Searching journal content for articles similar to Mateos et al. 12 (11): 1703.

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  1. Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
    • W.H. Adrian Tsui,
    • Spencer C. Ding,
    • Peiyong Jiang,
    • and Y.M. Dennis Lo
    Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
    ..., such as in Illumina's VeriSeq NIPT solution v2 assay, and also for single gene disorder analysis. For the latter, relative mutation dosage (RMD) (Lun et al. 2008) and relative haplotype dosage (RHDO) (Lo et al. 2010) establish statistical thresholds for classifying fetal monogenic disorders from maternal plasma DNA...
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  2. LETTER: A Gene Recommender Algorithm to Identify Coexpressed Genes in C. elegans
    • Art B. Owen,
    • Josh Stuart,
    • Kathy Mach,
    • Anne M. Villeneuve,
    • and Stuart Kim
    Genome Res. August 2003 13: 1828-1837; doi:10.1101/gr.1125403
    ...and Botstein 1999 ). A previous report compiled data from a large number of C. elegans DNA microarray experiments, and then used a variant of multidimensional scaling to generate a gene expression terrain map (a topomap; Kim et al. 2001 ). In this topomap, gene clusters are represented as different mountains...
  3. Method: Automated interpretable artificial intelligence genomic prediction with AlGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...and optimizing the hyperparameters. We demonstrate how gene-related biometrics influence target traits and how accounting for interaction effects enhances prediction accuracy. In addition, we apply Shapley additive explanations (SHAP) to quantify the SNP additive and epistatic effects. To bridge the gap between...
  4. Method: TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
    • Chen Li,
    • Sijie Chen,
    • Yixin Chen,
    • Haiyang Bian,
    • Minsheng Hao,
    • Lei Wei,
    • and Xuegong Zhang
    Genome Res. June 2025 35: 1429-1439; Published in Advance April 10, 2025, doi:10.1101/gr.279955.124
    ...for each gene. Then the DNA sequence of each correlated peak is used to scan TFs with the gimmemotifs v.5 vertebrate motif data set (https://gimmemotifs.readthedocs.io/en/master/). For the TFs that are not included in the gimmemotifs database, we searched the corresponding motifs in JASPAR database...
  5. METHODS: Spectral Biclustering of Microarray Data: Coclustering Genes and Conditions
    • Yuval Kluger,
    • Ronen Basri,
    • Joseph T. Chang,
    • and Mark Gerstein
    Genome Res. April 1, 2003 13: 703-716; doi:10.1101/gr.648603
    ...patients) index the columns j . Depending on the type of chip technology used, a value in this matrix A ij could either represent absolute expression levels (such as from Affymetrix GeneChips) or relative expression ratios (such as from cDNA microarrays). The methodology we will construct will apply...
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