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

Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function

(2022) Johann S. Hawe et al.   NATURE GENETICS

Cross-species identification of cancer resistance–associated genes that may mediate human cancer risk

(2022) Nishanth Ulhas Nair et al.   Science Advances

The emergence of the brain non-CpG methylation system in vertebrates

(2021) Alex de Mendoza et al.   Nature Ecology & Evolution

A chicken DNA methylation clock for the prediction of broiler health

(2021) Günter Raddatz et al.   Communications Biology

Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation

(2021) Devika Singh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation

(2021) Josine L. Min et al.   NATURE GENETICS

Developmental programming of DNA methylation and gene expression patterns is associated with extreme cardiovascular tolerance to anoxia in the common snapping turtle

(2021) Ilan Ruhr et al.   Epigenetics & Chromatin

Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns

(2020) Yang Zhou et al.   BMC BIOLOGY

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

A map of cis-regulatory elements and 3D genome structures in zebrafish

(2020) Hongbo Yang et al.   NATURE

Developmental remodelling of non-CG methylation at satellite DNA repeats

(2020) Samuel E Ross et al.   NUCLEIC ACIDS RESEARCH

The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease

(2019) Lindsay Kosack et al.   CANCER CELL

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Convergent evolution of a vertebrate-like methylome in a marine sponge

(2019) Alex de Mendoza et al.   Nature Ecology & Evolution

Revisiting the genomic hypomethylation hypothesis of aging

(2018) Archana Unnikrishnan et al.   Annals of the New York Academy of Sciences

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

gemBS: high throughput processing for DNA methylation data from bisulfite sequencing

(2018) Angelika Merkel et al.   BIOINFORMATICS

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space

(2018) Johanna Klughammer et al.   NATURE MEDICINE

R 2s for Correlated Data: Phylogenetic Models, LMMs, and GLMMs

(2018) Anthony R Ives   SYSTEMATIC BIOLOGY

GOnet: a tool for interactive Gene Ontology analysis

(2018) Mikhail Pomaznoy et al.   BMC BIOINFORMATICS

Amphioxus functional genomics and the origins of vertebrate gene regulation

(2018) Ferdinand Marlétaz et al.   NATURE

DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma

(2017) Nathan C Sheffield et al.   NATURE MEDICINE

The DNA methyltransferase family: a versatile toolkit for epigenetic regulation

(2017) Frank Lyko   NATURE REVIEWS GENETICS

TET-mediated active DNA demethylation: mechanism, function and beyond

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia

(2016) Sheng Li et al.   NATURE MEDICINE

Diagenode® Premium RRBS technology: cost-effective DNA methylation mapping with superior coverage

(2016) Anne-Clémence Veillard et al.   NATURE METHODS

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved

(2016) Hannah K. Long et al.   NUCLEIC ACIDS RESEARCH

Evolutionary signals of selection on cognition from the great tit genome and methylome

(2016) Veronika N. Laine et al.   Nature Communications

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns

(2016) Matthew Huska et al.   PLoS Computational Biology

Structural and biochemical characterization of the cell fate determining nucleotidyltransferase fold protein MAB21L1

(2016) Carina C. de Oliveira Mann et al.   Scientific Reports

DNA methylation and healthy human aging

(2015) Meaghan J. Jones et al.   AGING CELL

KeBABS: an R package for kernel-based analysis of biological sequences: Fig. 1.

(2015) Johannes Palme et al.   BIOINFORMATICS

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Differential DNA Methylation Analysis without a Reference Genome

(2015) Johanna Klughammer et al.   Cell Reports

Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas

(2015) Diane I. Schroeder et al.   PLoS Genetics

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

(2015) Weiwei Zhang et al.   GENOME BIOLOGY

Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation

(2015) Xiaotong Wang et al.   BMC GENOMICS

Genome-wide age-related changes in DNA methylation and gene expression in human PBMCs

(2014) Wilma T. Steegenga et al.   AGE

Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia

(2014) Dan A. Landau et al.   CANCER CELL

Reprogramming the Methylome: Erasing Memory and Creating Diversity

(2014) Heather J. Lee et al.   Cell Stem Cell

The evidence for functional non-CpG methylation in mammalian cells

(2014) Vibha Patil et al.   Epigenetics

Patterns of DNA Methylation in Animals: An Ecotoxicological Perspective

(2014) J. A. Head   INTEGRATIVE AND COMPARATIVE BIOLOGY

Comprehensive analysis of DNA methylation data with RnBeads

(2014) Yassen Assenov et al.   NATURE METHODS

A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models

(2014) Lam si Tung Ho et al.   SYSTEMATIC BIOLOGY

Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing

(2013) Junwen Wang et al.   BMC GENOMICS

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Naive pluripotency is associated with global DNA hypomethylation

(2013) Harry G Leitch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comparison of Methods for Quantification of Global DNA Methylation in Human Cells and Tissues

(2013) Sofia Lisanti et al.   PLoS One

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

Epigenetics and the environment: emerging patterns and implications

(2012) Robert Feil et al.   NATURE REVIEWS GENETICS

DNA methylation in metabolic disorders

(2011) Romain Barres et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Hypoxia and hypoxia inducible factors: Diverse roles in liver diseases

(2011) Bharath Nath et al.   HEPATOLOGY

Epigenetic alterations in autoimmune rheumatic diseases

(2011) Esteban Ballestar   Nature Reviews Rheumatology

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types

(2011) Michael J. Ziller et al.   PLoS Genetics

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

(2010) Hongcang Gu et al.   NATURE METHODS

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

Linking DNA methylation and histone modification: patterns and paradigms

(2009) Howard Cedar et al.   NATURE REVIEWS GENETICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution

(2009) Eva Jablonka et al.   QUARTERLY REVIEW OF BIOLOGY

DNA hypomethylation in cancer cells

(2009) Melanie Ehrlich   Epigenomics

Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context

(2009) Brock C. Christensen et al.   PLoS Genetics

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS