Jason Li

Combined Tumor Sequencing and Case-Control Analyses of RAD51C in Breast Cancer.

Na Li, Simone McInerny, Magnus Zethoven, Dane Cheasley, Belle WX Lim, Simone M Rowley, Lisa Devereux, Norah Grewal, Somayeh Ahmadloo, David Byrne, Jue Er Amanda Lee, Jason Li, Stephen B Fox, Thomas John, Yoland Antill, Kylie L Gorringe, Paul A James, Ian G Campbell

Journal article  |  2019  |  JNCI: Journal of the National Cancer Institute

BACKGROUND: Loss-of-function variants in RAD51C are associated with familial ovarian cancer, but its role in hereditary breast can..

The molecular origin and taxonomy of mucinous ovarian carcinoma

Dane Cheasley, Matthew J Wakefield, Georgina L Ryland, Prue E Allan, Kathryn Alsop, Kaushalya C Amarasinghe, Sumitra Ananda, Michael S Anglesio, George Au-Yeung, Maret Bohm, David Dl Bowtell, Alison Brand, Georgia Chenevix-Trench, Michael Christie, Yoke-Eng Chiew, Michael Churchman, Anna DeFazio, Renee Demeo, Rhiannon Dudley, Nicole Fairweather, et al.

Journal article  |  2019  |  Nature Communications

Survival Following Chemotherapy in Ovarian Clear Cell Carcinoma Is Not Associated with Pathological Misclassification of Tumor Histotype

Masataka Takenaka, Martin Kobel, Dale W Garsed, Sian Fereday, Ahwan Pandey, Dariush Etemadmoghadam, Joy Hendley, Ayako Kawabata, Daito Noguchi, Nozomu Yanaihara, Hiroyuki Takahashi, Takako Kiyokawa, Masahiro Ikegami, Hirokuni Takano, Seiji Isonishi, Kazuhiko Ochiai, Nadia Traficante, Sreeja Gadipally, Timothy Semple, Dane Vassiliadis, et al.

Journal article  |  2019  |  Clinical Cancer Research

Prediction and monitoring of relapse in stage III melanoma using circulating tumor DNA

L Tan, S Sandhu, RJ Lee, J Li, J Callahan, S Ftouni, N Dhomen, P Middlehurst, A Wallace, J Raleigh, A Hatzimihalis, MA Henderson, M Shackleton, A Haydon, V Mar, DE Gyorki, D Oudit, MA Dawson, RJ Hicks, P Lorigan, et al.

Journal article  |  2019  |  Annals of Oncology

BACKGROUND: The advent of effective adjuvant therapies for patients with resected melanoma has highlighted the need to stratify pa..

CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing

John F Markham, Satwica Yerneni, Georgina L Ryland, Huei San Leong, Andrew Fellowes, Ella R Thompson, Wasanthi De Silva, Amit Kumar, Richard Lupat, Jason Li, Jason Ellul, Stephen Fox, Michael Dickinson, Anthony T Papenfuss, Piers Blombery

Journal article  |  2019  |  Scientific Reports

Next Generation Sequencing is now routinely used in the practice of diagnostic pathology to detect clinically relevant somatic and..

Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis

Madison J Kelly, Joan So, Amy J Rogers, Gareth Gregory, Jason Li, Magnus Zethoven, Micah D Gearhart, Vivian J Bardwell, Ricky W Johnstone, Stephin J Vervoort, Lev M Kats

Journal article  |  2019  |  Nature Communications

Dynamic molecular monitoring reveals that SWI-SNF mutations mediate resistance to ibrutinib plus venetoclax in mantle cell lymphoma

Rishu Agarwal, Yih-Chih Chan, Constantine S Tam, Tane Hunter, Dane Vassiliadis, Charis E Teh, Rachel Thijssen, Paul Yeh, Stephen Q Wong, Sarah Ftouni, Enid YN Lam, Mary Ann Anderson, Christiane Pott, Omer Gilan, Charles C Bell, Kathy Knezevic, Piers Blombery, Kathleen Rayeroux, Adrian Zordan, Jason Li, et al.

