Publications

2026 onwards

• SpatialBench: Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue, bioRxiv
  Ashleigh Solano, Raymond K. H. Yip, Changqing Wang, Daniela Amann-Zalcenstein, Pradeep Rajasekhar, Ishrat Zaman, Allan Motyer, Marek Cmero, Yang Xu, Yining Pan, Casey J. A. Anttila, Stephanie I. Studniberg, Peter F. Hickey, Layla Wang, Callum J. Sargeant, Ling Ling, Yunshun Chen, Ruvimbo D. Mishi, Lisa J. Ioannidis, Kim L. Good-Jacobson, Hamish W. King, Kelly L. Rogers, Diana S. Hansen, Rory Bowden, Matthew E. Ritchie
  pipeline contribution code
• The germline and somatic origins of prostate cancer heterogeneity, Cancer Discovery
  Takafumi N Yamaguchi, Kathleen E Houlahan, Helen Zhu, Natalie Kurganovs, Julie Livingstone, Natalie S Fox, Jiapei Yuan, Jocelyn Sietsma Penington, Chol-Hee Jung, Tommer Schwarz, Weerachai Jaratlerdsiri, Job Van Riet, Peter Georgeson, Stefano Mangiola, Kodi Taraszka, Robert Lesurf, Jue Jiang, Ken Chow, Lawrence E Heisler, Yu-Jia Shiah, Susmita G Ramanand, Michael J Clarkson, Anne Nguyen, Shadrielle Melijah G Espiritu, Ryan Stuchbery, Richard Jovelin, Vincent Huang, Connor Bell, Edward O’connor, Patrick J McCoy, Christopher M Lalansingh, Marek Cmero, Adriana Salcedo, Eva KF Chan, Lydia Y Liu, Phillip D Stricker, Vinayak Bhandari, Riana MS Bornman, Dorota HS Sendorek, Andrew Lonie, Stephenie D Prokopec, Michael Fraser, Justin S Peters, Adrien Foucal, Shingai BA Mutambirwa, Lachlan Mcintosh, Michèle Orain, Matthew Wakefield, Valérie Picard, Daniel J Park, Hélène Hovington, Michael Kerger, Alain Bergeron, Veronica Sabelnykova, Ji-Heui Seo, Mark M Pomerantz, Noah Zaitlen, Sebastian M Waszak, Alexander Gusev, Louis Lacombe, Yves Fradet, Andrew Ryan, Amar U Kishan, Martijn P Lolkema, Joachim Weischenfeldt, Bernard Têtu, Anthony J Costello, Vanessa M Hayes, Rayjean J Hung, Housheng H He, John D McPherson, Bogdan Pasaniuc, Theodorus van der Kwast, Anthony T Papenfuss, Matthew L Freedman, Bernard J Pope, Robert G Bristow, Ram S Mani, Niall M Corcoran, Jüri Reimand, Christopher M Hovens, Paul C Boutros

2020–2025

• MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data, Genome Biology
  Marek Cmero, Breon Schmidt, Ian J. Majewski, Paul G. Ekert, Alicia Oshlack^, Nadia M. Davidson^
  code | analysis code | bioconda
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes, Cell
  Stefan C. Dentro, Ignaty Leshchiner, Kerstin Haase, Maxime Tarabichi, Jeff Wintersinger, Amit G. Deshwar, Kaixian Yu, Yulia Rubanova, Geoff Macintyre, Jonas Demeulemeester, Ignacio Vázquez-García, Kortine Kleinheinz, Dimitri G. Livitz, Salem Malikic, Nilgun Donmez, Subhajit Sengupta, Pavana Anur, Clemency Jolly, Marek Cmero, Daniel Rosebrock, Steven E. Schumacher, Yu Fan, Matthew Fittall, Ruben M.Drews, Xiaotong Yao, Thomas B.K. Watkins, Juhee Lee, Matthias Schlesner, Hongtu Zhu, David J. Adams, Nicholas McGranahan, Charles Swanton, Gad Getz, Paul C. Boutros, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Inigo Martincorena, Florian Markowetz, Ville Mustonen, Ke Yuan, Moritz Gerstung, Paul T. Spellman, Wenyi Wang, Quaid D. Morris, David C. Wedge, Peter Van Loo, on behalf of the PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium
  code
• Loss of SNAI in Prostate Cancer Correlates With Clinical Response to Androgen Deprivation Therapy, JCO Precision Oncology
  Marek Cmero^, Natalie J. Kurganovs^, Ryan Stuchbery, Patrick McCoy, Corrina Grima, Anne Ngyuen, Ken Chow, Stefano Mangiola, Geoff Macintyre, Nicholas Howard, Michael Kerger, Philip Dundee, Paul Ruljancich, David Clarke, Jeremy Grummet, Justin S. Peters, Anthony J. Costello, Sam Norden, Andrew Ryan, Phillip Parente, Christopher M. Hovens and Niall M. Corcoran
• MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data, bioRxiv
  Marek Cmero, Breon Schmidt, Ian J. Majewski, Paul G. Ekert, Alicia Oshlack, Nadia M. Davidson
  code | analysis code
• Prostate cancer cell‐intrinsic interferon signaling regulates dormancy and metastatic outgrowth in bone, EMBO Reports
  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, Shahneen Sandhu, Alexander Swarbrick, Niall M. Corcoran, Paul J. Hertzog, Peter I. Croucher, Chris Hovens, Belinda S. Parker
• Inferring structural variant cancer cell fraction, Nature Communications
  Marek Cmero^, Ke Yuan^, Cheng Soon Ong, Jan Schröder, PCAWG Evolution and Heterogeneity Working Group, Niall M. Corcoran, Tony Papenfuss, Christopher M. Hovens, Florian Markowetz, Geoff Macintyre, PCAWG Consortium
  code | analysis code | ccube code | simulation code | bioconda
• The evolutionary history of 2,658 cancers, Nature
  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 Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Marek Cmero, Jonas Demeulemeester, Steven Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D. Morris, PCAWG Evolution & Heterogeneity Working Group, Paul T. Spellman, David C. Wedge, Peter Van Loo, PCAWG Consortium
  code

