Marco Blanchette

The paper introduces RyboCypher, a platform that maps the dark transcriptome to unannotated peptides, identifying cryptic proteins in cancer cell lines, tumors, and healthy tissues.

The paper generates a collection of 65 isogenic human stem cell lines with PD-associated mutations to study Parkinson's disease, revealing that most genetic variation comes from cell culture rather than genome editing.

The paper develops HiDENSEC to analyze Hi-C data in heterogeneous cancer samples, identifying chromosomal rearrangements and their impact on melanoma progression.

The paper uses high-resolution CTCF MNase HiChIP data to analyze chromatin loop structures and introduces FactorFinder, finding that fully extruded CTCF-CTCF loops are rare and that chromatin state affects cohesin extrusion dynamics.

The paper shows that inducing DNA breaks accelerates aging-related chromatin changes and loss of cell identity in mammals.

This paper develops a method called Fix-C to detect structural variations in FFPE tumor samples, achieving high concordance with FISH assays and identifying novel variations.