Searching journal content for articles similar to Uhrig et al..

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  1. Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m3C sites in poly(A) RNA
    • Shuhei Mitsutomi,
    • Anzu Sugawara,
    • Masahide Seki,
    • Yutaka Suzuki,
    • Sotaro Miyao,
    • Haozhe Du,
    • Kenji Takahashi,
    • Yusuke Mizukami,
    • Kenzui Taniue,
    • and Nobuyoshi Akimitsu
    Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
    ..., long-read sequencing-based methods, using single-molecule real-time (SMRT) or nanopore sequencing technology, can directly detect modified bases, eliminating the need for such preprocessing (Moshitch-Moshkovitz et al. 2022; Kong et al. 2023). The SMRT sequencing platform has been adapted for direct RNA...
  2. Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
    • Arthur Dondi,
    • Nico Borgsmüller,
    • Pedro F. Ferreira,
    • Brian J. Haas,
    • Francis Jacob,
    • Viola Heinzelmann-Schwarz,
    • Tumor Profiler Consortium,
    • and Niko Beerenwinkel
    Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
    .... 2021, 2023) in SR scRNA-seq were developed, compensating the 3′ capture bias by pooling large amounts of cells or sequencing at very high read depths. However, SR scRNA-seq is unsuited to detect isoforms or gene fusions. Long-read (LR) scRNA-seq, in contrast, sequences full-length RNA molecules, and we...
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  3. Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
    • Qian Qin,
    • Victoria Popic,
    • Kirsty Wienand,
    • Houlin Yu,
    • Emily White,
    • Akanksha Khorgade,
    • Asa Shin,
    • Christophe Georgescu,
    • Catarina D. Campbell,
    • Arthur Dondi,
    • Niko Beerenwinkel,
    • Francisca Vazquez,
    • Aziz M. Al'Khafaji,
    • and Brian J. Haas
    Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
    .... During the past decade, RNA-seq has been the preferred assay for comprehensive gene fusion detection due to its lower cost than whole- sequencing (WGS) and directly measuring the transcripts arising from the gene fusions. Illumina short-read RNA-seq has become routine for such studies, and numerous...
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  4. Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
    • Meng Wang,
    • Yumei Li,
    • Jun Wang,
    • Soo Hwan Oh,
    • Yexuan Cao,
    • and Rui Chen
    Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
    ...the transcriptomic landscape. What is particularly noteworthy is that certain genes can fuse with others that are not immediately adjacent to them on the same chromosome, highlighting the complexity and flexibility of gene fusion events in the context of scRNA sequencing data. These findings may have implications...
  5. Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
    • Wenyu Zhang,
    • Anja Guenther,
    • Yuanxiao Gao,
    • Kristian Ullrich,
    • Bruno Huettel,
    • Aftab Ahmad,
    • Lei Duan,
    • Kaizong Wei,
    • and Diethard Tautz
    Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
    ...: wyzhang@nwpu.edu.cn, tautz@evolbio.mpg.deAbstractThe ability to generate multiple RNA transcript isoforms from the same gene is a general phenomenon in eukaryotes. However, the complexity and diversity of alternative isoforms in natural populations remain largely unexplored. Using a newly developed full...
  6. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...exon 1 of the APC gene (Fig. 2D). RNA-seq analysis revealed a substantial decrease in APC expression in the tumor sample (tumor fragments per kilobase of transcript per million fragments mapped (FPKM): 0.296 vs. normal FPKM: 2.262). The SV was not detected by short-read sequencing, likely because...
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  7. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...that enables the detection and quantification of RNA transcripts of interest. This method involves separating RNA molecules by size using gel electrophoresis, followed by immobilization onto a membrane for hybridization with a labeled sequence-specific probe (He and Green 2013). Despite its reliability, NB has...
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  8. Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
    • Joshua Lee,
    • Elizabeth A. Snell,
    • Joanne Brown,
    • Charlotte E. Booth,
    • Rosamonde E. Banks,
    • Daniel J. Turner,
    • Naveen S. Vasudev,
    • and Dimitris Lagos
    Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
    ...of disease relapse and the discovery of novel genes and transcripts with evidence of cancer cell-intrinsic expression and potential association with disease relapse.ResultsTo demonstrate the feasibility of utilizing long-read RNA sequencing technologies for characterizing ccRCC transcriptomes in archival...
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  9. Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
    • Irmgard U. Haussmann,
    • Thomas C. Dix,
    • David W.J. McQuarrie,
    • Veronica Dezi,
    • Abdullah I. Hans,
    • Roland Arnold,
    • and Matthias Soller
    Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
    ...selection of efficient sgRNAs, we developed web-based PlatinumCRISPr, an sgRNA design tool to evaluate base-pairing and sequence composition parameters for optimal design of highly efficient sgRNAs for Cas9 editing. We applied this tool to select sgRNAs to efficiently generate gene deletions in Drosophila...
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  10. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...variations in the noncoding regions that regulate RNA expression are not explored (Ramsuran et al. 2015). HLA typing on the PacBio platform was demonstrated by Albrecht et al. by combining highly accurate MiSeq data with lower accuracy full-length RS II data to sequence a long HLA amplicon. The full...
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