Searching journal content for articles similar to Roh et al. 17 (1): 74.

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  1. Research: Genome-wide analysis of histone modifications in human pancreatic islets
    • Reena Bhandare,
    • Jonathan Schug,
    • John Le Lay,
    • Alan Fox,
    • Olga Smirnova,
    • Chengyang Liu,
    • Ali Naji,
    • and Klaus H. Kaestner
    Genome Res. April 2010 20: 428-433; Published in Advance February 24, 2010, doi:10.1101/gr.102038.109
    .... The transcriptional response of the islet to pregnancy in mice. Mol Endocrinol 23: 1702–1712. Roh TY, Cuddapah S, Cui K, Zhao K. 2006. The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci 103: 15782– 15787. Roh TY, Wei G, Farrell CM, Zhao K. 2007. Genome-wide prediction of conserved...
  2. Method: Domain-adaptive neural networks improve cross-species prediction of transcription factor binding
    • Kelly Cochran,
    • Divyanshi Srivastava,
    • Avanti Shrikumar,
    • Akshay Balsubramani,
    • Ross C. Hardison,
    • Anshul Kundaje,
    • and Shaun Mahony
    Genome Res. March 2022 32: 512-523; Published in Advance January 18, 2022, doi:10.1101/gr.275394.121
    ...-negative prediction errors could be the result of differential TF activity across the two species. Such differential activities could result from gain or loss of TF expression patterns, nonconserved cooperative binding capabilities, or evolved sequence preferences of the TF itself. Our sequence composition domain...
  3. Resource: Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
    • Riu Yamashita,
    • Nuankanya P. Sathira,
    • Akinori Kanai,
    • Kousuke Tanimoto,
    • Takako Arauchi,
    • Yoshiaki Tanaka,
    • Shin-ichi Hashimoto,
    • Sumio Sugano,
    • Kenta Nakai,
    • and Yutaka Suzuki
    Genome Res. May 2011 21: 775-789; Published in Advance March 3, 2011, doi:10.1101/gr.110254.110
    ...Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis Riu Yamashita 1 , 2 , 6 , Nuankanya P. Sathira 3 , 6 , Akinori Kanai 3 , Kousuke Tanimoto 3 , Takako Arauchi 3 , Yoshiaki...
  4. Research: Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
    • Pouya Kheradpour,
    • Jason Ernst,
    • Alexandre Melnikov,
    • Peter Rogov,
    • Li Wang,
    • Xiaolan Zhang,
    • Jessica Alston,
    • Tarjei S. Mikkelsen,
    • and Manolis Kellis
    Genome Res. May 2013 23: 800-811; Published in Advance March 19, 2013, doi:10.1101/gr.144899.112
    ...conserved regulatory motif instances within enhancer chromatin states. We select five predicted activators (HNF1, HNF4, FOXA, GATA, NFE2L2) and two predicted repressors (GFI1, ZFP161) and measure reporter expression in erythroleukemia (K562) and liver carcinoma (HepG2) cell lines. We test 2104 wild...
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  5. Research: Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
    • Valer Gotea,
    • Axel Visel,
    • John M. Westlund,
    • Marcelo A. Nobrega,
    • Len A. Pennacchio,
    • and Ivan Ovcharenko
    Genome Res. May 2010 20: 565-577; Published in Advance April 2, 2010, doi:10.1101/gr.104471.109
    ...will be required to quantify the success rate of HCT-based prediction more accurately. We also observed that among the four HCTs that had enhancer activity in zebrafish, two were conserved in chicken and two were not. The same 1:1 ratio of elements deeply conserved and nondeeply conserved was observed for the set...
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  6. Resource: Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
    • Ozren Bogdanović,
    • Ana Fernandez-Miñán,
    • Juan J. Tena,
    • Elisa de la Calle-Mustienes,
    • Carmen Hidalgo,
    • Ila van Kruysbergen,
    • Simon J. van Heeringen,
    • Gert Jan C. Veenstra,
    • and José Luis Gómez-Skarmeta
    Genome Res. October 2012 22: 2043-2053; Published in Advance May 16, 2012, doi:10.1101/gr.134833.111
    ...their target genes. Studies performed on mammalian embryonic stem cells and Drosophila embryos suggest that active enhancers form part of a defined chromatin landscape marked by histone H3 lysine 4 mono-methylation (H3K4me1) and histone H3 lysine 27 acetylation (H3K27ac). Nevertheless, little is known about...
  7. Research: Maintaining replication origins in the face of genomic change
    • Sara C. Di Rienzi,
    • Kimberly C. Lindstrom,
    • Tobias Mann,
    • William S. Noble,
    • M.K. Raghuraman,
    • and Bonita J. Brewer
    Genome Res. October 2012 22: 1940-1952; Published in Advance June 4, 2012, doi:10.1101/gr.138248.112
    ...to predict to what extent and in what regard origins are conserved over evolutionary time. Here, through a comparative genomic analysis of replication origins and chromosomal replication patterns in the budding yeasts Saccharomyces cerevisiae and Lachancea waltii , we assess to what extent replication...
  8. Research: The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species
    • Jingping Yang,
    • Edward Ramos,
    • and Victor G. Corces
    Genome Res. November 2012 22: 2199-2207; Published in Advance August 15, 2012, doi:10.1101/gr.142125.112
    .... Insulators have been shown to contribute to the establishment of specific patterns of chromatin organization important for regulation of transcription by, at least in part, regulating interactions between enhancers and promoters (Phillips and Corces 2009; Handoko et al. 2011; Yang and Corces 2011...
  9. LETTER: Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
    • Yong Cheng,
    • David C. King,
    • Louis C. Dore,
    • Xinmin Zhang,
    • Yuepin Zhou,
    • Ying Zhang,
    • Christine Dorman,
    • Demesew Abebe,
    • Swathi A. Kumar,
    • Francesca Chiaromonte,
    • Webb Miller,
    • Roland D. Green,
    • Mitchell J. Weiss,
    • and Ross C. Hardison
    Genome Res. December 2008 18: 1896-1905; Published in Advance September 25, 2008, doi:10.1101/gr.083089.108
    ...invariant in multiple mammalian orders ( Visel et al. 2008 ) are active as enhancers during early development. Noncoding sequences that are conserved in placental mammals but are under less severe constraint can also be important regulatory regions. For example, noncoding sequences with patterns...
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  10. PERSPECTIVE: Raising the estimate of functional human sequences
    • Michael Pheasant and
    • John S. Mattick
    Genome Res. September 2007 17: 1245-1253; Published in Advance August 9, 2007, doi:10.1101/gr.6406307
    ...within them (∼600 long ncRNAs investigated in human and mouse) ( Pang et al. 2006 ) and 3122 other long ncRNAs show subtle evidence of selection ( Ponjavic et al. 2007 ). Genome-wide estimates of function from conservation Initial comparison of the mouse and human s led to the conclusion that ∼5...
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