Helene Kretzmer

Epigenetic regulators partition the genome by evolutionary and developmental constraint

The paper uses single-cell RNA sequencing to analyze mutant phenotypes of epigenetic regulators in mouse embryos, revealing how these regulators partition the genome based on developmental and evolutionary constraints.

Genome-wide multi-layered epigenomic profiling across human aging

This study investigates the relationship between age-related epigenetic changes in DNA methylation, chromatin accessibility, and histone modifications across human aging using integrated WGBS and ATAC-seq data.

Multimodal single-cell analysis uncovers transcription factor networks underlying T-cell aging

This study uses multimodal single-cell analysis to identify transcription factor networks involved in T-cell aging.

Nucleolus transformation and Pol1 activity pattern dual transcriptomes of neuronal subtype identity

The paper identifies that nucleolar restructuring and Pol1 activity patterns are linked to neuronal subtype identity through dual rRNA-mRNA transcriptomes in developing neocortex.

Human brain organoids record the passage of time over multiple years in culture

This study shows human brain organoids can mature over 5 years in culture, transcriptionally aging and retaining memory of time spent in vitro.

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold-standard

The paper benchmarks DNA methylation sequencing workflows against an experimental gold-standard, identifying superior workflows and developing a sustainable benchmarking platform.

An advanced head-to-tail mouse embryo model with hypoxia-mediated neural patterning

This paper develops a hypoxia-mediated mouse embryo model to study neural patterning and shows hypoxia enhances anterior neural cell identity through HIF1a and TGFβ modulation.

The Greenland shark (Somniosus microcephalus) genome provides insights into extremelongevity

The paper presents a chromosome-level genome assembly of the Greenland shark and identifies genomic features associated with its extreme longevity.

Discovery and characterization of LNCSOX17 as an essential regulator in human endoderm formation

The paper identifies and characterizes LNCSOX17, a lncRNA essential for human endoderm formation, showing its role in regulating transcriptome and differentiation.

Emergence and patterning dynamics of mouse definitive endoderm

This study investigates the emergence and patterning dynamics of mouse definitive endoderm using in vivo and in vitro models, revealing self-sorting and Sox17 expression patterns.

Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites

The paper describes a method to generate trunk-like structures from mouse embryonic stem cells that mimic embryonic development features.

Dissecting the DNA binding landscape and gene regulatory network of p63 and p53

The paper identifies p63 binding sites and predicts its gene regulatory network using ChIP-seq data and motif analysis, highlighting potential therapeutic targets in SCC.

Molecular recording of mammalian embryogenesis

The paper develops a molecular recorder to track lineage and define a mouse cell fate map using scRNA-seq, revealing transcriptional convergence of endodermal cells and estimating progenitor cell numbers.

Repeat expansion and methylation state analysis with nanopore sequencing

This paper develops a Cas12a-based enrichment strategy and algorithm for nanopore sequencing to quantify repeat expansions and their methylation status.

Disturbance of poised chromatin coincides with increased expression of developmental genes in cancer

The paper shows that hypermethylation of poised chromatin and up-regulation of corresponding developmental genes is a common feature in cancer, using large-scale expression and methylation data.