Journal article  |  2019  |  Nature Medicine

Mutations in RECQL are not associated with breast cancer risk in an Australian population

Na Li, Simone M Rowley, David L Goode, Kaushalya C Amarasinghe, Simone McInerny, Lisa Devereux, Michelle W Wong-Brown, Richard Lupat, Jue Er Amanda Lee, Siobhan Hughes, Ella R Thompson, Magnus Zethoven, Jason Li, Alison H Trainer, Kylie L Gorringe, Rodney J Scott, Paul A James, Ian G Campbell

Journal article  |  2018  |  Nature Genetics

Circulating tumour DNA analysis predicts relapse following resection in stage II and III melanoma

L Tan, SK Sandhu, R Lee, J Li, J Callahan, J Raleigh, A Hatzimihalis, P Middlehurst, M Henderson, M Shackleton, A Haydon, D Gyorki, D Oudit, RJ Hicks, P Lorigan, GA McArthur, R Marais, SQ Wong, S-J Dawson

Conference Proceedings  |  2018  |  ANNALS OF ONCOLOGY

Intraductal carcinoma of the prostate can evade androgen deprivation, with emergence of castrate-tolerant cells

Laura H Porter, Kohei Hashimoto, Mitchell G Lawrence, Carmel Pezaro, David Clouston, Hong Wang, Melissa Papargiris, Heather Thorne, Jason Li, Andrew Ryan, Sam Norden, Daniel Moon, Damien M Bolton, Shomik Sengupta, Mark Frydenberg, Declan G Murphy, Gail P Risbridger, Renea A Taylor

Journal article  |  2018  |  BJU International

Identification of Pik3ca Mutation as a Genetic Driver of Prostate Cancer That Cooperates with Pten Loss to Accelerate Progression and Castration-Resistant Growth

Helen B Pearson, Jason Li, Valerie S Meniel, Christina M Fennell, Paul Waring, Karen G Montgomery, Richard J Rebello, Arthi A Macpherson, Sarah Koushyar, Luc Furic, Carleen Cullinane, Richard W Clarkson, Matthew J Smalley, Kaylene J Simpson, Toby J Phesse, Peter R Shepherd, Patrick O Humbert, Owen J Sansom, Wayne A Phillips

Journal article  |  2018  |  Cancer Discovery

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

Dale W Garsed, Kathryn Alsop, Sian Fereday, Catherine Emmanuel, Catherine J Kennedy, Dariush Etemadmoghadam, Bo Gao, Val Gebski, Valerie Gares, Elizabeth L Christie, Maartje CA Wouters, Katy Milne, Joshy George, Ann-Marie Patch, Jason Li, Gisela Mir Arnau, Timothy Semple, Sreeja R Gadipally, Yoke-Eng Chiew, Joy Hendley, et al.

Journal article  |  2018  |  Clinical Cancer Research

Evaluating the breast cancer predisposition role of rare variants in genes associated with low-penetrance breast cancer risk SNPs

Na Li, Simone M Rowley, Ella R Thompson, Simone McInerny, Lisa Devereux, Kaushalya C Amarasinghe, Magnus Zethoven, Richard Lupat, David Goode, Jason Li, Alison H Trainer, Kylie L Gorringe, Paul A James, Ian G Campbell

Journal article  |  2018  |  Breast Cancer Research

TERT structural rearrangements in metastatic pheochromocytomas

Trisha Dwight, Aidan Flynn, Kaushalya Amarasinghe, Diana E Benn, Richard Lupat, Jason Li, Daniel L Cameron, Annette Hogg, Shiva Balachander, Ida LM Candiloro, Stephen Q Wong, Bruce G Robinson, Anthony T Papenfuss, Anthony J Gill, Alexander Dobrovic, Rodney J Hicks, Roderick J Clifton-Bligh, Richard W Tothill

Journal article  |  2018  |  Endocrine-Related Cancer

Genome-wide functional analysis reveals central signaling regulators of lymphatic endothelial cell migration and remodeling

Steven P Williams, Adam F Odell, Tara Karnezis, Rae H Farnsworth, Cathryn M Gould, Jason Li, Sophie Paquet-Fifield, Nicole C Harris, Anne Walter, Julia L Gregory, Sara F Lamont, Ruofei Liu, Elena A Takano, Cameron J Nowell, Neil I Bower, Daniel Resnick, Gordon K Smyth, Leigh Coultas, Benjamin M Hogan, Stephen B Fox, et al.

