ReviewBioinformatics and biology insights2015
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists.
Review in Bioinformatics and biology insights, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-omic network analysis identified betacellulin as a novel target of omega-3 fatty acid attenuation of western diet-induced nonalcoholic steatohepatitis.EMBO molecular medicine · 2023Pooled it
- A systems approach for elucidating the role of the microbiome in epigenetic cellular memory.mSystems · 2025Review
- Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions.Nature protocols · 2024Review
- Host response to cholestyramine can be mediated by the gut microbiota.Microbiome research reports · 2024Article
- Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome.Microbiome · 2023Article
- Lactiplantibacillus plantarum enables blood urate control in mice through degradation of nucleosides in gastrointestinal tract.Microbiome · 2023Article
- Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions.bioRxiv : the preprint server for biology · 2023Article
- Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages.The Journal of experimental medicine · 2022Article
- Microbiota triggers STING-type I IFN-dependent monocyte reprogramming of the tumor microenvironment.Cell · 2021Article
- Graphery: interactive tutorials for biological network algorithms.Nucleic acids research · 2021Article
- SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data.Journal of statistical software · 2021Article
- Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes.Nature communications · 2021Article
- Network analysis methods for studying microbial communities: A mini review.Computational and structural biotechnology journal · 2021Review
- The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State.Cell reports · 2020Article
- Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.BMC bioinformatics · 2020Article
- Dietary Indole-3-Carbinol Activates AhR in the Gut, Alters Th17-Microbe Interactions, and Exacerbates Insulitis in NOD Mice.Frontiers in immunology · 2020Article
- Improvements in Metabolic Syndrome by Xanthohumol Derivatives Are Linked to Altered Gut Microbiota and Bile Acid Metabolism.Molecular nutrition & food research · 2020Article
- Host and microbiome multi-omics integration: applications and methodologies.Biophysical reviews · 2019Review
- CVID enteropathy is characterized by exceeding low mucosal IgA levels and interferon-driven inflammation possibly related to the presence of a pathobiont.Clinical immunology (Orlando, Fla.) · 2018Article
- FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb.Scientific reports · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Omics technologies enable unbiased investigation of biological systems through massively parallel sequence acquisition or molecular measurements, bringing the life sciences into the era of Big Data. A central challenge posed by such omics datasets is how to transform these data into biological knowledge, for example, how to use these data to answer questions such as: Which functional pathways are involved in cell differentiation? Which genes should we target to stop cancer? Network analysis is a powerful and general approach to solve this problem consisting of two fundamental stages, network reconstruction, and network interrogation. Here we provide an overview of network analysis including a step-by-step guide on how to perform and use this approach to investigate a biological question. In this guide, we also include the software packages that we and others employ for each of the steps of a network analysis workflow.
Indexed as
Identifiers
What 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.