Tony Papenfuss

Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome

Alexandra J Roth-Schulze, Megan AS Penno, Katrina M Ngui, Helena Oakey, Esther Bandala-Sanchez, Alannah D Smith, Theo R Allnutt, Rebecca L Thomson, Peter J Vuillermin, Maria E Craig, William D Rawlinson, Elizabeth A Davis, Mark Harris, Georgia Soldatos, Peter G Colman, John M Wentworth, Aveni Haynes, Simon C Barry, Richard O Sinnott, Grant Morahan, et al.

Journal article  |  2021  |  MICROBIOME

BACKGROUND: The gut microbiome changes in response to a range of environmental conditions, life events and disease states. Pregnan..

Transcriptome sequencing and multi-plex imaging of prostate cancer microenvironment reveals a dominant role for monocytic cells in progression

Stefano Mangiola, Patrick McCoy, Martin Modrak, Fernando Souza-Fonseca-Guimaraes, Daniel Blashki, Ryan Stuchbery, Simon P Keam, Michael Kerger, Ken Chow, Chayanica Nasa, Melanie Le Page, Natalie Lister, Simon Monard, Justin Peters, Phil Dundee, Scott G Williams, Anthony J Costello, Paul J Neeson, Bhupinder Pal, Nicholas D Huntington, et al.

Journal article  |  2021  |  BMC CANCER

BACKGROUND: Prostate cancer is caused by genomic aberrations in normal epithelial cells, however clinical translation of findings ..

GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing

Daniel L Cameron, Jonathan Baber, Charles Shale, Jose Espejo Valle-Inclan, Nicolle Besselink, Arne van Hoeck, Roel Janssen, Edwin Cuppen, Peter Priestley, Anthony T Papenfuss

Journal article  |  2021  |  GENOME BIOLOGY

GRIDSS2 is the first structural variant caller to explicitly report single breakends-breakpoints in which only one side can be una..

The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile

Jean Berthelet, Verena C Wimmer, Holly J Whitfield, Antonin Serrano, Thomas Boudier, Stefano Mangiola, Michal Merdas, Farrah El-Saafin, David Baloyan, Jordan Wilcox, Steven Wilcox, Adam C Parslow, Anthony T Papenfuss, Belinda Yeo, Matthias Ernst, Bhupinder Pal, Robin L Anderson, Melissa J Davis, Kelly L Rogers, Frederic Hollande, et al.

Journal article  |  2021  |  SCIENCE ADVANCES

Intratumoral heterogeneity is a driver of breast cancer progression, but the nature of the clonal interactive network involved in ..

Detection of cell-free microbial DNA using a contaminant-controlled analysis framework

Enrique Zozaya-Valdes, Stephen Q Wong, Jeanette Raleigh, Athena Hatzimihalis, Sarah Ftouni, Anthony T Papenfuss, Shahneen Sandhu, Mark A Dawson, Sarah-Jane Dawson

Journal article  |  2021  |  GENOME BIOLOGY

BACKGROUND: The human microbiome plays an important role in cancer. Accumulating evidence indicates that commensal microbiome-deri..

Interfacing Seurat with the R tidy universe.

Stefano Mangiola, Maria A Doyle, Anthony T Papenfuss

Journal article  |  2021  |  Bioinformatics

MOTIVATION: Seurat is one of the most popular software suites for the analysis of single-cell RNA sequencing data. Considering the..

Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition

Simon J Hogg, Olga Motorna, Leonie A Cluse, Timothy M Johanson, Hannah D Coughlan, Ramya Raviram, Robert M Myers, Matteo Costacurta, Izabela Todorovski, Lizzy Pijpers, Stefan Bjelosevic, Tobias Williams, Shannon N Huskins, Conor J Kearney, Jennifer R Devlin, Zheng Fan, Jafar S Jabbari, Ben P Martin, Mohamed Fareh, Madison J Kelly, et al.

Journal article  |  2021  |  MOLECULAR CELL

To separate causal effects of histone acetylation on chromatin accessibility and transcriptional output, we used integrated epigen..

VIRUSBreakend: Viral Integration Recognition Using Single Breakends.

Daniel L Cameron, Nina Jacobs, Paul Roepman, Peter Priestley, Edwin Cuppen, Anthony T Papenfuss

Journal article  |  2021  |  Bioinformatics

MOTIVATION: Integration of viruses into infected host cell DNA can cause DNA damage and disrupt genes. Recent cost reductions and ..

A single-cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast

Bhupinder Pal, Yunshun Chen, Francois Vaillant, Bianca D Capaldo, Rachel Joyce, Xiaoyu Song, Vanessa L Bryant, Jocelyn S Penington, Leon Di Stefano, Nina Tubau Ribera, Stephen Wilcox, Gregory B Mann, Anthony T Papenfuss, Geoffrey J Lindeman, Gordon K Smyth, Jane E Visvader

Journal article  |  2021  |  EMBO JOURNAL

To examine global changes in breast heterogeneity across different states, we determined the single-cell transcriptomes of > 340,0..

First Description of the Composition and the Functional Capabilities of the Skin Microbial Community Accompanying Severe Scabies Infestation in Humans

Charlotte Bernigaud, Martha Zakrzewski, Sara Taylor, Pearl M Swe, Anthony T Papenfuss, Kadaba S Sriprakash, Deborah Holt, Olivier Chosidow, Bart J Currie, Katja Fischer

Journal article  |  2021  |  MICROORGANISMS

Epidemiological studies link Sarcoptes scabiei infection and impetigo. Scabies mites can promote Streptococcus pyogenes (Group A S..