Searching journal content for articles similar to Theilhaber et al. 12 (1): 165.

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  1. Method: Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
    • Vikram S. Shivakumar and
    • Ben Langmead
    Genome Res. February 2026 36: 397-404; Published in Advance November 7, 2025, doi:10.1101/gr.280940.125
    ...pans be scalable. Specifically, we wish to be able to find conserved elements across pans in a way that scales to large pans and that can be updated incrementally when the pan grows further. Such methods will allow us build the common coordinate systems that will underlie future studies (Taylor et al...
  2. Method: Robust 16S rRNA classification based on a compressed LCA index
    • Omar Ahmed,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
    ...offsets where the substring occurred. This subsampled SA fits in a space budget of words, where r is the number of BWT runs. Compressed indexes are relevant for taxonomic classification because they enable finding and locating substrings while also compressing away repetitive sequence content. In practice...
  3. Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
    • Jung-Wan Mok,
    • Shelley B. Gibson,
    • Haley A. Dostalik,
    • and Shinya Yamamoto
    Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
    .../AMP) guidelines to classify genetic variants into five categories: pathogenic, likely pathogenic, benign, likely benign, and variant(s) of uncertain significance (VUS) (Richards et al. 2015). Whereas the first four classifications could be useful in interpreting rare variants that are found in genes that have...
  4. Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
    • Paras Verma,
    • Deeksha Thakur,
    • Deepanshi Awasthi,
    • and Shashi Bhushan Pandit
    Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
    ...remains limited owing to dearth of subsequent proteogenomic consequences. To coalesce the genomic information embedded in exons with isoform sequences, we present an innovative framework, “Exon Nomenclature And Classification of Transcripts” (ENACT). This centralizes exonic loci such that protein sequence...
  5. Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
    • Jens-Uwe Ulrich and
    • Bernhard Y. Renard
    Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
    ...the highest F1- and F0.5-scores on the species level for the three mock communities, indicating the robustness of the findings. We attribute this improvement to using syncmers instead of minimizers, applying several iterative filter steps, and applying our EM algorithm for read classification refinement...
  6. Method: A simple method for finding related sequences by adding probabilities of alternative alignments
    • Martin C. Frith
    Genome Res. August 2024 34: 1165-1173; Published in Advance August 16, 2024, doi:10.1101/gr.279464.124
    ...: mcfrith@edu.k.u-tokyo.ac.jpAbstractThe main way of analyzing genetic sequences is by finding sequence regions that are related to each other. There are many methods to do that, usually based on this idea: Find an alignment of two sequence regions, which would be unlikely to exist between unrelated...
  7. Method: Semisupervised adversarial neural networks for single-cell classification
    • Jacob C. Kimmel and
    • David R. Kelley
    Genome Res. October 2021 31: 1781-1793; Published in Advance February 24, 2021, doi:10.1101/gr.268581.120
    .... Manual annotation is time-consuming, somewhat subjective, and error prone. Annotations influence the results of nearly all downstream analyses, motivating more robust algorithmic approaches for cell type annotation.Automated classification tools have been proposed to transfer annotations across data sets...
    OPEN ACCESS ARTICLE
  8. 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
    ...the heterozygous condition in Deafness nonsyndromic autosomal dominant 2 (DFNA2) patients caused by KCNQ4 variants, we coexpressed loss-of-function variants with wild-type KCNQ4 and found 516 variants showed impaired or only partially rescued heterogeneous channel function. Overall, our functional classification...
  9. Method: Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers
    • Minjie Zhang,
    • Irena T. Hwang,
    • Kongpan Li,
    • Jianhui Bai,
    • Jian-Fu Chen,
    • Tsachy Weissman,
    • James Y. Zou,
    • and Zhipeng Lu
    Genome Res. May 2022 32: 968-985; Published in Advance March 24, 2022, doi:10.1101/gr.275979.121
    ..., extracting structure information from such data presents unique challenges. Here, we introduce a set of computational tools for the systematic analysis of data from a wide variety of crosslink-ligation methods, specifically focusing on read mapping, alignment classification, and clustering. We design a new...
  10. Method: Centrifuge: rapid and sensitive classification of metagenomic sequences
    • Daehwan Kim,
    • Li Song,
    • Florian P. Breitwieser,
    • and Steven L. Salzberg
    Genome Res. December 2016 26: 1721-1729; Published in Advance October 17, 2016, doi:10.1101/gr.210641.116
    ...Centrifuge: rapid and sensitive classification of metagenomic sequences Daehwan Kim 1 , 4 , Li Song 1 , 2 , 4 , Florian P. Breitwieser 1 , 4 and Steven L. Salzberg 1 , 2 , 3 1Center for Computational Biology, Mc...
    OPEN ACCESS ARTICLE
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