ArticleGenome biology2023
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
28 citing papers in PubMed.
- Large-scale, interpretable gene regulatory network inference through biologically informed matrix factorization.bioRxiv : the preprint server for biology · 2026Article
- PARROT: Phase-Altering Regulatory Rewiring Over Time.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer.Scientific reports · 2026Article
- Gene regulatory network analysis identifies dysregulation of hypoxia pathways as contributing to glioblastoma treatment resistance in females.Biology of sex differences · 2026Article
- Multilayer network approaches to omics data integration in digital twins for cancer research.Frontiers in systems biology · 2026Review
- Sex differences in thyroid aging and their implications in thyroid disorders: insights from gene regulatory networks.bioRxiv : the preprint server for biology · 2025Article
- Multi-omics protein signaling networks identify sex-specific therapeutic candidates in lung adenocarcinoma.Biology of sex differences · 2025Article
- NetMedPy: a Python package for large-scale network medicine screening.Bioinformatics (Oxford, England) · 2025Article
- Aging-associated alterations in gene regulatory networks associate with risk, prognosis and response to therapy in lung adenocarcinoma.npj aging · 2025Article
- SPONGE: simple prior omics network GEnerator.Bioinformatics (Oxford, England) · 2025Article
- BiGSM: Bayesian inference of gene regulatory network via sparse modelling.Bioinformatics (Oxford, England) · 2025Article
- miRNA-mRNA network analysis identifies PAX5 as a potential regulator of adaptive immune response in COPD.bioRxiv : the preprint server for biology · 2025Article
- BLOBFISH: Bipartite Limited Subnetworks from Multiple Observations using Breadth-First Search with Constrained Hops.bioRxiv : the preprint server for biology · 2025Article
- Identifying Sex Differences in Lung Adenocarcinoma Using Multi-Omics Integrative Protein Signaling Networks.bioRxiv : the preprint server for biology · 2025Article
- Reproducible processing of TCGA regulatory networks.GigaScience · 2025Article
- Perspective on recent developments and challenges in regulatory and systems genomics.Bioinformatics advances · 2025Review
- Review
- Bayesian inference of sample-specific coexpression networks.Genome research · 2024Article
- Selective loss of Y chromosomes in lung adenocarcinoma modulates the tumor immune environment through cancer/testis antigens.bioRxiv : the preprint server for biology · 2024Article
- Higher-order correction of persistent batch effects in correlation networks.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
25 authors.
Funding
Abstract
Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source methods to infer GRNs, conduct differential network analyses, estimate community structure, and explore the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages and between methods to allow better integration of these tools into analytical pipelines. We demonstrate the utility using multi-omic data from the Cancer Cell Line Encyclopedia. We will continue to expand the netZoo to incorporate additional methods.
Indexed as
Identifiers
What Socratic 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 Socratic graph.