Author details

Full Name

Anthony T Papenfuss

Affiliation

ORCID

Career Start Year

2005

Papers

179

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36853190	7-<i>N</i>-Substituted-3-oxadiazole Quinolones with Potent Antimalarial Activity Target the Cytochrome <i>bc</i><sub>1</sub> Complex.	ACS Infect Dis	2023
36109686	Removing unwanted variation from large-scale RNA sequencing data with PRPS.	Nature Biotechnology	2023
38028140	The microtubule inhibitor eribulin demonstrates efficacy in platinum-resistant and refractory high-grade serous ovarian cancer patient-derived xenograft models.	Ther Adv Med Oncol	2023
37691350	Single-cell RNA sequencing captures patient-level heterogeneity and associated molecular phenotypes in breast cancer pleural effusions.		2023
37952182	cellsig plug-in enhances CIBERSORTx signature selection for multidataset transcriptomes with sparse multilevel modelling.		2023
37686662	A Matched Molecular and Clinical Analysis of the Epithelioid Haemangioendothelioma Cohort in the Stafford Fox Rare Cancer Program and Contextual Literature Review.	Cancers (Basel)	2023
37289866	Taurine deficiency as a driver of aging.		2023
37287132	A systematic review of computational methods for designing efficient guides for CRISPR DNA base editor systems.		2023
36648336	and mutations combine to amplify oncogenic stress and restrict liver overgrowth in a zebrafish model of hepatocellular carcinoma.		2023
37143137	Targeting homologous recombination deficiency in uterine leiomyosarcoma.	J Exp Clin Cancer Res	2023
35134827	StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem.	Bioinformatics	2022
36045381	Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers.	Genome Medicine	2022
36180431	A G358S mutation in the Plasmodium falciparum Na pump PfATP4 confers clinically-relevant resistance to cipargamin.	Nature Communications	2022
36151085	Relationship of circulating Plasmodium falciparum lifecycle stage to circulating parasitemia and total parasite biomass.	Nature Communications	2022
35550554	Tissue-resident memory T cells from a metastatic vaginal melanoma patient are tumor-responsive T cells and increase after anti-PD-1 treatment.	J Immunother Cancer	2022
37721410	Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants.	Gigascience	2022
36776527	Unscrambling cancer genomes via integrated analysis of structural variation and copy number.	Cell Genom	2022
36824522	svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data.	GigaByte	2022
34871039	Identifying Targets of Protective Antibodies against Severe Malaria in Papua, Indonesia, Using Locally Expressed Domains of Plasmodium falciparum Erythrocyte Membrane Protein 1.	Infection and Immunity	2022
34362459	Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome.	Microbiome	2021
34019788	Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition.	Mol Cell	2021
34294073	Transcriptome sequencing and multi-plex imaging of prostate cancer microenvironment reveals a dominant role for monocytic cells in progression.	BMC Cancer	2021
33482892	tidybulk: an R tidy framework for modular transcriptomic data analysis.	Genome Biol	2021
34233875	The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile.	Science advances	2021
33630855	Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents.	PLoS Genetics	2021
34162397	Detection of cell-free microbial DNA using a contaminant-controlled analysis framework.		2021
33678516	Ductal variant prostate carcinoma is associated with a significantly shorter metastasis-free survival.	Eur J Cancer	2021
33626043	Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome.	PLoS Neglected Tropical Diseases	2021
33950524	A single-cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast.	EMBO J	2021
33664264	Evolution of late-stage metastatic melanoma is dominated by aneuploidy and whole genome doubling.	Nat Commun	2021
34253237	GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing.	Genome Biol	2021
33927729	T-Cell Receptor Therapy in the Treatment of Ovarian Cancer: A Mini Review.	Frontiers in Immunology	2021
34028547	Interfacing Seurat with the R tidy universe.	Bioinformatics	2021
33922793	First Description of the Composition and the Functional Capabilities of the Skin Microbial Community Accompanying Severe Scabies Infestation in Humans.	Microorganisms	2021
33709073	Probabilistic outlier identification for RNA sequencing generalized linear models.	NAR Genomics and Bioinformatics	2021
33303574	Combined BRAF, MEK, and CDK4/6 Inhibition Depletes Intratumoral Immune-Potentiating Myeloid Populations in Melanoma.	Cancer Immunol Res	2021
34802442	Safety, infectivity and immunogenicity of a genetically attenuated blood-stage malaria vaccine.	BMC Med	2021
34625515	Melanoma brain metastases that progress on BRAF-MEK inhibitors demonstrate resistance to ipilimumab-nivolumab that is associated with the Innate PD-1 Resistance Signature (IPRES).	J Immunother Cancer	2021
33214714	Author Correction: Determination of RNA structural diversity and its role in HIV-1 RNA splicing.	Nature	2020
31800147	Higher frequency of vertebrate-infecting viruses in the gut of infants born to mothers with type 1 diabetes.	Pediatr Diabetes	2020
32358589	RAF1 rearrangements are common in pancreatic acinar cell carcinomas.	Mod Pathol	2020
32109369	Dual Plasmepsin-Targeting Antimalarial Agents Disrupt Multiple Stages of the Malaria Parasite Life Cycle.		2020
31981004	Tentacle Transcriptomes of the Speckled Anemone (Actiniaria: Actiniidae: Oulactis sp.): Venom-Related Components and Their Domain Structure.	Mar Biotechnol (NY)	2020
33205815	Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix.	GigaScience	2020
32576910	Publisher Correction: CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing.	Sci Rep	2020
32561850	The Hippo pathway oncoprotein YAP promotes melanoma cell invasion and spontaneous metastasis.	Oncogene	2020
33225957	Histone modifications associated with gene expression and genome accessibility are dynamically enriched at Plasmodium falciparum regulatory sequences.	Epigenetics and Chromatin	2020
33001992	High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite.	PLoS Neglected Tropical Diseases	2020
32555469	Determination of RNA structural diversity and its role in HIV-1 RNA splicing.	Nature	2020
32499442	MTOR signaling orchestrates stress-induced mutagenesis, facilitating adaptive evolution in cancer.	Science	2020