Prof Tony Papenfuss

Research interestWe develop novel bioinformatics methods to analyse and make sense of cancer '-omics' data. A major focus of our work is cancer evolution and intra-tumoral heterogeneity, particularly in melanoma.

One of our aims is to develop practical measures of tumour heterogeneity and test if these are predictive of patient outcome.

We are also interested in complex genomic rearrangements and the mechanisms underlying extreme amplification events in genomes. We have developed novel methods to identify these rearrangements and use mathematical models to make sense of them. With this approach we recently discovered the dynamic mechanisms underlying the formation of giant cancer-associated neochromosomes.

www.wehi.edu.au/people/tony-papenfuss

Find out more about Tony Papenfuss' experience

Tony Papenfuss' highlights

FEATURED Journal article

DNA repair processes are critical mediators of p53-dependent tumor suppression

Tony Papenfuss' selected work

Novel Blood-Based Biomarkers To Guide Immunotherapy Management In Early Stage Melanoma

Research Grant

The Architecture and Evolution of Cancer Neochromosomes

Journal article

Precept - Prostate Cancer Prognosis And Treatment

Research Grant

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and..

Journal article

Precept - Prostate Cancer Prognosis And Treatment

Research Grant

BRAF/NRAS Wild-Type Melanomas Have a High Mutation Load Correlating with Histologic and Mo..

Journal article

Projects

Displaying the 10 most recent projects by Tony Papenfuss.

Novel Blood-Based Biomarkers To Guide Immunotherapy Management In Early Stage Melanoma

2020 - 2024

Active

Discovering New Therapies For Castrate-Resistant Prostate Cancer Through Genome Profiling Of Patient Derived Xengraft Mouse Models

2018 - 2022

Active

Acrf Tumour Heterogeneity Program

2017 - 2024

Active

Novel Approaches For Overcoming Resistance To Therapies For Advanced Melanoma

2017 - 2022

Active

Neochromosomes In Well Differentiated Liposarcoma

Neochromosomes (NCs) are large chromosomes which are not usually found in a normal cell. Well differentiated liposarcoma (WDLPS) is a tumour..

2011 - 2013

Completed

10

Projects

Project Types

Research Grant

Scholarly Works

Displaying the 178 most recent scholarly works by Tony Papenfuss.

RAF1 rearrangements are common in pancreatic acinar cell carcinomas

Owen WJ Prall, Violeta Nastevski, Huiling Xu, Christopher RE McEvoy, Joep HA Vissers, David J Byrne, Elena Takano, Satwica Yerneni, Sarah Ellis, Thomas Green, Catherine A Mitchell, William K Murray, Clare L Scott, Sean M Grimmond, Oliver Hofmann, Anthony Papenfuss, Damien Kee, Andrew Fellowes, Ian S Brown, Gregory Miller, et al.

Journal article | 2020 | Modern Pathology

Higher frequency of vertebrate-infecting viruses in the gut of infants born to mothers with type 1 diabetes

Ki Wook Kim, Digby W Allen, Thomas Briese, Jennifer J Couper, Simon C Barry, Peter G Colman, Andrew M Cotterill, Elizabeth A Davis, Lynne C Giles, Leonard C Harrison, Mark Harris, Aveni Haynes, Jessica L Horton, Sonia R Isaacs, Komal Jain, Walter I Lipkin, Kelly McGorm, Grant Morahan, Claire Morbey, Ignatius CN Pang, et al.

Journal article | 2020 | Pediatric Diabetes

Background: Microbial exposures in utero and early life shape the infant microbiome, which can profoundly impact on health. Compar..

Inferring structural variant cancer cell fraction.

Marek Cmero, Ke Yuan, Cheng Soon Ong, Jan Schröder, undefined PCAWG Evolution and Heterogeneity Working Group, Niall M Corcoran, Tony Papenfuss, Christopher M Hovens, Florian Markowetz, Geoff Macintyre, undefined PCAWG Consortium

Journal article | 2020 | Nature Communications

We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whol..

Tentacle Transcriptomes of the Speckled Anemone (Actiniaria: Actiniidae: Oulactis sp.): Venom-Related Components and Their Domain Structure

Michela L Mitchell, Gerry Q Tonkin-Hill, Rodrigo A Morales, Anthony W Purcell, Anthony T Papenfuss, Raymond S Norton

Journal article | 2020 | Marine Biotechnology

Cnidarians are one of the oldest known animal lineages (ca. 700 million years), with a unique envenomation apparatus to deliver a ..

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

Daniel Esposito, Jochen Weile, Jay Shendure, Lea M Starita, Anthony T Papenfuss, Frederick P Roth, Douglas M Fowler, Alan F Rubin

Journal article | 2019 | Genome Biology

Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands o..

Regulation of PRMT5-MDM4 axis is critical in the response to CDK4/6 inhibitors in melanoma

Shatha AbuHammad, Carleen Cullinane, Claire Martin, Zoe Bacolas, Teresa Ward, Huiqin Chen, Alison Slater, Kerry Ardley, Laura Kirby, Keefe T Chan, Natalie Brajanovski, Lorey K Smith, Aparna D Rao, Emily J Lelliott, Margarete Kleinschmidt, Ismael A Vergara, Anthony T Papenfuss, Peter Lau, Prerana Ghosh, Sue Haupt, et al.

Journal article | 2019 | Proceedings of the National Academy of Sciences

Gut microbiome dysbiosis and increased intestinal permeability in children with islet autoimmunity and type 1 diabetes: A prospective cohort study

Jessica E Harbison, Alexandra J Roth-Schulze, Lynne C Giles, Cuong D Tran, Katrina M Ngui, Megan A Penno, Rebecca L Thomson, John M Wentworth, Peter G Colman, Maria E Craig, Grant Morahan, Anthony T Papenfuss, Simon C Barry, Leonard C Harrison, Jennifer J Couper

Journal article | 2019 | Pediatric Diabetes

Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software

Daniel L Cameron, Leon Di Stefano, Anthony T Papenfuss

Journal article | 2019 | Nature Communications

In recent years, many software packages for identifying structural variants (SVs) using whole-genome sequencing data have been rel..

A 4-cyano-3-methylisoquinoline inhibitor of Plasmodium falciparum growth targets the sodium efflux pump PfATP4

Paul R Gilson, Rasika Kumarasingha, Jennifer Thompson, Xinxin Zhang, Jocelyn Sietsma Penington, Robabeh Kalhor, Hayley E Bullen, Adele M Lehane, Madeline G Dans, Tania F de Koning-Ward, Jessica K Holien, Tatiana P Soares da Costa, Mark D Hulett, Melissa J Buskes, Brendan S Crabb, Kiaran Kirk, Anthony T Papenfuss, Alan F Cowman, Belinda M Abbott

Journal article | 2019 | Scientific Reports

Somatic Hypermutation of the YAP Oncogene in a Human Cutaneous Melanoma

Xiaomeng Zhang, Jian Zhong Tang, Ismael A Vergara, Youfang Zhang, Pacman Szeto, Lie Yang, Christopher Mintoff, Andrew Colebatch, Lachlan McIntosh, Katrina A Mitchell, Evangeline Shaw, Helen Rizos, Georgina Long, Nicholas Hayward, Grant A McArthur, Anthony T Papenfuss, Kieran F Harvey, Mark Shackleton

Journal article | 2019 | Molecular Cancer Research

Evolution of cnidarian trans-defensins: Sequence, structure and exploration of chemical space

Michela L Mitchell, Thomas Shafee, Anthony T Papenfuss, Raymond S Norton

Journal article | 2019 | Proteins: Structure, Function, and Bioinformatics

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

Charles C Bell, Katie A Fenne, 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, et al.

