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

Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications

(2020) Jingwei Liu et al.   Scientific Reports

Developmental remodelling of non-CG methylation at satellite DNA repeats

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

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons

(2019) Antonio Torres-Méndez et al.   Nature Ecology & Evolution

A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice

(2019) Gintarė Sendžikaitė et al.   Nature Communications

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs

(2019) Rafael Yaari et al.   Nature Communications

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

Evolution of DNA Methylome Diversity in Eukaryotes

(2019) Alex de Mendoza et al.   JOURNAL OF MOLECULAR BIOLOGY

MeCP2 Represses Enhancers through Chromosome Topology-Associated DNA Methylation

(2019) Adam W. Clemens et al.   MOLECULAR CELL

DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development

(2019) Keith D. Harris et al.   Epigenetics & Chromatin

OUP accepted manuscript

(2018)   BIOINFORMATICS

The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

(2018) Jeramiah J. Smith et al.   NATURE GENETICS

Amphioxus functional genomics and the origins of vertebrate gene regulation

(2018) Ferdinand Marlétaz et al.   NATURE

Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions

(2018) Patricia Heyn et al.   NATURE GENETICS

The DNA methyltransferase family: a versatile toolkit for epigenetic regulation

(2017) Frank Lyko   NATURE REVIEWS GENETICS

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s

(2017) Jong-Hun Lee et al.   Scientific Reports

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

(2017) Beatriz Albuixech-Crespo et al.   PLOS BIOLOGY

MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain

(2017) Sabine Lagger et al.   PLoS Genetics

Gene and transposable element methylation in great tit (Parus major) brain and blood

(2016) Martijn F. L. Derks et al.   BMC GENOMICS

Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain

(2016) Fumiaki Sugahara et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

From nerve net to nerve ring, nerve cord and brain — evolution of the nervous system

(2016) Detlev Arendt et al.   NATURE REVIEWS NEUROSCIENCE

On the origin and evolutionary consequences of gene body DNA methylation

(2016) Adam J. Bewick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Birds have primate-like numbers of neurons in the forebrain

(2016) Seweryn Olkowicz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Non-CG Methylation in the Human Genome

(2015) Yupeng He et al.   Annual Review of Genomics and Human Genetics

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

(2015) Harrison W. Gabel et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

The octopus genome and the evolution of cephalopod neural and morphological novelties

(2015) Caroline B. Albertin et al.   NATURE

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

(2015) Mark A Urich et al.   Nature Protocols

Rett syndrome: a complex disorder with simple roots

(2015) Matthew J. Lyst et al.   NATURE REVIEWS GENETICS

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Convergent evolution of complex brains and high intelligence

(2015) G. Roth   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

(2015) Benyam Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes

(2015) Carina F. Mugal et al.   G3-Genes Genomes Genetics

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

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

The glia/neuron ratio: How it varies uniformly across brain structures and species and what that means for brain physiology and evolution

(2014) Suzana Herculano-Houzel   GLIA

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability

(2014) Katrina Tatton-Brown et al.   NATURE GENETICS

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

(2013) Weilong Guo et al.   BMC GENOMICS

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Large conserved domains of low DNA methylation maintained by Dnmt3a

(2013) Mira Jeong et al.   NATURE GENETICS

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

(2013) Junjie U Guo et al.   NATURE NEUROSCIENCE

Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor

(2013) Matthew J Lyst et al.   NATURE NEUROSCIENCE

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Evolution of bilaterian central nervous systems: a single origin?

(2013) Linda Z Holland et al.   EvoDevo

DNA methylation in amphioxus: from ancestral functions to new roles in vertebrates

(2012) R. Albalat et al.   Briefings in Functional Genomics

Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome

(2012) Wei Xie et al.   CELL

Genome-wide and Caste-Specific DNA Methylomes of the Ants Camponotus floridanus and Harpegnathos saltator

(2012) Roberto Bonasio et al.   CURRENT BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

Expression of the dnmt3 genes in zebrafish development: similarity to Dnmt3a and Dnmt3b

(2011) Tamara H. L. Smith et al.   DEVELOPMENT GENES AND EVOLUTION

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

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

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Neuronal MeCP2 Is Expressed at Near Histone-Octamer Levels and Globally Alters the Chromatin State

(2010) Peter J. Skene et al.   MOLECULAR CELL

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

DNMT3L Modulates Significant and Distinct Flanking Sequence Preference for DNA Methylation by DNMT3A and DNMT3B In Vivo

(2010) Bethany L. Wienholz et al.   PLoS Genetics

Evolution of DNA-methylation machinery: DNA methyltransferases and methyl-DNA binding proteins in the amphioxus Branchiostoma floridae

(2008) Ricard Albalat   DEVELOPMENT GENES AND EVOLUTION

DNA methylation landscapes: provocative insights from epigenomics

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