2015–2019

• Using equivalence class counts for fast and accurate testing of differential transcript usage, F1000 Research
  Marek Cmero, Nadia M. Davidson, Alicia Oshlack
  pipeline code | analysis code | vignette
• Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types, bioRxiv
  Stefan C. Dentro, Ignaty Leshchiner, Kerstin Haase, Maxime Tarabichi, Jeff Wintersinger, Amit G. Deshwar, Kaixian Yu, Yulia Rubanova, Geoff Macintyre, Ignacio Vázquez-García, Kortine Kleinheinz, Dimitri G. Livitz, Salem Malikic, Nilgun Donmez, Subhajit Sengupta, Jonas Demeulemeester, Pavana Anur, Clemency Jolly, Marek Cmero, Daniel Rosebrock, Steven Schumacher, Yu Fan, Matthew Fittall, Ruben M. Drews, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Hongtu Zhu, David J. Adams, Gad Getz, Paul C. Boutros, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Inigo Martincorena, Florian Markowetz, Ville Mustonen, Ke Yuan, Moritz Gerstung, Paul T. Spellman, Wenyi Wang, Quaid D. Morris, David C. Wedge, Peter Van Loo
• Investigating the evolution of structural variation in cancer, PhD Thesis
  Marek Cmero, supervised by Christopher Hovens, Geoff Macintyre, Niall Corcoran, Cheng Soon Ong, Tony Papenfuss
• SVclone: inferring structural variant cancer cell fraction, bioRxiv
  Marek Cmero, Cheng Soon Ong, Ke Yuan, Jan Schröder, Kangbo Mo, PCAWG Evolution and Heterogeneity Working Group, Niall M. Corcoran, Anthony Troy Papenfuss, Christopher M. Hovens, Florian Markowetz, Geoff Macintyre
• Comparing nodal versus bony metastatic spread using tumour phylogenies, Nature Scientific Reports
  Stefano Mangiola, Matthew K. H. Hong, Marek Cmero, Natalie Kurganovs, Andrew Ryan, Anthony J. Costello, Niall M. Corcoran, Geoff Macintyre & Christopher M. Hovens
  code
• Reduction in expression of the benign AR transcriptome is a hallmark of localised prostate cancer progression, Oncotarget
  Ryan Stuchbery, Geoff Macintyre, Marek Cmero, Laurence M. Harewood, Justin S. Peters, Anthony J. Costello, Christopher M. Hovens, Niall M. Corcoran
• A urinary microRNA signature can predict the presence of bladder urothelial carcinoma in patients undergoing surveillance, British Journal of Cancer
  Nikhil Sapre, Geoff Macintyre, Michael Clarkson, Haroon Naeem, Marek Cmero, Adam Kowalczyk, Paul D. Anderson, Anthony J. Costello, Niall M. Corcoran, Christopher M. Hovens
• Drosha controls dendritic cell development by cleaving messenger RNAs encoding inhibitors of myelopoiesis, Nature Immunology
  Timothy M. Johanson, Ashleigh A. Keown, Marek Cmero, Janet H.C. Yeo, Amit Kumar, Andrew M. Lew, Yifan Zhan, Mark M.W. Chong
• Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer, Nature Communications
  Matthew K.H. Hong, Geoff Macintyre, David C. Wedge, Peter Van Loo, Keval Patel, Sebastian Lunke, Ludmil B. Alexandrov, Clare Sloggett, Marek Cmero, Francesco Marass, Dana Tsui, Stefano Mangiola, Andrew Lonie, Haroon Naeem, Nikhil Sapre, Pramit M. Phal, Natalie Kurganovs, Xiaowen Chin, Michael Kerger, Anne Y. Warren, David Neal, Vincent Gnanapragasam, Nitzan Rosenfeld, John S. Pedersen, Andrew Ryan, Izhak Haviv, Anthony J. Costello, Niall M. Corcoran, Christopher M. Hovens

Prior to 2015

• A microRNA expression atlas of mouse dendritic cell development, Immunology & Cell Biology
  Timothy M Johanson, Marek Cmero, James Wettenhall, Andrew M Lew, Yifan Zhan, Mark MW Chong
• Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads, Bioinformatics
  Jan Schröder, Arthur Hsu, Samantha E. Boyle, Geoff Macintyre, Marek Cmero, Richard W. Tothill, Ricky W. Johnstone, Mark Shackleton, Anthony T. Papenfuss.
  code

^ Equal contributions