Searching journal content for articles similar to Rao et al. 35 (8): 1842.

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  1. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ..., Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China 200438 ↵7 These authors contributed equally to this work. Corresponding author: hongliyan@smmu.edu.cnAbstractHepatitis B virus (HBV) integration is a key driver of hepatocellular carcinoma (HCC) occurrence and progression...
  2. Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
    • Yueqiang Song,
    • Fuyuan Li,
    • Shangzi Wang,
    • Yuntong Wang,
    • Cong Lai,
    • Lian Chen,
    • Ning Jiang,
    • Jin Li,
    • Xingdong Chen,
    • Swneke D. Bailey,
    • and Xiaoyang Zhang
    Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
    ...and Larsson 2021). As a major type of structural variants, duplication of oncogenes is a key cancer driver event causing oncogene overexpression (Stratton et al. 2009; Zack et al. 2013). In addition to the oncogenes themselves, we and others have recently shown that noncoding enhancers are also critical...
  3. Research: Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity
    • Zdenek Andrysik,
    • Matthew D. Galbraith,
    • Anna L. Guarnieri,
    • Sara Zaccara,
    • Kelly D. Sullivan,
    • Ahwan Pandey,
    • Morgan MacBeth,
    • Alberto Inga,
    • and Joaquín M. Espinosa
    Genome Res. October 2017 27: 1645-1657; Published in Advance September 13, 2017, doi:10.1101/gr.220533.117
    ...53 activity is abrogated by other oncogenic events, such as hyperactivation of its endogenous repressors MDM2 or MDM4. Despite identification of hundreds of genes regulated by this transcription factor, it remains unclear which direct target genes and downstream pathways are essential for the tumor...
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  4. Research: High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
    • Walter Muskovic,
    • Eve Slavich,
    • Ben Maslen,
    • Dominik C. Kaczorowski,
    • Joseph Cursons,
    • Edmund Crampin,
    • and Maria Kavallaris
    Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
    ...Corresponding authors: w.muskovic@garvan.org.au, m.kavallaris@ccia.unsw.edu.auAbstractThe advent of massively parallel sequencing revealed extensive transcription beyond protein-coding genes, identifying tens of thousands of long noncoding RNAs (lncRNAs). Selected functional examples raised the possibility...
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  5. Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
    • Parijat Senapati,
    • Masaru Miyano,
    • Rosalyn W. Sayaman,
    • Mudaser Basam,
    • Amy Leung,
    • Mark A. LaBarge,
    • and Dustin E. Schones
    Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
    ...-specific drivers of aging, which are essential to understand disease risk (Bell et al. 2019).Age is the most significant risk factor for breast cancer, as >75% of breast cancers are diagnosed in women over the age of 50 (Jemal et al. 2007). This is especially true for luminal subtypes of breast cancer, which...
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  6. Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
    • Swati Venkat,
    • Arwen A. Tisdale,
    • Johann R. Schwarz,
    • Abdulrahman A. Alahmari,
    • H. Carlo Maurer,
    • Kenneth P. Olive,
    • Kevin H. Eng,
    • and Michael E. Feigin
    Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
    ...Consortium 2015). We performed a systems level analysis to identify trends in APA, impacts on gene expression, and effects of miRNA regulation. Our in-depth analysis reveals APA as a recurrent, widespread mechanism underlying oncogenic gene expression changes through loss of tumor-suppressive mi...
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  7. Perspective: Linking RNA biology to lncRNAs
    • Loyal A. Goff and
    • John L. Rinn
    Genome Res. October 2015 25: 1456-1465; doi:10.1101/gr.191122.115
    ...Linking RNA biology to lncRNAs Loyal A. Goff 1 , 2 and John L. Rinn 3 , 4 , 5 1McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA; 2Department of Neuroscience, Johns Hopkins University...
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  8. Resource: Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes
    • Andrea Halaburkova,
    • Vincent Cahais,
    • Alexei Novoloaca,
    • Mariana Gomes da Silva Araujo,
    • Rita Khoueiry,
    • Akram Ghantous,
    • and Zdenko Herceg
    Genome Res. October 2020 30: 1517-1532; Published in Advance September 22, 2020, doi:10.1101/gr.268292.120
    ...; it is also the first experimental effort to specifically identify ERG drivers (epidrivers) and characterize their deregulation and functional impact in oncogenic processes.Although it has long been known that human cancers harbor both genetic and epigenetic changes, with an intricate interplay between...
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  9. Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
    • Yi Liao,
    • Xinwen Zhang,
    • Mahul Chakraborty,
    • and J.J. Emerson
    Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
    ...Topologically associating domains and their role in the evolution of structure and function in Drosophila Yi Liao1, Xinwen Zhang1, Mahul Chakraborty1 and J.J. Emerson1,2 1Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA; 2Center for Complex...
  10. Method: Mutual exclusivity analysis identifies oncogenic network modules
    • Giovanni Ciriello,
    • Ethan Cerami,
    • Chris Sander,
    • and Nikolaus Schultz
    Genome Res. February 2012 22: 398-406; Published in Advance September 9, 2011, doi:10.1101/gr.125567.111
    ...pathway analysis has been a powerful tool in cancer genomics, our knowledge of oncogenic pathway modules is incomplete. To systematically identify such modules, we have developed a novel method, Mutual Exclusivity Modules in cancer (MEMo). The method uses correlation analysis and statistical tests...
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