Publications by authors named "Geoff Macintyre"

32Publications

Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE).

Authors:
Aline Talhouk Joshy George Chen Wang Timothy Budden Tuan Zea Tan Derek S Chiu Stefan Kommoss Huei San Leong Stephanie Chen Maria P Intermaggio Blake Gilks Tayyebeh M Nazeran Mila Volchek Wafaa Elatre Rex C Bentley Janine Senz Amy Lum Veronica Chow Hanwei Sudderuddin Robertson Mackenzie Samuel C Y Leong Geyi Liu Dustin Johnson Billy Chen Aocs Group Jennifer Alsop Susana N Banerjee Sabine Behrens Clara Bodelon Alison H Brand Louise Brinton Michael E Carney Yoke-Eng Chiew Kara L Cushing-Haugen Cezary Cybulski Darren Ennis Sian Fereday Renée T Fortner Jesús García-Donas Aleksandra Gentry-Maharaj Rosalind Glasspool Teodora Goranova Casey S Greene Paul Haluska Holly R Harris Joy Hendley Brenda Y Hernandez Esther Herpel Mercedes Jimenez-Linan Chloe Karpinskyj Scott H Kaufmann Gary L Keeney Catherine J Kennedy Martin Köbel Jennifer M Koziak Melissa C Larson Jenny Lester Liz-Anne Lewsley Jolanta Lissowska Jan Lubiński Hugh Luk Geoff Macintyre Sven Mahner Iain A McNeish Janusz Menkiszak Nikilyn Nevins Ana Osorio Oleg Oszurek José Palacios Samantha Hinsley Celeste L Pearce Malcolm C Pike Anna M Piskorz Isabelle Ray-Coquard Valerie Rhenius Cristina Rodriguez-Antona Raghwa Sharma Mark E Sherman Dilrini De Silva Naveena Singh Peter Sinn Dennis Slamon Honglin Song Helen Steed Euan A Stronach Pamela J Thompson Aleksandra Tołoczko Britton Trabert Nadia Traficante Chiu-Chen Tseng Martin Widschwendter Lynne R Wilkens Stacey J Winham Boris Winterhoff Alicia Beeghly-Fadiel Javier Benitez Andrew Berchuck James D Brenton Robert Brown Jenny Chang-Claude Georgia Chenevix-Trench Anna deFazio Peter A Fasching María J García Simon A Gayther Marc T Goodman Jacek Gronwald Michelle J Henderson Beth Y Karlan Linda E Kelemen Usha Menon Sandra Orsulic Paul D P Pharoah Nicolas Wentzensen Anna H Wu Joellen M Schildkraut Mary Anne Rossing Gottfried E Konecny David G Huntsman Ruby Yun-Ju Huang Ellen L Goode Susan J Ramus Jennifer A Doherty David D Bowtell Michael S Anglesio

Clin Cancer Res 2020 Oct 17;26(20):5411-5423. Epub 2020 Jun 17.

British Columbia's Gynecological Cancer Research Program (OVCARE), BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1158/1078-0432.CCR-20-0103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7572656PMC
October 2020

Inferring structural variant cancer cell fraction.

Nat Commun 2020 02 5;11(1):730. Epub 2020 Feb 5.

Department of Computing and Information Systems, University of Melbourne, Parkville, VIC, 3010, Australia.

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http://dx.doi.org/10.1038/s41467-020-14351-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002525PMC
February 2020

Periprostatic fat tissue transcriptome reveals a signature diagnostic for high-risk prostate cancer.

Endocr Relat Cancer 2018 05 28;25(5):569-581. Epub 2018 Mar 28.

Australian Prostate Cancer Research Centre Epworth, Richmond, Victoria, Australia.

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http://dx.doi.org/10.1530/ERC-18-0058DOI Listing
May 2018

How Subclonal Modeling Is Changing the Metastatic Paradigm.

Clin Cancer Res 2017 Feb 18;23(3):630-635. Epub 2016 Nov 18.

Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, Australia.

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http://dx.doi.org/10.1158/1078-0432.CCR-16-0234DOI Listing
February 2017

Comparing nodal versus bony metastatic spread using tumour phylogenies.

Sci Rep 2016 Sep 22;6:33918. Epub 2016 Sep 22.

Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.

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http://dx.doi.org/10.1038/srep33918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031992PMC
September 2016

Sequencing Structural Variants in Cancer for Precision Therapeutics.

Trends Genet 2016 09 29;32(9):530-542. Epub 2016 Jul 29.

Cancer Research UK Cambridge Institute, University of Cambridge, UK. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2016.07.002DOI Listing
September 2016

A urinary microRNA signature can predict the presence of bladder urothelial carcinoma in patients undergoing surveillance.

Br J Cancer 2016 Feb 26;114(4):454-62. Epub 2016 Jan 26.

Department of Surgery, Division of Urology, Royal Melbourne Hospital, The University of Melbourne, Parkville, Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1038/bjc.2015.472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815774PMC
February 2016

Associating disease-related genetic variants in intergenic regions to the genes they impact.

PeerJ 2014 23;2:e639. Epub 2014 Oct 23.

Department of Computing and Information Systems, The University of Melbourne, VIC, Australia.

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http://dx.doi.org/10.7717/peerj.639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4217187PMC
November 2014

Establishing and managing a global student network.

