Searching journal content for articles similar to Gomes et al. 24 (10): 1686.

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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
    ...shared peaks. (C,D) Scatterplots of read counts (log2) on shared peaks, IGV (Robinson et al. 2011) tracks, and heatmaps of ±5 kb from the center of transcription start sites (TSSs) or peaks showing the automated ChIP-seq results of H3K27ac (C) and H3K27me3 (D) for evaluating cross-linking conditions, DSG...
  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. Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
    • Yiqiao Zheng,
    • Gary D. Stormo,
    • and Shiming Chen
    Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
    ...remodeling at photoreceptor CREs enriched with K50 HD motifs. (A) Heatmaps depicting the normalized ATAC-seq or CRX ChIP-seq signal intensities at CrxK88N-reduced accessible ATAC-seq peaks. (B) PWM logo and enrichment significance E-value of the STREME de novo discovered HD motif. (C) Line plot showing...
    OPEN ACCESS ARTICLE
  4. Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
    • Wei-Hao Lee,
    • Lechuan Li,
    • Ruth Dannenfelser,
    • and Vicky Yao
    Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
    ...to link genes with conditions, requiring the user to essentially reconstitute predicted counts and perform differential gene expression. In contrast, scParser (Zhao et al. 2024) adopts a matrix factorization framework combined with sparse representation learning to model multiple conditions, but because...
  5. Method: MAnorm2 for quantitatively comparing groups of ChIP-seq samples
    • Shiqi Tu,
    • Mushan Li,
    • Haojie Chen,
    • Fengxiang Tan,
    • Jian Xu,
    • David J. Waxman,
    • Yijing Zhang,
    • and Zhen Shao
    Genome Res. January 2021 31: 131-145; Published in Advance November 18, 2020, doi:10.1101/gr.262675.120
    ..., and the occupancy matrix uses a binary variable to indicate whether the interval is enriched with reads (or whether it is a peak region). Formally, MAnorm2 refers to a genomic interval as occupied by a ChIP-seq sample if the interval is enriched with reads in the sample.For each MAnorm2 analysis in this study, we...
  6. Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
    • Gianluca Mattei,
    • Marta Baragli,
    • Barbara Gega,
    • Alessandra Mingrino,
    • Martina Chieca,
    • Tommaso Ducci,
    • Gianmaria Frigè,
    • Luca Mazzarella,
    • Romina D'Aurizio,
    • Francesco De Logu,
    • Romina Nassini,
    • Pier Giuseppe Pelicci,
    • and Alberto Magi
    Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
    ...in at least 99% of the epi.At present, the methylation state of a CpG site is studied by using the methylation frequency β (calculated as the ratio between the total number of CpG sites predicted as methylated and the total number of reads aligned to that CpG) and differential methylation between test (T...
  7. 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
    ...ultimately be determined by local constellations of DNA-binding sites, current analysis is typically limited to identifying enriched motifs in ChIP-seq peaks. Here we present Crunch, a completely automated computational method that performs all ChIP-seq analysis from quality control through read mapping...
    OPEN ACCESS ARTICLE
  8. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ...species-specific modeling with ensemble deep learning architectures to systematically optimize feature encoding schemes. Evaluated across six species, EnDeep4mC demonstrates commendable prediction performance and significantly outperforms current state-of-the-art predictors. Cross-species validation...
    OPEN ACCESS ARTICLE
  9. Method: Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome
    • Dachang Dang,
    • Shao-Wu Zhang,
    • Ran Duan,
    • and Shihua Zhang
    Genome Res. March 2023 33: 386-400; Published in Advance March 9, 2023, doi:10.1101/gr.277187.122
    ..., and the boundary type components within each type of domains. (C) Hi-C contact maps of a region on Chromosome 2 of GM12878 accompanied by the ConsTADs (black frames in contact map), the corresponding boundary types and domain types, and ChIP-seq and Repli-seq profiles. (D) Five clusters of topological domains...
  10. 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
    ...Saturation analysis of ChIP-seq data for reproducible identification of binding peaks Peter Hansen 1 , 2 , Jochen Hecht 1 , 2 , 3 , Daniel M. Ibrahim 1 , 3 , Alexander Krannich 4 , Matthias Truss 5 and Peter N. Robinson 1 , 2...
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