Felix Krueger

This paper explores the use of LLM-based coding agents in scientific computing, presenting case studies in the life sciences and discussing their potential and challenges.

The paper examines genomic imprinting and X-chromosome inactivation stability in aging mouse brains, finding they remain largely stable despite epigenetic drift.

The paper shows NANOGP1, a duplicate of NANOG, has partial functional conservation in human naive pluripotent stem cells, contributing to pluripotency but not maintaining undifferentiated status.

The paper identifies sequence preferences of TET enzymes that target DNA demethylation to bHLH and bZIP transcription factor binding sites.

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 investigates how transcriptional activation of the CUP1 gene in budding yeast leads to copy number variation through replication stress and homologous recombination.

The paper examines how MEK and GSK3 inhibition affects the methylome and transcriptome of mouse embryonic stem cells, revealing distinct epigenetic and transcriptional changes.

This paper identifies 8-cell like cells (8CLCs) in human naive stem cells that model zygotic genome activation, expressing ZGA markers and transposable elements, and can be manipulated to enhance ZGA-like transcription.

This paper introduces TrAEL-seq, a method to detect DNA replication fork stalling and double strand breaks with high resolution, and demonstrates its application in yeast and mammalian cells.

The paper shows that histone modifications form cell-type-specific chromosomal patterns that remain stable through the cell cycle, helping maintain gene expression identity.

The paper shows that donor cell sex and reprogramming conditions affect imprinting defects in mouse iPSCs, with distinct methylation patterns observed under different culture conditions.

IMPLICON is a high-throughput method for measuring DNA methylation at imprinted regions with high coverage and resolution, validated in mice and adapted for human use to detect imprinting errors.

This study shows that transcription of the CUP1 gene in aged yeast leads to the formation of extrachromosomal DNA, which accumulates without phenotypic selection and is site-specific.

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.

This study shows that SmcHD1 prevents TAD formation on the inactive X chromosome by altering chromatin structure and epigenetic marks.

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 study compares WGBS library preparation methods and identifies biases in sequencing data, finding that bisulfite conversion and PCR amplification are major sources of bias.

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.

The paper develops a DNA methylation age predictor for mice, showing it accurately measures biological age and responds to interventions like ovariectomy and diet.