ArticleGenome biology2020
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 192 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
192 citing papers in PubMed.
- PROTACs in cancer therapy: targeted degradation of GPX4, PARP and epigenetic regulators.Journal of enzyme inhibition and medicinal chemistry · 2026Review
- The histone methyltransferase complex subunit RBBP5 serves as a central epigenetic regulator of proteostasis dynamics.PLoS biology · 2026Article
- Article
- Endurance exercise elicits a hepatic memory associated with improved metabolic function and protein secretion.Molecular metabolism · 2026Article
- Integrative analysis of the embryonic origin of adult neural stem cells in forebrain subventricular zones.National science review · 2026Article
- Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response.Nature communications · 2026Article
- Ribosome dynamics during skeletal muscle repair and regeneration in mice and humans.American journal of physiology. Cell physiology · 2026Article
- TRIAGE Toolkit: Streamlined Discovery of Regulatory Genes and Elements.Current protocols · 2026Article
- Computational blueprints for cell fate programming.Stem cell reports · 2026Review
- Computational modelling of cell identity.The Biochemical journal · 2026Review
- Article
- Epitranscriptomic regulation of mRNA stability in pivotal transcription factors modulates the second cell fate decision.Nature communications · 2026Article
- Targeting CDK12 disrupts estrogen-receptor chromatin recruitment and ER-MED1 transcription in advanced ER+ breast cancer.Journal of the National Cancer Institute · 2026Article
- Oxidized LDL Induces Pro-Inflammatory Transcriptomic and Epigenomic Responses in Human CD4FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- REV-ERB-alpha and -beta coordinately regulate astrocyte reactivity and proteostatic function.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Epstein-Barr Virus, Lower Vitamin D, Low Sun Exposure, and HLA-DRB1*1501 Risk Variant Share Common Epigenetic Pathways Leading to Multiple Sclerosis Onset.Annals of neurology · 2026Article
- Enhancing TFEA.ChIP with ENCODE regulatory maps for generalizable transcription factor enrichment.Briefings in bioinformatics · 2026Article
- Systemic control of HNF1B-driven redox homeostasis by N6-adenosine methylation.Nucleic acids research · 2026Article
- DNA methylation mediates the multiple sclerosis onset risk associated with HHV-6 DNA positivity.Environmental epigenetics · 2026Article
- Reference-guided computational framework identifies microenvironment metabolic subtypes and targets using pan-cancer single-cell datasets.Genome medicine · 2025Article
132 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
We developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes and outperformed alternative methods in identifying the perturbed TRs.
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.