Journal article | 2019 | Nature Communications

Androgen deprivation therapy promotes an obesity-like microenvironment in periprostatic fat

Stefano Mangiola, Ryan Stuchbery, Patrick McCoy, Ken Chow, Natalie Kurganovs, Michael Kerger, Anthony Papenfuss, Christopher M Hovens, Niall M Corcoran

Journal article | 2019 | Endocrine Connections

The effect of vitamin D supplementation on plasma non-oxidised PTH in a randomised clinical trial

Stan Ursem, Vito Francic, Martin Keppel, Verena Schwetz, Christian Trummer, Marlene Pandis, Felix Aberer, Martin R Grübler, Nicolas D Verheyen, Winfried März, Andreas Tomaschitz, Stefan Pilz, Barbara Obermayer-Pietsch, Annemieke C Heijboer

Journal article | 2019 | Endocrine Connections

Objective PTH can be oxidised in vivo, rendering it biologically inactive. Non-oxidised PTH (n-oxPTH) may therefore give a better ..

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..

Tasmanian devils with contagious cancer exhibit a constricted T-cell repertoire diversity

Yuanyuan Cheng, Mariano Makara, Emma Peel, Samantha Fox, Anthony T Papenfuss, Katherine Belov

Journal article | 2019 | Communications Biology

Deep multi-region whole-genome sequencing reveals heterogeneity and gene-by-environment interactions in treatment-naive, metastatic lung cancer

Tracy L Leong, Velimir Gayevskiy, Daniel P Steinfort, Marc R De Massy, Alvaro Gonzalez-Rajal, Kieren D Marini, Emily Stone, Venessa Chin, Adrian Havryk, Marshall Plit, Louis B Irving, Barton R Jennings, Rachael A McCloy, W Samantha N Jayasekara, Muhammad Alamgeer, Vishal Boolell, Andrew Field, Prudence A Russell, Beena Kumar, Daniel J Gough, et al.

Journal article | 2019 | Oncogene

Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer

Anna S Trigos, Richard B Pearson, Anthony T Papenfuss, David L Goode

Journal article | 2019 | eLife

An open-source platform to distribute and interpret data from multiplexed assays of variant effect

Daniel Esposito, Jochen Weile, Jay Shendure, Lea Starita, Anthony Papenfuss, Frederick Roth, Douglas Fowler, Alan Rubin

Journal article | 2019

Abstract Multiplex Assays of Variant Effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test th..

Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer

D Merino, TS Weber, A Serrano, F Vaillant, K Liu, B Pal, L Di Stefano, J Schreuder, D Lin, Y Chen, ML Asselin-Labat, TN Schumacher, D Cameron, GK Smyth, AT Papenfuss, GJ Lindeman, JE Visvader, SH Naik

Journal article | 2019 | Nature Communications

Distinct Gut Virome Profile of Pregnant Women With Type 1 Diabetes in the ENDIA Study

Ki Wook Kim, Digby W Allen, Thomas Briese, Jennifer J Couper, Simon C Barry, Peter G Colman, Andrew M Cotterill, Elizabeth A Davis, Lynne C Giles, Leonard C Harrison, Mark Harris, Aveni Haynes, Jessica L Horton, Sonia R Isaacs, Komal Jain, Walter Ian Lipkin, Grant Morahan, Claire Morbey, Ignatius CN Pang, Anthony T Papenfuss, et al.

Journal article | 2019 | Open Forum Infectious Diseases

GLOBAL STRUCTURE OF THE VAR GENES ENCODING THE MAJOR VARIANT SURFACE ANTIGEN OF PLASMODIUM FALCIPARUM

Gerry Tonkin-Hill, Shazia Ruybal-Pesantez, Kathryn E Tiedje, Virginie Rougeron, Sedigheh Zakeri, Tepanata Pumpaibool, Pingchai Harnyuttanakorn, OraLee H Branch, Lastenia Ruiz-Mesia, Michael F Duffy, Thomas S Rask, Franck Prugnolle, Yao-Ban Yao-Ban Chan, Anthony T Papenfuss, Karen P Day

Conference Proceedings | 2019 | AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

The inner ear proteome of fish

Oliver RB Thomas, Stephen E Swearer, Eugene A Kapp, Po Peng, Gerry Q Tonkin-Hill, Anthony Papenfuss, Anne Roberts, Pascal Bernard, Blaine R Roberts

Journal article | 2019 | The FEBS Journal

The Scalloped and Nerfin-1 Transcription Factors Cooperate to Maintain Neuronal Cell Fate

Joseph HA Vissers, Francesca Froldi, Jan Schroder, Anthony T Papenfuss, Louise Y Cheng, Kieran F Harvey

Journal article | 2018 | Cell Reports

Computational Tools for Deep Mutational Scanning

Alan F Rubin, Daniel Esposito, Jochen Weile, Frederick P Roth, Douglas M Fowler, Anthony T Papenfuss

Conference Proceedings | 2018 | PROTEIN SCIENCE

Detection of clinically relevant early genomic lesions in B-cell malignancies from circulating tumour DNA using a single hybridisation-based next generation sequencing assay

Piers A Blombery, Georgina L Ryland, John Markham, Jerick Guinto, Meaghan Wall, Michelle McBean, Kate Jones, Ella R Thompson, Daniel L Cameron, Anthony T Papenfuss, Miles H Prince, Michael Dickinson, David Alan Westerman

Journal article | 2018 | British Journal of Haematology

NLRP1 restricts butyrate producing commensals to exacerbate inflammatory bowel disease

Hazel Tye, Chien-Hsiung Yu, Lisa A Simms, Marcel R de Zoete, Man Lyang Kim, Martha Zakrzewski, Jocelyn S Penington, Cassandra R Harapas, Fernando Souza-Fonseca-Guimaraes, Leesa F Wockner, Adele Preaudet, Lisa A Mielke, Stephen A Wilcox, Yasunori Ogura, Sinead C Corr, Komal Kanojia, Konstantinos A Kouremenos, David P De Souza, Malcolm J McConville, Richard A Flavell, et al.

Journal article | 2018 | Nature Communications

TARGETING MYCN OVER-EXPRESSION WITH BRD4 INHIBITION IN THE PROLIFERATIVE C5 SUBTYPE OF HIGH GRADE SEROUS OVARIAN CANCER (HGSOC)

GY Ho, O Kondrashova, C Vandenberg, E Kyran, E Lieschke, V Heong, M Milevskiy, T Papenfuss, J Schroeder, J Weroha, M Dawson, D Bowtell, H Barker, M Wakefield, C Scott

Conference Proceedings | 2018 | INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER

Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer

Anna Trigos, Rick Pearson, Anthony Papenfuss, David Goode

Journal article | 2018 | eLife

Extensive transcriptional alterations are observed in cancer, many of which activate core biological processes established in unic..

