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

Bioinformatics, 2011-06, Vol.27 (11), p.1571-1572

2011

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Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Genome Biology, 2018-03, Vol.19 (1), p.33-33, Article 33

2018

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Multi-omics profiling of mouse gastrulation at single-cell resolution

Nature (London), 2019-12, Vol.576 (7787), p.487-491

2019

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Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

Science (American Association for the Advancement of Science), 2012-05, Vol.336 (6083), p.934-937

2012

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scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

Nature communications, 2018-02, Vol.9 (1), p.781-9, Article 781

2018

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Resetting transcription factor control circuitry toward ground-state pluripotency in human

Cell, 2014-09, Vol.158 (6), p.1254-1269

2014

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The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

Molecular cell, 2012-12, Vol.48 (6), p.849-862

2012

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Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq

PLoS biology, 2021-03, Vol.19 (3), p.e3000886-e3000886

2021

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Transcription-induced formation of extrachromosomal DNA during yeast ageing

PLoS biology, 2019-12, Vol.17 (12), p.e3000471

2019

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SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes [version 2; peer review: 3 approved]

F1000 research, 2016, Vol.5, p.1479-1479

2016

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Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism

Genome Biology, 2017-03, Vol.18 (1), p.56-56, Article 56

2017

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Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

Nature (London), 2011-05, Vol.473 (7347), p.398-402

2011

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Multi-tissue DNA methylation age predictor in mouse

Genome Biology, 2017-04, Vol.18 (1), p.68-68, Article 68

2017

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Dynamic CpG island methylation landscape in oocytes and preimplantation embryos

Nature genetics, 2011-08, Vol.43 (8), p.811-814

2011

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MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs

Cell reports (Cambridge), 2016-09, Vol.17 (1), p.179-192

2016

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FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency

Cell stem cell, 2013-09, Vol.13 (3), p.351-359

2013

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Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape

Genome Biology, 2015-09, Vol.16 (1), p.209-209, Article 209

2015

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Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions

Nature communications, 2020-03, Vol.11 (1), p.1528-1528, Article 1528

2020

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Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues

Genome Biology, 2019-10, Vol.20 (1), p.225-17, Article 225

2019

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The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome

Nature communications, 2019-01, Vol.10 (1), p.30-14, Article 30

2019

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Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

Genome Biology, 2015-05, Vol.16 (1), p.112-112, Article 112

2015

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Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis

Genome Biology, 2022-09, Vol.23 (1), p.202-20, Article 202

2022

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DNA Methylation Profiles Define Stem Cell Identity and Reveal a Tight Embryonic-Extraembryonic Lineage Boundary

Stem cells (Dayton, Ohio), 2012-12, Vol.30 (12), p.2732-2745

2012

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scEpiAge: an age predictor highlighting single-cell ageing heterogeneity in mouse blood

Nature communications, 2024-08, Vol.15 (1), p.7567-15, Article 7567

2024

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Large scale loss of data in low-diversity illumina sequencing libraries can be recovered by deferred cluster calling

PloS one, 2011-01, Vol.6 (1), p.e16607-e16607

2011

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

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Multi-omics profiling of mouse gastrulation at single-cell resolution

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

Resetting transcription factor control circuitry toward ground-state pluripotency in human

The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq

Transcription-induced formation of extrachromosomal DNA during yeast ageing

SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes [version 2; peer review: 3 approved]

Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

Multi-tissue DNA methylation age predictor in mouse

Dynamic CpG island methylation landscape in oocytes and preimplantation embryos

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs

FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency

Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape

Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions

Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues

The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome

Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis

DNA Methylation Profiles Define Stem Cell Identity and Reveal a Tight Embryonic-Extraembryonic Lineage Boundary

scEpiAge: an age predictor highlighting single-cell ageing heterogeneity in mouse blood

Large scale loss of data in low-diversity illumina sequencing libraries can be recovered by deferred cluster calling

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