Hakan Özadam

The paper analyzes ribosome profiling data to show translation efficiency covariation (TEC) is conserved across human and mouse cells, revealing gene functions not evident from RNA or protein co-expression.

RiboGraph provides an interactive visualization tool for ribosome profiling data, enabling real-time analysis at read length resolution without preprocessing.

The paper shows Reh1 remains on 60S subunits during early translation elongation and is displaced by the growing peptide chain.

This paper develops Ribo-ITP to measure ribosome occupancy in single cells during early mouse development, revealing differential translation efficiency and allele-specific ribosome engagement.

This study evaluates 3C-based assays to understand how experimental parameters affect chromatin interaction detection and quantification, leading to the development of Hi-C 3.0.

The paper identifies genes with 5' terminal oligopyrimidine tracts that escape suppression by SARS-CoV-2 NSP1 through RNA-Seq and ribosome profiling, revealing a role for LARP1 in their preferential translation.

The paper analyzes RNA expression and splicing in a family with a rare Mendelian disorder, revealing disrupted coordination between mitochondrial components and RPL11 transcripts.

The paper shows that during telophase, condensin-mediated loops are replaced by cohesin-mediated loops and TADs, revealing telophase as a critical transition in chromosome folding.

The paper evaluates reproducibility and quality measures for Hi-C data using real and simulated datasets, showing that specialized methods outperform simple correlation analysis.

This study shows that SmcHD1 prevents TAD formation on the inactive X chromosome by altering chromatin structure and epigenetic marks.

This study develops a method to probe mRNA 3D structures and finds that pre-translational mRNPs form linear rod-like structures without strong end interactions.

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

This study introduces spliceosome profiling to map intron excision sites with high resolution, revealing new introns and correcting misannotations in S. pombe.

The paper investigates the HoxD cluster's role as a dynamic TAD boundary in limb development, showing its resilience and ability to maintain regulatory segregation.