Searching journal content for articles similar to Bussotti et al. 26 (5): 705.

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  1. 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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  2. 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...
  3. 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...
  4. 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
    ...inaccessible AG′ within the RNA secondary structure (Kesarwani et al. 2017). Despite these hypotheses, the exact mechanism of the effect of mutations in SF3B1 is still not resolved.Here, we aimed to comprehensively characterize the effects of SF3B1 mutations in cancer using long-read transcriptome sequencing...
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  5. 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
    ...software, as many definitions rely on differences in the current intensity signals obtained from RNA ligated to the DNA adapter.MethodsPlasmid extraction and linearizationWe selected plasmids encoding in vitro transcripts from a T7 promoter that share little sequence similarity (see Supplemental Table S7...
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  6. 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
    ...sequences while acting as a major source to generate isoform diversity at the RNA level (Huang et al. 2021). These data illustrate the distinct roles of local AS events in contributing to isoform and ORF diversity in wild mice brain transcriptomes.DiscussionWe used PacBio Iso-Seq and Illumina RNA...
  7. Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
    • Mari B. Gornitzka,
    • Egil Røsjø,
    • Uddalok Jana,
    • Easton E. Ford,
    • Alan Tourancheau,
    • William D. Lees,
    • Zachary Vanwinkle,
    • Melissa L. Smith,
    • Corey T. Watson,
    • and Andreas Lossius
    Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
    ...SEQUEL II (HD1, MS1, and MS2) or REVIO (HD2).IgA and IgG FLAIRR-seqRNA was extracted from HD1 and HD2 PBMCs using the AllPrep DNA/RNA Mini Kit (Qiagen). IgG and IgA transcripts were resolved by targeted amplification using FLAIRR-seq as described previously (Ford et al. 2023). FLAIRR-seq cDNA libraries...
  8. Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
    • Yongkang Long,
    • Bin Zhang,
    • Shuye Tian,
    • Jia Jia Chan,
    • Juexiao Zhou,
    • Zhongxiao Li,
    • Yisheng Li,
    • Zheng An,
    • Xingyu Liao,
    • Yu Wang,
    • Shiwei Sun,
    • Ying Xu,
    • Yvonne Tay,
    • Wei Chen,
    • and Xin Gao
    Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
    ...for the identification and quantification of sample-specific APA events in a transcriptome-wide manner by enriching the 3′ end of RNA transcripts, followed by high-throughput sequencing (3′ end-seq), such as 3P-seq, Aseq, Poly(A)-seq, and 3′ READS (Jan et al. 2011; Derti et al. 2012; Martin et al. 2012; Hoque et al...
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  9. Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
    • Carolina Monzó,
    • Adam Frankish,
    • and Ana Conesa
    Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
    ...transcriptomic methods. For example, with a few years of completion of the human sequence, analysis of millions of EST, and cDNA sequences identified splicing complexity (Hayashizaki and Carninci 2006) as did RNA-seq assembly efforts from FANTOM (Hon et al. 2017) and MiTranscriptome (Iyer et al. 2015) a decade...
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  10. Method: A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data
    • Yi Qiao,
    • Xiaomeng Huang,
    • Philip J. Moos,
    • Jonathan M. Ahmann,
    • Anthony D. Pomicter,
    • Michael W. Deininger,
    • John C. Byrd,
    • Jennifer A. Woyach,
    • Deborah M. Stephens,
    • and Gabor T. Marth
    Genome Res. January 2024 34: 94-105; Published in Advance January 9, 2024, doi:10.1101/gr.278234.123
    ...-cell RNA sequencing (scRNA-seq), respectively. However, tools are currently lacking to link genomic tumor subclonality with transcriptomic heterogeneity by integrating genomic and single-cell transcriptomic data collected from the same tumor. To address this gap, we developed scBayes, a Bayesian...
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