Search Results - "Varley, E."

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  1. 1

    The lingering mysteries of metastatic recurrence in breast cancer by Riggio, Alessandra I., Varley, Katherine E., Welm, Alana L.

    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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    Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites by Gertz, Jason, Savic, Daniel, Varley, Katherine E., Partridge, E. Christopher, Safi, Alexias, Jain, Preti, Cooper, Gregory M., Reddy, Timothy E., Crawford, Gregory E., Myers, Richard M.

    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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    Dynamic DNA methylation across diverse human cell lines and tissues by Varley, Katherine E, Gertz, Jason, Bowling, Kevin M, Parker, Stephanie L, Reddy, Timothy E, Pauli-Behn, Florencia, Cross, Marie K, Williams, Brian A, Stamatoyannopoulos, John A, Crawford, Gregory E, Absher, Devin M, Wold, Barbara J, Myers, Richard M

    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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    Widespread plasticity in CTCF occupancy linked to DNA methylation by Wang, Hao, Maurano, Matthew T, Qu, Hongzhu, Varley, Katherine E, Gertz, Jason, Pauli, Florencia, Lee, Kristen, Canfield, Theresa, Weaver, Molly, Sandstrom, Richard, Thurman, Robert E, Kaul, Rajinder, Myers, Richard M, Stamatoyannopoulos, John A

    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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    Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation by Gertz, Jason, Varley, Katherine E, Reddy, Timothy E, Bowling, Kevin M, Pauli, Florencia, Parker, Stephanie L, Kucera, Katerina S, Willard, Huntington F, Myers, Richard M

    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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    CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice by Guo, Ya, Monahan, Kevin, Wu, Haiyang, Gertz, Jason, Varley, Katherine E., Li, Wei, Myers, Richard M., Maniatis, Tom, Wu, Qiang

    “…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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    TXNIP loss expands Myc-dependent transcriptional programs by increasing Myc genomic binding by Lim, Tian-Yeh, Wilde, Blake R, Thomas, Mallory L, Murphy, Kristin E, Vahrenkamp, Jeffery M, Conway, Megan E, Varley, Katherine E, Gertz, Jason, Ayer, Donald E

    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 by Gertz, Jason, Reddy, Timothy E, Varley, Katherine E, Garabedian, Michael J, Myers, Richard M

    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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    Recurrent read-through fusion transcripts in breast cancer by Varley, Katherine E., Gertz, Jason, Roberts, Brian S., Davis, Nicholas S., Bowling, Kevin M., Kirby, Marie K., Nesmith, Amy S., Oliver, Patsy G., Grizzle, William E., Forero, Andres, Buchsbaum, Donald J., LoBuglio, Albert F., Myers, Richard M.

    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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    3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression by Mortenson, Katelyn L., Dawes, Courtney, Wilson, Emily R., Patchen, Nathan E., Johnson, Hailey E., Gertz, Jason, Bailey, Swneke D., Liu, Yang, Varley, Katherine E., Zhang, Xiaoyang

    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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    CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing by Wallace, Amelia D, Sasani, Thomas A, Swanier, Jordan, Gates, Brooke L, Greenland, Jeff, Pedersen, Brent S, Varley, Katherine E, Quinlan, Aaron R

    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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    Transposase mediated construction of RNA-seq libraries by Gertz, Jason, Varley, Katherine E, Davis, Nicholas S, Baas, Bradley J, Goryshin, Igor Y, Vaidyanathan, Ramesh, Kuersten, Scott, Myers, Richard M

    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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    Quantification of rare allelic variants from pooled genomic DNA by Mitra, Robi D, Druley, Todd E, Vallania, Francesco L M, Wegner, Daniel J, Varley, Katherine E, Knowles, Olivia L, Bonds, Jacqueline A, Robison, Sarah W, Doniger, Scott W, Hamvas, Aaron, Cole, F Sessions, Fay, Justin C

    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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    Early de novo DNA methylation and prolonged demethylation in the muscle lineage by Tsumagari, Koji, Baribault, Carl, Terragni, Jolyon, Varley, Katherine E., Gertz, Jason, Pradhan, Sirharsa, Badoo, Melody, Crain, Charlene M., Song, Lingyun, Crawford, Gregory E., Myers, Richard M., Lacey, Michelle, Ehrlich, Melanie

    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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