemon-Tree.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 104 citations in OpenAlex.
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- SiRCle (Signature Regulatory Clustering) model integration reveals mechanisms of phenotype regulation in renal cancer.Genome medicine · 2024Article
- Comprehensive applications of the artificial intelligence technology in new drug research and development.Health information science and systems · 2024Review
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- Methods for multi-omic data integration in cancer research.Frontiers in genetics · 2024Review
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- Integrative multi-omics and systems bioinformatics in translational neuroscience: A data mining perspective.Journal of pharmaceutical analysis · 2023Review
- Network-based approaches for modeling disease regulation and progression.Computational and structural biotechnology journal · 2023Review
- A Machine Learning-Based Approach Using Multi-omics Data to Predict Metabolic Pathways.Methods in molecular biology (Clifton, N.J.) · 2023Article
- StabJGL: a stability approach to sparsity and similarity selection in multiple-network reconstruction.Bioinformatics advances · 2023Article
- Identification of functional gene modules by integrating multi-omics data and known molecular interactions.Frontiers in genetics · 2023Article
- SUBATOMIC: a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks.BMC bioinformatics · 2022Article
- A penalized linear mixed model with generalized method of moments for prediction analysis on high-dimensional multi-omics data.Briefings in bioinformatics · 2022Article
- Machine learning: its challenges and opportunities in plant system biology.Applied microbiology and biotechnology · 2022Review
- Network Analysis of Microarray Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Computational approaches for network-based integrative multi-omics analysis.Frontiers in molecular biosciences · 2022Review
- Multi-omics analysis: Paving the path toward achieving precision medicine in cancer treatment and immuno-oncology.Frontiers in molecular biosciences · 2022Review
- Network approaches for omics studies of neurodegenerative diseases.Frontiers in genetics · 2022Review
- Unsupervised Multi-Omics Data Integration Methods: A Comprehensive Review.Frontiers in genetics · 2022Review
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
Module network inference is an established statistical method to reconstruct co-expression modules and their upstream regulatory programs from integrated multi-omics datasets measuring the activity levels of various cellular components across different individuals, experimental conditions or time points of a dynamic process. We have developed Lemon-Tree, an open-source, platform-independent, modular, extensible software package implementing state-of-the-art ensemble methods for module network inference. We benchmarked Lemon-Tree using large-scale tumor datasets and showed that Lemon-Tree algorithms compare favorably with state-of-the-art module network inference software. We also analyzed a large dataset of somatic copy-number alterations and gene expression levels measured in glioblastoma samples from The Cancer Genome Atlas and found that Lemon-Tree correctly identifies known glioblastoma oncogenes and tumor suppressors as master regulators in the inferred module network. Novel candidate driver genes predicted by Lemon-Tree were validated using tumor pathway and survival analyses. Lemon-Tree is available from http://lemon-tree.googlecode.com under the GNU General Public License version 2.0.
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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.