Sean Grimmond

Sean Grimmond

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Sean Grimmond

Publications by authors named "Sean Grimmond"

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Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia.

Authors:
Charles C Bell Katie A Fennell Yih-Chih Chan Florian Rambow Miriam M Yeung Dane Vassiliadis Luis Lara Paul Yeh Luciano G Martelotto Aljosja Rogiers Brandon E Kremer Olena Barbash Helai P Mohammad Timothy M Johanson Marian L Burr Arindam Dhar Natalie Karpinich Luyi Tian Dean S Tyler Laura MacPherson Junwei Shi Nathan Pinnawala Chun Yew Fong Anthony T Papenfuss Sean M Grimmond Sarah-Jane Dawson Rhys S Allan Ryan G Kruger Christopher R Vakoc David L Goode Shalin H Naik Omer Gilan Enid Y N Lam Jean-Christophe Marine Rab K Prinjha Mark A Dawson

Nat Commun 2019 06 20;10(1):2723. Epub 2019 Jun 20.

Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.

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http://dx.doi.org/10.1038/s41467-019-10652-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586637PMC
June 2019

Platypus Induced Pluripotent Stem Cells: The Unique Pluripotency Signature of a Monotreme.

Authors:
Deanne J Whitworth Ioannis J Limnios Marie-Emilie Gauthier Prasanna Weeratunga Dmitry A Ovchinnikov Gregory Baillie Sean M Grimmond Jennifer A Marshall Graves Ernst J Wolvetang

Stem Cells Dev 2019 02 9;28(3):151-164. Epub 2019 Jan 9.

2 Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Australia.

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https://www.liebertpub.com/doi/10.1089/scd.2018.0179
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http://dx.doi.org/10.1089/scd.2018.0179DOI Listing
February 2019

Tailored first-line and second-line CDK4-targeting treatment combinations in mouse models of pancreatic cancer.

Authors:
Angela Chou Danielle Froio Adnan M Nagrial Ashleigh Parkin Kendelle J Murphy Venessa T Chin Dalia Wohl Angela Steinmann Rhys Stark Alison Drury Stacey N Walters Claire Vennin Andrew Burgess Mark Pinese Lorraine A Chantrill Mark J Cowley Timothy J Molloy Nicola Waddell Amber Johns Sean M Grimmond David K Chang Andrew V Biankin Owen J Sansom Jennifer P Morton Shane T Grey Thomas R Cox John Turchini Jaswinder Samra Stephen J Clarke Paul Timpson Anthony J Gill Marina Pajic

Gut 2018 12 28;67(12):2142-2155. Epub 2017 Oct 28.

The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.

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http://dx.doi.org/10.1136/gutjnl-2017-315144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6241608PMC
December 2018

Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer.

Authors:
Ben Lawrence Cherie Blenkiron Kate Parker Peter Tsai Sandra Fitzgerald Paula Shields Tamsin Robb Mee Ling Yeong Nicole Kramer Sarah James Mik Black Vicky Fan Nooriyah Poonawala Patrick Yap Esther Coats Braden Woodhouse Reena Ramsaroop Masato Yozu Bridget Robinson Kimiora Henare Jonathan Koea Peter Johnston Richard Carroll Saxon Connor Helen Morrin Marianne Elston Christopher Jackson Papaarangi Reid John Windsor Andrew MacCormick Richard Babor Adam Bartlett Dragan Damianovich Nicholas Knowlton Sean Grimmond Michael Findlay Cristin Print

NPJ Genom Med 2018 20;3:18. Epub 2018 Jul 20.

2Maurice Wilkins Centre hosted by the University of Auckland, Auckland, New Zealand.

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http://dx.doi.org/10.1038/s41525-018-0058-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054670PMC
July 2018

Telomere sequence content can be used to determine ALT activity in tumours.

Authors:
Michael Lee Erdahl T Teber Oliver Holmes Katia Nones Ann-Marie Patch Rebecca A Dagg Loretta M S Lau Joyce H Lee Christine E Napier Jonathan W Arthur Sean M Grimmond Nicholas K Hayward Peter A Johansson Graham J Mann Richard A Scolyer James S Wilmott Roger R Reddel John V Pearson Nicola Waddell Hilda A Pickett

Nucleic Acids Res 2018 06;46(10):4903-4918

Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia.

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http://dx.doi.org/10.1093/nar/gky297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007693PMC
June 2018

Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss Are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer.

Authors:
Dale W Garsed Kathryn Alsop Sian Fereday Catherine Emmanuel Catherine J Kennedy Dariush Etemadmoghadam Bo Gao Val Gebski Valérie Garès Elizabeth L Christie Maartje C A Wouters Katy Milne Joshy George Ann-Marie Patch Jason Li Gisela Mir Arnau Timothy Semple Sreeja R Gadipally Yoke-Eng Chiew Joy Hendley Thomas Mikeska Giada V Zapparoli Kaushalya Amarasinghe Sean M Grimmond John V Pearson Nicola Waddell Jillian Hung Colin J R Stewart Raghwa Sharma Prue E Allan Peter F Rambau Orla McNally Linda Mileshkin Anne Hamilton Sumitra Ananda Marisa Grossi Paul A Cohen Yee C Leung Robert M Rome Philip Beale Penny Blomfield Michael Friedlander Alison Brand Alexander Dobrovic Martin Köbel Paul Harnett Brad H Nelson David D L Bowtell Anna deFazio

Clin Cancer Res 2018 02 23;24(3):569-580. Epub 2017 Oct 23.

Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.

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http://dx.doi.org/10.1158/1078-0432.CCR-17-1621DOI Listing
February 2018

Exome-Wide Association Study of Pancreatic Cancer Risk.

Authors:
Robert C Grant Robert E Denroche Ayelet Borgida Carl Virtanen Natalie Cook Alyssa L Smith Ashton A Connor Julie M Wilson Gloria Peterson Nicholas J Roberts Alison P Klein Sean M Grimmond Andrew Biankin Sean Cleary Malcolm Moore Mathieu Lemire George Zogopoulos Lincoln Stein Steven Gallinger

Gastroenterology 2018 02 24;154(3):719-722.e3. Epub 2017 Oct 24.

Ontario Institute for Cancer Research, Toronto, Canada; Ontario Pancreas Cancer Study, Toronto, Canada. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2017.10.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5811358PMC
February 2018

Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumours.

Authors:
Aldo Scarpa David K Chang Katia Nones Vincenzo Corbo Ann-Marie Patch Peter Bailey Rita T Lawlor Amber L Johns David K Miller Andrea Mafficini Borislav Rusev Maria Scardoni Davide Antonello Stefano Barbi Katarzyna O Sikora Sara Cingarlini Caterina Vicentini Skye McKay Michael C J Quinn Timothy J C Bruxner Angelika N Christ Ivon Harliwong Senel Idrisoglu Suzanne McLean Craig Nourse Ehsan Nourbakhsh Peter J Wilson Matthew J Anderson J Lynn Fink Felicity Newell Nick Waddell Oliver Holmes Stephen H Kazakoff Conrad Leonard Scott Wood Qinying Xu Shivashankar Hiriyur Nagaraj Eliana Amato Irene Dalai Samantha Bersani Ivana Cataldo Angelo P Dei Tos Paola Capelli Maria Vittoria Davì Luca Landoni Anna Malpaga Marco Miotto Vicki L J Whitehall Barbara A Leggett Janelle L Harris Jonathan Harris Marc D Jones Jeremy Humphris Lorraine A Chantrill Venessa Chin Adnan M Nagrial Marina Pajic Christopher J Scarlett Andreia Pinho Ilse Rooman Christopher Toon Jianmin Wu Mark Pinese Mark Cowley Andrew Barbour Amanda Mawson Emily S Humphrey Emily K Colvin Angela Chou Jessica A Lovell Nigel B Jamieson Fraser Duthie Marie-Claude Gingras William E Fisher Rebecca A Dagg Loretta M S Lau Michael Lee Hilda A Pickett Roger R Reddel Jaswinder S Samra James G Kench Neil D Merrett Krishna Epari Nam Q Nguyen Nikolajs Zeps Massimo Falconi Michele Simbolo Giovanni Butturini George Van Buren Stefano Partelli Matteo Fassan Kum Kum Khanna Anthony J Gill David A Wheeler Richard A Gibbs Elizabeth A Musgrove Claudio Bassi Giampaolo Tortora Paolo Pederzoli John V Pearson Nicola Waddell Andrew V Biankin Sean M Grimmond

Nature 2017 10 27;550(7677):548. Epub 2017 Sep 27.

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http://dx.doi.org/10.1038/nature24026DOI Listing
October 2017

and Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas.

Authors:
Dariush Etemadmoghadam Walid J Azar Ying Lei Tania Moujaber Dale W Garsed Catherine J Kennedy Sian Fereday Chris Mitchell Yoke-Eng Chiew Joy Hendley Raghwa Sharma Paul R Harnett Jason Li Elizabeth L Christie Ann-Marie Patch Joshy George George Au-Yeung Gisela Mir Arnau Timothy P Holloway Timothy Semple John V Pearson Nicola Waddell Sean M Grimmond Martin Köbel Helen Rizos Ivan B Lomakin David D L Bowtell Anna deFazio

Cancer Res 2017 08 23;77(16):4268-4278. Epub 2017 Jun 23.

Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.

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http://dx.doi.org/10.1158/0008-5472.CAN-16-2224DOI Listing
August 2017

Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma.

Authors:
Michael E Feigin Tyler Garvin Peter Bailey Nicola Waddell David K Chang David R Kelley Shimin Shuai Steven Gallinger John D McPherson Sean M Grimmond Ekta Khurana Lincoln D Stein Andrew V Biankin Michael C Schatz David A Tuveson

Nat Genet 2017 Jun 8;49(6):825-833. Epub 2017 May 8.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

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http://dx.doi.org/10.1038/ng.3861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5659388PMC
June 2017

Whole-genome landscapes of major melanoma subtypes.

