Searching journal content for articles similar to Suzuki et al. 28 (9): 1364.

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  1. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ..., current long-read sequencing platforms have achieved high accuracy and throughput at competitive costs (Kovaka et al. 2023) promoting a variety of new applications.View larger version: In this window In a new window Figure 1. Overview of long-read sequencing protocols and analyses. (A) The overview...
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  2. Method: metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
    • Frank Jühling,
    • Helene Kretzmer,
    • Stephan H. Bernhart,
    • Christian Otto,
    • Peter F. Stadler,
    • and Steve Hoffmann
    Genome Res. February 2016 26: 256-262; Published in Advance December 2, 2015, doi:10.1101/gr.196394.115
    ...sequencing experiments (WGBS) and targeted protocols, e.g., reduced representation bisulfite sequencing (RRBS), made it possible to study cytosine methylation landscapes at single CpG resolution. Decreasing costs and a high availability of next-generation sequencing (NGS) facilities have made it feasible...
  3. Method: Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
    • Michael Stevens,
    • Jeffrey B. Cheng,
    • Daofeng Li,
    • Mingchao Xie,
    • Chibo Hong,
    • Cécile L. Maire,
    • Keith L. Ligon,
    • Martin Hirst,
    • Marco A. Marra,
    • Joseph F. Costello,
    • and Ting Wang
    Genome Res. September 2013 23: 1541-1553; Published in Advance June 26, 2013, doi:10.1101/gr.152231.112
    ...and experimental strategy to produce DNA methylomes of all 28 million CpGs in the human genome for a fraction (<10%) of the cost of whole-genome bisulfite sequencing methods. methylCRF was benchmarked for accuracy against Infinium arrays, RRBS, WGBS sequencing, and locus-specific bisulfite sequencing performed...
  4. Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
    • Bo Zhang,
    • Yan Zhou,
    • Nan Lin,
    • Rebecca F. Lowdon,
    • Chibo Hong,
    • Raman P. Nagarajan,
    • Jeffrey B. Cheng,
    • Daofeng Li,
    • Michael Stevens,
    • Hyung Joo Lee,
    • Xiaoyun Xing,
    • Jia Zhou,
    • Vasavi Sundaram,
    • GiNell Elliott,
    • Junchen Gu,
    • Taoping Shi,
    • Philippe Gascard,
    • Mahvash Sigaroudinia,
    • Thea D. Tlsty,
    • Theresa Kadlecek,
    • Arthur Weiss,
    • Henriette O’Geen,
    • Peggy J. Farnham,
    • Cécile L. Maire,
    • Keith L. Ligon,
    • Pamela A.F. Madden,
    • Angela Tam,
    • Richard Moore,
    • Martin Hirst,
    • Marco A. Marra,
    • Baoxue Zhang,
    • Joseph F. Costello,
    • and Ting Wang
    Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
    ...present a novel integrative statistical framework M&M (for integration of MeDIP-seq and MRE-seq) that dynamically scales, normalizes, and combines MeDIP-seq and MRE-seq data to detect differentially methylated regions. Using sample-matched whole-genome bisulfite sequencing (WGBS) as a gold standard...
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  5. Method: Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
    • Lukas Chavez,
    • Justyna Jozefczuk,
    • Christina Grimm,
    • Jörn Dietrich,
    • Bernd Timmermann,
    • Hans Lehrach,
    • Ralf Herwig,
    • and James Adjaye
    Genome Res. October 2010 20: 1441-1450; Published in Advance August 27, 2010, doi:10.1101/gr.110114.110
    ...show improved correlation of normalized MeDIP-seq data in comparison to available whole-genome bisulfite sequencing data, and investigated the effect of differential methylation on gene expression. Furthermore, we analyzed the interplay between DNA methylation, histone modifications, and transcription...
  6. ARTICLE: A Complete Sequence of the T. tengcongensis Genome
    • Qiyu Bao,
    • Yuqing Tian,
    • Wei Li,
    • Zuyuan Xu,
    • Zhenyu Xuan,
    • Songnian Hu,
    • Wei Dong,
    • Jian Yang,
    • Yanjiong Chen,
    • Yanfen Xue,
    • Yi Xu,
    • Xiaoqin Lai,
    • Li Huang,
    • Xiuzhu Dong,
    • Yanhe Ma,
    • Lunjiang Ling,
    • Huarong Tan,
    • Runsheng Chen,
    • Jian Wang,
    • Jun Yu,
    • and Huanming Yang
    Genome Res. May 1, 2002 12: 689-700; doi:10.1101/gr.219302
    ...100101, China; 4Genome Center, University of Washington, Seattle, Washington 98195, USA Abstract Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from a freshwater hot spring in Tengchong, China. Using a whole-genome-shotgun method, we...
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