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  1. Method: Robust chromatin state annotation
    • Mehdi Foroozandeh Shahraki,
    • Marjan Farahbod,
    • and Maxwell W. Libbrecht
    Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
    ...confidently annotate only a small fraction (<0.10), a 1.7-bit annotation confidently annotates 0.64 of the (Fig. 5F; Supplemental Figs. 14–16).DiscussionChromatin state annotations are essential for various downstream tasks, including identifying regulatory regions and cell type–specific activity patterns...
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  2. Method: Dynamic regulatory module networks for inference of cell type–specific transcriptional networks
    • Alireza Fotuhi Siahpirani,
    • Sara Knaack,
    • Deborah Chasman,
    • Morten Seirup,
    • Rupa Sridharan,
    • Ron Stewart,
    • James Thomson,
    • and Sushmita Roy
    Genome Res. July 2022 32: 1367-1384; Published in Advance June 15, 2022, doi:10.1101/gr.276542.121
    ....g., in the cellular differentiation study).Central to DRMN's modeling framework is joint learning of predictive regulatory programs for each cell type or time point by using multitask learning. Using two different approaches to multitask learning, we show that joint learning of regulatory programs is advantageous...
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  3. Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
    • Siyuan Chen,
    • Jiuming Wang,
    • Inkyung Jung,
    • Zhaowen Qiu,
    • Xin Gao,
    • and Yu Li
    Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
    ...and DNA methylation in single human cells. Nat Methods 16: 999–1006. doi:10.1038/s41592-019-0547-z ↵Li GQ, Liu YP, Zhang YX, Kubo N, Yu M, Fang RX, Kellis M, Ren B. 2019. Joint profiling of DNA methylation and chromatin architecture in single cells. Nat Methods 16: 991–993. doi:10.1038/s41592-019-0502-z...
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  4. Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
    • Shudi Zhao,
    • Yuedong Li,
    • Guanping Chen,
    • Xingyang Wang,
    • Nan Chen,
    • and Xiaofeng Wu
    Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
    ...be interpreted by the fact that all the associated enhancers of a certain gene exert the joint regulatory effect.View larger version: In this window In a new window Figure 8. Obstruction of the transcriptional activation of antiviral genes facilitates viral infection. (A) qRT-PCR analysis for changes...
  5. Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
    • Timothy J. Durham,
    • Riza M. Daza,
    • Louis Gevirtzman,
    • Darren A. Cusanovich,
    • Olubusayo Bolonduro,
    • William Stafford Noble,
    • Jay Shendure,
    • and Robert H. Waterston
    Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
    ...the sci-ATAC-seq assay in L2 larvae to match the available single-cell RNA-seq data set. By using a novel implementation of the latent Dirichlet allocation algorithm, we identify 37 clusters of cells that correspond to different cell types in the worm, providing new maps of putative cell type–specific...
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  6. Research: YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
    • Jonathan A. Beagan,
    • Michael T. Duong,
    • Katelyn R. Titus,
    • Linda Zhou,
    • Zhendong Cao,
    • Jingjing Ma,
    • Caroline V. Lachanski,
    • Daniel R. Gillis,
    • and Jennifer E. Phillips-Cremins
    Genome Res. July 2017 27: 1139-1152; Published in Advance May 23, 2017, doi:10.1101/gr.215160.116
    ...understand the CTCF sites that are dynamic among our cellular states, we parsedCTCFpeaks present in the ES 2i, ES serum, and NPC conditions into classes based on their cell-type–specific occupancy (Fig. 2A; Supplemental Methods). We identified 56,138, 50,185, and 28,860 binding sites in ES 2i, ES serum...
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  7. Research: The chromatin environment shapes DNA replication origin organization and defines origin classes
    • Christelle Cayrou,
    • Benoit Ballester,
    • Isabelle Peiffer,
    • Romain Fenouil,
    • Philippe Coulombe,
    • Jean-Christophe Andrau,
    • Jacques van Helden,
    • and Marcel Méchali
    Genome Res. December 2015 25: 1873-1885; Published in Advance November 11, 2015, doi:10.1101/gr.192799.115
    ...zones enriched in reads, whereas SWEMBL highlights the precise position of peaks (Supplemental Fig. S1D; Methods). This joint analysis returned 65,019 high-confidence peaks that identified the major IS of DNA replication and 35,512 initiation zones (IZ) that encompassed one or several closely associated...
  8. Method: Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs
    • Ziyan Rao,
    • Min Zhang,
    • Shaodong Huang,
    • Chenyang Wu,
    • Yuheng Zhou,
    • Weijie Zhang,
    • Xia Lin,
    • and Dongyu Zhao
    Genome Res. August 2025 35: 1842-1858; Published in Advance May 27, 2025, doi:10.1101/gr.280235.124
    ....CDT is an important feature in identifying cancer lncRNAsAs TADs are characterized by high-density chromatin contacts, and their alterations may cause aberrant gene expression (Valton and Dekker 2016), we considered TADs in cancer as functional units where lncRNAs may affect the expression of cancer driver PCGs. TADs...
  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
    ...of the relationships between the topological domains and chromatin states, gene expression, and DNA replication timing.Recent advances in imaging technologies (Bintu et al. 2018; Su et al. 2020) and chromosome conformation capture (3C)–based technologies such as Hi-C (Dekker et al. 2002; Dostie et al. 2006; Simonis et...
  10. 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
    ...structure in this case.Performance on simulated data setscisDIVERSITY can be thought of as a joint clustering and de novo motif discovery method. To systematically assess how well cisDIVERSITY is able to retrieve modules and motifs, we simulated more such data sets. To better emulate reality, we used random...
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