Search Results - "Varley, E."
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The lingering mysteries of metastatic recurrence in breast cancer
Published in British journal of cancer (05-01-2021)“…Despite being the hallmark of cancer that is responsible for the highest number of deaths, very little is known about the biology of metastasis. Metastatic…”
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2
Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites
Published in Molecular cell (10-10-2013)“…Most human transcription factors bind a small subset of potential genomic sites and often use different subsets in different cell types. To identify mechanisms…”
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3
Dynamic DNA methylation across diverse human cell lines and tissues
Published in Genome research (01-03-2013)“…As studies of DNA methylation increase in scope, it has become evident that methylation has a complex relationship with gene expression, plays an important…”
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4
Widespread plasticity in CTCF occupancy linked to DNA methylation
Published in Genome research (01-09-2012)“…CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin…”
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5
Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation
Published in PLoS genetics (01-08-2011)“…The methylation of cytosines in CpG dinucleotides is essential for cellular differentiation and the progression of many cancers, and it plays an important role…”
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6
CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice
Published in Proceedings of the National Academy of Sciences - PNAS (18-12-2012)“…The closely linked human protocadherin (Pcdh) α, β, and γ gene clusters encode 53 distinct protein isoforms, which are expressed in a combinatorial manner to…”
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7
TXNIP loss expands Myc-dependent transcriptional programs by increasing Myc genomic binding
Published in PLoS biology (17-03-2023)“…The c-Myc protooncogene places a demand on glucose uptake to drive glucose-dependent biosynthetic pathways. To meet this demand, c-Myc protein (Myc henceforth)…”
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Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner
Published in Genome research (01-11-2012)“…Endogenous estrogens that are synthesized in the body impact gene regulation by activating estrogen receptors in diverse cell types. Exogenous compounds that…”
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Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development
Published in Cell reports (Cambridge) (07-08-2018)“…The mammary gland consists of cells with gene expression patterns reflecting their cellular origins, function, and spatiotemporal context. However, knowledge…”
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10
Recurrent read-through fusion transcripts in breast cancer
Published in Breast cancer research and treatment (01-07-2014)“…Read-through fusion transcripts that result from the splicing of two adjacent genes in the same coding orientation are a recently discovered type of chimeric…”
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11
3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression
Published in Nature communications (20-07-2024)“…Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding…”
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12
CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing
Published in PloS one (08-04-2021)“…A substantial fraction of the human genome is difficult to interrogate with short-read DNA sequencing technologies due to paralogy, complex haplotype…”
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13
A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer
Published in Nature communications (08-12-2021)“…Amplification and overexpression of the SOX2 oncogene represent a hallmark of squamous cancers originating from diverse tissue types. Here, we find that…”
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14
Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells Is Associated with a Good Prognosis and Infiltrating Lymphocytes
Published in Cancer immunology research (01-05-2016)“…Triple-negative breast cancer (TNBC) is a subtype with heterogeneous patient outcomes. Approximately 40% of patients experience rapid relapse, while the…”
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Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
Published in Genome research (01-05-2012)“…A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation…”
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16
Transposase mediated construction of RNA-seq libraries
Published in Genome research (01-01-2012)“…RNA-seq has been widely adopted as a gene-expression measurement tool due to the detail, resolution, and sensitivity of transcript characterization that the…”
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17
Genomic regulation of invasion by STAT3 in triple negative breast cancer
Published in Oncotarget (31-01-2017)“…Breast cancer is a heterogeneous disease comprised of four molecular subtypes defined by whether the tumor-originating cells are luminal or basal epithelial…”
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18
Quantification of rare allelic variants from pooled genomic DNA
Published in Nature methods (01-04-2009)“…We report a targeted, cost-effective method to quantify rare single-nucleotide polymorphisms from pooled human genomic DNA using second-generation sequencing…”
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TBCRC 002: a phase II, randomized, open-label trial of preoperative letrozole with or without bevacizumab in postmenopausal women with newly diagnosed stage 2/3 hormone receptor-positive and HER2-negative breast cancer
Published in Breast cancer research : BCR (18-02-2020)“…In preclinical studies, the expression of vascular endothelial growth factor (VEGF) in hormone receptor-positive breast cancer is associated with…”
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20
Early de novo DNA methylation and prolonged demethylation in the muscle lineage
Published in Epigenetics (01-03-2013)“…Myogenic cell cultures derived from muscle biopsies are excellent models for human cell differentiation. We report the first comprehensive analysis of…”
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