Searching journal content for articles similar to Hu et al. 11 (7): 1237.

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  1. Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
    • Jonathan Cahn,
    • James P.B. Lloyd,
    • Ino D. Karemaker,
    • Pascal W.T.C. Jansen,
    • Jahnvi Pflueger,
    • Owen Duncan,
    • Jakob Petereit,
    • Ozren Bogdanovic,
    • A. Harvey Millar,
    • Michiel Vermeulen,
    • and Ryan Lister
    Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
    ...), or in controlling alternative splicing in male sex cells of meiosis factor MPS1 (AT5G57880) (Walker et al. 2018). Many genes (10%–20%) (Zhang et al. 2020) in euchromatic arms also harbor DNA methylation but only in the CG context, located in the gene body with a modest bias toward the 3′ end, called gene body...
  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
    ...underlying gene expression programs is of considerable interest to contemporary experimental and computational biology. A fundamental objective is to map the relationships between transcription regulators (TRs) and the sets of gene targets they functionally influence. TRs, which include DNA sequence...
  3. Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
    • Jun Kim,
    • Haoyu Wang,
    • and Sevinç Ercan
    Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
    ...-Rad 500-0006). One to two milligrams of protein extract was used per ChIP, and 5% was taken out to use as input DNA. The remaining protein extract was incubated with 3 to 10 μg of antibody rotating overnight at 4°C in a volume of 440 μL. Forty microliters of (1:1 V) Protein A and/or G-Sepharose beads...
  4. Method: A complete pedigree-based graph workflow for rare candidate variant analysis
    • Charles Markello,
    • Charles Huang,
    • Alex Rodriguez,
    • Andrew Carroll,
    • Pi-Chuan Chang,
    • Jordan Eizenga,
    • Thomas Markello,
    • David Haussler,
    • and Benedict Paten
    Genome Res. May 2022 32: 893-903; Published in Advance April 28, 2022, doi:10.1101/gr.276387.121
    ...-heterozygous variant with a nonsynonymous change in an exon and a change in an intronic/splice-site region. Of the two that were missed, one had a large structural variant deletion which the candidate analysis workflow was not designed to detect. The other was a male with a de novo variant on the X Chromosome...
  5. Method: Predicting transfer RNA gene activity from sequence and genome context
    • Bryan P. Thornlow,
    • Joel Armstrong,
    • Andrew D. Holmes,
    • Jonathan M. Howard,
    • Russell B. Corbett-Detig,
    • and Todd M. Lowe
    Genome Res. January 2020 30: 85-94; Published in Advance December 19, 2019, doi:10.1101/gr.256164.119
    ...to estimate the evolutionary rate of functional changes among orthologs. Our method adds a new dimension to large-scale tRNA functional prediction and will help prioritize characterization of functional tRNA variants. Its simplicity and robustness should enable development of similar approaches for other...
  6. Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
    ...As variation in DNA methylation can also be influenced by other genetic variants besides STRs (Kerkel et al. 2008; Gutierrez-Arcelus et al. 2013; Banovich et al. 2014; Smith et al. 2014), we next attempted to determine whether candidate mSTRs are the causal modulators of local DNA methylation or whether...
  7. Method: Ultrafast and scalable variant annotation and prioritization with big functional genomics data
    • Dandan Huang,
    • Xianfu Yi,
    • Yao Zhou,
    • Hongcheng Yao,
    • Hang Xu,
    • Jianhua Wang,
    • Shijie Zhang,
    • Wenyan Nong,
    • Panwen Wang,
    • Lei Shi,
    • Chenghao Xuan,
    • Miaoxin Li,
    • Junwen Wang,
    • Weidong Li,
    • Hoi Shan Kwan,
    • Pak Chung Sham,
    • Kai Wang,
    • and Mulin Jun Li
    Genome Res. December 2020 30: 1789-1801; Published in Advance October 15, 2020, doi:10.1101/gr.267997.120
    ...type–specific, -wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole- sequencing variants...
  8. 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
    ...@stat.wisc.edu Abstract RNA-seq is currently the technology of choice for global measurement of transcript abundances in cells. Despite its successes, isoform-level quantification remains difficult because short RNA-seq reads are often compatible with multiple alternatively spliced isoforms. Existing methods rely...
    OPEN ACCESS ARTICLE
  9. 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
    ..., there is far more variability in the human CTCF motif itself, and it does not appear to make as many indirect or nonspecific interactions with DNA. However, the ChIP signal is significantly higher at the module with the canonical motif, suggesting that the modules with the variants are less strongly occupied...
  10. Method: Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements
    • Xiaofei Song,
    • Christine R. Beck,
    • Renqian Du,
    • Ian M. Campbell,
    • Zeynep Coban-Akdemir,
    • Shen Gu,
    • Amy M. Breman,
    • Pawel Stankiewicz,
    • Grzegorz Ira,
    • Chad A. Shaw,
    • and James R. Lupski
    Genome Res. August 2018 28: 1228-1242; Published in Advance June 15, 2018, doi:10.1101/gr.229401.117
    ...′ CNV-Alu is pink. Ctrl-Alu elements not involved in AAMR are in blue. The microhomology generated at the breakpoint junction after the AAMR event is shown in green.CNVs and other structural variants (SVs) can result from distinct molecular mechanisms, including DNA recombination–associated processes...
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