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List of works by Anthony T. Papenfuss

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

scientific article published on 16 July 2019

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

scientific article published on 2 February 2016

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

scientific article published on 12 September 2016

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

scientific article published on 3 March 2017

A limited role for gene duplications in the evolution of platypus venom

scientific article published on 3 August 2011

A newly discovered protein export machine in malaria parasites

scientific article

A novel family of Apicomplexan glideosome-associated proteins with an inner membrane-anchoring role

scientific article (publication date: 11 September 2009)

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

scientific article published in June 2007

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

scholarly article

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

scientific article

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

scientific article published in November 2006

A phase I trial of humanized monoclonal antibody A33 in patients with colorectal carcinoma: biodistribution, pharmacokinetics, and quantitative tumor uptake

scientific article published on July 2005

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

scientific article

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

scientific article published on 4 November 2010

A statistical framework for analyzing deep mutational scanning data

scientific article published on 07 August 2017

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

scientific article published on 8 May 2017

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

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

scientific article published on 13 February 2007

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

scientific article published on 02 January 2009

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

scientific article published on 20 November 2020

BET inhibitor resistance emerges from leukaemia stem cells

scientific article published on 14 September 2015

BRAF/NRAS wild-type melanomas have a high mutation load correlating with histologic and molecular signatures of UV damage

scientific article published on 5 July 2013

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

scientific article published in Nature Communications

Bioinformatics Analysis of Sequence Data

scientific article published in 2016

Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment

scientific article

Blood-stage Plasmodium berghei infection generates a potent, specific CD8+ T-cell response despite residence largely in cells lacking MHC I processing machinery

scientific article published on 13 October 2011

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

scientific article published on 20 June 2016

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

scientific article published on 22 May 2014

CLOVE: classification of genomic fusions into structural variation events

scientific article published on 20 July 2017

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

scientific article published on 23 April 2019

Canary: an atomic pipeline for clinical amplicon assays

scientific article published on 15 December 2017

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

scientific article published on 10 May 2007

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

scientific article published on 17 March 2017

Clinical cancer genomic analysis: data engineering required

scientific article

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

scientific article published on 07 September 2016

Clustered somatic mutations are frequent in transcription factor binding sites in melanoma and other cutaneous malignancies

article

Combined BRAF, MEK and CDK4/6 inhibition depletes intratumoral immune-potentiating myeloid populations in melanoma

scientific article published on 10 December 2020

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

scientific article

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

scientific article published on 19 July 2019

Correction to: A statistical framework for analyzing deep mutational scanning data

scientific article published on 7 February 2018

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

scientific article published in March 2006

Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail

scientific article published on 23 August 2017

Crystal structure of theLeishmania majorMIX protein: A scaffold protein that mediates protein-protein interactions

scientific article

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

scientific article published on 11 June 2018

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

scientific article published on 19 September 2016

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

scientific article published on 21 August 2017

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

article

Defensins and the convergent evolution of platypus and reptile venom genes

scientific article published in June 2008

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

scientific article published on 7 September 2017

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

scientific article published on 06 May 2020

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

scientific article published on 7 October 2007

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

scientific article

Digital PCR of Genomic Rearrangements for Monitoring Circulating Tumour DNA.

scientific article published on January 2016

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

scientific article

Diversity of conotoxin gene superfamilies in the venomous snail, Conus victoriae

scientific article (publication date: 2014)

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

scientific article published on January 2009

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

scientific article published on 2 September 2016

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

scientific article

Enrich2: a statistical framework for analyzing deep mutational scanning data

scientific article published on 25 September 2016

Epidermal wound repair is regulated by the planar cell polarity signaling pathway

scientific article published on 20 July 2010

Evolution and comparative analysis of the MHC Class III inflammatory region

scientific article

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

scientific article published on 7 November 2012

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

scientific article published on 27 February 2019

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

scientific article

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

scientific article

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

scientific article published in September 2008

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

scientific article published on 12 July 2021

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

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

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article published in Nature

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

scientific article

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

scientific article

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

article

Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer

scientific article published in February 2012

Genomic Identification of Chemokines and Cytokines in Opossum

scientific article published in March 2011

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

scientific article published on 06 March 2017

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

scientific article published on 02 June 2016

Genomic restructuring in the Tasmanian devil facial tumour: chromosome painting and gene mapping provide clues to evolution of a transmissible tumour

scientific article

HYSYS: have you swapped your samples?

