Georgi K. Marinov

This study uses Hi-C data to challenge the Cholesteric Liquid Crystal model of dinoflagellate chromosomes by showing no evidence of cholesteric discs and demonstrating transcription occurs throughout chromosomes.

This study links in vitro transcription factor affinities to in vivo single-molecule chromatin states using thermodynamic models and experimental data for KLF1.

The paper identifies age-related microbiome metabolites that alter RNA splicing and chromatin accessibility in the mouse brain using metabolomics, transcriptomic, and multi-omic approaches.

This paper develops beCasKAS, a method to directly detect off-target base editor activity in primary cells, revealing distinct off-target profiles and enabling risk stratification of edits.

The paper introduces a high-resolution single-molecule chromatin accessibility mapping method to quantify transcription factor occupancy and co-accessibility in human cell lines.

The paper presents a single-cell multi-omics atlas of human development and uses deep learning to analyze regulatory DNA motifs and their impact on chromatin accessibility and gene expression.

The paper updates and reevaluates evidence for nuclear transcription factor occupancy over the mitochondrial genome using expanded ChIP-seq data and deep learning models.

The paper introduces KAS-ATAC, a method combining KAS-seq and ATAC-seq to simultaneously measure chromatin accessibility and single-stranded DNA, revealing insights into transcription and regulatory elements in the human genome.

The paper shows genome concentration limits transcription and affects proteome composition in E. coli, with effects detectable in nutrient-rich conditions.

This paper identifies transcription-replication conflict as a vulnerability in ecDNA-containing cancers and demonstrates that CHK1 inhibition selectively kills these tumors.

The paper trains a deep learning model to predict transcription initiation from DNA sequences, revealing shared cis-regulatory logic and epistatic interactions across promoters and enhancers.

This study shows that germline manipulation in killifish leads to sex-specific effects on longevity and repair mechanisms.

This study links transcription factor binding to gene expression by analyzing chromatin configurations using single-molecule footprinting in human cells.

This study uses ATAC-seq to map the chromatin accessibility of Haloferax volcanii and finds that promoter accessibility does not correlate with transcriptional activity, and archaeal chromatin is similarly accessible to eukaryotic chromatin.

The paper identifies RNAPII as the limiting factor for transcription scaling with cell size in budding yeast and shows that mRNA stability feedback compensates for sub-linear transcription growth.

This study maps chromatin accessibility, transcription, and 3D organization in Bdellovibrionota bacteria, revealing features similar to archaea and eukaryotes.

This study maps 5-hydroxymethyluracil and chromatin accessibility in Breviolum minutum to explore their genomic distribution and functional roles.

This study maps open chromatin, transcription, and 3D organization of the nucleomorph genome in Bigelowiella natans, revealing its highly accessible and transcribed state with strong nucleosome positioning and telomeric chromosome interactions.

This study examines the 3D genome organization of dinoflagellates, finding that transcription-induced supercoiling drives domain-scale structure without chromatin loops.

The paper introduces a method to profile off-target specificity of CRISPR enzymes using ssDNA mapping, applicable to both catalytically dead and active Cas9 variants.

The paper develops HT-recruit, a high-throughput assay to identify transcriptional effectors in human proteins, finding repressor function correlates with evolutionary age and discovering new activator domains.

This study identifies how mutant KRAS reprograms the noncoding transcriptome, upregulating repetitive noncoding RNAs and inducing IFN-stimulated genes through epigenetic and RNA-based mechanisms.

The paper quantifies the mouse embryo transcriptome from E10.5 to birth using whole-tissue and single-cell RNA-seq, identifying key gene expression patterns and cell types.

This paper introduces SMAC-seq, a method for long-range chromatin accessibility mapping in eukaryotes, and demonstrates its application in yeast.

The paper identifies off-target effects in CRISPR-Cas9 screens for non-coding elements and shows that strict filtering with specificity scores improves the identification of essential regulatory regions.

The paper introduces MPRA-DragoNN, a CNN model to predict regulatory DNA activity from MPRAs, identifies TF motifs, and explores variant effects in lipid-associated loci.