Journal Publications
2022
- R Drews, B Hernando, M Tarabichi, K Haase, T Lesluyes, P Smith, L Morrill Gavarró, D Couturier, L Liu, M Schneider, J Brenton, P Van Loo, G Macintyre# & Florian Markowetz#
A pan-cancer compendium of chromosomal instability
Nature - B Chaves-Urbano, B Hernando, M Garcia, G Macintyre#
CNpare: matching DNA copy number profiles
Bioinformatics - Z Cheng, H Mirza, D P Ennis, P Smith, L Morrill Gavarró, C Sokota, G Giannone, T Goranova, T Bradley, A Piskorz, M Lockley, BriTROC-1 Investigators, B Kaur, N Singh, L A Tookman, J Krell, J McDermott, G Macintyre, F Markowetz, J D Brenton, I A McNeish
The genomic landscape of early-stage ovarian high-grade serous carcinoma
Clinical Cancer Research
2021
- SC Dentro*, I Leshchiner*, K Haase*, M Tarabichi*, J Wintersinger*, AG Deshwar*, K Yu*, Y Rubanova*, G Macintyre*, I Vazquez-Garcia, K Kleinheinz, D G Livitz, S Malikic, N Donmez, S Sengupta, J Demeulemeester, P Anur, C Jolly, M Cmero, D Rosebrock, S Schumacher, Y Fan, M Fittall, R M Drews, X Yao, J Lee, M Schlesner, D J Adams, G Getz, P C Boutros, M Imielinski, R Beroukhim, S C Sahinalp, Y Ji, M Peifer, I Martincorena, F Markowetz, V Mustonen, K Yuan, M Gerstung, P T Spellman, W Wang, Q D Morris, D C Wedge, P Van Loo
Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes.
Cell - G Macintyre, A Piskorz, A Berman, E Ross, D B Morse, K Yuan, D Ennis, J Pike, T Goranova, I A McNeish, J Brenton, F Markowetz
FrenchFISH: Poisson Models for Quantifying DNA Copy Number From Fluorescence In Situ Hybridization of Tissue Sections
JCO Clinical Cancer Informatics
2020
- M Cmero, K Yuan, C Soon Ong, J Schröder, PCAWG Evolution and Heterogeneity Working Group, N M Corcoran, T Papenfuss, C M Hovens, F Markowetz, PCAWG consortium, G Macintyre#
SVclone: inferring structural variant cancer cell fraction
Nature Communications - A Jiménez-Sánchez*, P Cybulska*, K LaVigne Mager*, S Koplev , O Cast, D Couturier, D Memon, P Selenica, I Nikolovski, Y Mazaheri, Y Bykov, F C. Geyer, G Macintyre, L Morrill Gavarró, R M Drews, M B. Gill, A D. Papanastasiou, R E. Sosa, R A. Soslow, T Walther, R Shen, D S. Chi, K J. Park, T Hollmann, J S Reis-Filho, F Markowetz, P Beltrao, H Alberto Vargas, D Zamarin, J D. Brenton, A Snyder, B Weigelt, E Sala, M L Miller
Unraveling Tumor-Immune Heterogeneity in Advanced Ovarian Cancer Uncovers Immunogenic Effect of Chemotherapy
Nature Genetics - C Loveday, K Litchfield, P Z Proszek, A J Cornish, F Santo, M Levy, G Macintyre, A Holryod, P Broderick, D Dudakia, B Benton, M Al Bakir, C Hiley, E Grist, C Swanton, R Huddart, T Powles, S Chowdhury, J Shipley, S O’Connor, J D Brenton, A Reid, D Gonzalez de Castro, R S Houlston, C Turnbull
Genomic landscape of platinum resistant and sensitive testicular cancers
Nature Communications - M Gerstung, C Jolly, I Leshchiner, S C Dentro, S Gonzalez, D Rosebrock, T J Mitchell, Y Rubanova, P Anur, K Yu, M Tarabichi, A Deshwar, J Wintersinger, K Kleinheinz, I Vázquez-García, K Haase, L Jerman, S Sengupta, G Macintyre, S Malikic, N Donmez, D G. Livitz, M Cmero, J Demeulemeester, S Schumacher, Y Fan, X Yao, J Lee, M Schlesner, P C Boutros, D D Bowtell, H Zhu, G Getz, M Imielinski, R Beroukhim, S C Sahinalp, Y Ji, M Peifer, F Markowetz, V Mustonen, K Yuan, W Wang, Q D Morris, PCAWG Evolution & Heterogeneity Working Group, P T Spellman, D C Wedge, P Van Loo & PCAWG Consortium
