Ogün Adebalı

The paper reanalyzes APOBEC3 mutagenesis in MPXV genomes, showing mutations are enriched at TC motifs in hairpin loops and downstream guanine-rich sequences, with structural and sequence context playing distinct roles at different genomic scales.

PHACTn predicts nucleotide variant tolerability across the genome without training, outperforming existing tools on non-coding variants from ClinVar and OMIM.

The paper introduces the GPCR Evolution Database, which provides evolutionary analysis of GPCRs to study their function and conservation across species.

This study shows that RNAPII and XPC remodel chromatin loops and domains during UV repair, enhancing lesion recognition and repair efficiency.

The paper develops Brendo, a resource identifying BMEC-specific genes using bulk RNA-seq data and provides a web platform for exploring these genes.

The paper analyzes MPXV RNA-seq data to determine if APOBEC3 enzymes edit viral RNA, concluding that observed mutations result from DNA-level mutagenesis, not RNA editing.

This study investigates how UV radiation induces reorganization of the 3D genome and its role in DNA damage response and repair.

PHACE identifies co-evolving amino acid positions by incorporating phylogenetic dependencies, outperforming existing methods in accuracy.

PHACTboost improves missense variant pathogenicity prediction by integrating phylogenetic trees, multiple sequence alignments, and ancestral reconstruction, outperforming existing tools including AlphaMissense and CPT-1.

This study identifies NPAS4 downregulation in multiple brain regions and links it to glutamatergic signaling disruption in Major Depressive Disorder.

Boquila simulates NGS reads to correct nucleotide bias by mimicking true read profiles from specified genomic regions.

This study investigates heterodimer formation among ZBTB transcription factors, confirming physical interactions and co-expression in immune cells, and analyzing energetic determinants of homo and heterodimer formation.

The paper compares UV repair efficiency and patterns between humans and mouse lemurs, finding similar repair mechanisms but differences in efficiency.

The paper presents a deep learning framework to detect misannotated long non-coding RNAs by analyzing training dynamics, achieving high accuracy in distinguishing coding from non-coding sequences.

The paper analyzes SARS-CoV-2 genomes from Turkey to trace the virus's introduction and spread, identifying multiple international introductions and a transmission hub.