Searching journal content for articles similar to Landt et al. 22 (9): 1813.

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  1. 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
    ...for Biotechnology, Huntsville, Alabama 35806, USA; 6Department of Medicine, Division of Endocrinology & Metabolism, University of California San Diego, La Jolla, California 92093, USA Corresponding author: agoren@ucsd.eduAbstractChromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to study...
  2. Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
    • Alexander Morin,
    • Eric Ching-Pan Chu,
    • Aman Sharma,
    • Alex Adrian-Hamazaki,
    • and Paul Pavlidis
    Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
    ...literature-sourced data, motivating our use of the stringent approach for peak calling promoted by ENCODE. Peaks were assigned to genes using a continuous scoring metric (from here referred to as the binding score; see Methods), and the ChIP-seq data were thus represented and analyzed as gene...
  3. Method: Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs
    • Severin Berger,
    • Mikhail Pachkov,
    • Phil Arnold,
    • Saeed Omidi,
    • Nicholas Kelley,
    • Silvia Salatino,
    • and Erik van Nimwegen
    Genome Res. July 2019 29: 1164-1177; Published in Advance May 28, 2019, doi:10.1101/gr.239319.118
    ...immunoprecipitation with high-throughput sequencing to quantify the -wide binding patterns of any molecule that associates with the DNA. Apart from large-scale efforts, such as the ENCODE Project in which ChIP-seq was used to systematically map the binding patterns of many transcription factors (TFs) (The ENCODE...
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  4. Method: Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data
    • Mingxiang Teng and
    • Rafael A. Irizarry
    Genome Res. November 2017 27: 1930-1938; Published in Advance October 12, 2017, doi:10.1101/gr.220673.117
    ...than running a peak caller and IDR (https://www.encodeproject.org/chip-seq/transcription_factor/). If we simply run SPP followed by IDR, the improvements of our algorithm are even larger, since this approach produced 29.5% of regions reported by only one laboratory (Supplemental Fig. S3C). Figure 4...
  5. Method: Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq
    • Peng Liu,
    • Rajendran Sanalkumar,
    • Emery H. Bresnick,
    • Sündüz Keleş,
    • and Colin N. Dewey
    Genome Res. August 2016 26: 1124-1133; Published in Advance July 12, 2016, doi:10.1101/gr.199174.115
    ..., for instance, pRSEM has utilized the ENCODE standard protocol (SPP peak caller and IDR pipeline) (Landt et al. 2012) to obtain Pol II peaks (and signals, depending on the partition model). Precomputed ChIP-seq peaks can also be provided to pRSEM to speed up the process. In the second step, a training set...
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  6. Method: CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
    • Daniel Savic,
    • E. Christopher Partridge,
    • Kimberly M. Newberry,
    • Sophia B. Smith,
    • Sarah K. Meadows,
    • Brian S. Roberts,
    • Mark Mackiewicz,
    • Eric M. Mendenhall,
    • and Richard M. Myers
    Genome Res. October 2015 25: 1581-1589; Published in Advance September 9, 2015, doi:10.1101/gr.193540.115
    ...(ChIP-seq) is one of the most widely used and powerful methods for mapping regulatory elements and analyzing transcription factor (TF) function (The ENCODE Project Consortium 2007, 2012; Johnson et al. 2007). However, the measurement of -wide TF binding requires high-quality, validated antibodies...
  7. Method: Saturation analysis of ChIP-seq data for reproducible identification of binding peaks
    • Peter Hansen,
    • Jochen Hecht,
    • Daniel M. Ibrahim,
    • Alexander Krannich,
    • Matthias Truss,
    • and Peter N. Robinson
    Genome Res. September 2015 25: 1391-1400; Published in Advance July 10, 2015, doi:10.1101/gr.189894.115
    ...binding sites in ChIP-seq experiments. BMC Genomics 10: 618. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, et al. 2012. ChIP-seq guidelines and practices of the ENCODE andmod...
  8. Method: Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
    • Antonio L.C. Gomes,
    • Thomas Abeel,
    • Matthew Peterson,
    • Elham Azizi,
    • Anna Lyubetskaya,
    • Luís Carvalho,
    • and James Galagan
    Genome Res. October 2014 24: 1686-1697; Published in Advance July 14, 2014, doi:10.1101/gr.161711.113
    ...Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction Antonio L.C. Gomes 1 , Thomas Abeel 2 , 5 , Matthew Peterson 3 , Elham Azizi 1 , Anna Lyubetskaya 1...
  9. Method: Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
    • Nicolas Bonhoure,
    • Gergana Bounova,
    • David Bernasconi,
    • Viviane Praz,
    • Fabienne Lammers,
    • Donatella Canella,
    • Ian M. Willis,
    • Winship Herr,
    • Nouria Hernandez,
    • Mauro Delorenzi,
    • and The CycliX Consortium
    Genome Res. July 2014 24: 1157-1168; Published in Advance April 7, 2014, doi:10.1101/gr.168260.113
    .../brown.edu/bioinformatics-in-biomed/ spp-r-from-chip-seq) (Kharchenko et al. 2008). The samples, referred to as RPB2_95 and RPB2_90 (see Table 1), contained different percentages of human chromatin (which was managed in the analysis by the species-specific scaling) (step 2 in Fig. 2) but otherwise were derived from the same batch...
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  10. Method: Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
    • David U. Gorkin,
    • Dongwon Lee,
    • Xylena Reed,
    • Christopher Fletez-Brant,
    • Seneca L. Bessling,
    • Stacie K. Loftus,
    • Michael A. Beer,
    • William J. Pavan,
    • and Andrew S. McCallion
    Genome Res. November 2012 22: 2290-2301; Published in Advance September 27, 2012, doi:10.1101/gr.139360.112
    ...flanked regions; [light green] peaks that do not overlap H3K4me1-flanked regions). Data for Heart (C57bl/6 mouse tissue taken at 8 wk), mES (Mouse ES-Bruce 4), and GM12878 generated by ENCODE and modENCODE consortia. (B) Average number ChIP-seq reads per peak for Pol2 (top row), H3K4me3 (middle row...
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