This study maps epigenomic heterogeneity in prostate cancer by analyzing 3,001 methylomes and identifies four subtypes with distinct clinical and molecular features.

Cancer Discovery · Jun 17, 2026Peer-reviewedCancer Biology

Whole-genome pre-amplification as a viable approach for genomic screening of FFPE-derived DNA samples

Conrado Guerrero Quiles, Taha Lodhi, Robert Sellers, Sudhakar Sahoo, John Weightman, Wolfgang Breitwieser, Diego Sánchez Martinez, Matej Bartak, Amen Shamim, Steve Lyons, Kimberley Jayne Reeves, Rachel Reed, Peter Hoskin, Catharine West, Laura J. Forker, , Luisa Vanesa Biolatti

This study evaluates DLMDA for improving DNA yield from FFPE samples but finds it reduces CNA sensitivity.

bioRxiv · Mar 29, 2026 · PreprintMolecular Biology

Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities

Jenna Craddock, Pavlo Lutsik, Pamela X. Y. Soh, Melanie Louw, Md. Mehedi Hasan, Sean Mark Patrick, Shingai Bertrand Angelo Mutambirwa, Phillip D. Stricker, Hagen E. A. Förtsch, HEROIC PCaPH Africa1K, Co-principal investigators, Gail S. Prins, Peter Mungai Ngugi, Developmental team leads, Weerachai Jaratlerdsiri, , Vanessa M. Hayes

The paper investigates DNA methylation differences in prostate cancer across African, European, and Asian ancestries, finding ancestry-driven methylation patterns linked to disease aggressiveness in African tumors.

Molecular Systems Biology · Oct 7, 2025Peer-reviewedGenomics

CellPie: a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization

Sokratia Georgaka, William Geraint Morgans, Qian Zhao, Diego Fernando Sanchez, Amin Ali, Mohamed Ghafoor, Syed-Murtuza Baker, Robert Glen Bristow, Mudassar Iqbal, Magnus Rattray

CellPie is a fast, unsupervised method for factor discovery in spatial transcriptomics using joint non-negative matrix factorization, showing improved performance on human cancer datasets.

Nucleic Acids Research · Mar 20, 2025Peer-reviewedBioinformatics

The Telomere Length Landscape of Prostate Cancer

Julie M. Livingstone, Yu-Jia Shiah, Takafumi N. Yamaguchi, Lawrence E. Heisler, Vincent Huang, Robert Lesurf, Tsumugi Gebo, Benjamin Carlin, Stefan E. Eng, Erik Drysdale, Jeffrey D Green, Theodorus van der Kwast, Robert Glen Bristow, Michael E. Fraser, Paul Christopher Boutros

This study examines telomere length in prostate cancer, finding associations with genomic instability and clinical outcomes.

Nature Communications · Nov 25, 2021Peer-reviewedGenomics

Valection: Design Optimization for Validation and Verification Studies

SMC-DNA Challenge Participants, Christopher I. Cooper, Delia Yao, Dorota H.S. Sendorek, Takafumi N. Yamaguchi, Christine P’ng, Kathleen E. Houlahan, Cristian Caloian, Michael E. Fraser, Kyle Ellrott, Adam A Margolin, Robert Glen Bristow, Joshua M. Stuart, Paul Christopher Boutros

Valection optimizes the selection of verification candidates to estimate error profiles in genomics studies by evaluating different strategies on synthetic data.

BMC Bioinformatics · Sep 25, 2018Peer-reviewedBioinformatics