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

Displaying results 1-10 of 4512
For checked items
  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
    ..., unlike in tRNAs, m3C sites in poly(A) RNAs are not specifically associated with loop structures.METTL2A downregulates m3C RNAsTo investigate the role of METTL2A in pancreatic cancer cells, we analyzed METTL2A-regulated genes in AsPC-1 cells. Direct RNA sequencing revealed that METTL2A knockdown led...
  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. 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
    ...of RNA reads from the CAST allele for genes exhibiting CAST-biased ASM were 0.557 and 0.558 for long-read and short-read sequencing. Similarly, genes with B6-biased ASM had higher mean proportion of RNA reads from the B6 allele (0.460 and 0.398, respectively). These observations suggest that ASM...
  4. Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
    • Haiyue Liu and
    • Lea H. Gregersen
    Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
    ...and proceeds along the gene body to transcribe RNA (Jonkers and Lis 2015; Core and Adelman 2019; Noe Gonzalez et al. 2021; Aoi and Shilatifard 2023). As with all steps in the transcription process, elongation is tightly regulated to ensure that RNAPII travels along the gene at a proper speed (i.e., elongation...
    OPEN ACCESS ARTICLE
  5. Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
    • Karine Choquet,
    • Louis-Philippe Chaumont,
    • Simon Bache,
    • Autum R. Baxter-Koenigs,
    • and L. Stirling Churchman
    Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
    ...the many introns of a human gene are removed can substantially influence AS, while nascent RNA polyadenylation can affect RNA stability and decay. However, how splicing order and poly(A) tail length are regulated by genetic variation has never been explored. Here, we used direct RNA nanopore sequencing...
  6. 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
    ...increased insight and accuracy. When scRNA-seq data are collected at different times, with different protocols, technologies, or sequencing platforms, the integration becomes increasingly complex. All these factors can affect the expressions of genes in complex ways; some of these differences can...
    OPEN ACCESS ARTICLE
  7. Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
    • Kathleen Zeglinski,
    • Christian Montellese,
    • Matthew E. Ritchie,
    • Monther Alhamdoosh,
    • Cédric Vonarburg,
    • Rory Bowden,
    • Monika Jordi,
    • Quentin Gouil,
    • Florian Aeschimann,
    • and Arthur Hsu
    Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
    ...implementation of lentiviral gene therapies. Here, we compare three long-read sequencing technologies for their ability to detect issues in vector design and determine nanopore direct RNA sequencing to be the most powerful. We show how this approach identifies and quantifies incomplete RNA caused by cryptic...
  8. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...and mutations using data sets from tumor sequencing projects, such as The Cancer Genome Atlas (TCGA) (Hutter and Zenklusen 2018; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020). These tools employ a variety of approaches, including analysis of mutations using gene sequences, protein...
    OPEN ACCESS ARTICLE
  9. Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
    • Prashanthi Ravichandran,
    • Princy Parsana,
    • Rebecca Keener,
    • Kasper D. Hansen,
    • and Alexis Battle
    Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
    ...and AI Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: ajbattle@jhu.eduAbstractGene coexpression networks (GCNs) describe relationships among genes that maintain cellular identity and homeostasis. However, typical RNA-seq experiments often lack sufficient sample...
    OPEN ACCESS ARTICLE
  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...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research