Searching journal content for articles similar to Koga et al. 19 (8): 1462.

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  1. 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
    ...Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage Lukas Chavez 1 , 5 , Justyna Jozefczuk 1 , Christina Grimm 1 , Jörn Dietrich 1 , Bernd Timmermann 2...
  2. ARTICLE: A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes
    • Liora Z. Strichman-Almashanu,
    • Richard S. Lee,
    • Patrick O. Onyango,
    • Elizabeth Perlman,
    • Folke Flam,
    • Matthew B. Frieman,
    • and Andrew P. Feinberg
    Genome Res. April 1, 2002 12: 543-554; Published in Advance March 20, 2002, doi:10.1101/gr.224102
    ...A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes Liora Z. Strichman-Almashanu 1 , 4 , 5 , Richard S. Lee 1 , 5 , Patrick O. Onyango 1 , Elizabeth Perlman 2 , Folke Flam 3...
  3. Research: Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
    • Pedro G. Ferreira,
    • Pedro Jares,
    • Daniel Rico,
    • Gonzalo Gómez-López,
    • Alejandra Martínez-Trillos,
    • Neus Villamor,
    • Simone Ecker,
    • Abel González-Pérez,
    • David G. Knowles,
    • Jean Monlong,
    • Rory Johnson,
    • Victor Quesada,
    • Sarah Djebali,
    • Panagiotis Papasaikas,
    • Mónica López-Guerra,
    • Dolors Colomer,
    • Cristina Royo,
    • Maite Cazorla,
    • Magda Pinyol,
    • Guillem Clot,
    • Marta Aymerich,
    • Maria Rozman,
    • Marta Kulis,
    • David Tamborero,
    • Anaïs Gouin,
    • Julie Blanc,
    • Marta Gut,
    • Ivo Gut,
    • Xose S. Puente,
    • David G. Pisano,
    • José Ignacio Martin-Subero,
    • Nuria López-Bigas,
    • Armando López-Guillermo,
    • Alfonso Valencia,
    • Carlos López-Otín,
    • Elías Campo,
    • and Roderic Guigó
    Genome Res. February 2014 24: 212-226; Published in Advance November 21, 2013, doi:10.1101/gr.152132.112
    ...of the patients is largely unexplained by these simple genetic events. Genome-wide transcriptome analysis in cancer provides a global view of the expressed elements and networks that reshapes the biology of the normal cells in their transformation and progression to aggressive cancer cells. Microarray gene...
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  4. Research: Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer
    • Marcos R.H. Estécio,
    • Juan Gallegos,
    • Céline Vallot,
    • Ryan J. Castoro,
    • Woonbok Chung,
    • Shinji Maegawa,
    • Yasuhiro Oki,
    • Yutaka Kondo,
    • Jaroslav Jelinek,
    • Lanlan Shen,
    • Helge Hartung,
    • Peter D. Aplan,
    • Bogdan A. Czerniak,
    • Shoudan Liang,
    • and Jean-Pierre J. Issa
    Genome Res. October 2010 20: 1369-1382; Published in Advance August 17, 2010, doi:10.1101/gr.107318.110
    ...of SINE and LINE retrotransposons near their transcription start site. In several large testing sets, this distribution was highly predictive of promoter methylation. Genome-wide analysis showed that 22% of human genes were predicted to be methylation-prone in cancer; these tended to be genes...
  5. Method: Cross-species analysis of enhancer logic using deep learning
    • Liesbeth Minnoye,
    • Ibrahim Ihsan Taskiran,
    • David Mauduit,
    • Maurizio Fazio,
    • Linde Van Aerschot,
    • Gert Hulselmans,
    • Valerie Christiaens,
    • Samira Makhzami,
    • Monika Seltenhammer,
    • Panagiotis Karras,
    • Aline Primot,
    • Edouard Cadieu,
    • Ellen van Rooijen,
    • Jean-Christophe Marine,
    • Giorgia Egidy,
    • Ghanem-Elias Ghanem,
    • Leonard Zon,
    • Jasper Wouters,
    • and Stein Aerts
    Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
    ...species. We show the accuracy of DeepMEL predictions on the CAGI5 challenge, where it significantly outperforms existing models on the melanoma enhancer of IRF4. Next, we exploit DeepMEL to analyze enhancer architectures and identify accurate transcription factor binding sites for the core regulatory...