Using the evolutionary ages of genes to understand hallmark features of cancer

David L Goode, Anna S Trigos, Anthony T Papenfuss, Richard B Pearson

Conference Proceedings | 2018 | Bioinformatics and Systems Biology

DNA repair processes are critical mediators of p53-dependent tumor suppression

Ana Janic, Liz J Valente, Matthew J Wakefield, Leon Di Stefano, Liz Milla, Stephen Wilcox, Haoyu Yang, Lin Tai, Cassandra J Vandenberg, Andrew J Kueh, Shinsuke Mizutani, Margs S Brennan, Robyn L Schenk, Lisa M Lindqvist, Anthony T Papenfuss, Liam O'Connor, Andreas Strasser, Marco J Herold

Journal article | 2018 | Nature Medicine

Phylogenetic relationships, stage-specific expression and localisation of a unique family of inactive cysteine proteases in Sarcoptes scabiei

Deepani D Fernando, Simone L Reynolds, Martha Zakrzewski, Ehtesham Mofiz, Anthony T Papenfuss, Deborah Holt, Katja Fischer

Journal article | 2018 | Parasites & Vectors

Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer

Eva KF Chan, Daniel L Cameron, Desiree C Petersen, Ruth J Lyons, Benedetta F Baldi, Anthony T Papenfuss, David M Thomas, Vanessa M Hayes

Journal article | 2018 | Genome Research

Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis

Jocelyn Sietsma Penington, Megan AS Penno, Katrina M Ngui, Nadim J Ajami, Alexandra J Roth-Schulze, Stephen A Wilcox, Esther Bandala-Sanchez, John M Wentworth, Simon C Barry, Cheryl Y Brown, Jennifer J Couper, Joseph F Petrosino, Anthony T Papenfuss, Leonard C Harrison

Journal article | 2018 | Scientific Reports

The &ITPlasmodium falciparum &ITtranscriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen-encoding &ITvar &ITgenes

Gerry Q Tonkin-Hill, Leily Trianty, Rintis Noviyanti, Hanh HT Nguyen, Boni F Sebayang, Daniel A Lampah, Jutta Marfurt, Simon A Cobbold, Janavi S Rambhatla, Malcolm J McConville, Stephen J Rogerson, Graham Brown, Karen P Day, Ric N Price, Nicholas M Anstey, Anthony T Papenfuss, Michael F Duffy

Journal article | 2018 | PLOS Biology

A statistical framework for analyzing deep mutational scanning data (vol 18, 150, 2017)

Alan F Rubin, Hannah Gelman, Nathan Lucas, Sandra M Bajjalieh, Anthony T Papenfuss, Terence P Speed, Douglas M Fowler

Journal article | 2018 | Genome Biology

How the evolution of multicellularity set the stage for cancer

Anna S Trigos, Richard B Pearson, Anthony T Papenfuss, David L Goode

Journal article | 2018 | British Journal of Cancer

Transcriptome and proteome profiling reveals stress-induced expression signatures of imiquimod-treated Tasmanian devil facial tumor disease (DFTD) cells

AL Patchett, R Wilson, JC Charlesworth, LM Corcoran, AT Papenfuss, AB Lyons, GM Woods, C Tovar

Journal article | 2018 | Oncotarget

THE IMPACT OF SCABIES ON THE HEALTHY HUMAN SKIN MICROBIOTA

Katja Fischer, Charlotte Bernigaud, Martha Zakrzewski, Martha Zakrzewski, Pearl Swe, Anthony Papenfuss, Ehtesham Mofiz, Francoise Botterel, M Karmarkar, Deborah Holt, Bart Currie, Olivier Chosidow

Conference Proceedings | 2018 | AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

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

Canary: an atomic pipeline for clinical amplicon assays

Kenneth D Doig, Jason Ellul, Andrew Fellowes, Ella R Thompson, Georgina Ryland, Piers Blombery, Anthony T Papenfuss, Stephen B Fox

Journal article | 2017 | BMC Bioinformatics

Malaria parasite DNA-harbouring vesicles activate cytosolic immune sensors

Xavier Sisquella, Yifat Ofir-Birin, Matthew A Pimentel, Lesley Cheng, Paula Abou Karam, Natalia G Sampaio, Jocelyn Sietsma Penington, Dympna Connolly, Tal Giladi, Benjamin J Scicluna, Robyn A Sharples, Andreea Waltmann, Dror Avni, Eli Schwartz, Louis Schofield, Ziv Porat, Diana S Hansen, Anthony T Papenfuss, Emily M Eriksson, Motti Gerlic, et al.

Journal article | 2017 | Nature Communications

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

Daniel L Cameron, Jan Schroder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence P Speed, Anthony T Papenfuss

Journal article | 2017 | Genome Research

De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

Jared Mamrot, Roxane Legaie, Stacey J Ellery, Trevor Wilson, Torsten Seemann, David R Powell, David K Gardner, David W Walker, Peter Temple-Smith, Anthony T Papenfuss, Hayley Dickinson

Journal article | 2017 | Scientific Reports

A statistical framework for analyzing deep mutational scanning data

Alan F Rubin, Hannah Gelman, Nathan Lucas, Sandra M Bajjalieh, Anthony T Papenfuss, Terence P Speed, Douglas M Fowler

Journal article | 2017 | Genome Biology

SVclone: inferring structural variant cancer cell fraction

Marek Cmero, Cheng Soon Ong, Ke Yuan, Jan Schröder, Kangbo Mo, Niall Corcoran, Anthony Troy Papenfuss, Christopher Hovens, Florian Markowetz, Geoff Macintyre, undefined PCAWG Evolution and Heterogeneity Working Group

Journal article | 2017

We present SVclone, a computational method for inferring the cancer cell fraction of structural variant breakpoints from whole-gen..

CLOVE: classification of genomic fusions into structural variation events

Jan Schroder, Adrianto Wirawan, Bertil Schmidt, Anthony T Papenfuss

Journal article | 2017 | BMC Bioinformatics

Altered interactions between unicellular and multicellular genes drive hallmarks of transformation in a diverse range of solid tumors

Anna S Trigos, Richard B Pearson, Anthony T Papenfuss, David L Goode

Journal article | 2017 | Proceedings of the National Academy of Sciences

Whole genome analysis of a schistosomiasis-transmitting freshwater snail

Coen M Adema, LaDeana W Hillier, Catherine S Jones, Eric S Loker, Matty Knight, Patrick Minx, Guilherme Oliveira, Nithya Raghavan, Andrew Shedlock, Laurence Rodrigues do Amaral, Halime D Arican-Goktas, Juliana G Assis, Elio Hideo Baba, Olga L Baron, Christopher J Bayne, Utibe Bickham-Wright, Kyle K Biggar, Michael Blouin, Bryony C Bonning, Chris Botka, et al.

Journal article | 2017 | Nature Communications

A forward genetic screen identifies a negative regulator of rapid Ca2 -dependent cell egress (MS1) in the intracellular parasite Toxoplasma gondii

James M McCoy, Rebecca J Stewart, Alessandro D Uboldi, Dongdi Li, Jan Schroder, Nicollas E Scott, Anthony T Papenfuss, Adele M Lehane, Leonard J Foster, Christopher J Tonkin

Journal article | 2017 | Journal of Biological Chemistry

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

Hormone-like peptides in the venoms of marine cone snails

Samuel D Robinson, Qing Li, Pradip K Bandyopadhyay, Joanna Gajewiak, Mark Yandell, Anthony T Papenfuss, Anthony W Purcell, Raymond S Norton, Helena Safavi-Hemami

Journal article | 2017 | General and Comparative Endocrinology

Circulating tumour DNA reflects treatment response and clonal evolution in chronic lymphocytic leukaemia

Paul Yeh, Tane Hunter, Devbarna Sinha, Sarah Ftouni, Elise Wallach, Damian Jiang, Yih-Chih Chan, Stephen Q Wong, Maria Joao Silva, Ravikiran Vedururu, Kenneth Doig, Enid Lam, Gisela Mir Arnau, Timothy Semple, Meaghan Wall, Andjelija Zivanovic, Rishu Agarwal, Pasquale Petrone, Kate Jones, David Westerman, et al.

