Author details

Full Name

Ryan Lister

Affiliation

ORCID

Career Start Year

2001

Papers

101

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37483019	Exploring the identity of individual plant cells in space and time.		2023
37587336	Transient naive reprogramming corrects hiPS cells functionally and epigenetically.	Nature	2023
38000387	A modular dCas9-based recruitment platform for combinatorial epigenome editing.		2023
36637421	Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds.	Tree Physiol	2023
37308583	Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap.	Nat Plants	2023
37239317	Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development.	Genes (Basel)	2023
37228755	Single-nucleus RNA sequencing of pre-malignant liver reveals disease-associated hepatocyte state with HCC prognostic potential.		2023
34526697	Epigenome plasticity in plants.	Nature Reviews Genetics	2022
35710627	Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential.	NPJ Regen Med	2022
35883107	Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.	Genome Biol	2022
35788565	Synthetic memory circuits for stable cell reprogramming in plants.	Nature Biotechnology	2022
36318921	Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution.	Cell	2022
36463236	Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells.	Nat Commun	2022
35292647	Comprehensive evaluation of deconvolution methods for human brain gene expression.	Nature Communications	2022
33462491	The emergence of the brain non-CpG methylation system in vertebrates.	Nat Ecol Evol	2021
34021136	Transcriptional signature in microglia associated with AÎ² plaque phagocytosis.	Nat Commun	2021
34009614	Genomic Targeting of TET Activity for Targeted Demethylation Using CRISPR/Cas9.	Methods in Molecular Biology	2021
33738444	Cerebrospinal fluid liquid biopsy for detecting somatic mosaicism in brain.	Brain Communications	2021
33731926	Modelling human blastocysts by reprogramming fibroblasts into iBlastoids.	Nature	2021
32719321	Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri.	Nature Communications	2020
31794001	schex avoids overplotting for large single-cell RNA-sequencing datasets.		2020
31726061	Evolution of DNA Methylome Diversity in Eukaryotes.	Journal of Molecular Biology	2020
32487174	Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows.	Genome Biol	2020
32457347	Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings.	Nat Commun	2020
33313487	Depletion of Foxk transcription factors causes genome-wide transcriptional misregulation and developmental arrest in zebrafish embryos.		2020
33296673	TINC- A Method to Dissect Regulatory Complexes at Single-Locus Resolution- Reveals an Extensive Protein Complex at the Nanog Promoter.	Stem Cell Reports	2020
32939092	ReprogrammingÂ roadmap reveals route toÂ human induced trophoblast stem cells.	Nature	2020
31096906	HOME: a histogram based machine learning approach for effective identification of differentially methylated regions.	BMC Bioinformatics	2019
31724704	Harnessing targeted DNA methylation and demethylation using dCas9.	Essays in Biochemistry	2019
31768052	A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation.	Nat Neurosci	2019
31558833	Convergent evolution of a vertebrate-like methylome in a marine sponge.	Nature Ecology and Evolution	2019
31230816	LINE-1 Evasion of Epigenetic Repression in Humans.	Mol Cell	2019
31296860	Retention of paternal DNA methylome in the developing zebrafish germline.	Nature Communications	2019
31239280	Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family.	Genome Research	2019
29632298	Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.	Nature Communications	2018
29907613	A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs.	Genome Research	2018
30464347	Amphioxus functional genomics and the origins of vertebrate gene regulation.	Nature	2018
29717194	Author Correction: Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.	Nature Communications	2018
29524143	Approaches for theÂ Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data.	Methods in Molecular Biology	2018
29524142	Generation of Whole Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis.	Methods in Molecular Biology	2018
27859855	Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation.	Plant J	2017
28911330	Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination.		2017
28945704	Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming.	Nature Methods	2017
28451358	Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA.	Chem Sci	2017
28793267	Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases.	Cell Reports	2017
28705956	Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis.	Plant Cell	2017
28441589	Nutrient stress-induced chromatin changes in plants.	Current Opinion in Plant Biology	2017
28651214	DNA methylation and the preservation of cell identity.	Current Opinion in Genetics and Development	2017
29220667	Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming.		2017
29212013	Cell Type of Origin Dictates the Route to Pluripotency.	Cell Rep	2017