Authors:
Nicholas K Hayward James S Wilmott Nicola Waddell Peter A Johansson Matthew A Field Katia Nones Ann-Marie Patch Hojabr Kakavand Ludmil B Alexandrov Hazel Burke Valerie Jakrot Stephen Kazakoff Oliver Holmes Conrad Leonard Radhakrishnan Sabarinathan Loris Mularoni Scott Wood Qinying Xu Nick Waddell Varsha Tembe Gulietta M Pupo Ricardo De Paoli-Iseppi Ricardo E Vilain Ping Shang Loretta M S Lau Rebecca A Dagg Sarah-Jane Schramm Antonia Pritchard Ken Dutton-Regester Felicity Newell Anna Fitzgerald Catherine A Shang Sean M Grimmond Hilda A Pickett Jean Y Yang Jonathan R Stretch Andreas Behren Richard F Kefford Peter Hersey Georgina V Long Jonathan Cebon Mark Shackleton Andrew J Spillane Robyn P M Saw Núria López-Bigas John V Pearson John F Thompson Richard A Scolyer Graham J Mann

Nature 2017 05 3;545(7653):175-180. Epub 2017 May 3.

Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.

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http://dx.doi.org/10.1038/nature22071DOI Listing
May 2017

Lost in translation: returning germline genetic results in genome-scale cancer research.

Authors:
Amber L Johns Skye H McKay Jeremy L Humphris Mark Pinese Lorraine A Chantrill R Scott Mead Katherine Tucker Lesley Andrews Annabel Goodwin Conrad Leonard Hilda A High Katia Nones Ann-Marie Patch Neil D Merrett Nick Pavlakis Karin S Kassahn Jaswinder S Samra David K Miller David K Chang Marina Pajic John V Pearson Sean M Grimmond Nicola Waddell Nikolajs Zeps Anthony J Gill Andrew V Biankin

Genome Med 2017 04 28;9(1):41. Epub 2017 Apr 28.

Cancer Research Program, Garvan Institute of Medical Research, Kinghorn Cancer Centre, Sydney, Australia.

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http://dx.doi.org/10.1186/s13073-017-0430-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408494PMC
April 2017

Whole-genome landscape of pancreatic neuroendocrine tumours.

Authors:
Aldo Scarpa David K Chang Katia Nones Vincenzo Corbo Ann-Marie Patch Peter Bailey Rita T Lawlor Amber L Johns David K Miller Andrea Mafficini Borislav Rusev Maria Scardoni Davide Antonello Stefano Barbi Katarzyna O Sikora Sara Cingarlini Caterina Vicentini Skye McKay Michael C J Quinn Timothy J C Bruxner Angelika N Christ Ivon Harliwong Senel Idrisoglu Suzanne McLean Craig Nourse Ehsan Nourbakhsh Peter J Wilson Matthew J Anderson J Lynn Fink Felicity Newell Nick Waddell Oliver Holmes Stephen H Kazakoff Conrad Leonard Scott Wood Qinying Xu Shivashankar Hiriyur Nagaraj Eliana Amato Irene Dalai Samantha Bersani Ivana Cataldo Angelo P Dei Tos Paola Capelli Maria Vittoria Davì Luca Landoni Anna Malpaga Marco Miotto Vicki L J Whitehall Barbara A Leggett Janelle L Harris Jonathan Harris Marc D Jones Jeremy Humphris Lorraine A Chantrill Venessa Chin Adnan M Nagrial Marina Pajic Christopher J Scarlett Andreia Pinho Ilse Rooman Christopher Toon Jianmin Wu Mark Pinese Mark Cowley Andrew Barbour Amanda Mawson Emily S Humphrey Emily K Colvin Angela Chou Jessica A Lovell Nigel B Jamieson Fraser Duthie Marie-Claude Gingras William E Fisher Rebecca A Dagg Loretta M S Lau Michael Lee Hilda A Pickett Roger R Reddel Jaswinder S Samra James G Kench Neil D Merrett Krishna Epari Nam Q Nguyen Nikolajs Zeps Massimo Falconi Michele Simbolo Giovanni Butturini George Van Buren Stefano Partelli Matteo Fassan Kum Kum Khanna Anthony J Gill David A Wheeler Richard A Gibbs Elizabeth A Musgrove Claudio Bassi Giampaolo Tortora Paolo Pederzoli John V Pearson Nicola Waddell Andrew V Biankin Sean M Grimmond

Nature 2017 03 15;543(7643):65-71. Epub 2017 Feb 15.

University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, 3010, Victoria, Australia.

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http://dx.doi.org/10.1038/nature21063DOI Listing
March 2017

Hypermutation In Pancreatic Cancer.

Authors:
Jeremy L Humphris Ann-Marie Patch Katia Nones Peter J Bailey Amber L Johns Skye McKay David K Chang David K Miller Marina Pajic Karin S Kassahn Michael C J Quinn Timothy J C Bruxner Angelika N Christ Ivon Harliwong Senel Idrisoglu Suzanne Manning Craig Nourse Ehsan Nourbakhsh Andrew Stone Peter J Wilson Matthew Anderson J Lynn Fink Oliver Holmes Stephen Kazakoff Conrad Leonard Felicity Newell Nick Waddell Scott Wood Ronald S Mead Qinying Xu Jianmin Wu Mark Pinese Mark J Cowley Marc D Jones Adnan M Nagrial Venessa T Chin Lorraine A Chantrill Amanda Mawson Angela Chou Christopher J Scarlett Andreia V Pinho Ilse Rooman Marc Giry-Laterriere Jaswinder S Samra James G Kench Neil D Merrett Christopher W Toon Krishna Epari Nam Q Nguyen Andrew Barbour Nikolajs Zeps Nigel B Jamieson Colin J McKay C Ross Carter Euan J Dickson Janet S Graham Fraser Duthie Karin Oien Jane Hair Jennifer P Morton Owen J Sansom Robert Grützmann Ralph H Hruban Anirban Maitra Christine A Iacobuzio-Donahue Richard D Schulick Christopher L Wolfgang Richard A Morgan Rita T Lawlor Borislav Rusev Vincenzo Corbo Roberto Salvia Ivana Cataldo Giampaolo Tortora Margaret A Tempero Oliver Hofmann James R Eshleman Christian Pilarsky Aldo Scarpa Elizabeth A Musgrove Anthony J Gill John V Pearson Sean M Grimmond Nicola Waddell Andrew V Biankin

Gastroenterology 2017 01 15;152(1):68-74.e2. Epub 2016 Nov 15.

Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Department of Surgery, Bankstown Hospital, Bankstown, Sydney, New South Wales, Australia; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales Australia, Liverpool, New South Wales, Australia; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00165085163518
Publisher Site
http://dx.doi.org/10.1053/j.gastro.2016.09.060DOI Listing
January 2017

Mitochondrial mutations and metabolic adaptation in pancreatic cancer.

Authors:
Rae-Anne Hardie Ellen van Dam Mark Cowley Ting-Li Han Seher Balaban Marina Pajic Mark Pinese Mary Iconomou Robert F Shearer Jessie McKenna David Miller Nicola Waddell John V Pearson Sean M Grimmond Leonid Sazanov Andrew V Biankin Silas Villas-Boas Andrew J Hoy Nigel Turner Darren N Saunders

Cancer Metab 2017 30;5. Epub 2017 Jan 30.

The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia.

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http://dx.doi.org/10.1186/s40170-017-0164-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282905PMC
January 2017

Whole exome sequencing in patients with white matter abnormalities.

Authors:
Adeline Vanderver Cas Simons Guy Helman Joanna Crawford Nicole I Wolf Geneviève Bernard Amy Pizzino Johanna L Schmidt Asako Takanohashi David Miller Amirah Khouzam Vani Rajan Erica Ramos Shimul Chowdhury Tina Hambuch Kelin Ru Gregory J Baillie Sean M Grimmond Ljubica Caldovic Joseph Devaney Miriam Bloom Sarah H Evans Jennifer L P Murphy Nathan McNeill Brent L Fogel Raphael Schiffmann Marjo S van der Knaap Ryan J Taft

Ann Neurol 2016 06 9;79(6):1031-1037. Epub 2016 May 9.

School of Medicine and Health Sciences, George Washington University, Washington, DC.

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http://dx.doi.org/10.1002/ana.24650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5354169PMC
June 2016

Dual targeting of p53 and c-MYC selectively eliminates leukaemic stem cells.

Authors:
Sheela A Abraham Lisa E M Hopcroft Emma Carrick Mark E Drotar Karen Dunn Andrew J K Williamson Koorosh Korfi Pablo Baquero Laura E Park Mary T Scott Francesca Pellicano Andrew Pierce Mhairi Copland Craig Nourse Sean M Grimmond David Vetrie Anthony D Whetton Tessa L Holyoake

Nature 2016 06 8;534(7607):341-6. Epub 2016 Jun 8.

Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Gartnavel General Hospital, 1053 Great Western Road, Glasgow G12 0YN, UK.

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http://dx.doi.org/10.1038/nature18288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913876PMC
June 2016

Rapid identification of a novel complex I MT-ND3 m.10134C>A mutation in a Leigh syndrome patient.

Authors:
David K Miller Minal J Menezes Cas Simons Lisa G Riley Sandra T Cooper Sean M Grimmond David R Thorburn John Christodoulou Ryan J Taft

PLoS One 2014 12;9(8):e104879. Epub 2014 Aug 12.

Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia; Departments of Integrative Systems Biology and Pediatrics, George Washington University School of Medicine, Washington, D.C., United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0104879PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4130626PMC
April 2016

Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma.

Authors:
Lutz Krause Katia Nones Kelly A Loffler Derek Nancarrow Harald Oey Yue Hang Tang Nicola J Wayte Ann Marie Patch Kalpana Patel Sandra Brosda Suzanne Manning Guy Lampe Andrew Clouston Janine Thomas Jens Stoye Damian J Hussey David I Watson Reginald V Lord Wayne A Phillips David Gotley B Mark Smithers David C Whiteman Nicholas K Hayward Sean M Grimmond Nicola Waddell Andrew P Barbour

Carcinogenesis 2016 Apr 10;37(4):356-65. Epub 2016 Feb 10.

Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia, Department of Surgery, School of Medicine, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia and.

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http://dx.doi.org/10.1093/carcin/bgw018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806711PMC
April 2016

Genomic analyses identify molecular subtypes of pancreatic cancer.