Journal article  |  2017  |  Science Signaling

EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas

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, et al.

Journal article  |  2017  |  Cancer Research

A pharmacogenomic approach validates AG-221 as an effective and on-target therapy in IDH2 mutant AML

LM Kats, SJ Vervoort, R Cole, AJ Rogers, GP Gregory, E Vidacs, J Li, R Nagaraja, KE Yen, RW Johnstone

Journal article  |  2017  |  Leukemia

HDAC Inhibitor Panobinostat Engages Host Innate Immune Defenses to Promote the Tumoricidal Effects of Trastuzumab in HER2( ) Tumors

Mikolaj Medon, Eva Vidacs, Stephin J Vervoort, Jason Li, Misty R Jenkins, Kelly M Ramsbottom, Joseph A Trapani, Mark J Smyth, Phillip K Darcy, Peter W Atadja, Michael A Henderson, Ricky W Johnstone, Nicole M Haynes

Journal article  |  2017  |  Cancer Research

PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories

Kenneth D Doig, Andrew Fellowes, Anthony H Bell, Andrei Seleznev, David Ma, Jason Ellul, Jason Li, Maria A Doyle, Ella R Thompson, Amit Kumar, Luis Lara, Ravikiran Vedururu, Gareth Reid, Thomas Conway, Anthony T Papenfuss, Stephen B Fox

Journal article  |  2017  |  Genome Medicine

Genomic characterisation of E mu-Myc mouse lymphomas identifies Bcor as a Myc co-operative tumour-suppressor gene

Marcus Lefebure, Richard W Tothill, Elizabeth Kruse, Edwin D Hawkins, Jake Shortt, Geoffrey M Matthews, Gareth P Gregory, Benjamin P Martin, Madison J Kelly, Izabela Todorovski, Maria A Doyle, Richard Lupat, Jason Li, Jan Schroeder, Meaghan Wall, Stuart Craig, Gretchen Poortinga, Don Cameron, Megan Bywater, Lev Kats, et al.

Journal article  |  2017  |  Nature Communications

BET-Bromodomain Inhibitors Engage the Host Immune System and Regulate Expression of the Immune Checkpoint Ligand PD-L1

Simon J Hogg, Stephin J Vervoort, Sumit Deswal, Christopher J Ott, Jason Li, Leonie A Cluse, Paul A Beavis, Phillip K Darcy, Benjamin P Martin, Andrew Spencer, Anna K Traunbauer, Irina Sadovnik, Karin Bauer, Peter Valent, James E Bradner, Johannes Zuber, Jake Shortt, Ricky W Johnstone

Journal article  |  2017  |  Cell Reports

Circulating Tumor DNA Analysis and Functional Imaging Provide Complementary Approaches for Comprehensive Disease Monitoring in Metastatic Melanoma

Stephen Q Wong, Jeanette M Raleigh, Jason Callahan, Ismael A Vergara, Sarah Ftouni, Athena Hatzimihalis, Andrew J Colebatch, Jason Li, Timothy Semple, Kenneth Doig, Christopher Mintoff, Devbarna Sinha, Paul Yeh, Maria Joao Silva, Kathryn Alsop, Heather Thorne, David D Bowtell, David E Gyorki, Gisela Mir Arnau, Carleen Cullinane, et al.

