DNA methylation and transcriptome analysis reveal epigenomic differences among three macaque species

Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species

(2023) Johanna Klughammer et al.   Nature Communications

Multi-omics analysis reveals the host–microbe interactions in aged rhesus macaques

(2022) Jue Xu et al.   Frontiers in Microbiology

Sex-specific gene expression in the blood of four primates

(2021) Jiao Wang et al.   GENOMICS

Genomic copy number variation study of nine Macaca species provides new insights into their genetic divergence, adaptation and biomedical application

(2020) Jing Li et al.   Genome Biology and Evolution

Multi-dimensional Transcriptional Remodeling by Physiological Insulin In Vivo

(2019) Thiago M. Batista et al.   Cell Reports

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Regulation of INSR, the Insulin Receptor Gene

(2019) Sandhya Payankaulam et al.   Genes

Synthesizing the role of epigenetics in the response and adaptation of species to climate change in freshwater ecosystems

(2018) Guilherme Jeremias et al.   MOLECULAR ECOLOGY

Ancient hybridization and admixture in macaques (genus Macaca ) inferred from whole genome sequences

(2018) Zhenxin Fan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

(2016) Isabel Mendizabal et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-Genome Sequencing of Six Mauritian Cynomolgus Macaques (Macaca fascicularis) Reveals a Genome-Wide Pattern of Polymorphisms under Extreme Population Bottleneck

(2015) Naoki Osada et al.   Genome Biology and Evolution

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The interplay between DNA methylation and sequence divergence in recent human evolution

(2015) Irene Hernando-Herraez et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation: Insights into Human Evolution

(2015) Irene Hernando-Herraez et al.   PLoS Genetics

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Whole-Genome Sequencing of Tibetan Macaque (Macaca thibetana) Provides New Insight into the Macaque Evolutionary History

(2014) Zhenxin Fan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hydroxymethylation and DNA methylation profiles in the prefrontal cortex of the non-human primate rhesus macaque and the impact of maternal deprivation on hydroxymethylation

(2014) R. Massart et al.   NEUROSCIENCE

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data

(2014) Hao Feng et al.   NUCLEIC ACIDS RESEARCH

DNA methylation contributes to natural human variation

(2013) H. Heyn et al.   GENOME RESEARCH

DNA Methylation and Methyl-Binding Proteins Control Differential Gene Expression in Distinct Cortical Areas of Macaque Monkey

(2013) K. Hata et al.   JOURNAL OF NEUROSCIENCE

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Dynamics of DNA Methylation in Recent Human and Great Ape Evolution

(2013) Irene Hernando-Herraez et al.   PLoS Genetics

The Signature of Maternal Rearing in the Methylome in Rhesus Macaque Prefrontal Cortex and T Cells

(2012) N. Provencal et al.   JOURNAL OF NEUROSCIENCE

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility

(2012) Lovisa E. Reinius et al.   PLoS One

Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome

(2012) Atsunori Higashino et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

GABAB receptor modulation of synaptic function

(2011) Jason R Chalifoux et al.   CURRENT OPINION IN NEUROBIOLOGY

Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment

(2011) Emily Hodges et al.   MOLECULAR CELL

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

(2011) Guangmei Yan et al.   NATURE BIOTECHNOLOGY

Epigenetic Changes with Dietary Soy in Cynomolgus Monkeys

(2011) Timothy D. Howard et al.   PLoS One

A Molecular Phylogeny of Living Primates

(2011) Polina Perelman et al.   PLoS Genetics

Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque

(2011) Xiaodong Fang et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Molecular Aspects of Thyroid Hormone Actions

(2010) Sheue-Yann Cheng et al.   ENDOCRINE REVIEWS

Ancient genome-wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M. mulatta

(2010) NAOKI OSADA et al.   MOLECULAR ECOLOGY

Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after

(2010) BERNARD ANGERS et al.   MOLECULAR ECOLOGY

Pancreatic β-cell signaling: toward better understanding of diabetes and its treatment

(2010) Susumu SEINO et al.   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

DNA methylation profiles in monozygotic and dizygotic twins

(2009) Zachary A Kaminsky et al.   NATURE GENETICS

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta

(2008) Naoki Osada et al.   BMC GENOMICS

Morphine: A Protective or Destructive Role in Neurons?

(2008) Yan Zhang et al.   NEUROSCIENTIST

Nutritional Control of Reproductive Status in Honeybees via DNA Methylation

(2008) R. Kucharski et al.   SCIENCE