Authors:
Peter Bailey David K Chang Katia Nones Amber L Johns Ann-Marie Patch Marie-Claude Gingras David K Miller Angelika N Christ Tim J C Bruxner Michael C Quinn Craig Nourse L Charles Murtaugh Ivon Harliwong Senel Idrisoglu Suzanne Manning Ehsan Nourbakhsh Shivangi Wani Lynn Fink Oliver Holmes Venessa Chin Matthew J Anderson Stephen Kazakoff Conrad Leonard Felicity Newell Nick Waddell Scott Wood Qinying Xu Peter J Wilson Nicole Cloonan Karin S Kassahn Darrin Taylor Kelly Quek Alan Robertson Lorena Pantano Laura Mincarelli Luis N Sanchez Lisa Evers Jianmin Wu Mark Pinese Mark J Cowley Marc D Jones Emily K Colvin Adnan M Nagrial Emily S Humphrey Lorraine A Chantrill Amanda Mawson Jeremy Humphris Angela Chou Marina Pajic Christopher J Scarlett Andreia V Pinho Marc Giry-Laterriere Ilse Rooman Jaswinder S Samra James G Kench Jessica A Lovell Neil D Merrett Christopher W Toon Krishna Epari Nam Q Nguyen Andrew Barbour Nikolajs Zeps Kim Moran-Jones Nigel B Jamieson Janet S Graham Fraser Duthie Karin Oien Jane Hair Robert Grützmann Anirban Maitra Christine A Iacobuzio-Donahue Christopher L Wolfgang Richard A Morgan Rita T Lawlor Vincenzo Corbo Claudio Bassi Borislav Rusev Paola Capelli Roberto Salvia Giampaolo Tortora Debabrata Mukhopadhyay Gloria M Petersen Donna M Munzy William E Fisher Saadia A Karim James R Eshleman Ralph H Hruban Christian Pilarsky Jennifer P Morton Owen J Sansom Aldo Scarpa Elizabeth A Musgrove Ulla-Maja Hagbo Bailey Oliver Hofmann Robert L Sutherland David A Wheeler Anthony J Gill Richard A Gibbs John V Pearson Nicola Waddell Andrew V Biankin Sean M Grimmond

Nature 2016 Mar 24;531(7592):47-52. Epub 2016 Feb 24.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1038/nature16965DOI Listing
March 2016

Towards the systematic mapping and engineering of the protein prenylation machinery in Saccharomyces cerevisiae.

Authors:
Viktor Stein Marta H Kubala Jason Steen Sean M Grimmond Kirill Alexandrov

PLoS One 2015 13;10(3):e0120716. Epub 2015 Mar 13.

Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120716PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358939PMC
February 2016

Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data.

Authors:
David L A Wood Katia Nones Anita Steptoe Angelika Christ Ivon Harliwong Felicity Newell Timothy J C Bruxner David Miller Nicole Cloonan Sean M Grimmond

PLoS One 2015 12;10(5):e0126911. Epub 2015 May 12.

Translational Research Centre, University of Glasgow, Glasgow, Scotland; Queensland Centre for Medical Genomics, University of Queensland, Brisbane, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126911PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428808PMC
February 2016

Using the MCF10A/MCF10CA1a Breast Cancer Progression Cell Line Model to Investigate the Effect of Active, Mutant Forms of EGFR in Breast Cancer Development and Treatment Using Gefitinib.

Authors:
Darrell C Bessette Erik Tilch Tatjana Seidens Michael C J Quinn Adrian P Wiegmans Wei Shi Sibylle Cocciardi Amy McCart-Reed Jodi M Saunus Peter T Simpson Sean M Grimmond Sunil R Lakhani Kum Kum Khanna Nic Waddell Fares Al-Ejeh Georgia Chenevix-Trench

PLoS One 2015 13;10(5):e0125232. Epub 2015 May 13.

QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125232PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430383PMC
February 2016

Ampullary Cancers Harbor ELF3 Tumor Suppressor Gene Mutations and Exhibit Frequent WNT Dysregulation.

Authors:
Marie-Claude Gingras Kyle R Covington David K Chang Lawrence A Donehower Anthony J Gill Michael M Ittmann Chad J Creighton Amber L Johns Eve Shinbrot Ninad Dewal William E Fisher Christian Pilarsky Robert Grützmann Michael J Overman Nigel B Jamieson George Van Buren Jennifer Drummond Kimberly Walker Oliver A Hampton Liu Xi Donna M Muzny Harsha Doddapaneni Sandra L Lee Michelle Bellair Jianhong Hu Yi Han Huyen H Dinh Mike Dahdouli Jaswinder S Samra Peter Bailey Nicola Waddell John V Pearson Ivon Harliwong Huamin Wang Daniela Aust Karin A Oien Ralph H Hruban Sally E Hodges Amy McElhany Charupong Saengboonmee Fraser R Duthie Sean M Grimmond Andrew V Biankin David A Wheeler Richard A Gibbs

Cell Rep 2016 Feb 21;14(4):907-919. Epub 2016 Jan 21.

Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.celrep.2015.12.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982376PMC
February 2016

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Authors:
Tyler S Alioto Ivo Buchhalter Sophia Derdak Barbara Hutter Matthew D Eldridge Eivind Hovig Lawrence E Heisler Timothy A Beck Jared T Simpson Laurie Tonon Anne-Sophie Sertier Ann-Marie Patch Natalie Jäger Philip Ginsbach Ruben Drews Nagarajan Paramasivam Rolf Kabbe Sasithorn Chotewutmontri Nicolle Diessl Christopher Previti Sabine Schmidt Benedikt Brors Lars Feuerbach Michael Heinold Susanne Gröbner Andrey Korshunov Patrick S Tarpey Adam P Butler Jonathan Hinton David Jones Andrew Menzies Keiran Raine Rebecca Shepherd Lucy Stebbings Jon W Teague Paolo Ribeca Francesc Castro Giner Sergi Beltran Emanuele Raineri Marc Dabad Simon C Heath Marta Gut Robert E Denroche Nicholas J Harding Takafumi N Yamaguchi Akihiro Fujimoto Hidewaki Nakagawa Víctor Quesada Rafael Valdés-Mas Sigve Nakken Daniel Vodák Lawrence Bower Andrew G Lynch Charlotte L Anderson Nicola Waddell John V Pearson Sean M Grimmond Myron Peto Paul Spellman Minghui He Cyriac Kandoth Semin Lee John Zhang Louis Létourneau Singer Ma Sahil Seth David Torrents Liu Xi David A Wheeler Carlos López-Otín Elías Campo Peter J Campbell Paul C Boutros Xose S Puente Daniela S Gerhard Stefan M Pfister John D McPherson Thomas J Hudson Matthias Schlesner Peter Lichter Roland Eils David T W Jones Ivo G Gut

Nat Commun 2015 Dec 9;6:10001. Epub 2015 Dec 9.

CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1038/ncomms10001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682041PMC
December 2015

SOX9 regulates ERBB signalling in pancreatic cancer development.

Authors:
Adrien Grimont Andreia V Pinho Mark J Cowley Cécile Augereau Amanda Mawson Marc Giry-Laterrière Géraldine Van den Steen Nicola Waddell Marina Pajic Christine Sempoux Jianmin Wu Sean M Grimmond Andrew V Biankin Frédéric P Lemaigre Ilse Rooman Patrick Jacquemin

Gut 2015 Nov 21;64(11):1790-9. Epub 2014 Oct 21.

Université catholique de Louvain, de Duve Institute, Brussels, Belgium.

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http://dx.doi.org/10.1136/gutjnl-2014-307075DOI Listing
November 2015

Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance.

Authors:
Jodi M Saunus Michael C J Quinn Ann-Marie Patch John V Pearson Peter J Bailey Katia Nones Amy E McCart Reed David Miller Peter J Wilson Fares Al-Ejeh Mythily Mariasegaram Queenie Lau Teresa Withers Rosalind L Jeffree Lynne E Reid Leonard Da Silva Admire Matsika Colleen M Niland Margaret C Cummings Timothy J C Bruxner Angelika N Christ Ivon Harliwong Senel Idrisoglu Suzanne Manning Craig Nourse Ehsan Nourbakhsh Shivangi Wani Matthew J Anderson J Lynn Fink Oliver Holmes Stephen Kazakoff Conrad Leonard Felicity Newell Darrin Taylor Nick Waddell Scott Wood Qinying Xu Karin S Kassahn Vairavan Narayanan Nur Aishah Taib Soo-Hwang Teo Yock Ping Chow kConFab Parmjit S Jat Sebastian Brandner Adrienne M Flanagan Kum Kum Khanna Georgia Chenevix-Trench Sean M Grimmond Peter T Simpson Nicola Waddell Sunil R Lakhani

J Pathol 2015 Nov 19;237(3):363-78. Epub 2015 Aug 19.

University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia.

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November 2015

Corrigendum: Whole-genome characterization of chemoresistant ovarian cancer.

Authors:
Ann-Marie Patch Elizabeth L Christie Dariush Etemadmoghadam Dale W Garsed Joshy George Sian Fereday Katia Nones Prue Cowin Kathryn Alsop Peter J Bailey Karin S Kassahn Felicity Newell Michael C J Quinn Stephen Kazakoff Kelly Quek Charlotte Wilhelm-Benartzi Ed Curry Huei San Leong Anne Hamilton Linda Mileshkin George Au-Yeung Catherine Kennedy Jillian Hung Yoke-Eng Chiew Paul Harnett Michael Friedlander Michael Quinn Jan Pyman Stephen Cordner Patricia O'Brien Jodie Leditschke Greg Young Kate Strachan Paul Waring Walid Azar Chris Mitchell Nadia Traficante Joy Hendley Heather Thorne Mark Shackleton David K Miller Gisela Mir Arnau Richard W Tothill Timothy P Holloway Timothy Semple Ivon Harliwong Craig Nourse Ehsan Nourbakhsh Suzanne Manning Senel Idrisoglu Timothy J C Bruxner Angelika N Christ Barsha Poudel Oliver Holmes Matthew Anderson Conrad Leonard Andrew Lonie Nathan Hall Scott Wood Darrin F Taylor Qinying Xu J Lynn Fink Nick Waddell Ronny Drapkin Euan Stronach Hani Gabra Robert Brown Andrea Jewell Shivashankar H Nagaraj Emma Markham Peter J Wilson Jason Ellul Orla McNally Maria A Doyle Ravikiran Vedururu Collin Stewart Ernst Lengyel John V Pearson Nicola Waddell Anna deFazio Sean M Grimmond David D L Bowtell

Nature 2015 Nov 21;527(7578):398. Epub 2015 Oct 21.

