Csilla Várnai

The paper identifies six cis-regulatory elements controlling mdka expression in zebrafish telencephalic NSCs during development and regeneration, showing that their cooperation is necessary for full expression.

This study shows that HPV18 infection reprograms host transcription by altering CTCF binding and promoter-enhancer interactions, leading to repression of the tumor suppressor CADM1.

The paper differentiates agonists and competitive antagonists of the 5-HT3A receptor using Monte Carlo simulations and linear response theory.

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

This study examines how 3D chromatin organization in mouse liver changes throughout the circadian cycle, revealing dynamic domain assignments and promoter-specific chromatin contacts.

The paper analyzes promoter interactions in human pluripotent states to reveal hierarchical differences in genome organization using a network-graph approach.

This study demonstrates that CTCF, WAPL, and PDS5 proteins regulate TADs and loops by controlling cohesin's interaction with chromatin.

The paper shows that differential mobility of chromatin segments, influenced by protein occupancy, drives 3D genome organisation in yeast.

This study uses single-cell Hi-C to analyze chromosomal organization dynamics across the cell cycle, revealing distinct cell cycle-dependent changes in chromosomal compartments, TADs, and loops.

CHiCAGO detects DNA looping interactions in Capture Hi-C data by addressing statistical challenges with a background model and normalization algorithms, showing enrichment for regulatory features and disease SNPs.