ArticleGenome biology2013
jMOSAiCS: joint analysis of multiple ChIP-seq datasets.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Rescuing biologically relevant consensus regions across replicated samples.BMC bioinformatics · 2023Article
- Developing OCHROdb, a comprehensive quality checked database of open chromatin regions from sequencing data.Scientific reports · 2023Article
- Identification of Prostate Cancer Risk Genetics Biomarkers Based on Intergraded Bioinformatics Analysis.Frontiers in surgery · 2022Article
- ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements.PLoS computational biology · 2021Article
- Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.BMC genomics · 2021Article
- Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer.Frontiers in genetics · 2021Article
- Identification of ARHGEF38, NETO2, GOLM1, and SAPCD2 Associated With Prostate Cancer Progression by Bioinformatic Analysis and Experimental Validation.Frontiers in cell and developmental biology · 2021Article
- Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells.IUBMB life · 2020Review
- chromswitch: a flexible method to detect chromatin state switches.Bioinformatics (Oxford, England) · 2018Article
- Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling.Nucleic acids research · 2017Article
- Chromatin-state discovery and genome annotation with ChromHMM.Nature protocols · 2017Review
- Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes.Genome research · 2017Article
- A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Inference of cell type specific regulatory networks on mammalian lineages.Current opinion in systems biology · 2017Article
- Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.Briefings in bioinformatics · 2017Review
- A Hierarchical Framework for State-Space Matrix Inference and Clustering.The annals of applied statistics · 2016Article
- Jointly characterizing epigenetic dynamics across multiple human cell types.Nucleic acids research · 2016Article
- Genetic sources of population epigenomic variation.Nature reviews. Genetics · 2016Review
- The Hematopoietic Stem and Progenitor Cell Cistrome: GATA Factor-Dependent cis-Regulatory Mechanisms.Current topics in developmental biology · 2016Review
- Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type.Nature communications · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The ChIP-seq technique enables genome-wide mapping of in vivo protein-DNA interactions and chromatin states. Current analytical approaches for ChIP-seq analysis are largely geared towards single-sample investigations, and have limited applicability in comparative settings that aim to identify combinatorial patterns of enrichment across multiple datasets. We describe a novel probabilistic method, jMOSAiCS, for jointly analyzing multiple ChIP-seq datasets. We demonstrate its usefulness with a wide range of data-driven computational experiments and with a case study of histone modifications on GATA1-occupied segments during erythroid differentiation. jMOSAiCS is open source software and can be downloaded from Bioconductor 1.
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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.