Induction of APOBEC3-mediated genomic damage in urothelium implicates BK polyomavirus (BKPyV) as a hit-and-run driver for bladder cancer

CC and CXC chemokines play key roles in the development of polyomaviruses related pathological conditions

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The repertoire of mutational signatures in human cancer

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The landscape of viral associations in human cancers

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Procarcinogen Activation and Mutational Signatures Model the Initiation of Carcinogenesis in Human Urothelial Tissues In Vitro

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Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots

(2020) Pégah Jalili et al.   Nature Communications

Extensive heterogeneity in somatic mutation and selection in the human bladder

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Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B

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Polyomavirus T Antigen Induces APOBEC3B Expression Using an LXCXE-Dependent and TP53-Independent Mechanism

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Viral replication centers and the DNA damage response in JC virus-infected cells

(2019) Kimberly D. Erickson et al.   VIROLOGY

Temporal proteomic analysis of BK polyomavirus infection reveals virus-induced G2 arrest and highly effective evasion of innate immune sensing

(2019) Laura G. Caller et al.   JOURNAL OF VIROLOGY

Increasing of the interferon-γ gene expression during polyomavirus BK infection in kidney transplant patients

(2019) Neda Zareei et al.   MICROBIAL PATHOGENESIS

An immunoinformatic approach to universal therapeutic vaccine design against BK virus

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Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

APOBEC3A is a prominent cytidine deaminase in breast cancer

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CXCL9, CXCL10, CXCL11/CXCR3 axis for immune activation – A target for novel cancer therapy

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Agnoprotein Is an Essential Egress Factor during BK Polyomavirus Infection

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Defining the frequency of human papillomavirus and polyomavirus infection in urothelial bladder tumours

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Non-overlapping Control of Transcriptome by Promoter- and Super-Enhancer-Associated Dependencies in Multiple Myeloma

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Incidences and oncological outcomes of urothelial carcinoma in kidney transplant recipients

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Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells

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Census and evaluation of p53 target genes

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Functional Upregulation of the DNA Cytosine Deaminase APOBEC3B by Polyomaviruses

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Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors

(2016) Candace D Middlebrooks et al.   NATURE GENETICS

Brincidofovir (CMX001) Inhibits BK Polyomavirus Replication in Primary Human Urothelial Cells

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DNA double-strand break repair is impaired in presenescent Syrian hamster fibroblasts

(2015) Ljudmila Solovjeva et al.   BMC MOLECULAR BIOLOGY

Characteristics of polyomavirus BK (BKPyV) infection in primary human urothelial cells

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A novel significance score for gene selection and ranking

(2012) Yufei Xiao et al.   BIOINFORMATICS

The Forkhead Transcription Factor FOXM1 Controls Cell Cycle-Dependent Gene Expression through an Atypical Chromatin Binding Mechanism

(2012) X. Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

The variant call format and VCFtools

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Spectrum of Cancer Risk Among US Solid Organ Transplant Recipients

(2011) Eric A. Engels et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

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Innate Immune Signaling Induces High Levels of TC-specific Deaminase Activity in Primary Monocyte-derived Cells through Expression of APOBEC3A Isoforms

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Seroepidemiology of Human Polyomaviruses

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