Searching journal content for articles similar to Freiberg et al. 6 (7): 590.

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  1. Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
    • Shingo Kato,
    • Sachiko Masuda,
    • Arisa Shibata,
    • Takashi Itoh,
    • Mitsuo Sakamoto,
    • Ken Shirasu,
    • and Moriya Ohkuma
    Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
    .../contamination and also emphasize the necessity of more complete data set for more accurate estimation.Detection of extrachromosomal DNA fragmentsThe sequencing of the isolated strains indicated the presence of extrachromosomal DNA fragments, such as secondary replicons (diCenzo and Finan 2017) including plasmids...
  2. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ...of LILAP HiFi reads (∼5 kb; see comment about Illumina a few paragraphs above). One must also consider that Tn5 has its own sequence biases, which favor GC-rich regions (Kia et al. 2017), and that the LILAP protocol still includes a T4 ligase step to close the nick after the Tn5-mediated transposition...
  3. 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
    ..., Evers DJ, Barnes CL, Bignell HR, et al. 2008. Accurate whole human sequencing using reversible terminator chemistry. Nature 456: 53–59. doi:10.1038/nature07517 ↵Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, et al. 2011. The evolution...
  4. Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
    • Ezequiel Calvo-Roitberg,
    • Rachel F. Daniels,
    • and Athma A. Pai
    Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
    .../or stalling of the enzyme can lead to premature termination of cDNA synthesis and truncated molecules with 5′ ends that do not represent the true mRNA 5′ end (Wyman et al. 2020).RT processivity can be impacted by many factors, including sequence (i.e., stretches of GC-rich regions) (Minshall and Git 2020...
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  5. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...DNA fragments up to 100 kb in size into individual droplets. Target-specific amplification is performed along with an intercalating dye to identify which droplets contain DNA fragments of interest. In one example, Grosso et al. (2021) employed Xdrop for contiguous sequencing of the FMR1 repeat...
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  6. 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
    .... Building upon established bias-modeling methods that account for k-mer-based GC-content (Su et al. 2024b) and minimum free energy (MFE) (Su et al. 2024a), we begin our analysis with a one-dimensional (1D) examination of sequence characteristics. This initial phase specifically explores the potential impact...
  7. Research: A GC-rich sequence feature in the 3′ UTR directs UPF1-dependent mRNA decay in mammalian cells
    • Naoto Imamachi,
    • Kazi Abdus Salam,
    • Yutaka Suzuki,
    • and Nobuyoshi Akimitsu
    Genome Res. March 2017 27: 407-418; Published in Advance December 9, 2016, doi:10.1101/gr.206060.116
    ...-value (P = 4.0 × 10−107) is shown.We next sought to predict p-UPF1 binding motifs in 3′ UTR of UPF1 targets using the MEME software (Bailey et al. 2006). GC-rich motifs, which contain the CUG sequence, were identified in the 3′ UTRs of UPF1 targets, but not in the 5′ UTRs and CDSs (Fig. 2E; Supplemental...
  8. Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
    • Xuyan Liu,
    • Lin Xia,
    • Yixin Qiao,
    • Yang Li,
    • Yan Huang,
    • Bingyan Yue,
    • Xi Liang,
    • Xin Yang,
    • Honghui Zhang,
    • Jiaxun Zhang,
    • Xiao Chen,
    • Dan Xie,
    • and Jifeng Liu
    Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
    ...Nanopore sequencing identifies high-frequency somatic structural 1 variations in laryngeal squamous cell carcinoma s 2 Xuyan Liu1#, Lin Xia1#, Yixin Qiao2#, Yang Li1, Yan Huang1, Bingyan Yue2, Xi Liang2, Xin 3 Yang2, Honghui Zhang2, Jiaxun Zhang1, Xiao Chen1, Dan Xie1*, Jifeng Liu2,3* 4 1...
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  9. Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
    • Kristine Bilgrav Saether,
    • Angelo Salazar Mantero,
    • Marlene Ek,
    • Maria Pettersson,
    • Elisabeth Syk Lundberg,
    • Christopher M. Grochowski,
    • Claudia M.B. Carvalho,
    • Jesper Eisfeldt,
    • and Anna Lindstrand
    Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
    ...Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read sequencing Kristine Bilgrav Saether1,2,6, Angelo Salazar Mantero1,3,6, Marlene Ek1,3, Maria Pettersson1,3, Elisabeth Syk Lundberg1,3, Christopher M. Grochowski4, Claudia M...
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  10. 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
    .... Subsequently, the complementary DNA (cDNA) was amplified for 12 PCR cycles. We used AMPure XP bead cleanup (1.8×), followed by size selection using 3% agarose, dye-free gel cassettes with internal standards (Sage Science BDQ3010) on the BluePippin platform. Sequencing was performed on a NovaSeq 6000 platform...
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