Journal article  |  2017  |  JCO Precision Oncology

PREOPERATIVE SERUM microRNA PROFILING AS A DIAGNOSTIC TOOL IN GLIOMA

Andrew Morokoff, Iwan Bennett, Lucy Paradiso, Rod Luwor, Michael Wong, Rachel Koldej, Jason Li, Chenkai Ma, Kate Drummond, Stanley Stylli, Andrew Kaye, Tali Siegal

Conference Proceedings  |  2016  |  NEURO-ONCOLOGY

Whole exome sequencing reveals activating JAK1 and STAT3 mutations in breast implant-associated anaplastic large cell lymphoma anaplastic large cell lymphoma

Piers Blombery, Ella R Thompson, Kate Jones, Gisela Mir Arnau, Stephen Lade, John F Markham, Jason Li, Anand Deva, Ricky W Johnstone, Amit Khot, H Miles Prince, David Westerman

Journal article  |  2016  |  Haematologica

Id2 and E Proteins Orchestrate the Initiation and Maintenance of MLL-Rearranged Acute Myeloid Leukemia

Margherita Ghisi, Lev Kats, Frederick Masson, Jason Li, Tobias Kratina, Eva Vidacs, Omer Gilan, Maria A Doyle, Andrea Newbold, Jessica E Bolden, Kirsten A Fairfax, Carolyn A de Graaf, Matthew Firth, Johannes Zuber, Ross A Dickins, Lynn M Corcoran, Mark A Dawson, Gabrielle T Belz, Ricky W Johnstone

Journal article  |  2016  |  Cancer Cell

Long term, continuous exposure to panobinostat induces terminal differentiation and long term survival in the TH-MYCN neuroblastoma mouse model

Kelly Waldeck, Carleen Cullinane, Kerry Ardley, Jake Shortt, Ben Martin, Richard W Tothill, Jason Li, Ricky W Johnstone, Grant A McArthur, Rodney J Hicks, Paul J Wood

Journal article  |  2016  |  Int J Cancer

Pericytes Promote Malignant Ovarian Cancer Progression in Mice and Predict Poor Prognosis in Serous Ovarian Cancer Patients

Devbarna Sinha, Lynn Chong, Joshy George, Holger Schlueter, Susann Moenchgesang, Stuart Mills, Jason Li, Christopher Parish, David Bowtell, Pritinder Kaur

Journal article  |  2016  |  Clin Cancer Res

Searching for candidate genes in familial BRCAX mutation carriers with prostate cancer

Sally M Hunter, Simone M Rowley, David Clouston, Jason Li, Richard Lupat, Nishanth Krishnananthan, Gail Risbridger, Renea Taylor, Damien Bolton, Ian G Campbell, Heather Thorne

Journal article  |  2016  |  Urol Oncol

UV-Associated Mutations Underlie the Etiology of MCV-Negative Merkel Cell Carcinomas

Stephen Q Wong, Kelly Waldeck, Ismael A Vergara, Jan Schroeder, Jason Madore, James S Wilmott, Andrew J Colebatch, Ricardo De Paoli-Iseppi, Jason Li, Richard Lupat, Timothy Semple, Gisela Mir Arnau, Andrew Fellowes, J Helen Leonard, George Hruby, Graham J Mann, John F Thompson, Carleen Cullinane, Meredith Johnston, Mark Shackleton, et al.

Journal article  |  2015  |  Cancer Res

Molecular profiling of low grade serous ovarian tumours identifies novel candidate driver genes

Sally M Hunter, Michael S Anglesio, Georgina L Ryland, Raghwa Sharma, Yoke-Eng Chiew, Simone M Rowley, Maria A Doyle, Jason Li, C Blake Gilks, Phillip Moss, Prue E Allan, Andrew N Stephens, David G Huntsman, Anna deFazio, David D Bowtell, Kylie L Gorringe, Ian G Campbell

Journal article  |  2015  |  Oncotarget

Reevaluation of the BRCA2 truncating allele c.9976A > T (p.Lys3326Ter) in a familial breast cancer context

Ella R Thompson, Kylie L Gorringe, Simone M Rowley, Na Li, Simone McInerny, Michelle W Wong-Brown, Lisa Devereux, Jason Li, Alison H Trainer, Gillian Mitchell, Rodney J Scott, Paul A James, Ian G Campbell

