Research graph
References from Integrative genomics decoding DNA methylation-mediated genetic control of complex traits in pigs. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1007/978-3-319-43624-1_4
10.1007/978-3-319-43624-1_4 · External reference
CpG islands – ‘A rough guide.
10.1016/j.febslet.2009.04.012 · 2009 · External reference
Linking DNA methylation and histone modification: patterns and paradigms
10.1038/nrg2540 · 2009 · External reference
DNA Methylation and Its Basic Function
10.1038/npp.2012.112 · 2013 · External reference
Dynamics and Context-Dependent Roles of DNA Methylation
10.1016/j.jmb.2017.02.008 · 2017 · External reference
Molecular targets of epigenetic regulation and effectors of environmental influences
10.1016/j.taap.2010.03.022 · 2010 · External reference
Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions
10.1016/j.cell.2013.12.019 · 2014 · External reference
DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development
10.1038/s41467-022-28940-2 · 2022 · External reference
DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse
10.1016/j.xgen.2022.100144 · 2022 · External reference
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
10.1038/nrg2719 · 2010 · External reference
DNA methylation in genomic imprinting
10.1016/s1383-5742(96)00049-x · 1997 · External reference
DNA methylation: roles in mammalian development
10.1038/nrg3354 · 2013 · External reference
The potential of DNA methylation as a biomarker for obesity and smoking
10.1111/joim.13496 · 2022 · External reference
Epigenetic Regulation of Hepatic Lipid Metabolism by DNA Methylation
2023 · External reference
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease
10.1038/s41588-022-01097-w · 2022 · External reference
Genome-wide DNA methylation profiles in Tibetan and Yorkshire pigs under high-altitude hypoxia
10.1186/s40104-019-0316-y · 2019 · External reference
Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs
10.1186/s12863-021-00977-0 · 2021 · External reference
Differential DNA methylation analysis reveals key genes in Chinese Qingyu and Landrace pigs
10.1139/gen-2021-0006 · 2022 · External reference
Multi-omic characterization of allele-specific regulatory variation in hybrid pigs
10.1038/s41467-024-49923-5 · 2024 · External reference
A comprehensive epigenome atlas reveals DNA methylation regulating skeletal muscle development
10.1093/nar/gkaa1203 · 2021 · External reference
DNA methylation analysis of porcine mammary epithelial cells reveals differentially methylated loci associated with immune response against Escherichia coli challenge
10.1186/s12864-019-5976-7 · 2019 · External reference
Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits
10.1186/s12864-022-08773-5 · 2022 · External reference
The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project
10.1038/s41588-025-02121-5 · 2025 · External reference
A multi-tissue atlas of regulatory variants in cattle
10.1038/s41588-022-01153-5 · 2022 · External reference
Genetic regulation of gene expression across multiple tissues in chickens
10.1038/s41588-025-02155-9 · 2025 · External reference
10.1101/2025.06.23.661035
10.1101/2025.06.23.661035 · External reference
A compendium of genetic regulatory effects across pig tissues
10.1038/s41588-023-01585-7 · 2024 · External reference
Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function
10.1038/s41588-021-00969-x · 2022 · External reference
QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration
10.1038/s41467-024-46063-8 · 2024 · External reference
PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs
10.1093/nar/gkad1080 · 2024 · External reference
Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs
2025 · External reference
Pig genome functional annotation enhances the biological interpretation of complex traits and human disease
10.1038/s41467-021-26153-7 · 2021 · External reference
fastp: an ultra-fast all-in-one FASTQ preprocessor
10.1093/bioinformatics/bty560 · 2018 · External reference
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
10.1093/bioinformatics/btr167 · 2011 · External reference
Trimmomatic: a flexible trimmer for Illumina sequence data
10.1093/bioinformatics/btu170 · 2014 · External reference
STAR: ultrafast universal RNA-seq aligner
10.1093/bioinformatics/bts635 · 2013 · External reference
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
10.1093/bioinformatics/btt656 · 2014 · External reference
Transcript-level expression analysis of RNA-seq experiments with HISAT
10.1038/nprot.2016.095 · 2016 · External reference
Unresolved reference
External reference
PHARP: a pig haplotype reference panel for genotype imputation
10.1038/s41598-022-15851-x · 2022 · External reference