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November 2015

Corrigendum: Genome-wide characterization of the routes to pluripotency.

Authors:
Samer M I Hussein Mira C Puri Peter D Tonge Marco Benevento Andrew J Corso Jennifer L Clancy Rowland Mosbergen Mira Li Dong-Sung Lee Nicole Cloonan David L A Wood Javier Munoz Robert Middleton Othmar Korn Hardip R Patel Carl A White Jong-Yeon Shin Maely E Gauthier Kim-Anh Lê Cao Jong-Il Kim Jessica C Mar Nika Shakiba William Ritchie John E J Rasko Sean M Grimmond Peter W Zandstra Christine A Wells Thomas Preiss Jeong-Sun Seo Albert J R Heck Ian M Rogers Andras Nagy

Nature 2015 Jul 17;523(7562):626. Epub 2015 Jun 17.

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July 2015

Corrigendum: Divergent reprogramming routes lead to alternative stem-cell states.

Authors:
Peter D Tonge Andrew J Corso Claudio Monetti Samer M I Hussein Mira C Puri Iacovos P Michael Mira Li Dong-Sung Lee Jessica C Mar Nicole Cloonan David L Wood Maely E Gauthier Othmar Korn Jennifer L Clancy Thomas Preiss Sean M Grimmond Jong-Yeon Shin Jeong-Sun Seo Christine A Wells Ian M Rogers Andras Nagy

Nature 2015 Jul 17;523(7562):626. Epub 2015 Jun 17.

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July 2015

A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae.

Authors:
John M Atack Yogitha N Srikhanta Kate L Fox Joseph A Jurcisek Kenneth L Brockman Tyson A Clark Matthew Boitano Peter M Power Freda E-C Jen Alastair G McEwan Sean M Grimmond Arnold L Smith Stephen J Barenkamp Jonas Korlach Lauren O Bakaletz Michael P Jennings

Nat Commun 2015 Jul 28;6:7828. Epub 2015 Jul 28.

Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia.

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July 2015

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.

Authors:
Shivashankar H Nagaraj Nicola Waddell Anil K Madugundu Scott Wood Alun Jones Ramya A Mandyam Katia Nones John V Pearson Sean M Grimmond

J Proteome Res 2015 May 17;14(5):2255-66. Epub 2015 Apr 17.

§Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland G61 1BD, United Kingdom.

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May 2015

Precision Medicine for Advanced Pancreas Cancer: The Individualized Molecular Pancreatic Cancer Therapy (IMPaCT) Trial.

Authors:
Lorraine A Chantrill Adnan M Nagrial Clare Watson Amber L Johns Mona Martyn-Smith Skye Simpson Scott Mead Marc D Jones Jaswinder S Samra Anthony J Gill Nicole Watson Venessa T Chin Jeremy L Humphris Angela Chou Belinda Brown Adrienne Morey Marina Pajic Sean M Grimmond David K Chang David Thomas Lucille Sebastian Katrin Sjoquist Sonia Yip Nick Pavlakis Ray Asghari Sandra Harvey Peter Grimison John Simes Andrew V Biankin

Clin Cancer Res 2015 May;21(9):2029-37

The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia. Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland. Department of Surgery, Bankstown Hospital, Sydney, New South Wales, Australia. South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, New South Wales, Australia. West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom.

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May 2015

Whole-genome characterization of chemoresistant ovarian cancer.

Authors:
Ann-Marie Patch Elizabeth L Christie Dariush Etemadmoghadam Dale W Garsed Joshy George Sian Fereday Katia Nones Prue Cowin Kathryn Alsop Peter J Bailey Karin S Kassahn Felicity Newell Michael C J Quinn Stephen Kazakoff Kelly Quek Charlotte Wilhelm-Benartzi Ed Curry Huei San Leong Anne Hamilton Linda Mileshkin George Au-Yeung Catherine Kennedy Jillian Hung Yoke-Eng Chiew Paul Harnett Michael Friedlander Michael Quinn Jan Pyman Stephen Cordner Patricia O'Brien Jodie Leditschke Greg Young Kate Strachan Paul Waring Walid Azar Chris Mitchell Nadia Traficante Joy Hendley Heather Thorne Mark Shackleton David K Miller Gisela Mir Arnau Richard W Tothill Timothy P Holloway Timothy Semple Ivon Harliwong Craig Nourse Ehsan Nourbakhsh Suzanne Manning Senel Idrisoglu Timothy J C Bruxner Angelika N Christ Barsha Poudel Oliver Holmes Matthew Anderson Conrad Leonard Andrew Lonie Nathan Hall Scott Wood Darrin F Taylor Qinying Xu J Lynn Fink Nick Waddell Ronny Drapkin Euan Stronach Hani Gabra Robert Brown Andrea Jewell Shivashankar H Nagaraj Emma Markham Peter J Wilson Jason Ellul Orla McNally Maria A Doyle Ravikiran Vedururu Collin Stewart Ernst Lengyel John V Pearson Nicola Waddell Anna deFazio Sean M Grimmond David D L Bowtell

Nature 2015 May;521(7553):489-94

1] Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Department of Pathology, University of Melbourne, Parkville, Victoria 3052, Australia [3] Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria 3052, Australia [4] Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK [5] Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3052, Australia.

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May 2015

New RAS-mutant pancreatic adenocarcinoma with combined BRAF and MEK inhibition for metastatic melanoma.

Authors:
Matteo S Carlino Vu Kwan David K Miller Catherine A B Saunders Desmond Yip Adnan M Nagrial Jeanne Tomlinson Sean M Grimmond Richard A Scolyer Richard F Kefford Andrew V Biankin Georgina V Long

J Clin Oncol 2015 Apr 12;33(11):e52-6. Epub 2014 May 12.

Melanoma Institute Australia; The University of Sydney and Westmead Institute for Cancer Research, Sydney, Australia

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http://dx.doi.org/10.1200/JCO.2013.51.5783DOI Listing
April 2015

Somatic point mutation calling in low cellularity tumors.

Authors:
Karin S Kassahn Oliver Holmes Katia Nones Ann-Marie Patch David K Miller Angelika N Christ Ivon Harliwong Timothy J Bruxner Qinying Xu Matthew Anderson Scott Wood Conrad Leonard Darrin Taylor Felicity Newell Sarah Song Senel Idrisoglu Craig Nourse Ehsan Nourbakhsh Suzanne Manning Shivangi Wani Anita Steptoe Marina Pajic Mark J Cowley Mark Pinese David K Chang Anthony J Gill Amber L Johns Jianmin Wu Peter J Wilson Lynn Fink Andrew V Biankin Nicola Waddell Sean M Grimmond John V Pearson

PLoS One 2013 8;8(11):e74380. Epub 2013 Nov 8.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3826759PMC
March 2015

Corrigendum: Mutations in the voltage-gated potassium channel gene KCNH1 cause Temple-Baraitser syndrome and epilepsy.

Authors:
Cas Simons Lachlan D Rash Joanna Crawford Linlin Ma Ben Cristofori-Armstrong David Miller Kelin Ru Gregory J Baillie Yasemin Alanay Adeline Jacquinet François-Guillaume Debray Alain Verloes Joseph Shen Gözde Yesil Serhat Guler Adnan Yuksel John G Cleary Sean M Grimmond Julie McGaughran Glenn F King Michael T Gabbett Ryan J Taft

Nat Genet 2015 Mar;47(3):304

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March 2015

Whole genomes redefine the mutational landscape of pancreatic cancer.

Authors:
Nicola Waddell Marina Pajic Ann-Marie Patch David K Chang Karin S Kassahn Peter Bailey Amber L Johns David Miller Katia Nones Kelly Quek Michael C J Quinn Alan J Robertson Muhammad Z H Fadlullah Tim J C Bruxner Angelika N Christ Ivon Harliwong Senel Idrisoglu Suzanne Manning Craig Nourse Ehsan Nourbakhsh Shivangi Wani Peter J Wilson Emma Markham Nicole Cloonan Matthew J Anderson J Lynn Fink Oliver Holmes Stephen H Kazakoff Conrad Leonard Felicity Newell Barsha Poudel Sarah Song Darrin Taylor Nick Waddell Scott Wood Qinying Xu Jianmin Wu Mark Pinese Mark J Cowley Hong C Lee Marc D Jones Adnan M Nagrial Jeremy Humphris Lorraine A Chantrill Venessa Chin Angela M Steinmann Amanda Mawson Emily S Humphrey Emily K Colvin Angela Chou Christopher J Scarlett Andreia V Pinho Marc Giry-Laterriere Ilse Rooman Jaswinder S Samra James G Kench Jessica A Pettitt Neil D Merrett Christopher Toon Krishna Epari Nam Q Nguyen Andrew Barbour Nikolajs Zeps Nigel B Jamieson Janet S Graham Simone P Niclou Rolf Bjerkvig Robert Grützmann Daniela Aust Ralph H Hruban Anirban Maitra Christine A Iacobuzio-Donahue Christopher L Wolfgang Richard A Morgan Rita T Lawlor Vincenzo Corbo Claudio Bassi Massimo Falconi Giuseppe Zamboni Giampaolo Tortora Margaret A Tempero Anthony J Gill James R Eshleman Christian Pilarsky Aldo Scarpa Elizabeth A Musgrove John V Pearson Andrew V Biankin Sean M Grimmond

Nature 2015 Feb;518(7540):495-501

1] Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia [2] Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523082PMC
February 2015

SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample.

Authors:
Jesse M Gray David A Harmin Sarah A Boswell Nicole Cloonan Thomas E Mullen Joseph J Ling Nimrod Miller Scott Kuersten Yong-Chao Ma Steven A McCarroll Sean M Grimmond Michael Springer

PLoS One 2014 26;9(2):e89673. Epub 2014 Feb 26.

Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3935918PMC
January 2015

Mutations in the voltage-gated potassium channel gene KCNH1 cause Temple-Baraitser syndrome and epilepsy.

