Searching journal content for articles similar to Zhang et al. 34 (12): 2147.

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  1. Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
    • Natan Belchikov,
    • Justine Hsu,
    • Xiang Jennie Li,
    • Julien Jarroux,
    • Wen Hu,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
    ...on the spatial origins of sequenced molecules, though it was at first too low-resolution to separate molecules from different neighboring cells. Important advances have been made by combining long-read RNA sequencing with either single-cell or spatial approaches. This becomes especially useful for characterizing...
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  2. Resource: The accessible chromatin landscape of the murine hippocampus at single-cell resolution
    • John R. Sinnamon,
    • Kristof A. Torkenczy,
    • Michael W. Linhoff,
    • Sarah A. Vitak,
    • Ryan M. Mulqueen,
    • Hannah A. Pliner,
    • Cole Trapnell,
    • Frank J. Steemers,
    • Gail Mandel,
    • and Andrew C. Adey
    Genome Res. May 2019 29: 857-869; Published in Advance April 1, 2019, doi:10.1101/gr.243725.118
    .... Corresponding authors: adey@ohsu.edu, sinnamon@ohsu.eduAbstractHere we present a comprehensive map of the accessible chromatin landscape of the mouse hippocampus at single-cell resolution. Substantial advances of this work include the optimization of a single-cell combinatorial indexing assay for transposase...
  3. Perspective: The first five years of single-cell cancer genomics and beyond
    • Nicholas E. Navin
    Genome Res. October 2015 25: 1499-1507; doi:10.1101/gr.191098.115
    ...in the clinic, in areas such as early detection, noninvasive monitoring, and guiding targeted therapy. In this perspective, I discuss the progress that has been made and the myriad of unexplored applications that still lie ahead in cancer research and medicine. A single cell is the ultimate denomination...
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  4. Method: RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells
    • Christopher Jen-Yue Wei and
    • Kun Zhang
    Genome Res. April 2020 30: 602-610; Published in Advance March 3, 2020, doi:10.1101/gr.255851.119
    ...sequencing (Sos et al. 2016; Cao et al. 2017; Mulqueen et al. 2018). However, a high-resolution single-cell method for simultaneous phylogenetic fate mapping has yet to be established. In general, there are two broad paradigms of studying development: prospective and retrospective lineage tracing (Woodworth...
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  5. Research: Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes
    • Nathan Lawlor,
    • Joshy George,
    • Mohan Bolisetty,
    • Romy Kursawe,
    • Lili Sun,
    • V. Sivakamasundari,
    • Ina Kycia,
    • Paul Robson,
    • and Michael L. Stitzel
    Genome Res. February 2017 27: 208-222; Published in Advance November 18, 2016, doi:10.1101/gr.212720.116
    ...Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes Nathan Lawlor 1 , 4 , Joshy George 1 , 4 , Mohan Bolisetty 1 , Romy Kursawe 1 , Lili Sun 1 , V...
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  6. Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
    • Laura Blanco-Berdugo,
    • Alexis Garretson,
    • and Beth L. Dumont
    Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
    ...SNV identification, and application of a post hoc filtering pipeline informed by tailored simulations (see Methods) (Garretson et al. 2025). Our strategic use of the reference strain, C57BL/6J, effectively eliminates reference biases to maximize the accuracy of SNV calling and dnSNV discovery. On average, we...
  7. Perspective: Advances in spatial transcriptomic data analysis
    • Ruben Dries,
    • Jiaji Chen,
    • Natalie del Rossi,
    • Mohammed Muzamil Khan,
    • Adriana Sistig,
    • and Guo-Cheng Yuan
    Genome Res. October 2021 31: 1706-1718; doi:10.1101/gr.275224.121
    ...development of single-cell RNA-seq technology (scRNA-seq) applications that made it possible to profile and compare the gene expression patterns of a large number of individual cells within a tissue/organ (Svensson et al. 2018b). Together with the development of a rich set of computational methods for data...
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