The variant call format and VCFtools
10.1093/bioinformatics/btr330 · 2011 · External reference
Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data
10.1186/gb-2012-13-7-r61 · 2012 · External reference
A one-penny imputed genome from next generationreference panels
10.1016/j.ajhg.2018.07.015 · 2018 · External reference
10.1101/023754
10.1101/023754 · External reference
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
10.1086/519795 · 2007 · External reference
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data
10.1093/bioinformatics/btx595 · 2018 · External reference
10.1101/2024.05.08.593132
10.1101/2024.05.08.593132 · External reference
Scaling computational genomics to millions of individuals with GPUs
10.1186/s13059-019-1836-7 · 2019 · External reference
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
10.1038/nprot.2011.457 · 2012 · External reference
Matrix eQTL: ultra fast eQTL analysis via large matrix operations
10.1093/bioinformatics/bts163 · 2012 · External reference
GCTA: A Tool for Genome-wide Complex Trait Analysis
10.1016/j.ajhg.2010.11.011 · 2011 · External reference
10.1101/032003
10.1101/032003 · External reference
FIMO: scanning for occurrences of a given motif
10.1093/bioinformatics/btr064 · 2011 · External reference
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
10.1016/j.molcel.2010.05.004 · 2010 · External reference
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
10.1093/nar/gkad1059 · 2024 · External reference
Modeling the vertebrate regulatory sequence landscape by UUATAC-seq and deep learning
10.1016/j.cell.2025.06.020 · 2025 · External reference
Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics
10.1371/journal.pgen.1004383 · 2014 · External reference
A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits
10.1038/s41467-020-20885-8 · 2021 · External reference
Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets
10.1038/ng.3538 · 2016 · External reference
A Bayesian framework for multiple trait colocalization from summary association statistics
10.1093/bioinformatics/bty147 · 2018 · External reference
Joint analysis of GWAS and multi-omics QTL summary statistics reveals a large fraction of GWAS signals shared with molecular phenotypes
10.1016/j.xgen.2023.100344 · 2023 · External reference
Multivariable Mendelian Randomization: The Use of Pleiotropic Genetic Variants to Estimate Causal Effects
10.1093/aje/kwu283 · 2015 · External reference
Genome-wide efficient mixed-model analysis for association studies
10.1038/ng.2310 · 2012 · External reference
GPAT3 and GPAT4 are regulated by insulin-stimulated phosphorylation and play distinct roles in adipogenesis[S]
10.1194/jlr.m006304 · 2010 · External reference
The Role of SOCS3 in Regulating Meat Quality in Jinhua Pigs
10.3390/ijms241310593 · 2023 · External reference
Joint effects of porcine leptin and leptin receptor polymorphisms on productivity and quality traits
10.1111/j.1365-2052.2012.02338.x · 2012 · External reference
Silencing of Carbohydrate Sulfotransferase 15 Hinders Murine Pulmonary Fibrosis Development
10.1016/j.omtn.2016.12.008 · 2017 · External reference
meQTL mapping in the GENOA study reveals genetic determinants of DNA methylation in African Americans
10.1038/s41467-023-37961-4 · 2023 · External reference
Functions of DNA methylation: islands, start sites, gene bodies and beyond
10.1038/nrg3230 · 2012 · External reference
Expression Quantitative Trait Methylation Analysis Reveals Methylomic Associations With Gene Expression in Childhood Asthma
10.1016/j.chest.2020.05.601 · 2020 · External reference
Genome-Wide Methylation Analysis Reveals a KCNK3-Prominent Causal Cascade on Hypertension
2024 · External reference
The role of DNA methylation in alcohol-mediated neurodevelopmental toxicity
10.1016/j.tox.2025.154315 · 2026 · External reference
Differential Methylation of the Genes PAX8 and GATA4 Alters Their Expression in the Heart during Hypertrophic Cardiomyopathy
10.1134/s1607672925601131 · 2025 · External reference
Deficiency of Transcription Factor Sp1 Contributes to Hypertrophic Cardiomyopathy
10.1161/circresaha.123.323272 · 2024 · External reference
SP1 undergoes phase separation and activates RGS20 expression through super-enhancers to promote lung adenocarcinoma progression
10.1073/pnas.2401834121 · 2024 · External reference
10.21203/rs.3.rs-3959082/v1
10.21203/rs.3.rs-3959082/v1 · External reference
Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits
10.1038/s41588-023-01494-9 · 2024 · External reference
Two-step epigenetic Mendelian randomization: a strategy for establishing the causal role of epigenetic processes in pathways to disease
10.1093/ije/dyr233 · 2012 · External reference