Authors:
Cas Simons Lachlan D Rash Joanna Crawford Linlin Ma Ben Cristofori-Armstrong David Miller Kelin Ru Gregory J Baillie Yasemin Alanay Adeline Jacquinet François-Guillaume Debray Alain Verloes Joseph Shen Gözde Yesil Serhat Guler Adnan Yuksel John G Cleary Sean M Grimmond Julie McGaughran Glenn F King Michael T Gabbett Ryan J Taft

Nat Genet 2015 Jan 24;47(1):73-7. Epub 2014 Nov 24.

1] Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia. [2] Department of Integrated Systems Biology, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA. [3] Department of Pediatrics, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA. [4] Illumina, Inc., San Diego, California, USA.

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http://www.nature.com/articles/ng.3153
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January 2015

Clinical and pathologic features of familial pancreatic cancer.

Authors:
Jeremy L Humphris Amber L Johns Skye H Simpson Mark J Cowley Marina Pajic David K Chang Adnan M Nagrial Venessa T Chin Lorraine A Chantrill Mark Pinese R Scott Mead Anthony J Gill Jaswinder S Samra James G Kench Elizabeth A Musgrove Katherine M Tucker Allan D Spigelman Nic Waddell Sean M Grimmond Andrew V Biankin

Cancer 2014 Dec 14;120(23):3669-75. Epub 2014 Oct 14.

The Kinghorn Cancer Center, Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.

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http://dx.doi.org/10.1002/cncr.28863DOI Listing
December 2014

An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator.

Authors:
Dong-Sung Lee Jong-Yeon Shin Peter D Tonge Mira C Puri Seungbok Lee Hansoo Park Won-Chul Lee Samer M I Hussein Thomas Bleazard Ji-Young Yun Jihye Kim Mira Li Nicole Cloonan David Wood Jennifer L Clancy Rowland Mosbergen Jae-Hyuk Yi Kap-Seok Yang Hyungtae Kim Hwanseok Rhee Christine A Wells Thomas Preiss Sean M Grimmond Ian M Rogers Andras Nagy Jeong-Sun Seo

Nat Commun 2014 Dec 10;5:5619. Epub 2014 Dec 10.

1] Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul 110-799, Korea [2] Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Korea [3] Department of Biochemistry, Seoul National University College of Medicine, Seoul 110-799, Korea [4] Life Science Institute, Macrogen Inc., Seoul 153-781, Korea.

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http://dx.doi.org/10.1038/ncomms6619DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284806PMC
December 2014

Small RNA changes en route to distinct cellular states of induced pluripotency.

Authors:
Jennifer L Clancy Hardip R Patel Samer M I Hussein Peter D Tonge Nicole Cloonan Andrew J Corso Mira Li Dong-Sung Lee Jong-Yeon Shin Justin J L Wong Charles G Bailey Marco Benevento Javier Munoz Aaron Chuah David Wood John E J Rasko Albert J R Heck Sean M Grimmond Ian M Rogers Jeong-Sun Seo Christine A Wells Mira C Puri Andras Nagy Thomas Preiss

Nat Commun 2014 Dec 10;5:5522. Epub 2014 Dec 10.

1] Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia [2] Molecular, Structural &Computational Biology Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia.

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http://dx.doi.org/10.1038/ncomms6522DOI Listing
December 2014

Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks.

Authors:
Marco Benevento Peter D Tonge Mira C Puri Samer M I Hussein Nicole Cloonan David L Wood Sean M Grimmond Andras Nagy Javier Munoz Albert J R Heck

Nat Commun 2014 Dec 10;5:5613. Epub 2014 Dec 10.

1] Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands [2] Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands.

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December 2014

Divergent reprogramming routes lead to alternative stem-cell states.

Authors:
Peter D Tonge Andrew J Corso Claudio Monetti Samer M I Hussein Mira C Puri Iacovos P Michael Mira Li Dong-Sung Lee Jessica C Mar Nicole Cloonan David L Wood Maely E Gauthier Othmar Korn Jennifer L Clancy Thomas Preiss Sean M Grimmond Jong-Yeon Shin Jeong-Sun Seo Christine A Wells Ian M Rogers Andras Nagy

Nature 2014 Dec;516(7530):192-7

1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 3H7, Canada [3] Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario M5T 3H7, Canada.

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http://dx.doi.org/10.1038/nature14047DOI Listing
December 2014

Genome-wide characterization of the routes to pluripotency.

Authors:
Samer M I Hussein Mira C Puri Peter D Tonge Marco Benevento Andrew J Corso Jennifer L Clancy Rowland Mosbergen Mira Li Dong-Sung Lee Nicole Cloonan David L A Wood Javier Munoz Robert Middleton Othmar Korn Hardip R Patel Carl A White Jong-Yeon Shin Maely E Gauthier Kim-Anh Lê Cao Jong-Il Kim Jessica C Mar Nika Shakiba William Ritchie John E J Rasko Sean M Grimmond Peter W Zandstra Christine A Wells Thomas Preiss Jeong-Sun Seo Albert J R Heck Ian M Rogers Andras Nagy

Nature 2014 Dec;516(7530):198-206

1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 3H7, Canada [3] Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario M5S 1E2, Canada.

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December 2014

Ferrets exclusively synthesize Neu5Ac and express naturally humanized influenza A virus receptors.

Authors:
Preston S K Ng Raphael Böhm Lauren E Hartley-Tassell Jason A Steen Hui Wang Samuel W Lukowski Paula L Hawthorne Ann E O Trezise Peter J Coloe Sean M Grimmond Thomas Haselhorst Mark von Itzstein Adrienne W Paton James C Paton Michael P Jennings

Nat Commun 2014 Dec 17;5:5750. Epub 2014 Dec 17.

Institute For Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351649PMC
December 2014

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis.

Authors:
Katia Nones Nicola Waddell Nicci Wayte Ann-Marie Patch Peter Bailey Felicity Newell Oliver Holmes J Lynn Fink Michael C J Quinn Yue Hang Tang Guy Lampe Kelly Quek Kelly A Loffler Suzanne Manning Senel Idrisoglu David Miller Qinying Xu Nick Waddell Peter J Wilson Timothy J C Bruxner Angelika N Christ Ivon Harliwong Craig Nourse Ehsan Nourbakhsh Matthew Anderson Stephen Kazakoff Conrad Leonard Scott Wood Peter T Simpson Lynne E Reid Lutz Krause Damian J Hussey David I Watson Reginald V Lord Derek Nancarrow Wayne A Phillips David Gotley B Mark Smithers David C Whiteman Nicholas K Hayward Peter J Campbell John V Pearson Sean M Grimmond Andrew P Barbour

Nat Commun 2014 Oct 29;5:5224. Epub 2014 Oct 29.

Surgical Oncology Group, School of Medicine, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane, Queensland 4102, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596003PMC
October 2014

Stromal protein Ecm1 regulates ureteric bud patterning and branching.

Authors:
Suneeta S Paroly Fengwei Wang Lee Spraggon Joseph Merregaert Ekatherina Batourina Benjamin Tycko Kai M Schmidt-Ott Sean Grimmond Melissa Little Cathy Mendelsohn

PLoS One 2013 31;8(12):e84155. Epub 2013 Dec 31.

Department of Urology, Irving Cancer Research Center, Columbia University, New York, New York, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877229PMC
September 2014

Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling.

Authors:
Katia Nones Nic Waddell Sarah Song Ann-Marie Patch David Miller Amber Johns Jianmin Wu Karin S Kassahn David Wood Peter Bailey Lynn Fink Suzanne Manning Angelika N Christ Craig Nourse Stephen Kazakoff Darrin Taylor Conrad Leonard David K Chang Marc D Jones Michelle Thomas Clare Watson Mark Pinese Mark Cowley Ilse Rooman Marina Pajic Giovanni Butturini Anna Malpaga Vincenzo Corbo Stefano Crippa Massimo Falconi Giuseppe Zamboni Paola Castelli Rita T Lawlor Anthony J Gill Aldo Scarpa John V Pearson Andrew V Biankin Sean M Grimmond

Int J Cancer 2014 Sep 9;135(5):1110-8. Epub 2014 May 9.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia.

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September 2014

Targeting mTOR dependency in pancreatic cancer.

Authors:
Douglas C Morran Jianmin Wu Nigel B Jamieson Agata Mrowinska Gabriela Kalna Saadia A Karim Amy Y M Au Christopher J Scarlett David K Chang Malgorzata Z Pajak Karin A Oien Colin J McKay C Ross Carter Gerry Gillen Sue Champion Sally L Pimlott Kurt I Anderson T R Jeffry Evans Sean M Grimmond Andrew V Biankin Owen J Sansom Jennifer P Morton

Gut 2014 Sep 9;63(9):1481-9. Epub 2014 Apr 9.

CRUK Beatson Institute, Glasgow, UK.

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September 2014

Transcriptional switching in macrophages associated with the peritoneal foreign body response.

Authors:
Jane E Mooney Kim M Summers Milena Gongora Sean M Grimmond Julie H Campbell David A Hume Barbara E Rolfe

Immunol Cell Biol 2014 Jul 18;92(6):518-26. Epub 2014 Mar 18.

Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia.

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July 2014

PRMT2 and RORγ expression are associated with breast cancer survival outcomes.

Authors:
Tae Gyu Oh Peter Bailey Eloise Dray Aaron G Smith Joel Goode Natalie Eriksson John W Funder Peter J Fuller Evan R Simpson Wayne D Tilley Peter J Leedman Christine L Clarke Sean Grimmond Dennis H Dowhan George E O Muscat

Mol Endocrinol 2014 Jul 9;28(7):1166-85. Epub 2014 Jun 9.

Institute for Molecular Bioscience (T.G.O., P.B., J.G., N.E., S.G., D.H.D., G.E.O.M.) and School of Biomedical Science (A.G.S.), The University of Queensland, Brisbane, Queensland 4072, Australia; Institute of Health and Biomedical Innovation (E.D.), Queensland University of Technology, Translational Research Institute, Brisbane, Queensland 4102, Australia; Prince Henry's Institute of Medical Research (J.W.F., P.J.F., E.R.S.), Clayton, Victoria 3168, Australia; Dame Roma Mitchell Cancer Research Laboratory (W.D.T.), School of Medicine, The University of Adelaide, Adelaide 5005, South Australia, Australia; Western Australian Institute for Medical Research (P.J.L.), University of Western Australia, Perth, Western Australia 6009, Australia; Westmead Millennium Institute (C.L.C.), Sydney Medical School, Westmead, University of Sydney, New South Wales 2006, Australia; and Department of Molecular and Clinical Medicine/Wallenberg Laboratory (G.E.O.M.), University of Gothenburg, S-405 30 Gothenburg, Sweden.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5414829PMC
July 2014

A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing.

