Tony Papenfuss

Evolution of late-stage metastatic melanoma is dominated by aneuploidy and whole genome doubling

Ismael A Vergara, Christopher P Mintoff, Shahneen Sandhu, Lachlan McIntosh, Richard J Young, Stephen Q Wong, Andrew Colebatch, Daniel L Cameron, Julia Lai Kwon, Rory Wolfe, Angela Peng, Jason Ellul, Xuelin Dou, Clare Fedele, Samantha Boyle, Gisela Mir Arnau, Jeanette Raleigh, Athena Hatzimihalis, Pacman Szeto, Jennifer Mooi, et al.

Journal article  |  2021  |  Nature Communications

Although melanoma is initiated by acquisition of point mutations and limited focal copy number alterations in melanocytes-of-origi..

Combined BRAF, MEK, and CDK4/6 Inhibition Depletes Intratumoral Immune-Potentiating Myeloid Populations in Melanoma

Emily J Lelliott, Stefano Mangiola, Kelly M Ramsbottom, Magnus Zethoven, Lydia Lim, Peter KH Lau, Amanda J Oliver, Luciano G Martelotto, Laura Kirby, Claire Martin, Riyaben P Patel, Alison Slater, Carleen Cullinane, Anthony T Papenfuss, Nicole M Haynes, Grant A McArthur, Jane Oliaro, Karen E Sheppard

Journal article  |  2021  |  Cancer Immunology Research

Combined inhibition of BRAF, MEK, and CDK4/6 is currently under evaluation in clinical trials for patients with melanoma harboring..

tidybulk: an R tidy framework for modular transcriptomic data analysis

Stefano Mangiola, Ramyar Molania, Ruining Dong, Maria A Doyle, Anthony T Papenfuss

Journal article  |  2021  |  Genome Biology

Recently, efforts have been made toward the harmonization of transcriptomic data structures and workflows using the concept of dat..

Histone modifications associated with gene expression and genome accessibility are dynamically enriched at Plasmodium falciparum regulatory sequences

Jingyi Tang, Scott A Chisholm, Lee M Yeoh, Paul R Gilson, Anthony T Papenfuss, Karen P Day, Michaela Petter, Michael F Duffy

Journal article  |  2020  |  Epigenetics and Chromatin

BACKGROUND: The malaria parasite Plasmodium falciparum has an unusually euchromatic genome with poorly conserved positioning of nu..

Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix.

Justin Bedo, Leon Di Stefano, Anthony T Papenfuss

Journal article  |  2020  |  GigaScience

MOTIVATION: A challenge for computational biologists is to make our analyses reproducible-i.e. to rerun, combine, and share, with ..

CD8 TISSUE-RESIDENT MEMORY T CELLS ARE TUMOUR REACTIVE AND INCREASE AFTER IMMUNOTHERAPY IN A CASE OF METASTATIC MUCOSAL MELANOMA

Angela Pizzolla, Simon Keam, Ismael Vergara, Franco Caramia, Minyu Wang, Nikolce Kocovski, Nguyen ThuNgoc, Sean Macdonald, Daniela Tantalo, Pasquale Petrone, Han Xian Aw Yeang, David Gyorki, Alison Weppler, George Au-Yeung, Shahneen Sandhu, Maurizio Perdicchio, Grant McArthur, Tony Papenfuss, Paul Neeson

Conference Proceedings  |  2020  |  Journal for ImmunoTherapy of Cancer

High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite

Pasi K Korhonen, Robin B Gasser, Guangxu Ma, Tao Wang, Andreas J Stroehlein, Neil D Young, Ching-Seng Ang, Deepani D Fernando, Hieng C Lu, Sara Taylor, Simone L Reynolds, Ehtesham Mofiz, Shivashankar H Najaraj, Harsha Gowda, Anil Madugundu, Santosh Renuse, Deborah Holt, Akhilesh Pandey, Anthony T Papenfuss, Katja Fischer

Journal article  |  2020  |  PLoS Neglected Tropical Diseases

The parasitic mite Sarcoptes scabiei is an economically highly significant parasite of the skin of humans and animals worldwide. I..

The Hippo pathway in melanoma.

Xiaomeng Zhang, Lie Yang, Ismael Vergara, Pacman Szeto, Youfang Zhang, Anthony Papenfuss, Mark Shackleton, Kieran Harvey

Conference Proceedings  |  2020  |  MOLECULAR CANCER RESEARCH

The Hippo pathway oncoprotein YAP promotes melanoma cell invasion and spontaneous metastasis

Xiaomeng Zhang, Lie Yang, Pacman Szeto, Gamze Kuser Abali, Youfang Zhang, Aishwarya Kulkarni, Kaushalya Amarasinghe, Jason Li, Ismael A Vergara, Ramyar Molania, Anthony T Papenfuss, Catriona McLean, Mark Shackleton, Kieran F Harvey

Journal article  |  2020  |  Oncogene

Determination of RNA structural diversity and its role in HIV-1 RNA splicing

Phillip J Tomezsko, Vincent DA Corbin, Paromita Gupta, Harish Swaminathan, Margalit Glasgow, Sitara Persad, Matthew D Edwards, Lachlan Mcintosh, Anthony T Papenfuss, Ann Emery, Ronald Swanstrom, Trinity Zang, Tammy CT Lan, Paul Bieniasz, Daniel R Kuritzkes, Athe Tsibris, Silvi Rouskin

Journal article  |  2020  |  Nature

Human immunodeficiency virus 1 (HIV-1) is a retrovirus with a ten-kilobase single-stranded RNA genome. HIV-1 must express all of i..