Journal article  |  2015  |  Sci Rep

Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour

Katie T Huang, Thomas Mikeska, Jason Li, Elena A Takano, Ewan KA Millar, Peter H Graham, Samantha E Boyle, Ian G Campbell, Terence P Speed, Alexander Dobrovic, Stephen B Fox

Journal article  |  2015  |  BMC Cancer

Prevalence of PALB2 mutations in Australian familial breast cancer cases and controls

Ella R Thompson, Kylie L Gorringe, Simone M Rowley, Michelle W Wong-Brown, Simone McInerny, Na Li, Alison H Trainer, Lisa Devereux, Maria A Doyle, Jason Li, Richard Lupat, Martin B Delatycki, Gillian Mitchell, Paul A James, Rodney J Scott, Ian G Campbell

Journal article  |  2015  |  Breast Cancer Res

Cooperation of the BTB-Zinc finger protein, Abrupt, with cytoskeletal regulators in Drosophila epithelial tumorigenesis

Nezaket Turkel, Marta Portela, Carole Poon, Jason Li, Anthony M Brumby, Helena E Richardson

Journal article  |  2015  |  Biology Open

Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors

Georgina L Ryland, Sally M Hunter, Maria A Doyle, Franco Caramia, Jason Li, Simone M Rowley, Michael Christie, Prue E Allan, Andrew N Stephens, David DL Bowtell, Ian G Campbell, Kylie L Gorringe

Journal article  |  2015  |  Genome Med

Loss of heterozygosity: what is it good for?

Georgina L Ryland, Maria A Doyle, David Goode, Samantha E Boyle, David YH Choong, Simone M Rowley, Jason Li, David DL Bowtell, Richard W Tothill, Ian G Campbell, Kylie L Gorringe

Journal article  |  2015  |  BMC Med Genomics

Altered significance of D'Amico risk classification in patients with prostate cancer linked to a familial breast cancer (kConFab) cohort

Damien Bolton, Yuan Cheng, Amber J Willems-Jones, Jason Li, Eveline Niedermeyr, Gillian Mitchell, David Clouston, Nathan Lawrentschuk, Ania Sliwinski, Stephen Fox, Heather Thorne

Journal article  |  2015  |  BJU Int

The genomic landscape of phaeochromocytoma

Aidan Flynn, Diana Benn, Roderick Clifton-Bligh, Bruce Robinson, Alison H Trainer, Paul James, Annette Hogg, Kelly Waldeck, Joshy George, Jason Li, Stephen B Fox, Anthony J Gill, Grant McArthur, Rodney J Hicks, Richard W Tothill

Journal article  |  2015  |  J Pathol

Patient-derived Xenografts Reveal that Intraductal Carcinoma of the Prostate Is a Prominent Pathology in BRCA2 Mutation Carriers with Prostate Cancer and Correlates with Poor Prognosis

Gail P Risbridger, Renea A Taylor, David Clouston, Ania Sliwinski, Heather Thorne, Sally Hunter, Jason Li, Gillian Mitchell, Declan Murphy, Mark Frydenberg, David Pook, John Pedersen, Roxanne Toivanen, Hong Wang, Melissa Papargiris, Mitchell G Lawrence, Damien M Bolton

Journal article  |  2015  |  Eur Urol

Functional and molecular characterisation of EO771.LMB tumours, a new C57BL/6-mouse-derived model of spontaneously metastatic mammary cancer

Cameron N Johnstone, Yvonne E Smith, Yuan Cao, Allan D Burrows, Ryan SN Cross, Xiawei Ling, Richard P Redvers, Judy P Doherty, Bedrich L Eckhardt, Anthony L Natoli, Christina M Restall, Erin Lucas, Helen B Pearson, Siddhartha Deb, Kara L Britt, Alexandra Rizzitelli, Jason Li, Judith H Harmey, Normand Pouliot, Robin L Anderson

