Searching journal content for articles similar to Morrissey et al. 34 (6): 937.

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  1. Method: Accurate and efficient detection of gene fusions from RNA sequencing data
    • Sebastian Uhrig,
    • Julia Ellermann,
    • Tatjana Walther,
    • Pauline Burkhardt,
    • Martina Fröhlich,
    • Barbara Hutter,
    • Umut H. Toprak,
    • Olaf Neumann,
    • Albrecht Stenzinger,
    • Claudia Scholl,
    • Stefan Fröhling,
    • and Benedikt Brors
    Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
    ...in STAR's proprietary data format (the file Chimeric.out.junction). Once STAR reports multimapping chimeric alignments in a SAM-compliant format, Arriba can be enhanced to detect fusions that are supported by multimapping reads.Relevance of gene fusions in pancreatic cancerWe combined published data from...
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  2. Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
    • Hyung Joo Lee,
    • Yiran Hou,
    • Ju Heon Maeng,
    • Nakul M. Shah,
    • Yujie Chen,
    • Heather A. Lawson,
    • Hongbo Yang,
    • Feng Yue,
    • and Ting Wang
    Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
    ...). For example, SINE3-1a and HATN9_DR contributed 1016 and 647 CTCF-bound sites in total, respectively.Expression analysis of TE-derived transcriptsTo investigate TE expression levels across different zebrafish tissues, we first used three classical approaches to allocate multimapped reads to genomic loci: equal...
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  3. Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
    • Jiawei Shen,
    • Siyuan Cheng,
    • Deepak Purushotham,
    • Xiaoyu Zhuo,
    • Alan Y Du,
    • Wenjin Zhang,
    • Daofeng Li,
    • and Ting Wang
    Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
    ...at both the individual copy level and at the repeat subfamily level (Figure 1A). Raw genomic sequencing data in FASTQ format were first mapped to the assembly while retaining multi-mapped reads. We then implemented a tool called iteres to access the alignment statistics of repeats in each dataset (Figure...
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