Authors:
Kelly Quek Katia Nones Ann-Marie Patch J Lynn Fink Felicity Newell Nicole Cloonan David Miller Muhammad Z H Fadlullah Karin Kassahn Angelika N Christ Timothy J C Bruxner Suzanne Manning Ivon Harliwong Senel Idrisoglu Craig Nourse Ehsan Nourbakhsh Shivangi Wani Anita Steptoe Matthew Anderson Oliver Holmes Conrad Leonard Darrin Taylor Scott Wood Qinying Xu Peter Wilson Andrew V Biankin John V Pearson Nic Waddell Sean M Grimmond

Biotechniques 2014 Jul 1;57(1):31-8. Epub 2014 Jul 1.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD, Australia; Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom.

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July 2014

Gemcitabine and CHK1 inhibition potentiate EGFR-directed radioimmunotherapy against pancreatic ductal adenocarcinoma.

Authors:
Fares Al-Ejeh Marina Pajic Wei Shi Murugan Kalimutho Mariska Miranda Adnan M Nagrial Angela Chou Andrew V Biankin Sean M Grimmond Michael P Brown Kum Kum Khanna

Clin Cancer Res 2014 Jun 16;20(12):3187-97. Epub 2014 May 16.

Authors' Affiliations: Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Herston; Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland; The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research; St Vincent's Clinical School, Faculty of Medicine, University of NSW; Department of Anatomical Pathology, SYDPATH, St Vincent's Hospital, Darlinghurst, New South Wales; Australian Pancreatic Cancer Genome Initiative, for the full list of contributors see http://www.pancreaticcancer.net.au/apgi/collaborators; Cancer Clinical Trials Unit, Royal Adelaide Hospital Cancer Centre, and Centre for Cancer Biology, SA Pathology; School of Medicine, University of Adelaide, Adelaide, Australia; and Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United KingdomAuthors' Affiliations: Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Herston; Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland; The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research; St Vincent's Clinical School, Faculty of Medicine, University of NSW; Department of Anatomical Pathology, SYDPATH, St Vincent's Hospital, Darlinghurst, New South Wales; Australian Pancreatic Cancer Genome Initiative, for the full list of contributors see http://www.pancreaticcancer.net.au/apgi/collaborators; Cancer Clinical Trials Unit, Royal Adelaide Hospital Cancer Centre, and Centre for Cancer Biology, SA Pathology; School of Medicine, University of Adelaide, Adelaide, Australia; and Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom.

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June 2014

Returning individual research results for genome sequences of pancreatic cancer.

Authors:
Amber L Johns David K Miller Skye H Simpson Anthony J Gill Karin S Kassahn Jeremy L Humphris Jaswinder S Samra Katherine Tucker Lesley Andrews David K Chang Nicola Waddell Marina Pajic John V Pearson Sean M Grimmond Andrew V Biankin Nikolajs Zeps

Genome Med 2014 29;6(5):42. Epub 2014 May 29.

St John of God Subiaco, Perth, WA, 6008, Australia ; School of Surgery, The University of Western Australia, Perth, WA, 6009, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4067993PMC
June 2014

Novel cancer drivers: mining the kinome.

Authors:
Andrew V Biankin Sean M Grimmond

Genome Med 2013 28;5(2):19. Epub 2013 Feb 28.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.

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May 2014

Clinical and molecular characterization of HER2 amplified-pancreatic cancer.

Authors:
Angela Chou Nicola Waddell Mark J Cowley Anthony J Gill David K Chang Ann-Marie Patch Katia Nones Jianmin Wu Mark Pinese Amber L Johns David K Miller Karin S Kassahn Adnan M Nagrial Harpreet Wasan David Goldstein Christopher W Toon Venessa Chin Lorraine Chantrill Jeremy Humphris R Scott Mead Ilse Rooman Jaswinder S Samra Marina Pajic Elizabeth A Musgrove John V Pearson Adrienne L Morey Sean M Grimmond Andrew V Biankin

Genome Med 2013 31;5(8):78. Epub 2013 Aug 31.

Kinghorn Cancer Centre and Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia ; Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK ; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK.

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May 2014

Can we move towards personalised pancreatic cancer therapy?

Authors:
Nigel Balfour Jamieson David K Chang Sean M Grimmond Andrew V Biankin

Expert Rev Gastroenterol Hepatol 2014 May 4;8(4):335-8. Epub 2014 Apr 4.

Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, UK.

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May 2014

Mining the genomes of exceptional responders.

Authors:
David K Chang Sean M Grimmond T R Jeffry Evans Andrew V Biankin

Nat Rev Cancer 2014 05;14(5):291-2

Wolfson Wohl Cancer Research Centre, Insitute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, UK; The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, 364 Victoria Street, Darlinghurst, Sydney, New South Wales 2010, Australia.

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May 2014

Interaction of c-Myb with p300 is required for the induction of acute myeloid leukemia (AML) by human AML oncogenes.

Authors:
Diwakar R Pattabiraman Crystal McGirr Konstantin Shakhbazov Valerie Barbier Keerthana Krishnan Pamela Mukhopadhyay Paula Hawthorne Ann Trezise Jianmin Ding Sean M Grimmond Peter Papathanasiou Warren S Alexander Andrew C Perkins Jean-Pierre Levesque Ingrid G Winkler Thomas J Gonda

Blood 2014 Apr 4;123(17):2682-90. Epub 2014 Mar 4.

Diamantina Institute.

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April 2014

Mutant p53 drives pancreatic cancer metastasis through cell-autonomous PDGF receptor β signaling.

Authors:
Susann Weissmueller Eusebio Manchado Michael Saborowski John P Morris Elvin Wagenblast Carrie A Davis Sung-Hwan Moon Neil T Pfister Darjus F Tschaharganeh Thomas Kitzing Daniela Aust Elke K Markert Jianmin Wu Sean M Grimmond Christian Pilarsky Carol Prives Andrew V Biankin Scott W Lowe

Cell 2014 Apr;157(2):382-394

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4001090PMC
April 2014

Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs.

Authors:
Hilary C Martin Shivangi Wani Anita L Steptoe Keerthana Krishnan Katia Nones Ehsan Nourbakhsh Alexander Vlassov Sean M Grimmond Nicole Cloonan

Genome Biol 2014 Mar 14;15(3):R51. Epub 2014 Mar 14.

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March 2014

In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale?

Authors:
Sebastiaan J van Hal Jason A Steen Björn A Espedido Sean M Grimmond Matthew A Cooper Matthew T G Holden Stephen D Bentley Iain B Gosbell Slade O Jensen

J Antimicrob Chemother 2014 Feb 18;69(2):363-7. Epub 2013 Sep 18.

Antibiotic Resistance & Mobile Elements Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886930PMC
February 2014

Pancreatic cancer genomics.

Authors:
David K Chang Sean M Grimmond Andrew V Biankin

Curr Opin Genet Dev 2014 Feb 28;24:74-81. Epub 2014 Jan 28.

Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland G4 0SF, United Kingdom; The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of NSW, Australia; Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, NSW 2200, Australia; South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, NSW 2170, Australia. Electronic address:

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February 2014

Minor class splicing shapes the zebrafish transcriptome during development.

Authors:
Sebastian Markmiller Nicole Cloonan Rea M Lardelli Karen Doggett Maria-Cristina Keightley Yeliz Boglev Andrew J Trotter Annie Y Ng Simon J Wilkins Heather Verkade Elke A Ober Holly A Field Sean M Grimmond Graham J Lieschke Didier Y R Stainier Joan K Heath

Proc Natl Acad Sci U S A 2014 Feb 10;111(8):3062-7. Epub 2014 Feb 10.

Ludwig Institute for Cancer Research, Melbourne-Parkville Branch, Parkville, VIC 3050, Australia.

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February 2014

Whole genome sequence analysis of the first Australian OXA-48-producing outbreak-associated Klebsiella pneumoniae isolates: the resistome and in vivo evolution.

Authors:
Björn A Espedido Jason A Steen Helen Ziochos Sean M Grimmond Matthew A Cooper Iain B Gosbell Sebastiaan J van Hal Slade O Jensen

PLoS One 2013 29;8(3):e59920. Epub 2013 Mar 29.

Antibiotic Resistance and Mobile Elements Group, School of Medicine, University of Western Sydney, New South Wales, Australia.

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January 2014

Identification of a novel de novo p.Phe932Ile KCNT1 mutation in a patient with leukoencephalopathy and severe epilepsy.

Authors:
Adeline Vanderver Cas Simons Johanna L Schmidt Philip L Pearl Miriam Bloom Bennett Lavenstein David Miller Sean M Grimmond Ryan J Taft

Pediatr Neurol 2014 Jan 10;50(1):112-4. Epub 2013 Oct 10.

Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia. Electronic address:

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January 2014

miR-139-5p is a regulator of metastatic pathways in breast cancer.

Authors:
Keerthana Krishnan Anita L Steptoe Hilary C Martin Diwakar R Pattabiraman Katia Nones Nic Waddell Mythily Mariasegaram Peter T Simpson Sunil R Lakhani Alexander Vlassov Sean M Grimmond Nicole Cloonan

RNA 2013 Dec 24;19(12):1767-80. Epub 2013 Oct 24.

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December 2013

Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline.

Authors:
Dhirendra Kumar Amit Kumar Yadav Puneet Kumar Kadimi Shivashankar H Nagaraj Sean M Grimmond Debasis Dash

Mol Cell Proteomics 2013 Nov 23;12(11):3388-97. Epub 2013 Jul 23.

G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India;

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November 2013

Understanding pancreatic cancer genomes.

