Searching journal content for articles similar to Lalonde et al. 21 (4): 545.

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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
    ...into the effects of genetic variation on splicing and RNA abundance. Furthermore, the ability to directly sequence RNA enables the detection of RNA modifications in tandem with ascertaining the allelic origin of each molecule. Here, we leverage these advantages to determine allele-biased patterns of N6...
  2. 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...
  3. 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...
  4. Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
    • Hsin-Yen Larry Wu,
    • Isaiah D. Kaufman,
    • and Polly Yingshan Hsu
    Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
    ...range are shown in gray. Genomic or transcript coordinates on the chromosomes are indicated below the gene models. (A) Only Ribo-seq and RNA-seq profiles are presented on top of the annotated gene models. (B) An additional DNA sequence track was added, but only the start and stop codons are displayed...
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  5. 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
    ..., in which the expression of the mutation was confirmed in the TRACERx cohort by RNA-seq (Supplemental Table 5; Frankell et al. 2023). Positive CESs were observed in FIEs in a majority of these functional families (n = 24/28 families) in TCGA pancancer (Supplemental Fig. 17), with somewhat larger effects...
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  6. 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
    ...editing sites overlap regions which are likely to produce strong intramolecular dsRNA structures, while the gene overlap region itself shows no significant editing (Supplementary Figure S5). Consistent with this finding, our exploration of the human revealed that while cis-NAT expression is not rare...
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  7. Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
    • Yuange Duan,
    • Min Huang,
    • Lin Ye,
    • Ling Ma,
    • Yashuai Wu,
    • Yating Du,
    • Jiyao Liu,
    • Fan Song,
    • Li Tian,
    • Wanzhi Cai,
    • Hu Li,
    • Xin Zhou,
    • and Shiqi Luo
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
    ...sites in GF mapped to 12 unique genes, with no significant difference in expression level between two conditions (P=0.48, Wilcoxon rank-sum test). This suggests that the differential RNA editing levels at specific sites are more likely to reflect changes in editing Table 1. Sequencing depth of samples...
  8. 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
    ...: wyzhang@nwpu.edu.cn, tautz@evolbio.mpg.deAbstractThe ability to generate multiple RNA transcript isoforms from the same gene is a general phenomenon in eukaryotes. However, the complexity and diversity of alternative isoforms in natural populations remain largely unexplored. Using a newly developed full...
  9. Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
    • Pengju Zhao,
    • Jiayi He,
    • Chen Peng,
    • Yuelang Zhang,
    • Chong Wang,
    • Dongyou Yu,
    • Lingzhao Fang,
    • and Zhengguang Wang
    Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
    ...in RepeatMasker, 146 we found that an average of 20.94% of ruminant s consisted of high-precision TE 147 sequences. The main TE families, by genomic size, included LINE/RTE-BovB (averaging 148 55.7% of total TE content), followed by LINE/L1 (18.13%), SINE/tRNA-Core-RTE 149 (13.07%), and SINE/Core-RTE (8...
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  10. Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
    • Chencheng Xu,
    • Suying Bao,
    • Ye Wang,
    • Wenxing Li,
    • Hao Chen,
    • Yufeng Shen,
    • Tao Jiang,
    • and Chaolin Zhang
    Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
    ...of modulating gene expression using therapeutically compatible approaches (El Marabti and Abdel-Wahab 2021).A longstanding question in the splicing field is the possibility to derive a “splicing code,” which can accurately predict splice sites and their quantitative usage from pre-mRNA sequences, including...
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