Searching journal content for articles similar to Battle et al. 24 (1): 14.

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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
    ...), and the development of microarrays first (Schena et al. 1995) and high-throughput sequencing later (Margulies et al. 2005) boosted our capacity to analyze transcriptomes. Nowadays, the most common technique to analyze gene expression is RNA sequencing (RNA-seq). This technique consists of first isolating RNA from...
  2. 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
    ...and is expected to improve the interpretation of transcriptomic data in future genomic studies.RNA sequencing (RNA-seq) has become an essential tool for characterizing transcriptomes (Stark et al. 2019), enabling comprehensive profiling of gene expression, including tissue-specific patterns, disease...
  3. 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
    ..., the distribution and function of m3C in poly(A) RNA remain largely unknown.In this study, we aim to identify METTL2A-mediated m3C sites in poly(A) RNA using nanopore-based comparative direct RNA sequencing to characterize their distribution and function.ResultsMETTL2A is required for the proliferation...
  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
    ...short-read sequencing strategies to detect m6A are inherently limited to aggregate measurements and are incapable of quantification at an individual molecular level.In contrast, Oxford Nanopore Technologies (ONT) RNA sequencing enables direct detection of RNA modifications such as m6A with single...
  5. Method: Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated
    • Sindri Emmanúel Antonsson and
    • Páll Melsted
    Genome Res. August 2025 35: 1832-1841; Published in Advance July 7, 2025, doi:10.1101/gr.279886.124
    ..., Miller HW, McElrath MJ, Prlic M, et al. 2015. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol 16: 278. doi:10.1186/s13059-015-0844-5 ↵Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C...
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  6. 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
    ...-Marín et al. 2021).Single-cell RNA sequencing (scRNA-seq) has widely been used to characterize cell-specific transcriptomic differences in various neuronal tissues (Tian et al. 2021). Currently, scRNA-seq data primarily consist of short-read sequencing technologies because of their high accuracy...
  7. Method: Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads
    • Seong Woo Han,
    • San Jewell,
    • Andrei Thomas-Tikhonenko,
    • and Yoseph Barash
    Genome Res. October 2024 34: 1624-1635; Published in Advance September 25, 2024, doi:10.1101/gr.278659.123
    ...These authors contributed equally to this work. Corresponding author: yosephb@upenn.eduAbstractMapping transcriptomic variations using either short- or long-read RNA sequencing is a staple of genomic research. Long reads are able to capture entire isoforms and overcome repetitive regions, whereas short reads...
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  8. Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
    • Gage S. Black,
    • Xiaomeng Huang,
    • Yi Qiao,
    • Philip Moos,
    • Deepa Sampath,
    • Deborah M. Stephens,
    • Jennifer A. Woyach,
    • and Gabor T. Marth
    Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
    ...-mutated subclones exhibit distinct transcriptomic behavior when compared to other cancer subclones. To achieve these goals, we use scBayes, which integrates bulk DNA sequencing and single-cell RNA sequencing (scRNA-seq) data to genotype individual cells for subclone-defining mutations. Although the most common...
  9. 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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  10. Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ..., catalyzed by the adenosine deaminase acting on RNA (ADAR) enzymes, is a posttranscriptional process that modifies RNA sequences and diversifies the transcriptome. ADARs bind to double-stranded RNA (dsRNA) and their specificity and efficiency are affected by the structural properties of these substructures...
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