Marek Cmero

Sex differences in oncogenic mutational processes.

Constance H Li, Stephenie D Prokopec, Ren X Sun, Fouad Yousif, Nathaniel Schmitz, undefined PCAWG Tumour Subtypes and Clinical Translation, Paul C Boutros, undefined PCAWG Consortium

Journal article  |  2020  |  Nature Communications

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside t..

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

Marek Cmero, Breon Schmidt, Ian Majewski, Paul Ekert, Alicia Oshlack, Nadia Davidson

Journal article  |  2020

Genomic rearrangements can modify gene function by altering transcript sequences, and have been shown to be drivers in both cancer..

Prostate cancer cell-intrinsic interferon signaling regulates dormancy and metastatic outgrowth in bone

Katie L Owen, Linden J Gearing, Damien J Zanker, Natasha K Brockwell, Weng Hua Khoo, Daniel L Roden, Marek Cmero, Stefano Mangiola, Matthew K Hong, Alex J Spurling, Michelle McDonald, Chia-Ling Chan, Anupama Pasam, Ruth J Lyons, Hendrika M Duivenvoorden, Andrew Ryan, Lisa M Butler, John M Mariadason, Tri Giang Phan, Vanessa M Hayes, et al.

Journal article  |  2020  |  EMBO Reports

The latency associated with bone metastasis emergence in castrate-resistant prostate cancer is attributed to dormancy, a state in ..

The evolutionary history of 2,658 cancers

Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vazquez-Garcia, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, et al.

Journal article  |  2020  |  Nature

Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this proce..

Pan-cancer analysis of whole genomes

Peter J Campbell, Gad Getz, Jan O Korbel, Joshua M Stuart, Jennifer L Jennings, Lincoln D Stein, Marc D Perry, Hardeep K Nahal-Bose, BF Francis Ouellette, Constance H Li, Esther Rheinbay, G Petur Nielsen, Dennis C Sgroi, Chin-Lee Wu, William C Faquin, Vikram Deshpande, Paul C Boutros, Alexander J Lazar, Katherine A Hoadley, David N Louis, et al.

Journal article  |  2020  |  Nature

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this v..

Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig

Yulia Rubanova, Ruian Shi, Caitlin F Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit Deshwar, undefined PCAWG Evolution and Heterogeneity Working Group, Quaid Morris, undefined PCAWG Consortium

Journal article  |  2020  |  Nature Communications

The type and genomic context of cancer mutations depend on their causes. These causes have been characterized using signatures tha..

Inferring structural variant cancer cell fraction

Marek Cmero, Ke Yuan, Cheng Soon Ong, Jan Schröder, undefined PCAWG Evolution and Heterogeneity Working Group, Niall M Corcoran, Tony Papenfuss, Christopher M Hovens, Florian Markowetz, Geoff Macintyre, undefined PCAWG Consortium

Journal article  |  2020  |  Nature Communications

We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whol..

A community effort to create standards for evaluating tumor subclonal reconstruction

Adriana Salcedo, Maxime Tarabichi, Shadrielle Melijah G Espiritu, Amit G Deshwar, Matei David, Nathan M Wilson, Stefan Dentro, Jeff A Wintersinger, Lydia Y Liu, Minjeong Ko, Srinivasan Sivanandan, Hongjiu Zhang, Kaiyi Zhu, Tai-Hsien Ou Yang, John M Chilton, Alex Buchanan, Christopher M Lalansingh, Christine P'ng, Catalina V Anghel, Imaad Umar, et al.

Journal article  |  2020  |  Nature Biotechnology

Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dyn..

Using equivalence class counts for fast and accurate testing of differential transcript usage

Marek Cmero, Nadia M Davidson, Alicia Oshlack

Journal article  |  2019  |  F1000Research

Background: RNA sequencing has enabled high-throughput and fine-grained quantitative analyses of the transcriptome. While differen..

Fast and accurate differential transcript usage by testing equivalence class counts [version 1; peer review: 3 approved with reservations]

M Cmero, NM Davidson, A Oshlack

Journal article  |  2019  |  F1000Research

Background: RNA sequencing has enabled high-throughput and fine-grained quantitative analyses of the transcriptome. While differen..