Searching journal content for articles similar to Neuwald et al. 13 (4): 673.

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  1. Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
    • David R. Lougheed,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
    ...memory usage. LongTR is the most memory-efficient STR caller for the GIAB trio samples sequenced with both ONT sequencing data sets.Read-level genotyping of targeted LRS data captures known instability in a pathogenic expansionWe ran STRkit and other tandem repeat callers on targeted CCS sequencing data...
  2. Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
    • Hsin-Yen Larry Wu,
    • Isaiah D. Kaufman,
    • and Polly Yingshan Hsu
    Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
    ...understanding of gene regulation. A tutorial detailing the setup, requirements, and example code of the ggRibo package is available on the ggRibo GitHub site.Visualizing translated ORFs using human and rice dataTo demonstrate ggRibo’s basic usage, we first provide an example in the human MRPL11 gene (Fig. 3...
    OPEN ACCESS ARTICLE
  3. Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
    • Laura Blanco-Berdugo,
    • Alexis Garretson,
    • and Beth L. Dumont
    Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
    ...transfer) affects stability. Age-matched cohorts of 12 ART-derived and 16 naturally conceived C57BL/6J inbred mice were reared in a controlled setting and whole--sequenced to ∼50× coverage. Using a rigorous pipeline for de novo single-nucleotide variant (dnSNV) discovery, we observe a ∼30% (95% CI: 4...
  4. Resource: Proactive functional classification of all possible missense single-nucleotide variants in KCNQ4
    • Honglan Zheng,
    • Xinhao Yan,
    • Guanluan Li,
    • Hengwei Lin,
    • Siqi Deng,
    • Wenhui Zhuang,
    • Fuqiang Yao,
    • Yu Lu,
    • Xin Xia,
    • Huijun Yuan,
    • Li Jin,
    • and Zhiqiang Yan
    Genome Res. August 2022 32: 1573-1584; Published in Advance June 27, 2022, doi:10.1101/gr.276562.122
    .... To prospectively characterize the function of all 4085 possible missense SNVs of human KCNQ4, we recorded the whole-cell currents using the patch-clamp technique and categorized 1068 missense SNVs as loss of function, as well as 728 loss-of-function SNVs located in the transmembrane domains. Further, to mimic...
  5. Research: Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors
    • Bradford H. Casey,
    • Rahul K. Kollipara,
    • Karine Pozo,
    • and Jane E. Johnson
    Genome Res. April 2018 28: 484-496; Published in Advance March 2, 2018, doi:10.1101/gr.224360.117
    ...related factors retain specificity, especially when they recognize the same DNA motifs, is not understood. We address this paradox using basic helix-loop-helix (bHLH) transcription factors ASCL1, ASCL2, and MYOD1, crucial mediators of lineage specification. In vivo, these factors recognize the same DNA...
  6. Research: A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization
    • Adam J. Litterman,
    • Robin Kageyama,
    • Olivier Le Tonqueze,
    • Wenxue Zhao,
    • John D. Gagnon,
    • Hani Goodarzi,
    • David J. Erle,
    • and K. Mark Ansel
    Genome Res. June 2019 29: 896-906; Published in Advance May 31, 2019, doi:10.1101/gr.242552.118
    ...Adam J. Litterman1, Robin Kageyama1, Olivier Le Tonqueze2, Wenxue Zhao2,3, John D. Gagnon1, Hani Goodarzi4, David J. Erle2 and K. Mark Ansel1 1Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California 94143...
  7. Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
    • Juniper J. Elacqua,
    • Navpreet Ranu,
    • Sarah E. DiIorio,
    • and Paul C. Blainey
    Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
    ..., toxicity, and cell death (Wu et al. 2014; Zhang et al. 2015). In efforts to make precise edits and minimize off-target DSB toxicity, Cas9's engineered nickase variants are an increasing focus in editing applications (Davis and Maizels 2011, 2014; Jinek et al. 2012; Ran et al. 2013; Komor et al. 2016...
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  8. Resource: Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants
    • Michael N. Edmonson,
    • Aman N. Patel,
    • Dale J. Hedges,
    • Zhaoming Wang,
    • Evadnie Rampersaud,
    • Chimene A. Kesserwan,
    • Xin Zhou,
    • Yanling Liu,
    • Scott Newman,
    • Michael C. Rusch,
    • Clay L. McLeod,
    • Mark R. Wilkinson,
    • Stephen V. Rice,
    • Thierry Soussi,
    • J. Paul Taylor,
    • Michael Benatar,
    • Jared B. Becksfort,
    • Kim E. Nichols,
    • Leslie L. Robison,
    • James R. Downing,
    • and Jinghui Zhang
    Genome Res. September 2019 29: 1555-1565; Published in Advance August 22, 2019, doi:10.1101/gr.250357.119
    ...to expand the repertoire of functional data generated by basic research scientists.View larger version: In this window In a new window Figure 3. Annotation interface. Excerpts of PeCanPIE annotation interface. (A) Results for Genome in a Bottle WGS data set. Variant page details for NOTCH1 R1350L: (B...
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  9. Research: Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer
    • Myrthe Jager,
    • Francis Blokzijl,
    • Ewart Kuijk,
    • Johanna Bertl,
    • Maria Vougioukalaki,
    • Roel Janssen,
    • Nicolle Besselink,
    • Sander Boymans,
    • Joep de Ligt,
    • Jakob Skou Pedersen,
    • Jan Hoeijmakers,
    • Joris Pothof,
    • Ruben van Boxtel,
    • and Edwin Cuppen
    Genome Res. July 2019 29: 1067-1077; Published in Advance June 20, 2019, doi:10.1101/gr.246223.118
    ...differentially expressed between WT and Ercc1−/Δ in both liver and small intestinal ASCs (P < 0.05, negative binomial test) (Fig. 1B), confirming the anticipated effects of the Ercc1 mutations at the mRNA level. While there is some Ercc1 expression in Ercc1−/Δ ASCs, the C-terminal domain of ERCC1 is essential...
    OPEN ACCESS ARTICLE
  10. Method: Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution
    • Hongyang Li and
    • Yuanfang Guan
    Genome Res. April 2021 31: 721-731; Published in Advance March 19, 2021, doi:10.1101/gr.269613.120
    ...). A relaxed cutoff of P = 0.01 was used to locate all the potential binding sites.The neural network architecture of LeopardThe Leopard architecture has two components, the encoder and the decoder (Fig. 1B). The basic building unit of the encoder is the convolution-convolution-pooling (ccp) block, which...
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