scientific article

Hatching time for monotreme immunology

scientific article published in 2009

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

scientific article published in October 2020

Hormone-like peptides in the venoms of marine cone snails

scientific article published on 21 August 2015

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

scientific article published on January 2013

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

scientific article published on 26 November 2015

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

scientific article published on 24 March 2014

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

scientific article published on 14 July 2009

Immunome database for marsupials and monotremes

scientific article

Improving the Power of Structural Variation Detection by Augmenting the Reference

scientific article published on 31 August 2015

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

scientific article

Inferring structural variant cancer cell fraction

scientific article published on 05 February 2020

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

scientific article

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

scientific article published on 3 March 2015

Insight into Evolution of Gene Regulation Networks from the Opossum Genome

scientific article published in 2010

Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants

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

scientific article published on 12 June 2009

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

scientific article published in December 2006

MTOR signaling orchestrates stress-induced mutagenesis, facilitating adaptive evolution in cancer

scientific article published on 01 June 2020

Malaria parasite DNA-harbouring vesicles activate cytosolic immune sensors

scientific article

Marsupial Sequencing Projects and Bioinformatics Challenges

scientific article published in 2010

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

scientific article published on 22 July 2015

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

scientific article published on 04 November 2019

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

scientific article published on 12 February 2016

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

scientific article published on 20 April 2009

NLRP1 restricts butyrate producing commensals to exacerbate inflammatory bowel disease

scientific article published in Nature Communications

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

scientific article published in 2009

Novel venom gene discovery in the platypus.

scientific article published on 29 September 2010

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

scientific article published on 4 April 2018

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

scientific article published on 09 December 2016

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

scientific article

Phase I trial of 131I-huA33 in patients with advanced colorectal carcinoma

scientific article

Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles.

scientific article

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

scientific article published on 24 April 2019

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

scientific article published on 23 June 2020

RAF1 rearrangements are common in pancreatic acinar cell carcinomas

scientific article published on 01 May 2020

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

scientific article published in March 2006

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

scientific article published on 9 March 2017

Regulation of apicomplexan actin-based motility

scientific article published on August 2006

SVclone: inferring structural variant cancer cell fraction

scientific article published on 4 August 2017

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

scientific article published on 16 March 2017

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

scientific article published on 22 January 2014

Somatic Hypermutation of the YAP Oncogene in a Human Cutaneous Melanoma

scholarly article published on 04 March 2019

TERT structural rearrangements in metastatic pheochromocytomas

scientific article published on 3 October 2017

Targeting of the tumor suppressor GRHL3 by a miR-21-dependent proto-oncogenic network results in PTEN loss and tumorigenesis.

scientific article published in November 2011

Taurine deficiency as a driver of aging

scientific article published on 08 June 2023

Telomere dynamics and homeostasis in a transmissible cancer

scientific article published on 29 August 2012

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

scientific article published on 24 January 2020

The Tasmanian devil microbiome-implications for conservation and management

scientific article published on 21 December 2015

The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer

scientific article

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

scientific article published on 8 November 2016

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

scientific article published in 2017

The architecture and evolution of cancer neochromosomes

scientific article published on 10 November 2014

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

scientific article published on 12 January 2016

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

scientific article (publication date: 20 June 2012)

The life history of neochromosomes revealed.

scientific article published on 23 January 2015

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

scientific article published on 11 December 2007

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

scientific article published in January 2015

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

scientific article published on 23 March 2018

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

scientific article published on 22 July 2021

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

scientific article published on 19 August 2011

Transmissible cancers in an evolutionary context

scientific article published on July 2016

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

scientific article published on 7 March 2011

Two of a kind: transmissible Schwann cell cancers in the endangered Tasmanian devil (Sarcophilus harrisii)

scientific article published on 02 August 2019

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

scientific article published on 15 December 2015

Understanding and utilising mammalian venom via a platypus venom transcriptome

scientific article published on 25 December 2008

Unscrambling cancer genomes via integrated analysis of structural variation and copy number

scientific article published in 2022

Whole genome analysis of a schistosomiasis-transmitting freshwater snail.

scientific article published on 16 May 2017

tidyHeatmap: an R package for modular heatmap production based on tidy principles

scientific article published on 03 August 2020

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