The evolutionary history of 2,658 cancers
Nature
2018
- G Macintyre*, T Goranova*, D De Silva, D Ennis, A Piskorz, M Eldridge, D Sie, LA Lewsley, A Hanif, C Wilson, S Dawson, RM Glasspool, M Lockley, E Brockbank, A Montes, A Walther, S Sundar, R Edmondson, GD Hall, A Clamp, C Gourley, M Hall, C Fotopoulou, H Gabra, J Paul, A Supernat, D Millan, A Hoyle, G Bryson, C Nourse, L Mincarelli, L Navarro Sanchez, B Ylstra, M Jimenez-Linan, L Moore, O Hofmann, F Markowetz#, IA McNeish#, JD Brenton#
Copy-number signatures and mutational processes in ovarian carcinoma
Nature Genetics
2017
- T Goranova, D Ennis, AM Piskorz, Geoff Macintyre, LA Lewsley, J Stobo, C Wilson, D Kay, RM Glasspool, M Lockley, E Brockbank, A Montes, A Walther, S Sundar, R Edmondson, GD Hall, A Clamp, C Gourley, M Hall, C Fotopoulou, H Gabra, S Freeman, L Moore, M Jimenez-Linan, J Paul, JD Brenton, IA McNeish
Safety and utility of image-guided research biopsies in relapsed high-grade serous ovarian carcinoma—experience of the BriTROC consortium
British Journal of Cancer - Geoff Macintyre, Peter Van Loo, Niall M Corcoran, David C Wedge, Florian Markowetz, Christopher M Hovens
How Subclonal Modeling Is Changing the Metastatic Paradigm
Clinical Cancer Research
2016
- Stefano Mangiola, Matthew KH Hong, Marek Cmero, Natalie Kurganovs, Andrew Ryan, Anthony J Costello, Niall M Corcoran, Geoff Macintyre#, Christopher M Hovens#
Comparing nodal versus bony metastatic spread using tumour phylogenies
Scientific Reports - Geoff Macintyre, Bauke Ylstra, James D Brenton
Sequencing structural variants in cancer for precision therapeutics. 2016
Trends in Genetics - Ryan Stuchbery, Geoff Macintyre, M Cmero, LM Harewood, JS Peters, AJ Costello, CM Hovens, NM Corcoran
Reduction in expression of the benign AR transcriptome is a hallmark of localised prostate cancer progression.
Oncotarget - Nikhil Sapre, Geoff Macintyre, Michael Clarkson, Haroon Naeem, Marek Cmero, Adam Kowalczyk, Paul D. Anderson, Anthony J. Costello, Niall M. Corcoran and Christopher M. Hovens
A urinary microRNA signature can predict the presence of bladder urothelial carcinoma in patients undergoing surveillance. 2016
British Journal of Cancer
2015
- A. Piskorz* , D. Ennis*, G. Macintyre*, T. E. Goranova , M. Eldridge , N. SeguiGracia , M. Valganon , A. Hoyle , C. Orange , L. Moore, M. Jimenez-Linan, D. Millan , I. A. McNeish, J. D. Brenton
Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples, 2015
Annals of Oncology - Matthew Hong*, Geoff Macintyre*, David Wedge*, Peter Van Loo, Keval Patel, Sebastian Lunke, Ludmil Alexandrov, Clare Sloggett, Marek Cmero, Francesco Marass, Dana Tsui, Stefano Mangiola, Andrew Lonie, Haroon Naeem, Nikhil Sapre, Pramit Phal, Natalie Kurganovs, Xiaowen Chin, Michael Kerger, Anne Warren, David Neal, Vincent Gnanapragasam, Nitzan Rosenfeld, John Pedersen, Andrew Ryan, Izhak Haviv, Anthony Costello, Niall Corcoran, and Christopher Hovens.
Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer. 2015
Nature Communications.
Covered in Nature News and Views.
2014
- Geoff Macintyre*, Antonio Jimeno Yepes*, Cheng Soon Ong, Karin Verspoor
Associating disease-related genetic variants in intergenic regions to the genes they impact. 2014
PeerJ - Avinash Shanmugam, Geoff Macintyre.
Establishing and Managing a Global Student Network. 2014
PLOS Computational Biology - Olugbenga Oluwagbemi, Marion Adebiyi, Segun Fatumo, Geoff Macintyre
Paving the way towards a successful and fulfilling career in Computational Biology. 2014
PLOS Computational Biology. - Matthew Fankhauser, Yuen Tan, Geoff Macintyre, Izhak Haviv, Matthew KH Hong, Thanh Nguyen, John Pedersen, Anthony J Costello, Christopher M Hovens, Niall M Corcoran
Canonical Androstenedione Reduction is the Predominant Source of Signalling Androgens in Hormone Refractory Prostate Cancer. 2014
Clinical Cancer Research. - Nikhil Sapre, Matthew KH Hong, Geoff Macintyre, Heather Lewis, Adam Kowalczyk, Anthony J. Costello, Niall M. Corcoran, Christopher M. Hovens
Curated MicroRNAs in Urine and Blood Fail to Validate as Predictive Biomarkers for High-Risk Prostate Cancer. 2014
PLOS One - Segun Fatumo, Sayane Shome, Geoff Macintyre
Workshops: A Great Way to Enhance and Supplement a Degree. 2014
PLOS Computational Biology - Haroon Naeem, Nicholas Wong, Zac Chatterton, Matthew K H Hong, John S Pedersen, Niall M Corcoran, Christopher M Hovens, Geoff Macintyre
Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array. 2014
BMC Genomics
2013
- Jan Schroeder, Arthur Hsu, Samantha E Boyle, Geoff MacIntyre, Marek Cmero, Richard W Tothill, Ricky W Johnstone, Mark Shackleton, Anthony T Papenfuss.
Socrates: Identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads. 2013
Bioinformatics. - Miranda Stobbe, Tarun Mishra, Geoff Macintyre.
Breaking the Ice and Forging Links: The Importance of Socializing in Research. 2013
PLOS Computational Biology - Avinash Kumar Shanmugam, Geoff Macintyre, Magali Michaut, Thomas Abeel.
Ten Simple Rules for Starting a Regional Student Group. 2013
PLOS Computational Biology - Jeroen de Ridder, Yana Bromberg, Magali Michaut, Venkata P Satagopam, Manuel Corpas, Geoff Macintyre, Theodore Alexandrov.
The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.2013
PLOS Computational Biology - Geoff Macintyre, Magali Michaut, Thomas Abeel.
The Regional Student Group Program of the ISCB Student Council: Stories from the Road. 2013
PLOS Computational Biology - Alex Bateman, Janet Kelso, Daniel Mietchen, Geoff Macintyre, Tomás Di Domenico, Thomas Abeel, Darren W Logan, Predrag Radivojac, Burkhard Rost.
ISCB Computational Biology Wikipedia Competition. 2013
PLOS Computational Biology - Matthew KH Hong, Nikhil Sapre, Pramit M Phal, Geoff Macintyre, Xiaowen Chin, John S Pedersen, Andrew Ryan, Michael Kerger, Anthony J Costello, Niall M Corcoran, Christopher M Hovens.