Journal article | 2017 | Nature Communications

Significant decline in anticancer immune capacity during puberty in the Tasmanian devil

Yuanyuan Cheng, Kim Heasman, Sarah Peck, Emma Peel, Rebecca M Gooley, Anthony T Papenfuss, Carolyn J Hogg, Katherine Belov

Journal article | 2017 | Scientific Reports

Regression of devil facial tumour disease following immunotherapy in immunised Tasmanian devils

Cesar Tovar, Ruth J Pye, Alexandre Kreiss, Yuanyuan Cheng, Gabriella K Brown, Jocelyn Darby, Roslyn C Malley, Hannah VT Siddle, Karsten Skjodt, Jim Kaufman, Anabel Silva, Adriana Baz Morelli, Anthony T Papenfuss, Lynn M Corcoran, James M Murphy, Martin J Pearse, Katherine Belov, A Bruce Lyons, Gregory M Woods

Journal article | 2017 | Scientific Reports

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

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

Daniel Cameron, Jan Schroeder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence Speed, Anthony Papenfuss

Journal article | 2017

ABSTRACT The identification of genomic rearrangements, particularly in cancers, with high sensitivity and specificity using massiv..

HYSYS: have you swapped your samples?

Jan Schroder, Vincent Corbin, Anthony T Papenfuss

Journal article | 2017 | Bioinformatics

Bioinformatics analysis of sequence data

AT Papenfuss, D Cameron, J Schroeder, I Vergara

Book Chapter | 2017

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

The Use of Imaging Mass Spectrometry to Study Peptide Toxin Distribution in Australian Sea Anemones

Michela L Mitchell, Brett R Hamilton, Bruno Madio, Rodrigo AV Morales, Gerry Q Tonkin-Hill, Anthony T Papenfuss, Anthony W Purcell, Glenn F King, Eivind AB Undheim, Raymond S Norton

Journal article | 2017 | Australian Journal of Chemistry

PD-L1 Is Not Constitutively Expressed on Tasmanian Devil Facial Tumor Cells but Is Strongly Upregulated in Response to IFN-gamma and Can Be Expressed in the Tumor Microenvironment

Andrew S Flies, A Bruce Lyons, Lynn M Corcoran, Anthony T Papenfuss, James M Murphy, Graeme W Knowles, Gregory M Woods, John D Hayball

Journal article | 2016 | Frontiers in Immunology

The UT family of MHC class I loci unique to non-eutherian mammals has limited polymorphism and tissue specific patterns of expression in the opossum

Katina V Krasnec, Anthony T Papenfuss, Robert D Miller

Journal article | 2016 | BMC Immunology

Clustered somatic mutations are frequent in transcription factor binding motifs within proximal promoter regions in melanoma and other cutaneous malignancies

Andrew J Colebatch, Leon Di Stefano, Stephen Q Wong, Ross D Hannan, Paul M Waring, Alexander Dobrovic, Grant A McArthur, Anthony T Papenfuss

Journal article | 2016 | Oncotarget

Elementary: breast cancer culprits leave their signatures on the double helix

Delphine Merino, Bhupinder Pal, Anthony T Papenfuss

Journal article | 2016 | Cell Death & Differentiation

A community-based model of rapid autopsy in end-stage cancer patients

Kathryn Alsop, Heather Thorne, Shahneen Sandhu, Anne Hamilton, Christopher Mintoff, Elizabeth Christie, Odette Spruyt, Scott Williams, Orla McNally, Linda Mileshkin, Sumitra Ananda, Julene Hallo, Sherene Loi, Clare Scott, Peter Savas, Lisa Devereux, Patricia O'Brien, Sameera Gunawardena, Clare Hampson, Kate Strachan, et al.

Journal article | 2016 | Nature Biotechnology

Enrich2: a statistical framework for analyzing deep mutational scanning data

Alan Rubin, Nathan Lucas, Sandra Bajjalieh, Anthony Papenfuss, Terence Speed, Douglas Fowler

Journal article | 2016

Abstract Measuring the functional consequences of protein variants can reveal how a protein works or help unlock the meaning of an..

De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

Jared Mamrot, Roxane Legaie, Stacey Ellery, Trevor Wilson, David Gardner, David Walker, Peter Temple-Smith, Anthony Papenfuss, Hayley Dickinson

Journal article | 2016

Abstract Background: Spiny mice of the genus Acomys are small desert-dwelling rodents that display physiological characteristics n..

Transmissible cancers in an evolutionary context

Beata Ujvari, Anthony T Papenfuss, Katherine Belov

Journal article | 2016 | BioEssays

CD271 Expression on Patient Melanoma Cells Is Unstable and Unlinked to Tumorigenicity

Samantha E Boyle, Clare G Fedele, Vincent Corbin, Elisha Wybacz, Pacman Szeto, Jeremy Lewin, Richard J Young, Annie Wong, Robert Fuller, John Spillane, David Speakman, Simon Donahoe, Miklos Pohl, David Gyorki, Michael A Henderson, Ricky W Johnstone, Anthony T Papenfuss, Mark Shackleton

Journal article | 2016 | Cancer Research

Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suis

Ehtesham Mofiz, Deborah C Holt, Torsten Seemann, Bart J Currie, Katja Fischer, Anthony T Papenfuss

Journal article | 2016 | GigaScience

Differences in PfEMP1s recognized by antibodies from patients with uncomplicated or severe malaria

Michael F Duffy, Rintis Noviyanti, Takafumi Tsuboi, Zhi-Ping Feng, Leily Trianty, Boni F Sebayang, Eizo Takashima, Fransisca Sumardy, Daniel A Lampah, Louise Turner, Thomas Lavstsen, Freya JI Fowkes, Peter Siba, Stephen J Rogerson, Thor G Theander, Jutta Marfurt, Ric N Price, Nicholas M Anstey, Graham V Brown, Anthony T Papenfuss

Journal article | 2016 | Malaria Journal

A Naturally Occurring Peptide with an Elementary Single Disulfide-Directed beta-Hairpin Fold

Samuel D Robinson, Sandeep Chhabra, Alessia Belgi, Balasubramanyam Chittoor, Helena Safavi-Hemami, Andrea J Robinson, Anthony T Papenfuss, Anthony W Purcell, Raymond S Norton

Journal article | 2016 | Structure

Complementarity and redundancy of IL-22-producing innate lymphoid cells

Lucille C Rankin, Mathilde JH Girard-Madoux, Cyril Seillet, Lisa A Mielke, Yann Kerdiles, Aurore Fenis, Elisabeth Wieduwild, Tracy Putoczki, Stanislas Mondot, Olivier Lantz, Dieter Demon, Anthony T Papenfuss, Gordon K Smyth, Mohamed Lamkanfi, Sebastian Carotta, Jean-Christophe Renauld, Wei Shi, Sabrina Carpentier, Tim Soos, Christopher Arendt, et al.

