Searching journal content for articles similar to Li and Guan 31 (4): 721.

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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
    ...in modeling gene expression changes resulting from sequence variants. Yet, few methods operate at the resolution necessary to capture subtle effects of single-nucleotide changes. Furthermore, it remains unclear which architectural components, such as residual connections, normalization strategies...
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  2. Review: Navigating the landscape of epitranscriptomics and host immunity
    • Elaine Huang,
    • Clara Frydman,
    • and Xinshu Xiao
    Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
    ...to enable isoform-level characterization of methylated transcripts (Molinie et al. 2016). These methods were followed by single-nucleotide resolution antibody-free approaches, including m6A-REF-seq (Zhang et al. 2019) and MAZTER-seq (Garcia-Campos et al. 2019), both of which enable m6A detection using...
  3. Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
    • Bo Yan,
    • Duan Wang,
    • Romualdas Vaisvila,
    • Zhiyi Sun,
    • and Laurence Ettwiller
    Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
    ...sequence instead of bisulfite-converted probes that are specific to methylation. Subsequently, the methylation and variation can be phased together at molecule resolution while the redundancy of the complementary strands increases the accuracy of variant detection. In addition, methylation motifs can also...
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  4. Research: AP-1 subunits converge promiscuously at enhancers to potentiate transcription
    • Jungkyun Seo,
    • D. Dewran Koçak,
    • Luke C. Bartelt,
    • Courtney A. Williams,
    • Alejandro Barrera,
    • Charles A. Gersbach,
    • and Timothy E. Reddy
    Genome Res. April 2021 31: 538-550; Published in Advance March 5, 2021, doi:10.1101/gr.267898.120
    ...single nucleotides polymorphisms (SNPs) associated with diverse phenotypic traits and diseases in 2596 published -wide association studies (MacArthur et al. 2017). These SNPs were identified for a trait in at least two independent studies. Of those SNPs, 93% were localized within noncoding regions...
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  5. Method: Evidence of widespread, independent sequence signature for transcription factor cobinding
    • Manqi Zhou,
    • Hongyang Li,
    • Xueqing Wang,
    • and Yuanfang Guan
    Genome Res. February 2021 31: 265-278; Published in Advance December 10, 2020, doi:10.1101/gr.267310.120
    ...the mechanisms underlying gene expression and human diseases is how to analyze and delineate the -wide landscape of multiple characteristic biochemical signatures. An important aspect is the regulation of transcription factors (TFs), which bind to DNAs and drive the expression or suppression of genes. TFs do...
  6. Research: A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells
    • Gurdeep Singh,
    • Shanelle Mullany,
    • Sakthi D. Moorthy,
    • Richard Zhang,
    • Tahmid Mehdi,
    • Ruxiao Tian,
    • Andrew G. Duncan,
    • Alan M. Moses,
    • and Jennifer A. Mitchell
    Genome Res. April 2021 31: 564-575; Published in Advance March 12, 2021, doi:10.1101/gr.272468.120
    ...are required to regulate tissue-specific gene expression during normal development, and -wide association studies (GWASs) reveal that disease-associated SNPs (single nucleotide polymorphisms) are more often found in noncoding regions of the displaying chromatin features associated with transcriptional...
  7. 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...
  8. Letter: Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
    • Jeremy R. Sanford,
    • Xin Wang,
    • Matthew Mort,
    • Natalia VanDuyn,
    • David N. Cooper,
    • Sean D. Mooney,
    • Howard J. Edenberg,
    • and Yunlong Liu
    Genome Res. March 2009 19: 381-394; Published in Advance December 30, 2008, doi:10.1101/gr.082503.108
    ...Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts Jeremy R. Sanford 1 , 6 , Xin Wang 2 , Matthew Mort 3 , Natalia VanDuyn 4 , David N. Cooper 3 , Sean D. Mooney 5 , Howard J. Edenberg 4...
  9. Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
    • Qiuhan Wen,
    • Zhen Wang,
    • Qi Bao,
    • Tianli Ding,
    • Haihan Zhang,
    • Jianbo Li,
    • Zhuang Liu,
    • Jieping Huang,
    • and Guoqiang Yi
    Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
    ...polyadenylation (APA) plays a crucial role in gene regulation and phenotypic diversity. Whereas extensive studies have explored the global APA landscape using bulk RNA-seq data, in-depth analyses of APA events at the single-cell level remain limited—particularly in farm animals. In this study, we construct...
  10. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...important to this day due to their predictable performance and low costs.More recently, short-read sequencing has gained widespread adoption for cancer research as it enables the -wide identification of alterations, including single-nucleotide variants (SNVs), small insertions and deletions (indels), copy...
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