Searching journal content for articles similar to Diensthuber et al. 34 (11): 1865.

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  1. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...-methyladenosine (m6A) modifications in native mRNA. We used human and mouse cells with known genetic variants to assign the allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses reveal the importance of sequences adjacent...
  2. Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
    • Xudong Liu,
    • Ying Ni,
    • Lianwei Ye,
    • Zhihao Guo,
    • Lu Tan,
    • Jun Li,
    • Mengsu Yang,
    • Sheng Chen,
    • and Runsheng Li
    Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
    ...by bacterial DNA modifications (Rand et al. 2017; Wick et al. 2019). Bacterial DNA methylation can occur frequently in diverse sequence contexts. In nanopore direct RNA sequencing, mismatches in modified RNA molecules can be used to detect modifications (Liu et al. 2019). However, this feature has not been...
  3. Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
    • Gianluca Mattei,
    • Marta Baragli,
    • Barbara Gega,
    • Alessandra Mingrino,
    • Martina Chieca,
    • Tommaso Ducci,
    • Gianmaria Frigè,
    • Luca Mazzarella,
    • Romina D'Aurizio,
    • Francesco De Logu,
    • Romina Nassini,
    • Pier Giuseppe Pelicci,
    • and Alberto Magi
    Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
    ...://ftp.ebi.ac.uk/pub/databases/gencode/). Consequently, PoreMeth2 contains the annotation of a large number of possible biotypes that include protein-coding genes, long noncoding RNAs, pseudogenes, and small RNAs.For each gene/transcript, PoreMeth2 considers the longest transcript with the highest number of exons, and the gene model annotations...
  4. Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
    • Alexander Zee,
    • Dori Z.Q. Deng,
    • Matthew Adams,
    • Kayla D. Schimke,
    • Russell Corbett-Detig,
    • Shelbi L. Russell,
    • Xuan Zhang,
    • Robert J. Schmitz,
    • and Christopher Vollmers
    Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
    ...this capability by producing and benchmarking RNA-seq, ChIP-seq, and regular and target-enriched Tn5 libraries. We also explore the use of this approach for rapid evaluation of sequencing library metrics by implementing a real-time analysis workflow.Over the past 15 years, high-throughput short-read sequencing...
  5. Method: Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
    • Haotian Teng,
    • Marcus Stoiber,
    • Ziv Bar-Joseph,
    • and Carl Kingsford
    Genome Res. November 2024 34: 1987-1999; Published in Advance October 15, 2024, doi:10.1101/gr.278960.124
    ...of overfitting. In addition, these methods usually can only provide site-level methylation, losing read-level resolution. We developed an end-to-end m6A modification detection system for nanopore direct RNA sequencing and were among the first to create an m6A-distinguishing base caller. Our system, Xron...
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  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. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ..., expanding the applicability of long-read sequencing across diverse genomic studies (Wenger et al. 2019; Koren et al. 2024). Both platforms are capable of DNA and cDNA sequencing and detecting DNA methylation. At the same time, ONT offers additional functionalities such as adaptive sampling and direct RNA...
  8. Method: Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads
    • Netanya Keil,
    • Carolina Monzó,
    • Lauren McIntyre,
    • and Ana Conesa
    Genome Res. April 2025 35: 987-998; Published in Advance March 3, 2025, doi:10.1101/gr.280021.124
    ...of the quality of transcript models, to develop a read-level quality control framework for replicated long-read RNA-seq experiments. The number and distribution of reads, as well as the number and distribution of unique junction chains (transcript splicing patterns), in SQANTI3 structural categories...
  9. 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
    ...short-read sequences. Recent advances in long-read isoform sequencing enable the detection of fusion transcripts at unprecedented resolution in bulk and single-cell samples. Here, we developed a new computational tool, CTAT-LR-Fusion, to detect fusion transcripts from long-read RNA-seq with or without...
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  10. Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
    • Ezequiel Calvo-Roitberg,
    • Rachel F. Daniels,
    • and Athma A. Pai
    Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
    .... Overview of current long-read RNA sequencing technologiesTwo main companies, Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) offer commercial solutions for long-read RNA sequencing.PacBio. In this technology, a single-stranded circularized cDNA molecule is generated by ligating hairpin...
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