PLoS Comput Biol 2014 Oct 30;10(10):e1003920. Epub 2014 Oct 30.

The Centre for Neural Engineering, University of Melbourne, Parkville, Victoria, Australia.

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http://dx.doi.org/10.1371/journal.pcbi.1003920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214619PMC
October 2014

Paving the way towards a successful and fulfilling career in computational biology.

PLoS Comput Biol 2014 May 1;10(5):e1003593. Epub 2014 May 1.

Centre for Neural Engineering, The University of Melbourne, Carlton, Victoria, Australia; Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia.

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http://dx.doi.org/10.1371/journal.pcbi.1003593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006700PMC
May 2014

Canonical androstenedione reduction is the predominant source of signaling androgens in hormone-refractory prostate cancer.

Clin Cancer Res 2014 Nov 25;20(21):5547-57. Epub 2014 Apr 25.

Departments of Urology and Surgery, Royal Melbourne Hospital; Australian Prostate Cancer Research Centre Epworth, Richmond, Victoria, Australia

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http://dx.doi.org/10.1158/1078-0432.CCR-13-3483DOI Listing
November 2014

Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads.

Bioinformatics 2014 04 2;30(8):1064-1072. Epub 2014 Jan 2.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Department of Medical Biology, University of Melbourne, Victoria 3010, Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Department of Pathology, The University of Melbourne, Victoria 3010, NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, Department of Computing and Information Systems, University of Melbourne, Victoria 3010, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Department of Medical Biology, University of Melbourne, Victoria 3010, Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Department of Pathology, The University of Melbourne, Victoria 3010, NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, Department of Computing and Information Systems, University of Melbourne, Victoria 3010, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Department of Medical Biology, University of Melbourne, Victoria 3010, Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Department of Pathology, The University of Melbourne, Victoria 3010, NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, Department of Computing and Information Systems, University of Melbourne, Victoria 3010, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Department of Medical Biology, University of Melbourne, Victoria 3010, Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Department of Pathology, The University of Melbourne, Victoria 3010, NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, Department of Computing and Information Systems, University of Melbourne, Victoria 3010, Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btt767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982158PMC
April 2014

Curated microRNAs in urine and blood fail to validate as predictive biomarkers for high-risk prostate cancer.

PLoS One 2014 4;9(4):e91729. Epub 2014 Apr 4.

Division of Urology, Department of Surgery, Royal Melbourne Hospital and the University of Melbourne, Parkville, Victoria, Australia; Australian Prostate Cancer Research Epworth, Richmond, Victoria, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091729PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976264PMC
June 2015

Workshops: a great way to enhance and supplement a degree.

PLoS Comput Biol 2014 Feb 27;10(2):e1003497. Epub 2014 Feb 27.

NICTA Victoria Research Laboratory, Department of Electrical and Electronic Engineering, The University of Melbourne, Victoria, Australia ; Department of Computing and Information Systems, The University of Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1371/journal.pcbi.1003497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937119PMC
February 2014

Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array.

BMC Genomics 2014 Jan 22;15:51. Epub 2014 Jan 22.

NICTA Victoria Research Laboratory, Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.

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http://dx.doi.org/10.1186/1471-2164-15-51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943510PMC
January 2014

Breaking the ice and forging links: the importance of socializing in research.

PLoS Comput Biol 2013 21;9(11):e1003355. Epub 2013 Nov 21.

Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands ; Netherlands Bioinformatics Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1003355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836699PMC
July 2014

Ten simple rules for starting a regional student group.

PLoS Comput Biol 2013 21;9(11):e1003340. Epub 2013 Nov 21.

Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836698PMC
July 2014

The young PI buzz: learning from the organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.

PLoS Comput Biol 2013 7;9(11):e1003350. Epub 2013 Nov 7.

Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1003350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820508PMC
July 2014

The regional student group program of the ISCB student council: stories from the road.

PLoS Comput Biol 2013 26;9(9):e1003241. Epub 2013 Sep 26.

NICTA Victoria Research Laboratory, University of Melbourne, Parkville, Victoria, Australia.

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http://dx.doi.org/10.1371/journal.pcbi.1003241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784494PMC
April 2014

Percutaneous image-guided biopsy of prostate cancer metastases yields samples suitable for genomics and personalised oncology.

Clin Exp Metastasis 2014 Feb 2;31(2):159-67. Epub 2013 Oct 2.

Division of Urology, Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC, Australia,

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http://link.springer.com/10.1007/s10585-013-9617-2
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http://dx.doi.org/10.1007/s10585-013-9617-2DOI Listing
February 2014

ISCB computational biology Wikipedia competition.

PLoS Comput Biol 2013 19;9(9):e1003242. Epub 2013 Sep 19.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777890PMC
April 2014

Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells.

Genome Res 2011 Oct 2;21(10):1601-15. Epub 2011 Sep 2.

Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia.

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http://dx.doi.org/10.1101/gr.116095.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202278PMC
October 2011

is-rSNP: a novel technique for in silico regulatory SNP detection.

Bioinformatics 2010 Sep;26(18):i524-30

Department of Computer Science and Software Engineering, University of Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btq378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935445PMC
September 2010

A voting approach to identify a small number of highly predictive genes using multiple classifiers.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S19. Epub 2009 Jan 30.

Department of Computer Science and Software Engineering, The University of Melbourne, Victoria 3010, Australia.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648737PMC
January 2009