Percutaneous image-guided biopsy of prostate cancer metastases yields samples suitable for genomics and personalised oncology. 2013
Clinical & Experimental Metastasis. - Sibgat Choudhury, Vanessa Almendro, Vanessa F. Merino, Zhenhua Wu, Reo Maruyama, Ying Su, Filipe C. Martins, Mary Jo Fackler, Marina Bessarabova, Adam Kowalczyk, Thomas Conway, Bryan Beresford-Smith, Geoff Macintyre, Yu-Kang Cheng, Zoila Lopez-Bujanda, Antony Kaspi, Rong Hu, Judith Robens, Tatiana Nikolskaya, Vilde D. Haakensen, Stuart J. Schnitt, Pedram Argani, Gabrielle Ethington, Laura Panos, Michael Grant, Jason Clark, William Herlihy, S. Joyce Lin, Grace Chew, Erik W. Thompson, April Greene-Colozzi, Andrea L. Richardson, Gedge D. Rosson, Malcolm Pike, Judy E. Garber, Yuri Nikolsky, Joanne L. Blum, Alfred Au, E. Shelley Hwang, Rulla M. Tamimi, Franziska Michor, Izhak Haviv, X. Shirley Liu, Saraswati Sukumar, Kornelia Polyak.
Molecular Profiling of Human Mammary Gland Links Breast Cancer Risk to a p27+ Cell Population with Progenitor Characteristics. 2013
Cell Stem Cell
2012
- Alexander Goncearenco, Priscila Grynberg; Olga B. Botvinnik, Geoff Macintyre, Thomas Abeel.
Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012. 2012
BMC Bioinformatics
2011
- Luciano Pirola, Aneta Balcerczyk, Richard W. Tothill, Izhak Haviv, Antony Kaspi, Sebastian Lunke, Mark Ziemann, Tom Karagiannis, Stephen Tonna, Adam Kowalczyk, Bryan Beresford-Smith, Geoff Macintyre, Ma Kelong, Zhang Hongyu, Jingde Zhu, and Assam El-Osta.
Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells. 2011
Genome Research 21, 1601 -1615.
2010
- Geoff Macintyre, James Bailey, Izhak Haviv and Adam Kowalczyk.
is-rSNP: A novel technique for in silico regulatory SNP detection. 2010
Bioinformatics 26, i542-i530. - Fan Shi, Christopher Leckie, Geoff Macintyre, Izhak Haviv, Alex Boussioutas and Adam Kowalczyk.
A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer. 2010
BMC Bioinformatics, 11:477 - Geoff Macintyre, James Bailey, Daniel Gustafsson, Izhak Haviv and Adam Kowalczyk.
Using Gene Ontology annotations in exploratory microarray clustering to understand cancer etiology. 2010
Pattern Recognition Letters 13, 2138-2146
2009
- Md. Rafiul Hassan, M. Maruf Hossain, James Bailey, Geoff Macintyre, Joshua W. K. Ho and Kotagiri Ramamohanarao.
A voting approach to identify a small number of highly predictive genes using multiple classifiers. 2009
BMC Bioinformatics, 10 (Suppl 1), S19.
Conference proceedings
2011
- Benjamin Goudey, Qiao Wang, Dave Rawlinson, Armita Zarnegar, Eder Kikianty, John Markham, Geoff Macintyre, Gad Abraham, Linda Stern, Michael Inouye, Izhak Haviv, Adam Kowalczyk.
Replication of epistatic DNA loci in two case-control GWAS studies using OPE algorithm.
BMC Bioinformatics
2008
- Geoff Macintyre, James Bailey, Daniel Gustafsson, Adam Kowalczyk, Alex Boussioutas and Izhak Haviv.
Gene Ontology Assisted Exploratory Microarray Clustering and its Application to Cancer.
Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB), Lecture Notes in Computer Science. Springer Berlin/Heidelberg. (pp. 400-411). - Fan Shi, Geoff Macintyre, Chris Leckie, Izhak Haviv, Alex Boussioutas, Adam Kowalczyk. A Bi-ordering approach to Linking Gene Expression with Clinical Annotations in Cancer. 2008,
Proceedings of the second International Workshop on Machine Learning in Systems Biology. (pp 95-103).
Patents
- Geoff MACINTYRE, Adam KOWALCZYK, Izhak HAVIV, James BAILEY. METHOD AND SYSTEM FOR DETECTING REGULATORY SINGLE NUCLEOTIDE POLYMORPHISMS. WO/2011/127527.