Journal article | 2016 | Nature Immunology

Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections

Ehtesham Mofiz, Torsten Seemann, Melanie Bahlo, Deborah Holt, Bart J Currie, Katja Fischer, Anthony T Papenfuss

Journal article | 2016 | PLoS Negl Trop Dis

The identification of immune genes in the milk transcriptome of the Tasmanian devil (Sarcophilus harrisii)

Rehana V Hewavisenti, Katrina M Morris, Denis O'Meally, Yuanyuan Cheng, Anthony T Papenfuss, Katherine Belov

Journal article | 2016 | PeerJ

Digital PCR of Genomic Rearrangements for Monitoring Circulating Tumour DNA

Hongdo Do, Daniel Cameron, Ramyar Molania, Bibhusal Thapa, Gareth Rivalland, Paul L Mitchell, Carmel Murone, Thomas John, Anthony Papenfuss, Alexander Dobrovic

Journal article | 2016 | Advances in Experimental Medicine and Biology

The Tasmanian devil microbiome-implications for conservation and management

Yuanyuan Cheng, Samantha Fox, David Pemberton, Carolyn Hogg, Anthony T Papenfuss, Katherine Belov

Journal article | 2015 | Microbiome

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

Identification and analysis of divergent immune gene families within the Tasmanian devil genome

Katrina M Morris, Yuanyuan Cheng, Wesley Warren, Anthony T Papenfuss, Katherine Belov

Journal article | 2015 | BMC Genomics

Expression of a Chimeric Antigen Receptor in Multiple Leukocyte Lineages in Transgenic Mice

Carmen SM Yong, Jennifer A Westwood, Jan Schroeder, Anthony T Papenfuss, Bianca von Scheidt, Maria Moeller, Christel Devaud, Phillip K Darcy, Michael H Kershaw

Journal article | 2015 | PLOS ONE

BET inhibitor resistance emerges from leukaemia stem cells

Chun Yew Fong, Omer Gilan, Enid YN Lam, Alan F Rubin, Sarah Ftouni, Dean Tyler, Kym Stanley, Devbarna Sinha, Paul Yeh, Jessica Morison, George Giotopoulos, Dave Lugo, Philip Jeffrey, Stanley Chun-Wei Lee, Christopher Carpenter, Richard Gregory, Robert G Ramsay, Steven W Lane, Omar Abdel-Wahab, Tony Kouzarides, et al.

Journal article | 2015 | Nature

Embryonic Lethality in Homozygous Human Her-2 Transgenic Mice Due to Disruption of the Pds5b Gene

Carmen SM Yong, Janelle Sharkey, Belinda Duscio, Ben Venville, Wei-Zen Wei, Richard F Jones, Clare Y Slaney, Gisela Mir Arnau, Anthony T Papenfuss, Jan Schroeder, Phillip K Darcy, Michael H Kershaw

Journal article | 2015 | PLOS ONE

Clinical cancer genomic analysis: data engineering required

Kenneth Doig, Anthony T Papenfuss, Stephen Fox

Journal article | 2015 | The Lancet Oncology

Improving the Power of Structural Variation Detection by Augmenting the Reference

Jan Schroeder, Santhosh Girirajan, Anthony T Papenfuss, Paul Medvedev

Journal article | 2015 | PLOS ONE

Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage

Anthony T Papenfuss, Zhi-Ping Feng, Katina Krasnec, Janine E Deakin, Michelle L Baker, Robert D Miller

Journal article | 2015 | BMC Genomics

Inositol polyphosphate 4-phosphatase II (INPP4B) is associated with chemoresistance and poor outcome in AML

Sewa Rijal, Shaun Fleming, Nik Cummings, Natalie K Rynkiewicz, Lisa M Ooms, Nhu-Y N Nguyen, Tse-Chieh Teh, Sharon Avery, Julie F McManus, Anthony T Papenfuss, Catriona McLean, Mark A Guthridge, Christina A Mitchell, Andrew H Wei

Journal article | 2015 | Blood

Discovery by proteogenomics and characterization of an RF-amide neuropeptide from cone snail venom

Samuel D Robinson, Helena Safavi-Hemami, Shrinivasan Raghuraman, Julita S Imperial, Anthony T Papenfuss, Russell W Teichert, Anthony W Purcell, Baldomero M Olivera, Raymond S Norton

Journal article | 2015 | Journal of Proteomics

The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells

Francesca Froldi, Milan Szuperak, Chen-Fang Weng, Wei Shi, Anthony T Papenfuss, Louise Y Cheng

Journal article | 2015 | Genes & Development

The life history of neochromosomes revealed

Anthony T Papenfuss, David M Thomas

Journal article | 2015 | Molecular & Cellular Oncology

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

Identification of Dendritic Cells, B Cell and T Cell Subsets in Tasmanian Devil Lymphoid Tissue; Evidence for Poor Immune Cell Infiltration into Devil Facial Tumors

Lauren J Howson, Katrina M Morris, Takumi Kobayashi, Cesar Tovar, Alexandre Kreiss, Anthony T Papenfuss, Lynn Corcoran, Katherine Belov, Gregory M Woods

Journal article | 2014 | The Anatomical Record

CD8( ) T Cells from a Novel T Cell Receptor Transgenic Mouse Induce Liver-Stage Immunity That Can Be Boosted by Blood-Stage Infection in Rodent Malaria

Lei Shong Lau, Daniel Fernandez-Ruiz, Vanessa Mollard, Angelika Sturm, Michelle A Neller, Anton Cozijnsen, Julia L Gregory, Gayle M Davey, Claerwen M Jones, Yi-Hsuan Lin, Ashraful Haque, Christian R Engwerda, Catherine Q Nie, Diana S Hansen, Kenneth M Murphy, Anthony T Papenfuss, John J Miles, Scott R Burrows, Tania de Koning-Ward, Geoffrey I McFadden, et al.

Journal article | 2014 | PLoS Pathogens

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

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

Jan Schroeder, Arthur Hsu, Samantha E Boyle, Geoff Macintyre, Marek Cmero, Richard W Tothill, Ricky W Johnstone, Mark Shackleton, Anthony T Papenfuss

Journal article | 2014 | Bioinformatics

Diversity of Conotoxin Gene Superfamilies in the Venomous Snail, Conus victoriae

Samuel D Robinson, Helena Safavi-Hemami, Lachlan D McIntosh, Anthony W Purcell, Raymond S Norton, Anthony T Papenfuss

Journal article | 2014 | PLoS One

IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling

Shuo Li, Marie-Paule Lefranc, John J Miles, Eltaf Alamyar, Veronique Giudicelli, Patrice Duroux, J Douglas Freeman, Vincent DA Corbin, Jean-Pierre Scheerlinck, Michael A Frohman, Paul U Cameron, Magdalena Plebanski, Bruce Loveland, Scott R Burrows, Anthony T Papenfuss, Eric J Gowans

Journal article | 2013 | Nature Communications

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

Evolution of a contagious cancer: epigenetic variation in Devil Facial Tumour Disease

Beata Ujvari, Anne-Maree Pearse, Sarah Peck, Collette Harmsen, Robyn Taylor, Stephen Pyecroft, Thomas Madsen, Anthony T Papenfuss, Katherine Belov

Journal article | 2013 | Royal Society of London. Proceedings B. Biological Sciences

Proteomics and Deep Sequencing Comparison of Seasonally Active Venom Glands in the Platypus Reveals Novel Venom Peptides and Distinct Expression Profiles

Emily SW Wong, David Morgenstern, Ehtesham Mofiz, Sara Gombert, Katrina M Morris, Peter Temple-Smith, Marilyn B Renfree, Camilla M Whittington, Glenn F King, Wesley C Warren, Anthony T Papenfuss, Katherine Belov

