Searching journal content for articles similar to Han et al. 34 (10): 1624.

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  1. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...when we exclude reads of size ≤25 nt (likely miRNAs) except for testis samples (piRNAs). In addition, we showed that read complexity of sRNA-seq experiments is not a determinant either. It is therefore recommended that ≥25 nt fraction at a sequencing depth of 5 million or more reads should be used per...
  2. 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
    ...a systematic comparison between single-cell long-read and conventional short-read RNA sequencing techniques. The transcriptome of approximately 30,000 mouse retina cells was profiled using 1.54 billion Illumina short reads and 1.40 billion Oxford Nanopore Technologies long reads. Consequently, we identify 44...
  3. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...). These structures are central to RNA function and similarly affect RNA-to-read conversion in sequencing, where enzymes, RNA templates, and primer ligands interact. By linking local RNA structures to sequencing efficiency, it becomes possible to identify major contributors to complex biases and design more...
  4. 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
    ...et al. 2022).Transcriptome-wide patterns of m6A RNA modifications have typically been studied using short-read sequencing coupled with either antibody-dependent methods such as methylated RNA immunoprecipitation sequencing (MeRIP-seq) (Meyer et al. 2012) or enzymatic/chemical approaches (Garcia...
  5. 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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  6. Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
    • Alicja Pacholewska,
    • Matthias Lienhard,
    • Mirko Brüggemann,
    • Heike Hänel,
    • Lorina Bilalli,
    • Anja Königs,
    • Felix Heß,
    • Kerstin Becker,
    • Karl Köhrer,
    • Jesko Kaiser,
    • Holger Gohlke,
    • Norbert Gattermann,
    • Michael Hallek,
    • Carmen D. Herling,
    • Julian König,
    • Christina Grimm,
    • Ralf Herwig,
    • Kathi Zarnack,
    • and Michal R. Schweiger
    Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
    ...diversity, and its dysregulation has been linked to various diseases, including cancer. Yet, complex transcriptome studies are challenging to perform with classical RNA-seq owing to the frequent ambiguity in mapping short reads and the difficulties in identifying novel isoforms (Rehrauer et al. 2013; Hooper...
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  7. Method: Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
    • Leszek P. Pryszcz,
    • Gregor Diensthuber,
    • Laia Llovera,
    • Rebeca Medina,
    • Anna Delgado-Tejedor,
    • Luca Cozzuto,
    • Julia Ponomarenko,
    • and Eva Maria Novoa
    Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
    ..., many DRS-related software, such as DeePlexiCon, were trained on polyadenylated RNA molecules, and rely on the identification of the poly(A) homopolymeric region to segment the barcode signal.Recent works have shown that it is possible to sequence very short RNA reads using DRS (e.g., tRNAs) (Thomas et...
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  8. 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
    ...and transcriptomic variants. However, those protocols can only capture RNA molecules via their 3′ or 5′ ends, and short-read (SR) scRNA-seq coverage is heavily biased toward the 3′/5′ end of genes. Recently, methods to call SNVs (Zhang et al. 2023; Muyas et al. 2024) and CNAs (Serin Harmanci et al. 2020; Gao et al...
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  9. 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
    ...splicing sites.Short-read RNA sequencing (srRNA-seq) is the most common and cost-effective approach for studying the transcriptome. In srRNA-seq, transcripts must be inferred computationally, which can lead to inaccuracies in transcript identification (Liu et al. 2016; Newman et al. 2018). Recent advances...
  10. Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
    • Jack A.S. Tierney,
    • Michał Świrski,
    • Håkon Tjeldnes,
    • Jonathan M. Mudge,
    • Joanna Kufel,
    • Nicola Whiffin,
    • Eivind Valen,
    • and Pavel V. Baranov
    Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
    ...representation of biological sequences as graphs, from to transcriptome to translatome.ConclusionThe RDG concept has the potential to significantly impact the study of RNA translation complexity. RDGs, in combination with Ribo-seq data, may shift the focus of differential translation analysis from changes...
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