Searching journal content for articles similar to Giresi et al. 17 (6): 877.

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  1. Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
    • Aayush Grover,
    • Till Muser,
    • Liine Kasak,
    • Lin Zhang,
    • Ekaterina Krymova,
    • and Valentina Boeva
    Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
    ...of noncoding genetic variants and the decoding of regulatory element architecture (Zhou and Troyanskaya 2015; Kelley et al. 2018; Avsec et al. 2021a; Pampari et al. 2024). Accurate, high-resolution maps of chromatin accessibility are essential for downstream tasks such as identifying regulatory elements...
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  2. Research: Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity
    • Sudhir Thakurela,
    • Sanjeeb Kumar Sahu,
    • Angela Garding,
    • and Vijay K. Tiwari
    Genome Res. September 2015 25: 1309-1324; Published in Advance July 13, 2015, doi:10.1101/gr.190926.115
    ...commitment. One of themost effectivemeans of discovering these regulatory elements is through the identification of nucleosome-depleted regions (“open chromatin”). The FAIRE assay has emergedas a simple, unbiasedbut robust, andhigh-throughput method to identify such functional regulatory regions in a broad...
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  3. Method: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
    • Emily R. Miraldi,
    • Maria Pokrovskii,
    • Aaron Watters,
    • Dayanne M. Castro,
    • Nicholas De Veaux,
    • Jason A. Hall,
    • June-Yong Lee,
    • Maria Ciofani,
    • Aviv Madar,
    • Nick Carriero,
    • Dan R. Littman,
    • and Richard Bonneau
    Genome Res. March 2019 29: 449-463; Published in Advance January 29, 2019, doi:10.1101/gr.238253.118
    ...false-positive and false-negative TF–gene interactions expected from chromatin-state data analyzed in isolation (Äijö and Bonneau 2016; Siahpirani and Roy 2016). Sources of false positives and negatives include (1) nonfunctional binding, (2) long-range interactions between genes and regulatory regions...
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  4. Resource: Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    • Lingyun Song,
    • Zhancheng Zhang,
    • Linda L. Grasfeder,
    • Alan P. Boyle,
    • Paul G. Giresi,
    • Bum-Kyu Lee,
    • Nathan C. Sheffield,
    • Stefan Gräf,
    • Mikael Huss,
    • Damian Keefe,
    • Zheng Liu,
    • Darin London,
    • Ryan M. McDaniell,
    • Yoichiro Shibata,
    • Kimberly A. Showers,
    • Jeremy M. Simon,
    • Teresa Vales,
    • Tianyuan Wang,
    • Deborah Winter,
    • Zhuzhu Zhang,
    • Neil D. Clarke,
    • Ewan Birney,
    • Vishwanath R. Iyer,
    • Gregory E. Crawford,
    • Jason D. Lieb,
    • and Terrence S. Furey
    Genome Res. October 2011 21: 1757-1767; Published in Advance July 12, 2011, doi:10.1101/gr.121541.111
    ...encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq (Formaldehyde Assisted Isolation of Regulatory Elements) to map “open chromatin.” Over 870,000 DNaseI or FAIRE sites, which correspond tightly...
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  5. Method: A universal framework for detecting cis-regulatory diversity in DNA regions
    • Anushua Biswas and
    • Leelavati Narlikar
    Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
    ...ENCODE phase III, where The ENCODE Project Consortium et al. (2020) have published a registry of candidate cis-regulatory elements based on results from multiple high-throughput experiments. They report two disjoint subsets, which they propose have distal enhancer-like signatures (dELSs) and proximal...
  6. Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    • Phillippa C. Taberlay,
    • Aaron L. Statham,
    • Theresa K. Kelly,
    • Susan J. Clark,
    • and Peter A. Jones
    Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
    ...Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer Phillippa C. Taberlay 1 , 2 , 3 , 6 , Aaron L. Statham 1 , 6 , Theresa K. Kelly 2 , 4...
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  7. Method: Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors
    • Shelsa S. Marcel,
    • Austin L. Quimby,
    • Melodie P. Noel,
    • Oscar C. Jaimes,
    • Marjan Mehrab-Mohseni,
    • Suud A. Ashur,
    • Brian Velasco,
    • James K. Tsuruta,
    • Sandeep K. Kasoji,
    • Charlene M. Santos,
    • Paul A. Dayton,
    • Joel S. Parker,
    • Ian J. Davis,
    • and Samantha G. Pattenden
    Genome Res. December 2021 31: 2327-2339; Published in Advance November 23, 2021, doi:10.1101/gr.275219.121
    ...of nanodroplets during the extraction of chromatin from FFPE tissues enhances the recovery of intact accessible and nucleosome-bound chromatin. We show that the addition of nanodroplets to the chromatin accessibility assay formaldehyde-assisted isolation of regulatory elements (FAIRE), does not affect...
  8. Method: NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution
    • Zhengyu Luo,
    • Ran Zhang,
    • Tengfei Hu,
    • Yuting Zhu,
    • Yueming Wu,
    • Wenfei Li,
    • Zhi Zhang,
    • Xuebiao Yao,
    • Haiyi Liang,
    • and Xiaoyuan Song
    Genome Res. March 2022 32: 534-544; Published in Advance February 1, 2022, doi:10.1101/gr.275986.121
    ....celrep.2016.04.085 ↵Giresi PG, Lieb JD. 2009. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (formaldehyde assisted isolation of regulatory elements). Methods 48: 233–239. doi:10.1016/j.ymeth.2009.03.003 ↵Hsieh TS, Cattoglio C, Slobodyanyuk E, Hansen AS, Rando OJ, Tjian R...
  9. Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
    • Aaron C. Daugherty,
    • Robin W. Yeo,
    • Jason D. Buenrostro,
    • William J. Greenleaf,
    • Anshul Kundaje,
    • and Anne Brunet
    Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
    ...applied to whole organisms or complex samples composed of diverse cellular populations, this approach could capture regulatory regions that may have been missed in studies of isolated cell populations.Specific motifs for transcription factors predict changes in chromatin accessibilityTo explore...
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  10. LETTER: Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
    • David C. King,
    • James Taylor,
    • Ying Zhang,
    • Yong Cheng,
    • Heather A. Lawson,
    • Joel Martin,
    • ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis,
    • Francesca Chiaromonte,
    • Webb Miller,
    • and Ross C. Hardison
    Genome Res. June 2007 17: 775-786; doi:10.1101/gr.5592107
    .... 2005 ), formaldehyde-assisted isolation of regulatory elements (FAIRE) ( Giresi et al. 2007 ), DNaseI hypersensitive sites measured in CaCo2, HeLa, SKnSH cell lines/phenotypes ( Sabo et al. 2006 ), and moderate MCSs generated by the ENCODE Multispecies Analysis group ( Margulies et al. 2007 ). Recent...
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