ArticleNature communications2024
MOCHA's advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- Multi-omic profiling of human antibody-secreting cells reveals diverse subsets sustain durable humoral immunity.bioRxiv : the preprint server for biology · 2026Article
- iAODE for benchmarking and continuum modeling of single-cell chromatin accessibility.Communications biology · 2026Article
- A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.Nature communications · 2026Article
- Genome- and peak-informed two-stage framework for scATAC-seq cell type identification.Bioinformatics (Oxford, England) · 2026Article
- Progression to rheumatoid arthritis in at-risk individuals is defined by systemic inflammation and by T and B cell dysregulation.Science translational medicine · 2025Article
- annATAC: automatic cell type annotation for scATAC-seq data based on language model.BMC biology · 2025Article
- AI enhancing prefabricated aesthetics and low carbon coupled with 3D printing in chain hotel buildings from multidimensional neural networks.Scientific reports · 2025Article
- Mapping TAM-tumor crosstalk in glioma via ligand-receptor multi-omics: mechanisms of immune evasion.Frontiers in immunology · 2025Review
- Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.Frontiers in genetics · 2025Article
- Systemic inflammation and lymphocyte activation precede rheumatoid arthritis.bioRxiv : the preprint server for biology · 2024Article
- MOCHA's advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts.Nature communications · 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
12 authors.
Funding
Abstract
Single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) is being increasingly used to study gene regulation. However, major analytical gaps limit its utility in studying gene regulatory programs in complex diseases. In response, MOCHA (Model-based single cell Open CHromatin Analysis) presents major advances over existing analysis tools, including: 1) improving identification of sample-specific open chromatin, 2) statistical modeling of technical drop-out with zero-inflated methods, 3) mitigation of false positives in single cell analysis, 4) identification of alternative transcription-starting-site regulation, and 5) modules for inferring temporal gene regulatory networks from longitudinal data. These advances, in addition to open chromatin analyses, provide a robust framework after quality control and cell labeling to study gene regulatory programs in human disease. We benchmark MOCHA with four state-of-the-art tools to demonstrate its advances. We also construct cross-sectional and longitudinal gene regulatory networks, identifying potential mechanisms of COVID-19 response. MOCHA provides researchers with a robust analytical tool for functional genomic inference from scATAC-seq data.
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.