This paper introduces refLinker, a method for haplotype-resolved analysis of cancer karyotypes, revealing transcriptional consequences of somatic Xi rearrangements.

Cell Systems · Mar 1, 2026Peer-reviewedGenomics

Determination of complete chromosomal haplotypes by bulk DNA sequencing

Richard W. Tourdot, Gregory J. Brunette, Ricardo A. Pinto, Cheng‐Zhong Zhang

This paper presents a computational method to determine complete chromosomal haplotypes using bulk long-range sequencing and Hi-C data, achieving high precision and completeness in diploid human genomes.

Genome biology · May 6, 2021Peer-reviewedGenomics

Genomic signatures of past and present chromosomal instability in the evolution of Barretts esophagus to esophageal adenocarcinoma

Matthew D. Stachler, Chunyang Bao, Richard W. Tourdot, Gregory J. Brunette, Chip Stewart, Lili Sun, Hideo Baba, Masayuki Watanabe, Agoston Agoston, Kunal Jajoo, Jon M. Davison, Katie Sue Nason, Gad A. Getz, Kenneth K. Wang, Yu Imamura, , Cheng‐Zhong Zhang

This study identifies genomic signatures of chromosomal instability in Barrett's esophagus progressing to esophageal adenocarcinoma, showing sloping copy-number variation as a precursor to complexity.

bioRxiv · Mar 26, 2021 · PreprintCancer Biology

Identification of MCM8IP, an interactor of MCM8-9 and RPA1 that promotes homologous recombination and DNA synthesis in response to DNA damage

Jen‐Wei Huang, Angelo Taglialatela, Ananya Acharya, Giuseppe Leuzzi, Tarun S. Nambiar, Raquel Cuella-Martin, Samuel B. Hayward, Gregory J. Brunette, Roopesh Anand, Rajesh Kumar Soni, Nathan L Clark, Kara Anne Bernstein, Petr Ćejka, Alberto Ciccia

This study identifies MCM8IP as a DNA repair factor that promotes homologous recombination and DNA synthesis in response to DNA damage by interacting with MCM8-9 and RPA1.

bioRxiv · Sep 3, 2019 · PreprintGenetics