List of works by Ryan Lister

A link between RNA metabolism and silencing affecting Arabidopsis development.

scientific article published on 22 May 2008

A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs

scientific article published on 15 June 2018

A plant outer mitochondrial membrane protein with high amino acid sequence identity to a chloroplast protein import receptor

scientific article published on 16 December 2003

A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation

scientific article published on 01 December 2019

A transcriptomic and proteomic characterization of the Arabidopsis mitochondrial protein import apparatus and its response to mitochondrial dysfunction

scientific article published on 15 January 2004

Active DNA demethylation at enhancers during the vertebrate phylotypic period

scientific article published on 29 February 2016

Amphioxus functional genomics and the origins of vertebrate gene regulation

scientific article published in Nature

Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation

scientific article

Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data.

scientific article published in January 2018

Arabidopsis thaliana ferrochelatase-I and -II are not imported into Arabidopsis mitochondria

scientific article published on 01 October 2001

Author Correction: Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.

scientific article published in May 2018

CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity

scientific article published on 07 April 2014

Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family

scientific article published on 25 June 2019

Cell Type of Origin Dictates the Route to Pluripotency.

scientific article published in December 2017

Cerebrospinal fluid liquid biopsy for detecting somatic mosaicism in brain

scientific article published on 21 January 2021

Characterization of the preprotein and amino acid transporter gene family in Arabidopsis

scientific article published on 10 November 2006

Characterization of the regulatory and expression context of an alternative oxidase gene provides insights into cyanide-insensitive respiration during growth and development.

scientific article published on 23 February 2007

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

scientific article

Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming

scientific article published on 25 September 2017

Comprehensive evaluation of deconvolution methods for human brain gene expression

scientific article published on 15 March 2022

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

scientific article published on 26 September 2019

DNA methylation and the preservation of cell identity

scientific article published on 23 June 2017

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

scientific article published on 09 September 2016

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

scientific article

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation

scientific article published on 12 November 2016

Embryonic transcription is controlled by maternally defined chromatin state.

scientific article

Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases.

scientific article published on August 2017

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

scientific article published on June 2015

Epigenomic analysis of multilineage differentiation of human embryonic stem cells

scientific article published on 09 May 2013

Epigenomic landscapes of retinal rods and cones

scientific article

Erratum: Embryonic transcription is controlled by maternally defined chromatin state

scientific article published on 5 July 2016

Evolution of DNA Methylome Diversity in Eukaryotes

scientific article published on 11 November 2019

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination.

scientific article published on 15 September 2017

Finding the fifth base: genome-wide sequencing of cytosine methylation.

scientific article published on 09 March 2009

Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

article

Functional definition of outer membrane proteins involved in preprotein import into mitochondria

scientific article published in 2007

Generation of Whole Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis

scientific article published on 01 January 2018

Genome evolution in the allotetraploid frog Xenopus laevis

scientific article

Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways

scientific article

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

scientific article

Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings

scientific article published on 26 May 2020

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

scientific article published on 7 December 2011

Global epigenomic reconfiguration during mammalian brain development

scientific article (publication date: 9 August 2013)

HOME: a histogram based machine learning approach for effective identification of differentially methylated regions

scientific article published on 16 May 2019

Harnessing targeted DNA methylation and demethylation using dCas9

scientific article published on 14 November 2019

Highly integrated single-base resolution maps of the epigenome in Arabidopsis

scientific article (publication date: 2 May 2008)

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

scientific article

Human DNA methylomes at base resolution show widespread epigenomic differences

scientific article

Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis

scientific article published on 20 June 2008

Identification, expression, and import of components 17 and 23 of the inner mitochondrial membrane translocase from Arabidopsis.

scientific article published in April 2003

LINE-1 Evasion of Epigenetic Repression in Humans

scientific article published on 20 June 2019

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

scientific article published on 18 February 2015

Mitochondrial Protein Import: Convergent Solutions for Receptor Structure

scientific article published on 01 March 2006

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

scientific article published on 20 January 2009

Nutrient stress-induced chromatin changes in plants

scientific article

Of Mice and Man: Differential DNMT Dependence in Mammalian ESCs.

scientific article published in May 2015

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

scientific article published on 02 December 2016

Protein import into mitochondria: origins and functions today (review).

scientific article

Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis.

scientific article published on 13 July 2017

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.

scientific article published on 9 April 2018

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

scientific article published on 24 October 2017

Retention of paternal DNA methylome in the developing zebrafish germline

scientific article published on 11 July 2019

Retrograde signalling caused by heritable mitochondrial dysfunction is partially mediated by ANAC017 and improves plant performance

scientific article published on 18 July 2016

STAR: an integrated solution to management and visualization of sequencing data

scientific article

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

scientific article

Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana.

scientific article published in May 2005

Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA.

scientific article published on 27 January 2017

Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells.

scientific article published on 05 December 2013

The Arabidopsis glutathione transferase gene family displays complex stress regulation and co-silencing multiple genes results in altered metabolic sensitivity to oxidative stress

scientific article

The Mitochondrial Protein Import Machinery of Plants (MPIMP) database

scientific article published on January 2003

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

scientific article published on 27 July 2020

Transcriptional signature in microglia associated with Aβ plaque phagocytosis

scientific article published on 21 May 2021

Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming

scientific article published in December 2017

Turning over DNA methylation in the mind

scientific article (publication date: 2015)

Unique cell-type-specific patterns of DNA methylation in the root meristem.

scientific article

Zinc-dependent intermembrane space proteins stimulate import of carrier proteins into plant mitochondria.

scientific article published in June 2002

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data

scientific article

schex avoids overplotting for large single-cell RNA-sequencing datasets

scientific article published on 01 April 2020

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