Journal article  |  2015  |  Dis Model Mech

Whole exome sequencing identifies a recurrent RQCD1 P131L mutation in cutaneous melanoma

Stephen Q Wong, Andreas Behren, Victoria J Mar, Katherine Woods, Jason Li, Claire Martin, Karen E Sheppard, Rory Wolfe, John Kelly, Jonathan Cebon, Alexander Dobrovic, Grant A McArthur

Journal article  |  2015  |  Oncotarget

Mutational profiling of familial male breast cancers reveals similarities with luminal A female breast cancer with rare TP53 mutations

S Deb, SQ Wong, J Li, H Do, J Weiss, D Byrne, A Chakrabarti, T Bosma, A Fellowes, A Dobrovic, SB Fox

Journal article  |  2014  |  Br J Cancer

The Architecture and Evolution of Cancer Neochromosomes

Dale W Garsed, Owen J Marshall, Vincent DA Corbin, Arthur Hsu, Leon Di Stefano, Jan Schroeder, Jason Li, Zhi-Ping Feng, Bo W Kim, Mark Kowarsky, Ben Lansdell, Ross Brookwell, Ola Myklebost, Leonardo Meza-Zepeda, Andrew J Holloway, Florence Pedeutour, KH Andy Choo, Michael A Damore, Andrew J Deans, Anthony T Papenfuss, et al.

Journal article  |  2014  |  Cancer Cell

Foxp3 Expression in Macrophages Associated with RENCA Tumors in Mice

Christel Devaud, Carmen SM Yong, Liza B John, Jennifer A Westwood, Connie PM Duong, Colin M House, Delphine Denoyer, Jason Li, Phillip K Darcy, Michael H Kershaw

Journal article  |  2014  |  PLoS ONE

Inferring copy number and genotype in tumour exome data

Kaushalya C Amarasinghe, Jason Li, Sally M Hunter, Georgina L Ryland, Prue A Cowin, Ian G Campbell, Saman K Halgamuge

Journal article  |  2014  |  BMC Genomics

Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing

Stephen Q Wong, Jason Li, Angela Y-C Tan, Ravikiran Vedururu, Jia-Min B Pang, Hongdo Do, Jason Ellul, Ken Doig, Anthony Bell, Grant A McArthur, Stephen B Fox, David M Thomas, Andrew Fellowes, John P Parisot, Alexander Dobrovic

Journal article  |  2014  |  BMC Medical Genomics

Identification of a radiation sensitivity gene expression profile in primary fibroblasts derived from patients who developed radiotherapy-induced fibrosis

Helen B Forrester, Jason Li, Trevor Leong, Michael J Mckay, Carl N Sprung

Journal article  |  2014  |  Radiotherapy and Oncology

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment

Jason Li, Maria A Doyle, Isaam Saeed, Stephen Q Wong, Victoria Mar, David L Goode, Franco Caramia, Ken Doig, Georgina L Ryland, Ella R Thompson, Sally M Hunter, Saman K Halgamuge, Jason Ellul, Alexander Dobrovic, Ian G Campbell, Anthony T Papenfuss, Grant A McArthur, Richard W Tothill

Journal article  |  2014  |  PLoS One

Response of BRAF-Mutant Melanoma to BRAF Inhibition Is Mediated by a Network of Transcriptional Regulators of Glycolysis

Tiffany J Parmenter, Margarete Kleinschmidt, Kathryn M Kinross, Simon T Bond, Jason Li, Mohan R Kaadige, Aparna Rao, Karen E Sheppard, Willy Hugo, Gulietta M Pupo, Richard B Pearson, Sean L Mcgee, Georgina V Long, Richard A Scolyer, Helen Rizos, Roger S Lo, Carleen Cullinane, Donald E Ayer, Antoni Ribas, Ricky W Johnstone, et al.

