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GREG—studying transcriptional regulation using integrative graph databases

https://doi.org/10.1093/database/baz162
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-030-06016-9_3openalex-snapshot
Construction and Visualization of Dynamic Biological Networks: Benchmarking the Neo4J Graph Database
inferredcites →https://doi.org/10.1016/j.celrep.2016.09.002openalex-snapshot
Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes
inferredcites →https://doi.org/10.1038/emboj.2011.492openalex-snapshot
Oxidative stress induces an ATM‐independent senescence pathway through p38 MAPK‐mediated lamin B1 accumulation
inferredcites →https://doi.org/10.1042/bj20080134openalex-snapshot
The pluripotency rheostat Nanog functions as a dimer
inferredcites →https://doi.org/10.1089/omi.2011.0118openalex-snapshot
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
inferredcites →https://doi.org/10.1093/bioinformatics/btt549openalex-snapshot
Are graph databases ready for bioinformatics?
inferredcites →https://doi.org/10.1093/bioinformatics/btv158openalex-snapshot
4DGenome: a comprehensive database of chromatin interactions
inferredcites →https://doi.org/10.1093/bioinformatics/btv460openalex-snapshot
cyNeo4j: connecting Neo4j and Cytoscape
inferredcites →https://doi.org/10.1093/bioinformatics/btw375openalex-snapshot
4DGenome: a comprehensive database of chromatin interactions
inferredcites →https://doi.org/10.1093/database/baq023openalex-snapshot
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence
inferredcites →https://doi.org/10.1093/database/bay039openalex-snapshot
LnChrom: a resource of experimentally validated lncRNA–chromatin interactions in human and mouse
inferredcites →https://doi.org/10.1093/hmg/ddi479openalex-snapshot
Loss of emerin at the nuclear envelope disrupts the Rb1/E2F and MyoD pathways during muscle regeneration
inferredcites →https://doi.org/10.1093/ije/dyx251openalex-snapshot
MELODI: Mining Enriched Literature Objects to Derive Intermediates
inferredcites →https://doi.org/10.1093/nar/gkt1248openalex-snapshot
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data
inferredcites →https://doi.org/10.1093/nar/gky1094openalex-snapshot
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis
inferredcites →https://doi.org/10.1093/nar/gky955openalex-snapshot
GENCODE reference annotation for the human and mouse genomes
inferredcites →https://doi.org/10.1101/gad.217281.113openalex-snapshot
Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence
inferredcites →https://doi.org/10.1172/jci60324openalex-snapshot
Pathogenesis of chronic obstructive pulmonary disease
inferredcites →https://doi.org/10.1186/1471-2105-12-455openalex-snapshot
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database
inferredcites →https://doi.org/10.1186/1471-2105-9-405openalex-snapshot
iRefIndex: A consolidated protein interaction database with provenance
inferredcites →https://doi.org/10.1186/s12918-018-0616-4openalex-snapshot
BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources
inferredcites →https://doi.org/10.1371/journal.pcbi.1005968openalex-snapshot
Reactome graph database: Efficient access to complex pathway data
inferredcites →https://doi.org/10.2147/copd.s80227openalex-snapshot
Candidate genes for COPD: current evidence and research
inferredcites →https://doi.org/10.22029/jlupub-10477openalex-snapshot
The role of lamin B1 in lung cancer development and metastasis
inferredcites →https://doi.org/10.4049/jimmunol.1801293openalex-snapshot
Involvement of Lamin B1 Reduction in Accelerated Cellular Senescence during Chronic Obstructive Pulmonary Disease Pathogenesis

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.5281/zenodo.4265559zenodo-depositor-declared
inferred← citeshttps://doi.org/10.1016/j.comtox.2024.100308openalex-snapshot
AOPWIKI-EXPLORER: An interactive graph-based query engine leveraging large language models
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.07.002openalex-snapshot
Chromatin Hubs: A biological and computational outlook
inferred← citeshttps://doi.org/10.1093/bib/bbae561openalex-snapshot
Graph databases in systems biology: a systematic review
inferred← citeshttps://doi.org/10.1093/database/baab026openalex-snapshot
An overview of graph databases and their applications in the biomedical domain
inferred← citeshttps://doi.org/10.1093/database/baac044openalex-snapshot
FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank
inferred← citeshttps://doi.org/10.20944/preprints202403.1289.v1openalex-snapshot
The Use of Graph Databases in Systems Biology: A Systematic Review
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.