Stephen J. Clark

This study introduces scIRES-seq to analyze CTCs from cervical cancer, revealing multimodal molecular heterogeneity through integrated genetic, epigenomic, and transcriptomic profiling.

The paper identifies average polycomb CpG methylation as a hallmark of cellular aging using single-cell whole-genome methylation data, showing cell-to-cell variability and accelerated aging in faster proliferating cells.

This paper introduces scDynaBar, a method using CRISPR barcoding to track temporal cellular events at single-cell resolution, showing the transient nature of the 2C-like state in mESCs.

The paper identifies Eomes's role in directing the formation of distinct extra-embryonic hematovascular tissues in mice, revealing functional and mechanistic diversity in their development.

The paper shows that DNA translesion synthesis is essential for primordial germ cell development and DNA demethylation in mammals, linking DDR to fertility.

This study shows that ectodermal Wnt signalling restricts Shh signal transduction and chondrogenesis to the posterior gill arch environment in skates, establishing skeletal polarity.

A mouse embryo multiome atlas (E7.5 to E8.75) and an unsupervised transcription factor binding predictor; a Brachyury knockout supports its network predictions in neuromesodermal progenitors.

The paper shows that H3K4me1 retention in enhancers supports germline competence by maintaining enhancer accessibility and responsiveness during in vitro differentiation.

The paper uses single-cell bisulfite sequencing to analyze DNA methylation in spermatozoa from lean and obese humans, revealing distinct epigenetic patterns that may affect intergenerational health outcomes.

The paper identifies conserved and unique transcriptional features in pharyngeal arches of skates, supporting serial homology of jaw and gill arches while highlighting distinct developmental mechanisms.

This paper develops a framework to infer spatio-temporal processes in the nucleus from single-cell methylome data, showing feedback between DNA methylation and chromatin condensates during pluripotency exit.

This study identifies Dppa2/4 as epigenetic factors that establish bivalency at developmental promoters, enabling lineage commitment by maintaining poised RNA polymerase and preventing DNA methylation.

This study shows that ageing increases transcriptional heterogeneity and DNA methylation drift in muscle stem cells, disrupting transcriptional networks and stem cell function.

The paper uses single-cell profiling of expression and DNA methylation to study splicing regulation and heterogeneity in human induced pluripotent stem cells.

The paper uses single cell triple-omics analysis to reveal how epigenetic changes drive germ layer specification in mouse embryos, showing distinct epigenetic priming and remodeling in different lineages.

The paper shows that during exit from pluripotency, coexpression of DNMT3s and TETs drives genome-scale DNA methylation oscillations, with amplitude dependent on CpG density, observed both in vitro and in vivo.

This paper introduces scNMT-seq, a method for joint profiling of chromatin accessibility, DNA methylation, and transcription in single cells, and validates it in differentiating mouse embryonic stem cells.