Journal article  |  2014  |  Cancer Discov

RAD21 cohesin overexpression is a prognostic and predictive marker exacerbating poor prognosis in KRAS mutant colorectal carcinomas

S Deb, H Xu, J Tuynman, J George, Y Yan, J Li, RL Ward, N Mortensen, NJ Hawkins, MJ McKay, RG Ramsay, SB Fox

Journal article  |  2014  |  British Journal of Cancer

Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data

Ingrid M Loennstedt, Franco Caramia, Jason Li, Debora Fumagalli, Roberto Salgado, Andrew Rowan, Max Salm, Nnennaya Kanu, Peter Savas, Stuart Horswell, Stephan Gade, Sibylle Loibl, Patrick Neven, Christos Sotiriou, Charles Swanton, Sherene Loi, Terence P Speed

Journal article  |  2014  |  Genome Biol

Studying Cancer Genomics Through Next-Generation DNA Sequencing and Bioinformatics

Maria A Doyle, Jason Li, Ken Doig, Andrew Fellowes, Stephen Q Wong

Journal article  |  2014  |  Methods Mol Biol

Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours

Stephen Q Wong, Jason Li, Renato Salemi, Karen E Sheppard, Hongdo Do, Richard W Tothill, Grant A McArthur, Alexander Dobrovic

Journal article  |  2013  |  Scientific Reports

Massively-parallel sequencing assists the diagnosis and guided treatment of cancers of unknown primary

Richard W Tothill, Jason Li, Linda Mileshkin, Ken Doig, Terence Siganakis, Prue Cowin, Andrew Fellowes, Timothy Semple, Stephen Fox, Keith Byron, Adam Kowalczyk, David Thomas, Penelope Schofield, David D Bowtell

Journal article  |  2013  |  Journal of Pathology

Next-Generation Sequence Analysis of Cancer Xenograft Models

Fernando J Rossello, Richard W Tothill, Kara Britt, Kieren D Marini, Jeanette Falzon, David M Thomas, Craig D Peacock, Luigi Marchionni, Jason Li, Samara Bennett, Erwin Tantoso, Tracey Brown, Philip Chan, Luciano G Martelotto, D Neil Watkins

Journal article  |  2013  |  PLoS One

Reducing Sequence Artifacts in Amplicon-Based Massively Parallel Sequencing of Formalin-Fixed Paraffin-Embedded DNA by Enzymatic Depletion of Uracil-Containing Templates

Hongdo Do, Stephen Q Wong, Jason Li, Alexander Dobrovic

Journal article  |  2013  |  Clinical Chemistry: international journal of molecular diagnostics and laboratory medicine

BRAF/NRAS Wild-Type Melanomas Have a High Mutation Load Correlating with Histologic and Molecular Signatures of UV Damage

Victoria J Mar, Stephen Q Wong, Jason Li, Richard A Scolyer, Catriona McLean, Anthony T Papenfuss, Richard W Tothill, Hojabr Kakavand, Graham J Mann, John F Thompson, Andreas Behren, Jonathan S Cebon, Rory Wolfe, John W Kelly, Alexander Dobrovic, Grant A McArthur

Journal article  |  2013  |  Clinical Cancer Research

CoNVEX: copy number variation estimation in exome sequencing data using HMM

Kaushalya C Amarasinghe, Jason Li, Saman K Halgamuge

Journal article  |  2013  |  BMC Bioinformatics

DNA Repair Genes: Alternative Transcription and Gene Expression at the Exon Level in Response to the DNA Damaging Agent, Ionizing Radiation

Helen B Forrester, Jason Li, Daniel Hovan, Alesia N Ivashkevich, Carl N Sprung

Journal article  |  2012  |  PLoS One

Genome-Wide Transcription Responses to Synchrotron Microbeam Radiotherapy

Carl N Sprung, Yuqing Yang, Helen B Forrester, Jason Li, Marina Zaitseva, Leonie Cann, Tina Restall, Robin L Anderson, Jeffrey C Crosbie, Peter AW Rogers

Journal article  |  2012  |  Radiation Research

Exome Sequencing Identifies Rare Deleterious Mutations in DNA Repair Genes FANCC and BLM as Potential Breast Cancer Susceptibility Alleles