Authors:
Mark J Cowley David K Chang Marina Pajic Amber L Johns Nicola Waddell Sean M Grimmond Andrew V Biankin

J Hepatobiliary Pancreat Sci 2013 Aug;20(6):549-56

The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, Australia; Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia.

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August 2013

Identification of unsafe human induced pluripotent stem cell lines using a robust surrogate assay for pluripotency.

Authors:
Juan Carlos Polanco Mirabelle S H Ho Bei Wang Qi Zhou Ernst Wolvetang Elizabeth Mason Christine A Wells Gabriel Kolle Sean M Grimmond Ivan Bertoncello Carmel O'Brien Andrew L Laslett

Stem Cells 2013 Aug;31(8):1498-510

CSIRO, Materials Science and Engineering, Clayton, Victoria, Australia; Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia.

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August 2013

Signatures of mutational processes in human cancer.

Authors:
Ludmil B Alexandrov Serena Nik-Zainal David C Wedge Samuel A J R Aparicio Sam Behjati Andrew V Biankin Graham R Bignell Niccolò Bolli Ake Borg Anne-Lise Børresen-Dale Sandrine Boyault Birgit Burkhardt Adam P Butler Carlos Caldas Helen R Davies Christine Desmedt Roland Eils Jórunn Erla Eyfjörd John A Foekens Mel Greaves Fumie Hosoda Barbara Hutter Tomislav Ilicic Sandrine Imbeaud Marcin Imielinski Marcin Imielinsk Natalie Jäger David T W Jones David Jones Stian Knappskog Marcel Kool Sunil R Lakhani Carlos López-Otín Sancha Martin Nikhil C Munshi Hiromi Nakamura Paul A Northcott Marina Pajic Elli Papaemmanuil Angelo Paradiso John V Pearson Xose S Puente Keiran Raine Manasa Ramakrishna Andrea L Richardson Julia Richter Philip Rosenstiel Matthias Schlesner Ton N Schumacher Paul N Span Jon W Teague Yasushi Totoki Andrew N J Tutt Rafael Valdés-Mas Marit M van Buuren Laura van 't Veer Anne Vincent-Salomon Nicola Waddell Lucy R Yates Jessica Zucman-Rossi P Andrew Futreal Ultan McDermott Peter Lichter Matthew Meyerson Sean M Grimmond Reiner Siebert Elías Campo Tatsuhiro Shibata Stefan M Pfister Peter J Campbell Michael R Stratton

Nature 2013 Aug 14;500(7463):415-21. Epub 2013 Aug 14.

Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

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August 2013

Neuropilin-2 promotes extravasation and metastasis by interacting with endothelial α5 integrin.

Authors:
Ying Cao Luke H Hoeppner Steven Bach Guangqi E Yan Guo Enfeng Wang Jianmin Wu Mark J Cowley David K Chang Nicola Waddell Sean M Grimmond Andrew V Biankin Roger J Daly Xiaohui Zhang Debabrata Mukhopadhyay

Cancer Res 2013 Jul 20;73(14):4579-4590. Epub 2013 May 20.

Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, MN 55905.

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July 2013

Caveolin-1 is necessary for hepatic oxidative lipid metabolism: evidence for crosstalk between caveolin-1 and bile acid signaling.

Authors:
Manuel A Fernández-Rojo Milena Gongora Rebecca L Fitzsimmons Nick Martel Sheree D Martin Susan J Nixon Andrew J Brooks Maria P Ikonomopoulou Sally Martin Harriet P Lo Stephen A Myers Christina Restall Charles Ferguson Paul F Pilch Sean L McGee Robin L Anderson Michael J Waters John F Hancock Sean M Grimmond George E O Muscat Robert G Parton

Cell Rep 2013 Jul 11;4(2):238-47. Epub 2013 Jul 11.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4067, Australia.

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July 2013

Characterization of an ntrX mutant of Neisseria gonorrhoeae reveals a response regulator that controls expression of respiratory enzymes in oxidase-positive proteobacteria.

Authors:
John M Atack Yogitha N Srikhanta Karrera Y Djoko Jessica P Welch Norain H M Hasri Christopher T Steichen Rachel N Vanden Hoven Sean M Grimmond Dk Seti Maimonah Pg Othman Ulrike Kappler Michael A Apicella Michael P Jennings Jennifer L Edwards Alastair G McEwan

J Bacteriol 2013 Jun 5;195(11):2632-41. Epub 2013 Apr 5.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.

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June 2013

MicroRNAs-140-5p/140-3p modulate Leydig cell numbers in the developing mouse testis.

Authors:
Joanna Rakoczy Selene L Fernandez-Valverde Evgeny A Glazov Elanor N Wainwright Tempei Sato Shuji Takada Alexander N Combes Darren J Korbie David Miller Sean M Grimmond Melissa H Little Hiroshi Asahara John S Mattick Ryan J Taft Dagmar Wilhelm

Biol Reprod 2013 Jun 6;88(6):143. Epub 2013 Jun 6.

Division of Molecular Genetics and Development, Institute for Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.

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June 2013

qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles.

Authors:
Sarah Song Katia Nones David Miller Ivon Harliwong Karin S Kassahn Mark Pinese Marina Pajic Anthony J Gill Amber L Johns Matthew Anderson Oliver Holmes Conrad Leonard Darrin Taylor Scott Wood Qinying Xu Felicity Newell Mark J Cowley Jianmin Wu Peter Wilson Lynn Fink Andrew V Biankin Nic Waddell Sean M Grimmond John V Pearson

PLoS One 2012 25;7(9):e45835. Epub 2012 Sep 25.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland, Australia.

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May 2013

A de novo mutation in the β-tubulin gene TUBB4A results in the leukoencephalopathy hypomyelination with atrophy of the basal ganglia and cerebellum.

Authors:
Cas Simons Nicole I Wolf Nathan McNeil Ljubica Caldovic Joseph M Devaney Asako Takanohashi Joanna Crawford Kelin Ru Sean M Grimmond David Miller Davide Tonduti Johanna L Schmidt Robert S Chudnow Rudy van Coster Lieven Lagae Jill Kisler Jürgen Sperner Marjo S van der Knaap Raphael Schiffmann Ryan J Taft Adeline Vanderver

Am J Hum Genet 2013 May 11;92(5):767-73. Epub 2013 Apr 11.

Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644625PMC
May 2013

Mutations in DARS cause hypomyelination with brain stem and spinal cord involvement and leg spasticity.

Authors:
Ryan J Taft Adeline Vanderver Richard J Leventer Stephen A Damiani Cas Simons Sean M Grimmond David Miller Johanna Schmidt Paul J Lockhart Kate Pope Kelin Ru Joanna Crawford Tena Rosser Irenaeus F M de Coo Monica Juneja Ishwar C Verma Prab Prabhakar Susan Blaser Julian Raiman Petra J W Pouwels Marianna R Bevova Truus E M Abbink Marjo S van der Knaap Nicole I Wolf

Am J Hum Genet 2013 May;92(5):774-80

Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072, Australia.

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May 2013

Integration-free induced pluripotent stem cells model genetic and neural developmental features of down syndrome etiology.

Authors:
James A Briggs Jane Sun Jill Shepherd Dmitry A Ovchinnikov Tung-Liang Chung Sam P Nayler Li-Pin Kao Carl A Morrow Nilay Y Thakar Set-Yen Soo Teija Peura Sean Grimmond Ernst J Wolvetang

Stem Cells 2013 Mar;31(3):467-78

Australian Institute for Bioengineering and Nanotechnology,The University of Queensland, St Lucia, Queensland, Australia.

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March 2013

MicroRNA-182-5p targets a network of genes involved in DNA repair.

Authors:
Keerthana Krishnan Anita L Steptoe Hilary C Martin Shivangi Wani Katia Nones Nic Waddell Mythily Mariasegaram Peter T Simpson Sunil R Lakhani Brian Gabrielli Alexander Vlassov Nicole Cloonan Sean M Grimmond

RNA 2013 Feb 18;19(2):230-42. Epub 2012 Dec 18.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543090PMC
February 2013

Identification of novel markers of mouse fetal ovary development.

Authors:
Huijun Chen James S Palmer Rathi D Thiagarajan Marcel E Dinger Emmanuelle Lesieur Hansheng Chiu Alexandra Schulz Cassy Spiller Sean M Grimmond Melissa H Little Peter Koopman Dagmar Wilhelm

PLoS One 2012 26;7(7):e41683. Epub 2012 Jul 26.

Division of Molecular Genetics and Development, Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia.

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November 2012

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

Authors:
Andrew V Biankin Nicola Waddell Karin S Kassahn Marie-Claude Gingras Lakshmi B Muthuswamy Amber L Johns David K Miller Peter J Wilson Ann-Marie Patch Jianmin Wu David K Chang Mark J Cowley Brooke B Gardiner Sarah Song Ivon Harliwong Senel Idrisoglu Craig Nourse Ehsan Nourbakhsh Suzanne Manning Shivangi Wani Milena Gongora Marina Pajic Christopher J Scarlett Anthony J Gill Andreia V Pinho Ilse Rooman Matthew Anderson Oliver Holmes Conrad Leonard Darrin Taylor Scott Wood Qinying Xu Katia Nones J Lynn Fink Angelika Christ Tim Bruxner Nicole Cloonan Gabriel Kolle Felicity Newell Mark Pinese R Scott Mead Jeremy L Humphris Warren Kaplan Marc D Jones Emily K Colvin Adnan M Nagrial Emily S Humphrey Angela Chou Venessa T Chin Lorraine A Chantrill Amanda Mawson Jaswinder S Samra James G Kench Jessica A Lovell Roger J Daly Neil D Merrett Christopher Toon Krishna Epari Nam Q Nguyen Andrew Barbour Nikolajs Zeps Nipun Kakkar Fengmei Zhao Yuan Qing Wu Min Wang Donna M Muzny William E Fisher F Charles Brunicardi Sally E Hodges Jeffrey G Reid Jennifer Drummond Kyle Chang Yi Han Lora R Lewis Huyen Dinh Christian J Buhay Timothy Beck Lee Timms Michelle Sam Kimberly Begley Andrew Brown Deepa Pai Ami Panchal Nicholas Buchner Richard De Borja Robert E Denroche Christina K Yung Stefano Serra Nicole Onetto Debabrata Mukhopadhyay Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Steven Gallinger Ralph H Hruban Anirban Maitra Christine A Iacobuzio-Donahue Richard D Schulick Christopher L Wolfgang Richard A Morgan Rita T Lawlor Paola Capelli Vincenzo Corbo Maria Scardoni Giampaolo Tortora Margaret A Tempero Karen M Mann Nancy A Jenkins Pedro A Perez-Mancera David J Adams David A Largaespada Lodewyk F A Wessels Alistair G Rust Lincoln D Stein David A Tuveson Neal G Copeland Elizabeth A Musgrove Aldo Scarpa James R Eshleman Thomas J Hudson Robert L Sutherland David A Wheeler John V Pearson John D McPherson Richard A Gibbs Sean M Grimmond

Nature 2012 Nov 24;491(7424):399-405. Epub 2012 Oct 24.