Journal article | 2012 | Molecular and Cellular Proteomics

Telomere Dynamics and Homeostasis in a Transmissible Cancer

Beata Ujvari, Anne-Maree Pearse, Robyn Taylor, Stephen Pyecroft, Cassandra Flanagan, Sara Gombert, Anthony T Papenfuss, Thomas Madsen, Katherine Belov

Journal article | 2012 | PLoS One

The immune gene repertoire of an important viral reservoir, the Australian black flying fox

Anthony T Papenfuss, Michelle L Baker, Zhi-Ping Feng, Mary Tachedjian, Gary Crameri, Chris Cowled, Justin Ng, Vijaya Janardhana, Hume E Field, Lin-Fa Wang

Journal article | 2012 | BMC Genomics

Evolution of coding and non-coding genes in HOX clusters of a marsupial

Hongshi Yu, James Lindsay, Zhi-Ping Feng, Stephen Frankenberg, Yanqiu Hu, Dawn Carone, Geoff Shaw, Andrew J Pask, Rachel O'Neill, Anthony T Papenfuss, Marilyn B Renfree

Journal article | 2012 | BMC Genomics

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

Elizabeth P Murchison, Ole B Schulz-Trieglaff, Zemin Ning, Ludmil B Alexandrov, Markus J Bauer, Beiyuan Fu, Matthew Hims, Zhihao Ding, Sergii Ivakhno, Caitlin Stewart, Bee Ling Ng, Wendy Wong, Bronwen Aken, Simon White, Amber Alsop, Jennifer Becq, Graham R Bignell, R Keira Cheetham, William Cheng, Thomas R Connor, et al.

Journal article | 2012 | Cell

Genomic Restructuring in the Tasmanian Devil Facial Tumour: Chromosome Painting and Gene Mapping Provide Clues to Evolution of a Transmissible Tumour

Janine E Deakin, Hannah S Bender, Anne-Maree Pearse, Willem Rens, Patricia CM O'Brien, Malcolm A Ferguson-Smith, Yuanyuan Cheng, Katrina Morris, Robyn Taylor, Andrew Stuart, Katherine Belov, Chris T Amemiya, Elizabeth P Murchison, Anthony T Papenfuss, Jennifer A Marshall Graves

Journal article | 2012 | PLoS Genetics

A Limited Role for Gene Duplications in the Evolution of Platypus Venom

Emily SW Wong, Anthony T Papenfuss, Camilla M Whittington, Wesley C Warren, Katherine Belov

Journal article | 2012 | Molecular Biology and Evolution

Blood-Stage Plasmodium berghei Infection Generates a Potent, Specific CD8( ) T-Cell Response Despite Residence Largely in Cells Lacking MHC I Processing Machinery

Lei Shong Lau, Daniel Fernandez Ruiz, Gayle M Davey, Tania F de Koning-Ward, Anthony T Papenfuss, Francis R Carbone, Andrew G Brooks, Brendan S Crabb, William R Heath

Journal article | 2011 | Journal of Infectious Diseases

Targeting of the Tumor Suppressor GRHL3 by a miR-21-Dependent Proto-Oncogenic Network Results in PTEN Loss and Tumorigenesis

Charbel Darido, Smitha R Georgy, Tomasz Wilanowski, Sebastian Dworkin, Alana Auden, Quan Zhao, Gerhard Rank, Seema Srivastava, Moira J Finlay, Anthony T Papenfuss, Pier Paolo Pandolfi, Richard B Pearson, Stephen M Jane

Journal article | 2011 | Cancer Cell

Tumor-Specific Diagnostic Marker for Transmissible Facial Tumors of Tasmanian Devils: Immunohistochemistry Studies

C Tovar, D Obendorf, EP Murchison, AT Papenfuss, A Kreiss, GM Woods

Journal article | 2011 | Veterinary Pathology

Immunome database for marsupials and monotremes

Emily SW Wong, Anthony T Papenfuss, Katherine Belov

Journal article | 2011 | BMC Immunology

Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby

Emily SW Wong, Anthony T Papenfuss, Andreas Heger, Arthur L Hsu, Chris P Ponting, Robert D Miller, Jane C Fenelon, Marilyn B Renfree, Richard A Gibbs, Katherine Belov

Journal article | 2011 | BMC Genomics

Investigation of hypoxia and carbonic anhydrase IX expression in a renal cell carcinoma xenograft model with oxygen tension measurements and I-124-cG250 PET/CT

Nathan Lawrentschuk, Fook T Lee, Gareth Jones, Angela Rigcpoulos, Angela Mountain, Graeme O'Keefe, Anthony T Papenfuss, Damien M Bolton, Ian D Davis, Andrew M Scott

Journal article | 2011 | Urologic Oncology - Seminars and Original Investigations

Crystal structure of the Leishmania major MIX protein: A scaffold protein that mediates protein-protein interactions

Michael A Gorman, Alex D Uboldi, Peter J Walsh, Kher Shing Tan, Guido Hansen, Trevor Huyton, Hong Ji, Joan Curtis, Lukasz Kedzierski, Anthony T Papenfuss, Con Dogovski, Matthew A Perugini, Richard J Simpson, Emanuela Handman, Michael W Parker

Journal article | 2011 | Protein Science

Genomic Identification of Chemokines and Cytokines in Opossum

Emily SW Wong, Anthony T Papenfuss, Katherine Belov

Journal article | 2011 | Journal of Interferon & Cytokine Research

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily Swwong, Christophe M Lefevre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, et al.

Journal article | 2011 | Genome Biology

A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility

Iris KL Tan, Leanne Mackin, Nancy Wang, Anthony T Papenfuss, Colleen M Elso, Michelle P Ashton, Fiona Quirk, Belinda Phipson, Melanie Bahlo, Terence P Speed, Gordon K Smyth, Grant Morahan, Thomas C Brodnicki

Journal article | 2010 | Genome Research

Epidermal Wound Repair Is Regulated by the Planar Cell Polarity Signaling Pathway (vol 19, pg 138, 2010)

Jacinta Caddy, Tomasz Wilanowski, Charbel Darido, Sebastian Dworkin, Stephen B Ting, Quan Zhao, Gerhard Rank, Alana Auden, Seema Srivastava, Tony A Papenfuss, Jennifer N Murdoch, Patrick O Humbert, Vishwas Parekh, Nidal Boulos, Thomas Weber, Jian Zuo, John M Cunningham, Stephen M Jane

Journal article | 2010 | Developmental Cell

Epidermal Wound Repair Is Regulated by the Planar Cell Polarity Signaling Pathway

Jacinta Caddy, Tomasz Wilanowski, Charbel Darido, Sebastian Dworkin, Stephen B Ting, Quan Zhao, Gerhard Rank, Alana Auden, Seema Srivastava, Tony A Papenfuss, Jennifer N Murdoch, Patrick O Humbert, Nidal Boulos, Thomas Weber, Jian Zuo, John M Cunningham, Stephen M Jane

Journal article | 2010 | Developmental Cell

Insight into Evolution of Gene Regulation Networks from the Opossum Genome

Matthew J Wakefield, Anthony T Papenfuss

Book Chapter | 2010

Marsupial Sequencing Projects and Bioinformatics Challenges

Anthony T Papenfuss, Arthur Hsu, Matthew Wakefield

Book Chapter | 2010

The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer

Elizabeth P Murchison, Cesar Tovar, Arthur Hsu, Hannah S Bender, Pouya Kheradpour, Clare A Rebbeck, David Obendorf, Carly Conlan, Melanie Bahlo, Catherine A Blizzard, Stephen Pyecroft, Alexandre Kreiss, Manolis Kellis, Alexander Stark, Timothy T Harkins, Jennifer A Marshall Graves, Gregory M Woods, Gregory J Hannon, Anthony T Papenfuss