Ella R Thompson, Maria A Doyle, Georgina L Ryland, Simone M Rowley, David YH Choong, Richard W Tothill, Heather Thorne, Daniel R Barnes, Jason Li, Jason Ellul, Gayle K Philip, Yoland C Antill, Paul A James, Alison H Trainer, Gillian Mitchell, Ian G Campbell

Journal article  |  2012  |  PLoS Genetics

CONTRA: copy number analysis for targeted resequencing

Jason Li, Richard Lupat, Kaushalya C Amarasinghe, Ella R Thompson, Maria A Doyle, Georgina L Ryland, Richard W Tothill, Saman K Halgamuge, Ian G Campbell, Kylie L Gorringe

Journal article  |  2012  |  Bioinformatics

Alternative Transcript Initiation and Splicing as a Response to DNA Damage

Carl N Sprung, Jason Li, Daniel Hovan, Michael J Mckay, Helen B Forrester

Journal article  |  2011  |  PLoS One

Functional Characterization of Quiescent Keratinocyte Stem Cells and Their Progeny Reveals a Hierarchical Organization in Human Skin Epidermis

Holger Schlueter, Sophie Paquet-Fifield, Pradnya Gangatirkar, Jason Li, Pritinder Kaur

Journal article  |  2011  |  Stem Cells

Decreased Prostate Cancer-Specific Survival of Men with BRCA2 Mutations from Multiple Breast Cancer Families

Heather Thorne, Amber J Willems, Eveline Niedermayr, Ivan MY Hoh, Jason Li, David Clouston, Gillian Mitchell, Stephen Fox, John L Hopper, Damien Bolton

Journal article  |  2011  |  Cancer prevention research

Integrated mutation, copy number and expression profiling in resectable non-small cell lung cancer

Genni M Newnham, Matthew Conron, SueAnne McLachlan, Alexander Dobrovic, Hongdo Do, Jason Li, Kenneth Opeskin, Natalie Thompson, Gavin M Wright, David M Thomas

Journal article  |  2011  |  BMC Cancer

2154 BRCA2 MUTATION WITH A DIAGNOSIS OF PROSTATE CANCER FROM HIGH RISK BREAST CANCER FAMILIES CONFERS A SUBSTANTIALLY INCREASED RISK OF CANCER RELATED MORTALITY

Ivan Ho, Heather Thorne, Amber Willems, David Clouston, Stephen Fox, Jason Li, Damien Bolton

Journal article  |  2010  |  The Journal of Urology

Are There Any More Ovarian Tumor Suppressor Genes? A New Perspective Using Ultra High-Resolution Copy Number and Loss of Heterozygosity Analysis

Kylie L Gorringe, Manasa Ramakrishna, Louise H Williams, Anita Sridhar, Samantha E Boyle, Jennifer L Bearfoot, Jason Li, Michael S Anglesio, Ian G Campbell

Journal article  |  2009  |  Genes, Chromosomes & Cancer

A role for pericytes as microenvironmental regulators of human skin tissue regeneration

Sophie Paquet-Fifield, Holger Schlueter, Amy Li, Tara Aitken, Pradnya Gangatirkar, Daniel Blashki, Rachel Koelmeyer, Normand Pouliot, Manuela Palatsides, Sarah Ellis, Nathalie Brouard, Andrew Zannettino, Nick Saunders, Natalie Thompson, Jason Li, Pritinder Kaur

Journal article  |  2009  |  Journal of Clinical Investigation

Genome classification by gene distribution: An overlapping subspace clustering approach

Jason Li, Saman K Halgamuge, Sen-Lin Tang

Journal article  |  2008  |  BMC Evolutionary Biology

Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages

J Li, SK Halgamuge, CI Kells, SL Tang

Journal article  |  2007  |  BMC Bioinformatics

BACKGROUND: Existing methods for whole-genome comparisons require prior knowledge of related species and provide little automation..

Splice site identification using probabilistic parameters and SVM classification

AKMA Baten, BCH Chang, SK Halgamuge, Jason Li

Journal article  |  2006  |  BMC Bioinformatics