Ekaterina E. Khrameeva

The paper integrates exome and transcriptome data from a schizophrenia case with low polygenic risk to identify potential variants and transcriptomic abnormalities, revealing biological alterations linked to cerebrovascular disease.

This study investigates how CTCF's functional properties evolved across bilaterian species, revealing gradual changes in its ability to regulate chromatin structure and transcription.

This study compares chromatin architecture in iPSC-derived neurons to fetal and mature neurons, finding iPSC-derived neurons resemble fetal neurons and have distinct chromatin features.

This study evaluates SIRT6 as an aging biomarker by analyzing transcriptomic data across species and identifies context-dependent dysregulation in Alzheimer's disease.

The paper estimates human lifespan limits by modeling the impact of somatic mutations, finding they reduce lifespan from 430 to 169 years but cannot fully explain mortality.

This study identifies accelerated aging patterns in 3D genome organization and transcriptome in schizophrenia using Hi-C data and transcriptomic analysis.

This paper presents the first chromosome-level genome assembly of the sponge Halisarca dujardinii, along with mitochondrial genome and comprehensive annotation.

This paper develops a reversible SIRT6 deficiency model to study brain aging and neurodegeneration, finding transcriptomic changes resembling aging and Alzheimer's disease.

This study compares 3D genome changes in aging and neurodegenerative mouse models using Hi-C, finding shared early features and distinct later changes linked to DNA damage.

The paper investigates how Polycomb proteins regulate gene expression in human cortical neurons through long-range chromatin interactions, showing their role in cell-type specification.

ComputAgeBench benchmarks epigenetic aging clocks by comparing 13 models on 66 harmonized blood DNA methylation datasets to evaluate their ability to distinguish healthy individuals from those with aging-accelerating conditions.

The paper analyzes how epistemic uncertainty affects the reliability of aging clocks in predicting rejuvenation effects during cellular reprogramming.

The paper identifies Elys as a nucleoporin linking peripheral chromatin to nuclear pores in interphase nuclei and shows its role in chromatin organization and gene regulation.

The paper investigates chromatin looping in Dictyostelium discoideum, finding that convergent gene pairs act as directional barriers for chromatin extrusion during development.

The paper maps 3D genome architecture in neuronal and non-neuronal cells, finding reduced compartmentalization and increased long-range polycomb interactions in neurons.

The paper introduces optimalTAD, an algorithm for identifying TADs by maximizing chromatin mark enrichment differences between TADs and boundaries, showing it works across species and cell types.

This study identifies a transcriptomic signature of reprogramming in mouse and human cells that reverses age-related gene expression changes and reveals mechanisms of rejuvenation independent of pluripotency gain.

This paper develops deep-learning methods to enhance Hi-C data resolution using genome sequence information and provides open-source code.