Alexander Kukalev

The paper introduces CoPhasing, a method to phase chromatin contacts with haplotype specificity, revealing structural differences between homologous chromosomes.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

The paper compares super-enhancer networks in embryonic stem cells and dopaminergic neurons, revealing their structural differences and functional roles in transcriptional regulation.

The paper uses GAM to study haplotype-specific 3D chromatin structures in mESCs, finding extensive allelic differences in chromatin architecture and gene expression mediated by Polycomb repression.

This study shows that ecDNA mis-segregation leads to micronuclei formation, reduced oncogene transcription, and improved patient survival in neuroblastoma.

This study shows that a single cocaine exposure causes long-lasting 3D genome structure changes in midbrain dopamine neurons, affecting gene regulation and synaptic plasticity.

This study shows that SRRM2 splicing factor dosage affects embryonic stem cell pluripotency and lineage commitment, with implications for developmental diseases and tumorigenesis.

The paper introduces multiplex-GAM, a ligation-free method for genome-wide chromatin contact mapping, showing it detects different strong contacts compared to Hi-C, particularly involving active genomic regions.

The paper examines 3D genome structures in mouse blastocyst cells to identify lineage-specific chromatin organization differences between epiblast and primitive endoderm cells.

GAMIBHEAR reconstructs haplotypes from Genome Architecture Mapping data to enable allele-specific chromatin conformation analysis.

The paper investigates cell-type specific 3D chromatin structures in the brain using immunoGAM, finding TAD melting, neuron-specific contacts, and compartmentalization patterns related to gene expression and neurodegenerative diseases.