ArticleFunctional & integrative genomics2022
BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction.
Article in Functional & integrative genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 2 of them syntheses that pooled it.
What it found
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Who cites it
57 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Genome-wide transcriptional analysis of rapeseed (Brassica napus L.) responses to heat stress: an integrated RNA-Seq meta-analysis, gene co-expression, and gene regulatory network study.BMC plant biology · 2025Pooled it
- Cross-species transcriptomics uncovers shared responses to water deficiency in plants.The plant genome · 2026Article
- Integrative analysis identifies candidate biomarkers for bladder cancer: evidence from genomic and clinical validation.Molecular biology reports · 2026Article
- Convergent genomic trajectories shape adaptation to life on land across animal lineages.Nature communications · 2026Article
- Opposing Changes in Cerebellar Dopaminergic Genes Co-Expression Networks in Different Models of Neurodevelopmental Disorders.International journal of molecular sciences · 2026Article
- Alterations of microRNAs across human and mouse limbic brain areas: molecular mechanisms and biological processes involved in major depressive disorder.Neurobiology of stress · 2026Article
- Coregulated metabolite networks associated with global protein crotonylation are central pathophysiological processes in prediabetes and diabetes.medRxiv : the preprint server for health sciences · 2026Article
- Integrative Transcriptome Analysis and WGCNA Uncover the Growth Regulatory Mechanisms inAnimals : an open access journal from MDPI · 2026Article
- Transcriptional footprints associated with bud fertility in grapevine development (Vitis vinifera L.).Planta · 2026Article
- Antimicrobial Peptides and Systemic Inflammation: A Network Analysis.Immunity, inflammation and disease · 2026Article
- Molecular mechanisms associated with rootstock-scion interactions in rubber trees.The plant genome · 2026Article
- Temperature changes reveal different transcriptional responses in the larvae of the bark beetle Dendroctonus rhizophagus during the cold season.Scientific reports · 2026Article
- Rhythmic Mechanisms Governing CAM Photosynthesis inInternational journal of molecular sciences · 2026Article
- SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.Briefings in bioinformatics · 2026Article
- Applications of the Soybean Expression Atlas in Genomics and Transcriptomics Research.Methods in molecular biology (Clifton, N.J.) · 2026Article
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- Intratumoral Microbiota Correlates with AP-2 Expression: A Pan-Cancer Map with Cohort-Specific Prognostic and Molecular Footprints.International journal of molecular sciences · 2025Article
- Mapping atherogenesis mechanisms in smooth muscle cells by targeting genes linked to coronary artery disease.iScience · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Currently, standard network analysis workflows rely on many different packages, often requiring users to have a solid statistics and programming background. Here, we present BioNERO, an R package that aims to integrate all aspects of network analysis workflows, including expression data preprocessing, gene coexpression and regulatory network inference, functional analyses, and intraspecies and interspecies network comparisons. The state-of-the-art methods implemented in BioNERO ensure that users can perform all analyses with a single package in a simple pipeline, without needing to learn a myriad of package-specific syntaxes. BioNERO offers a user-friendly framework that can be easily incorporated in systems biology pipelines.
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34787733What 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.