Journal article | 2010 | Science

Novel venom gene discovery in the platypus

Camilla M Whittington, Anthony T Papenfuss, Devin P Locke, Elaine R Mardis, Richard K Wilson, Sahar Abubucker, Makedonka Mitreva, Emily SW Wong, Arthur L Hsu, Philip W Kuchel, Katherine Belov, Wesley C Warren

Journal article | 2010 | Genome Biology

A Novel Family of Apicomplexan Glideosome-associated Proteins with an Inner Membrane-anchoring Role

Hayley E Bullen, Christopher J Tonkin, Rebecca A O'Donnell, Wai-Hong Tham, Anthony T Papenfuss, Sven Gould, Alan F Cowman, Brendan S Crabb, Paul R Gilson

Journal article | 2009 | Journal of Biological Chemistry

Identification of natural killer cell receptor clusters in the platypus genome reveals an expansion of C-type lectin genes

Emily SW Wong, Claire E Sanderson, Janine E Deakin, Camilla M Whittington, Anthony T Papenfuss, Katherine Belov

Journal article | 2009 | Immunogenetics

A newly discovered protein export machine in malaria parasites

Tania F de Koning-Ward, Paul R Gilson, Justin A Boddey, Melanie Rug, Brian J Smith, Anthony T Papenfuss, Paul R Sanders, Rachel J Lundie, Alexander G Maier, Alan F Cowman, Brendan S Crabb

Journal article | 2009 | Nature

Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites

Jake Baum, Anthony T Papenfuss, Gunnar R Mair, Chris J Janse, Dina Vlachou, Andrew P Waters, Alan F Cowman, Brendan S Crabb, Tania F de Koning-Ward

Journal article | 2009 | Nucleic Acids Research

Understanding and utilising mammalian venom via a platypus venom transcriptome

Camilla M Whittington, Jennifer MS Koh, Wesley C Warren, Anthony T Papenfuss, Allan M Torres, Philip W Kuchel, Katherine Belov

Journal article | 2009 | Journal of Proteomics

Analysis of the platypus genome suggests a transposon origin for mammalian imprinting

Andrew J Pask, Anthony T Papenfuss, Eleanor I Ager, Kaighin A Mccoll, Terence P Speed, Marilyn B Renfree

Journal article | 2009 | Genome Biology

No evidence of expression of two classes of natural antibiotics (cathelicidins and defensins) in a sample of platypus milk

Camilla M Whittington, Julie A Sharp, Anthony Papenfuss, Katherine Belov

Journal article | 2009 | Australian Journal of Zoology

Eggs, embryos and the evolution of imprinting: insights from the platypus genome

Marilyn B Renfree, Anthony T Papenfuss, Geoff Shaw, Andrew J Pask

Journal article | 2009 | Reproduction, Fertility and Development

Hatching time for monotreme immunology

Emily SW Wong, Anthony T Papenfuss, Robert D Miller, Katherine Belov

Journal article | 2009 | Australian Journal of Zoology

REMOTE AIRPORT TRAFFIC CONTROL CENTER WITH AUGMENTED VISION VIDEO PANORAMA

M Schmidt, M Rudolph, A Papenfuss, M Friedrich, C Moehlenbrink, S Kaltenhaeuser, N Fuerstenau

Conference Proceedings | 2009 | 2009 IEEE/AIAA 28TH DIGITAL AVIONICS SYSTEMS CONFERENCE, VOLS 1-3

Expression patterns of platypus defensin and related venom genes across a range of tissue types reveal the possibility of broader functions for OvDLPs than previously suspected

Camilla M Whittington, Anthony T Papenfuss, Philip W Kuchel, Katherine Belov

Journal article | 2008 | Toxicon

Genome analysis of the platypus reveals unique signatures of evolution (vol 453, pg 175, 2008)

Wesley C Warren, LaDeana W Hillier, Jennifer A Marshall Graves, Ewan Birney, Chris P Ponting, Frank Grutzner, Katherine Belov, Webb Miller, Laura Clarke, Asif T Chinwalla, Shiaw-Pyng Yang, Andreas Heger, Devin P Locke, Pat Miethke, Paul D Waters, Frederic Veyrunes, Lucinda Fulton, Bob Fulton, Tina Graves, John Wallis, et al.

Journal article | 2008 | Nature

Defensins and the convergent evolution of platypus and reptile venom genes

Camilla M Whittington, Anthony T Papenfuss, Paramjit Bansal, Allan M Torres, Emily SW Wong, Janine E Deakin, Tina Graves, Amber Alsop, Kyriena Schatzkamer, Colin Kremitzki, Chris P Ponting, Peter Temple-Smith, Wesley C Warren, Philip W Kuchel, Katherine Belov

Journal article | 2008 | Genome Res.

Genome analysis of the platypus reveals unique signatures of evolution

Journal article | 2008 | Nature

The role of osmiophilic bodies and Pfg377 expression in female gametocyte emergence and mosquito infectivity in the human malaria parasite Plasmodium falciparum

Tania F de Koning-Ward, Anna Olivieri, Lucia Bertuccini, Andrew Hood, Francesco Silvestrini, Konstantinos Charvalias, Pedro Berzosa Diaz, Grazia Camarda, Terry F McElwain, Tony Papenfuss, Julie Healer, Lucilla Baldassarri, Brendan S Crabb, Pietro Alano, Lisa C Ranford-Cartwright

Journal article | 2008 | Molecular Microbiology

Erratum: Development of plasmacytoid and conventional dendritic cell subtypes from single precursor cells derived in vitro and in vivo (Nature Immunology (2007) 10.1038/ni1522)

SH Naik, P Sathe, HY Park, D Metcalf, AI Proietto, A Dakic, S Carotta, M O'Keeffe, M Bahlo, A Papenfuss, JY Kwak, L Wu, K Shortman

Journal article | 2007 | Nature Immunology

Development of plasmacytoid and conventional dendritic cell subtypes from single precursor cells derived in vitro and in vivo

Shalin H Naik, Priyanka Sathe, Hae-Young Park, Donald Metcalf, Anna I Proietto, Aleksander Dakic, Sebastian Carotta, Meredith O'Keeffe, Melanie Bahlo, Anthony Papenfuss, Jong-Young Kwak, Li Wu, Ken Shortman

Journal article | 2007 | Nature Immunology

A phase I clinical trial with monoclonal antibody ch806 targeting transitional state and mutant epidermal growth factor receptors (vol 104, pg 4071, 2007)

Andrew M Scott, Fook-Thean Lee, Niall Tebbutt, Rebecca Herbertson, Sanjeev S Gill, Zhanqi Liu, Effie Skrinos, Carmel Murone, Timothy H Saunder, Bridget Chappell, Anthony T Papenfuss, Aurora MT Poon, Wendie Hopkins, Fiona E Smyth, Duncan MacGregor, Lawrence M Cher, Achim A Jungbluth, Gerd Ritter, Martin W Brechbiel, Roger Murphy, et al.

Journal article | 2007 | Proceedings of the National Academy of Sciences

A phase I multiple dose, dose escalation study of cG250 monoclonal antibody in patients with advanced renal cell carcinoma.