The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, Sydney, New South Wales 2010, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530898PMC
November 2012

Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites.

Authors:
Martin Hemberg Jesse M Gray Nicole Cloonan Scott Kuersten Sean Grimmond Michael E Greenberg Gabriel Kreiman

Nucleic Acids Res 2012 Sep 8;40(16):7858-69. Epub 2012 Jun 8.

Department of Ophthalmology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gks477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439890PMC
September 2012

RON is not a prognostic marker for resectable pancreatic cancer.

Authors:
Carole M Tactacan David K Chang Mark J Cowley Emily S Humphrey Jianmin Wu Anthony J Gill Angela Chou Katia Nones Sean M Grimmond Robert L Sutherland Andrew V Biankin Roger J Daly

BMC Cancer 2012 Sep 7;12:395. Epub 2012 Sep 7.

Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532183PMC
September 2012

Phasevarion mediated epigenetic gene regulation in Helicobacter pylori.

Authors:
Yogitha N Srikhanta Rebecca J Gorrell Jason A Steen Jayde A Gawthorne Terry Kwok Sean M Grimmond Roy M Robins-Browne Michael P Jennings

PLoS One 2011 5;6(12):e27569. Epub 2011 Dec 5.

Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia.

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July 2012

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney.

Authors:
Jing Yu M Todd Valerius Mary Duah Karl Staser Jennifer K Hansard Jin-Jin Guo Jill McMahon Joe Vaughan Diane Faria Kylie Georgas Bree Rumballe Qun Ren A Michaela Krautzberger Jan P Junker Rathi D Thiagarajan Philip Machanick Paul A Gray Alexander van Oudenaarden David H Rowitch Charles D Stiles Qiufu Ma Sean M Grimmond Timothy L Bailey Melissa H Little Andrew P McMahon

Development 2012 May;139(10):1863-73

Department of Stem Cell and Regenerative Biology, Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1242/dev.074005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328182PMC
May 2012

Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma.

Authors:
Karen M Mann Jerrold M Ward Christopher Chin Kuan Yew Anne Kovochich David W Dawson Michael A Black Benjamin T Brett Todd E Sheetz Adam J Dupuy David K Chang Andrew V Biankin Nicola Waddell Karin S Kassahn Sean M Grimmond Alistair G Rust David J Adams Nancy A Jenkins Neal G Copeland

Proc Natl Acad Sci U S A 2012 Apr 15;109(16):5934-41. Epub 2012 Mar 15.

Division of Genetics and Genomics, Institute of Molecular and Cell Biology, Singapore 138673.

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http://dx.doi.org/10.1073/pnas.1202490109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3341075PMC
April 2012

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.

Authors:
Kate Schroder Katharine M Irvine Martin S Taylor Nilesh J Bokil Kim-Anh Le Cao Kelly-Anne Masterman Larisa I Labzin Colin A Semple Ronan Kapetanovic Lynsey Fairbairn Altuna Akalin Geoffrey J Faulkner John Kenneth Baillie Milena Gongora Carsten O Daub Hideya Kawaji Geoffrey J McLachlan Nick Goldman Sean M Grimmond Piero Carninci Harukazu Suzuki Yoshihide Hayashizaki Boris Lenhard David A Hume Matthew J Sweet

Proc Natl Acad Sci U S A 2012 Apr 26;109(16):E944-53. Epub 2012 Mar 26.

Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia.

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http://dx.doi.org/10.1073/pnas.1110156109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3341041PMC
April 2012

The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma.

Authors:
Pedro A Pérez-Mancera Alistair G Rust Louise van der Weyden Glen Kristiansen Allen Li Aaron L Sarver Kevin A T Silverstein Robert Grützmann Daniela Aust Petra Rümmele Thomas Knösel Colin Herd Derek L Stemple Ross Kettleborough Jacqueline A Brosnan Ang Li Richard Morgan Spencer Knight Jun Yu Shane Stegeman Lara S Collier Jelle J ten Hoeve Jeroen de Ridder Alison P Klein Michael Goggins Ralph H Hruban David K Chang Andrew V Biankin Sean M Grimmond Lodewyk F A Wessels Stephen A Wood Christine A Iacobuzio-Donahue Christian Pilarsky David A Largaespada David J Adams David A Tuveson

Nature 2012 Apr 29;486(7402):266-70. Epub 2012 Apr 29.

Li Ka Shing Centre, Cambridge Research Institute, Cancer Research UK, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1038/nature11114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376394PMC
April 2012

PINA v2.0: mining interactome modules.

Authors:
Mark J Cowley Mark Pinese Karin S Kassahn Nic Waddell John V Pearson Sean M Grimmond Andrew V Biankin Sampsa Hautaniemi Jianmin Wu

Nucleic Acids Res 2012 Jan 8;40(Database issue):D862-5. Epub 2011 Nov 8.

Cancer Research Program, Peter Wills Bioinformatics Centre, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244997PMC
January 2012

Comprehensive transcriptome and immunophenotype analysis of renal and cardiac MSC-like populations supports strong congruence with bone marrow MSC despite maintenance of distinct identities.

Authors:
Rebecca A Pelekanos Joan Li Milena Gongora Vashe Chandrakanthan Janelle Scown Norseha Suhaimi Gary Brooke Melinda E Christensen Tram Doan Alison M Rice Geoffrey W Osborne Sean M Grimmond Richard P Harvey Kerry Atkinson Melissa H Little

Stem Cell Res 2012 Jan 17;8(1):58-73. Epub 2011 Aug 17.

Australian Stem Cell Centre, Monash University, Clayton, Victoria, Australia.

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http://dx.doi.org/10.1016/j.scr.2011.08.003DOI Listing
January 2012

Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells.

Authors:
Gabriel Kolle Jill L Shepherd Brooke Gardiner Karin S Kassahn Nicole Cloonan David L A Wood Ehsan Nourbakhsh Darrin F Taylor Shivangi Wani Hun S Chy Qi Zhou Kevin McKernan Scott Kuersten Andrew L Laslett Sean M Grimmond

Genome Res 2011 Dec 31;21(12):2014-25. Epub 2011 Oct 31.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Queensland 4072, Australia.

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http://genome.cshlp.org/content/early/2011/10/31/gr.119321.1
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http://genome.cshlp.org/cgi/doi/10.1101/gr.119321.110
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http://dx.doi.org/10.1101/gr.119321.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227092PMC
December 2011

MicroRNAs and their isomiRs function cooperatively to target common biological pathways.

Authors:
Nicole Cloonan Shivangi Wani Qinying Xu Jian Gu Kristi Lea Sheila Heater Catalin Barbacioru Anita L Steptoe Hilary C Martin Ehsan Nourbakhsh Keerthana Krishnan Brooke Gardiner Xiaohui Wang Katia Nones Jason A Steen Nicholas A Matigian David L Wood Karin S Kassahn Nic Waddell Jill Shepherd Clarence Lee Jeff Ichikawa Kevin McKernan Kelli Bramlett Scott Kuersten Sean M Grimmond

Genome Biol 2011 Dec 30;12(12):R126. Epub 2011 Dec 30.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia.

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http://dx.doi.org/10.1186/gb-2011-12-12-r126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334621PMC
December 2011

A high-throughput platform for lentiviral overexpression screening of the human ORFeome.

Authors:
Dubravka Škalamera Max V Ranall Benjamin M Wilson Paul Leo Amy S Purdon Carolyn Hyde Ehsan Nourbakhsh Sean M Grimmond Simon C Barry Brian Gabrielli Thomas J Gonda

PLoS One 2011 24;6(5):e20057. Epub 2011 May 24.

University of Queensland Diamantina Institute, Princess Alexandra Hospital, Brisbane, Queensland, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020057PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101218PMC
September 2011

Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling.

Authors:
Rathi D Thiagarajan Nicole Cloonan Brooke B Gardiner Tim R Mercer Gabriel Kolle Ehsan Nourbakhsh Shivangi Wani Dave Tang Keerthana Krishnan Kylie M Georgas Bree A Rumballe Han S Chiu Jason A Steen John S Mattick Melissa H Little Sean M Grimmond

BMC Genomics 2011 Sep 5;12:441. Epub 2011 Sep 5.

Institute for Molecular Bioscience, The University of Queensland, St, Lucia QLD 4072, Australia.

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http://dx.doi.org/10.1186/1471-2164-12-441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180702PMC
September 2011

Sequencing transcriptomes in toto.

Authors:
Karin S Kassahn Nic Waddell Sean M Grimmond

Integr Biol (Camb) 2011 May 4;3(5):522-8. Epub 2011 Feb 4.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, Brisbane, Australia.

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http://dx.doi.org/10.1039/c0ib00062kDOI Listing
May 2011

X-MATE: a flexible system for mapping short read data.

Authors:
David L A Wood Qinying Xu John V Pearson Nicole Cloonan Sean M Grimmond

Bioinformatics 2011 Feb 6;27(4):580-1. Epub 2011 Jan 6.

The University of Queensland, Queensland, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btq698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035802PMC
February 2011

Identification of anchor genes during kidney development defines ontological relationships, molecular subcompartments and regulatory pathways.

Authors:
Rathi D Thiagarajan Kylie M Georgas Bree A Rumballe Emmanuelle Lesieur Han Sheng Chiu Darrin Taylor Dave T P Tang Sean M Grimmond Melissa H Little

PLoS One 2011 Feb 28;6(2):e17286. Epub 2011 Feb 28.

Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017286PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046260PMC
February 2011