Searching journal content for articles similar to Kiyosawa et al. 13 (6b): 1554.

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  1. 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
    ...provide examples of multiomic comparisons that reveal insights that connect the transcriptome, translatome, and degradome. In summary, ggRibo is an advanced single-gene viewer that offers a valuable resource for studying gene expression regulation through its intuitive and flexible platform...
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  2. Resource: Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)
    • Sanjida H. Rangwala,
    • Anatoliy Kuznetsov,
    • Victor Ananiev,
    • Andrea Asztalos,
    • Evgeny Borodin,
    • Vladislav Evgeniev,
    • Victor Joukov,
    • Vadim Lotov,
    • Ravinder Pannu,
    • Dmitry Rudnev,
    • Andrew Shkeda,
    • Eric M. Weitz,
    • and Valerie A. Schneider
    Genome Res. January 2021 31: 159-169; Published in Advance November 25, 2020, doi:10.1101/gr.266932.120
    ...access to a wide range and large volume of biological sequence data and literature. Staff scientists at NCBI analyze user-submitted data in the archive, producing gene and SNP annotation and generating sequence alignment tools. NCBI's flagship browser, Genome Data Viewer (GDV), displays our in-house Ref...
  3. Resource: LookSeq: A browser-based viewer for deep sequencing data
    • Heinrich Magnus Manske and
    • Dominic P. Kwiatkowski
    Genome Res. November 2009 19: 2125-2132; Published in Advance August 13, 2009, doi:10.1101/gr.093443.109
    ...LookSeq: A browser-based viewer for deep sequencing data Heinrich Magnus Manske 1 and Dominic P. Kwiatkowski Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom Abstract Sequencing a genome to great depth can be highly...
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  4. RESOURCE: EagleView: A genome assembly viewer for next-generation sequencing technologies
    • Weichun Huang and
    • Gabor Marth
    Genome Res. September 2008 18: 1538-1543; Published in Advance June 11, 2008, doi:10.1101/gr.076067.108
    ...EagleView: A genome assembly viewer for next-generation sequencing technologies Weichun Huang and Gabor Marth 1 Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA Abstract The emergence of high-throughput next...
  5. Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
    • Zepu Miao and
    • Jia-Xing Yue
    Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
    ...one-dimensional local graph structure rendering. Another tool, PanGraphViewer (Yuan et al. 2023), while still being built for graph topology visualization, enables a coordinate-based graph querying and can be used for genomic variant examination when a VCF file is provided. Although these tools...
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  6. 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
    ...through spatial proximity. These findings underscore the potential of long-read 33 sequencing and SomaGauss-SV for uncovering recurrent somatic SVs in LSCC, providing 34 valuable resources for biomarker discovery. 35 36 Introduction 37 Laryngeal squamous cell carcinoma (LSCC) is the second most common...
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  7. Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
    • Yuwei Cao,
    • Lauren Patel,
    • Lauren Alcoser,
    • Eric Mendenhall,
    • Christopher Benner,
    • Sven Heinz,
    • and Alon Goren
    Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
    ...the genomic localization of DNA-associated proteins. However, conventional protocols include multiple manual steps that can introduce inconsistency and limit scalability, thereby restricting the inclusion of appropriate replicates and controls. Although the introduction of liquid handling platforms has...
  8. Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
    • Jacob Stewart-Ornstein,
    • Matthew J. Irby,
    • Marina K. Lilieholm,
    • Dylan Laprise,
    • Maria D. Collier,
    • Thomas Aunins,
    • Dewi Harjanto,
    • Aaron N. Chang,
    • Deepak Reyon,
    • and Jeremy S. Duffield
    Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
    ...improvement of in silico algorithms to capture the unique signatures of SSBs induced by the RuvC and HNH domains of SpCas9. More generally, as described in the introduction, there are many potential methods to detect off-target activity of PE, including PE-tag (Liang et al. 2023), and biochemical approaches...
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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
    ...structure of the derivative Chromosome 7 identified in RD_P328. (B) Integrative Genomics Viewer images of short-read sequencing (srGS) and long-read sequencing (lrGS) data for each BPJ. (C) Breakpoint sequences of the two BPJs with the chimeric sequence in the center aligned to the reference sequences shown...
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  10. RESOURCE: The Mammalian Protein–Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer
    • Harukazu Suzuki,
    • Rintaro Saito,
    • Mutsumi Kanamori,
    • Chikatoshi Kai,
    • Christian Schönbach,
    • Takeshi Nagashima,
    • Junko Hosaka,
    • and Yoshihide Hayashizaki
    Genome Res. June 2003 13: 1534-1541; doi:10.1101/gr.956303
    ...The Mammalian Protein–Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer Harukazu Suzuki 1 , 3 , 6 , Rintaro Saito 1 , 5 , Mutsumi Kanamori 1 , Chikatoshi Kai 1 , Christian Schönbach 4...
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