Ian D Davis, Gregory A Wiseman, Fook-Thean Lee, Denise N Gansen, Wendie Hopkins, Anthony T Papenfuss, Zhanqi Liu, Timothy J Moynihan, Gary A Croghan, Alex A Adjei, Eric W Hoffman, James N Ingle, Lloyd J Old, Andrew M Scott

Journal article | 2007 | Cancer Immunity

The chimeric monoclonal antibody cG250 recognises the G250/CAIX/MN antigen found on 95% of clear cell renal cell carcinomas (RCCs)..

A pilot study of monoclonal antibody cG250 and low dose subcutaneous IL-2 in patients with advanced renal cell carcinoma.

Ian D Davis, Zhanqi Liu, Wayne Saunders, Fook-Thean Lee, Violeta Spirkoska, Wendie Hopkins, Fiona E Smyth, Geoffrey Chong, Anthony T Papenfuss, Bridget Chappell, Aurora Poon, Timothy H Saunder, Eric W Hoffman, Lloyd J Old, Andrew M Scott

Journal article | 2007 | Cancer Immunity

The chimeric monoclonal antibody cG250 recognizes the CAIX/MN antigen. cG250 induces antibody-dependent cellular cytotoxicity (ADC..

Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system

Katherine Belov, Claire E Sanderson, Janine E Deakin, Emily SW Wong, Daniel Assange, Kaighin A McColl, Alex Gout, Bernard de Bono, Alexander D Barrow, Terence P Speed, John Trowsdale, Anthony T Papenfuss

Journal article | 2007 | Genome Research

A phase I biodistribution and pharmacokinetic trial of humanized monoclonal antibody Hu3s193 in patients with advanced epithelial cancers that express the Lewis-Y antigen

Andrew M Scott, Niall Tebbutt, Fook-Thean Lee, Tina Cavicchiolo, Zhanqi Liu, Sanjeev Gill, Aurora MT Poon, Wendie Hopkins, Fiona E Smyth, Carmel Murone, Duncan MacGregor, Anthony T Papenfuss, Bridget Chappell, Timothy H Saunder, Martin W Brechbiel, Ian D Davis, Roger Murphy, Geoffrey Chong, Eric W Hoffman, Lloyd J Old

Journal article | 2007 | Clinical Cancer Research

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Tarjei S Mikkelsen, Matthew J Wakefield, Bronwen Aken, Chris T Amemiya, Jean L Chang, Shannon Duke, Manuel Garber, Andrew J Gentles, Leo Goodstadt, Andreas Heger, Jerzy Jurka, Michael Kamal, Evan Mauceli, Stephen MJ Searle, Ted Sharpe, Michelle L Baker, Mark A Batzer, Panayiotis V Benos, Katherine Belov, Michele Clamp, et al.

Journal article | 2007 | Nature

A phase I clinical trial with monoclonal antibody ch806 targeting transitional state and mutant epidermal growth factor receptors

Andrew M Scott, Fook-Thean Lee, Niall Tebbutt, Rebecca Herbertson, Sanjeev S Gill, Zhanqi Liu, Effie Skrinos, Carmel Murone, Timothy H Saunder, Bridget Chappell, Anthony T Papenfuss, Aurora MT Poon, Wendie Hopkins, Fiona E Smyth, Duncan MacGregor, Lawrence M Cher, Achim A Jungbluth, Martin W Brechbiel, Roger Murphy, Antony W Burgess, et al.

Journal article | 2007 | Proceedings of the National Academy of Sciences of the United States of America

Analysis of a set of Australian northern brown bandicoot expressed sequence tags with comparison to the genome sequence of the South American grey short tailed opossum

Michelle L Baker, Sandra Indiviglio, April M Nyberg, George H Rosenberg, Kerstin Lindblad-Toh, Robert D Miller, Anthony T Papenfuss

Journal article | 2007 | BMC Genomics

Lack of correlation of hypoxic cell fraction and angiogenesis with glucose metabolic rate in non-small cell lung cancer assessed by F-18-fluoromisonidazole and F-18-FDG PET

Martin H Cherk, Serene S Foo, Aurora MT Poon, Simon R Knight, Carmel Murone, Anthony T Papenfuss, John I Sachinidis, Timothy HC Saunder, Graeme J O'Keefe, Andrew M Scott

Journal article | 2006 | Journal of Nuclear Medicine

In silico identification of opossum cytokine genes suggests the complexity of the marsupial immune system rivals that of eutherian mammals.

Emily Sw Wong, Lauren J Young, Anthony T Papenfuss, Katherine Belov

Journal article | 2006 | Immunome Research

BACKGROUND: Cytokines are small proteins that regulate immunity in vertebrate species. Marsupial and eutherian mammals last shared..

Evolution and comparative analysis of the MHC Class III inflammatory region

Janine E Deakin, Anthony T Papenfuss, Katherine Belov, Joseph GR Cross, Penny Coggill, Sophie Palmer, Sarah Sims, Terence P Speed, Stephan Beck, Jennifer A Marshall Graves

Journal article | 2006 | BMC Genomics

A phase I radioimmunolocalization trial of humanized monoclonal antibody huA33 in patients with gastric carcinoma

Junichi Sakamoto, Noboru Oriuchi, Erito Mochiki, Takayuki Asao, Andrew M Scott, Eric W Hoffman, Achim A Jungbluth, Takanori Matsui, FT Lee, Anthony Papenfuss, Hiroyuki Kuwano, Toshitada Takahashi, Keigo Endo, Lloyd J Old

Journal article | 2006 | Cancer Science

Mapping of the Plasmodium chabaudi resistance locus char2

Enmoore Lin, Tony Pappenfuss, Rachel B Tan, Danielle Senyschyn, Melanie Bahlo, Terence P Speed, Simon J Foote

Journal article | 2006 | Infection and Immunity

Regulation of apicomplexan actin-based motility

Jake Baum, Anthony T Papenfuss, Buzz Baum, Terence P Speed, Alan F Cowman

Journal article | 2006 | Nature Reviews Microbiology

Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex

K Belov, JE Deakin, AT Papenfuss, ML Baker, SD Melman, HV Siddle, N Gouin, DL Goode, TJ Sargeant, MD Robinson, MJ Wakefield, S Mahony, JGR Cross, PV Benos, PB Samollow, TP Speed, JAM Graves, RD Miller

Journal article | 2006 | PLoS Biology

Correlation of hypoxic cell fraction and angiogenesis with glucose metabolic rate in gliomas using F-18-fluoromisonidazole, F-18-FDG PET, and immunohistochemical studies

Lawrence M Cher, Carmel Murone, Nathan Lawrentschuk, Shanker Ramdave, Anthony Papenfuss, Anthony Hannah, Graeme J O'Keefe, John I Sachinidis, Salvatore U Berlangieri, Gavin Fabinyi, Andrew M Scott

Journal article | 2006 | Journal of Nuclear Medicine

Pharmacokinetics and biodistribution of humanized monoclonal antibody hu3S193 in a phase I trial of patients with advanced epithelial cancers which express the Lewis-gamma antigen

Z Liu, N Tebbutt, F Lee, T Cavicchiolo, S Gill, AMT Poon, W Hopkins, FE Smyth, C Murone, D MacGregor, A Papenfuss, B Chappell, TH Saunder, NW Brechbiel, ID Davis, R Murphy, G Chong, E Stockert, G Ritter

Journal article | 2005 | Tissue Antigens