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  6. Review: Navigating the landscape of epitranscriptomics and host immunity
    • Elaine Huang,
    • Clara Frydman,
    • and Xinshu Xiao
    Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
    ...of pseudouridine within in vivo systems have drawn mixed conclusions, including increasing (Schwartz et al. 2014; Dai et al. 2023), decreasing (Nakamoto et al. 2017), and having no effect on mRNA stability (Zhang et al. 2023).Genome-wide identification of RNA modificationsA-to-I and C-to-U RNA editing events can...
  7. Resource: Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types
    • Peng Xu and
    • Bin Zhang
    Genome Res. October 2023 33: 1806-1817; Published in Advance October 31, 2023, doi:10.1101/gr.278063.123
    ...detection via MCODE. Raina et al. (2023) established a database of coexpression networks from TCGA data sets using the weighted Pearson correlation method, without subsequent modularity and prognostic marker identification. Although prior research has identified coexpression network modules in a few cancers...
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  8. Research: Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways
    • Sanchari Bhattacharyya,
    • Kith Pradhan,
    • Nathaniel Campbell,
    • Jozef Mazdo,
    • Aparna Vasantkumar,
    • Shahina Maqbool,
    • Tushar D. Bhagat,
    • Sonal Gupta,
    • Masako Suzuki,
    • Yiting Yu,
    • John M. Greally,
    • Ulrich Steidl,
    • James Bradner,
    • Meelad Dawlaty,
    • Lucy Godley,
    • Anirban Maitra,
    • and Amit Verma
    Genome Res. November 2017 27: 1830-1842; Published in Advance October 6, 2017, doi:10.1101/gr.222794.117
    ...of cancer and can be due to epigenetic alterations. 5-Hydroxymethylcytosine (5-hmC) is an epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC-enriched loci with hmC-seal was conducted in a cohort of low-passage pancreatic cancer cell lines, primary patient...
  9. Research: Age-related epigenetic drift in the pathogenesis of MDS and AML
    • Shinji Maegawa,
    • Sheryl M. Gough,
    • Naoko Watanabe-Okochi,
    • Yue Lu,
    • Nianxiang Zhang,
    • Ryan J. Castoro,
    • Marcos R.H. Estecio,
    • Jaroslav Jelinek,
    • Shoudan Liang,
    • Toshio Kitamura,
    • Peter D. Aplan,
    • and Jean-Pierre J. Issa
    Genome Res. April 2014 24: 580-591; Published in Advance January 10, 2014, doi:10.1101/gr.157529.113
    ...-axis) with age (x-axis) for significant genes. DNA methylation in MDS model mice Genome Research 583 www..org Figure 3. Hierarchical clustering analysis of methylation markers in mouse. (A) Hierarchical clustering analysis in bone marrow. Green to red cells indicate the range ofmethylation percentage from 0...
  10. Research: Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer
    • Noriomi Matsumura,
    • Zhiqing Huang,
    • Seiichi Mori,
    • Tsukasa Baba,
    • Shingo Fujii,
    • Ikuo Konishi,
    • Edwin S. Iversen,
    • Andrew Berchuck,
    • and Susan K. Murphy
    Genome Res. January 2011 21: 74-82; Published in Advance December 14, 2010, doi:10.1101/gr.108803.110
    ...of an effective screening strategy. Epigenetic mechanisms of gene regulation, including DNA methylation, are fundamental to normal cellular function and also play a major role in carcinogenesis. To elucidate the biological and clinical relevance of DNA methylation in ovarian cancer, we conducted expression...
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