Searching journal content for articles similar to Burch et al. 34 (9): 1304.

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  1. Method: Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
    • Van Hoan Do,
    • Francisca Rojas Ringeling,
    • and Stefan Canzar
    Genome Res. April 2021 31: 677-688; Published in Advance February 24, 2021, doi:10.1101/gr.267906.120
    ...data points, spectral clustering computes eigenvectors of an n × n affinity matrix, which incurs a computational cost of . For scRNA-seq data sets with n in the order of ten thousands up to the millions, this presents a prohibitive cost that has thus prevented the application of spectral clustering...
  2. Method: Likelihood-based deconvolution of bulk gene expression data using single-cell references
    • Dan D. Erdmann-Pham,
    • Jonathan Fischer,
    • Justin Hong,
    • and Yun S. Song
    Genome Res. October 2021 31: 1794-1806; Published in Advance July 22, 2021, doi:10.1101/gr.272344.120
    ...mathematically as (1) where M is a gene-by-cell type matrix of cell type–specific gene expression averages, α is a vector of cell type mixing proportions, and b is a vector of gene expression values in a bulk RNA-seq experiment. Depending on which of M, α, and b are measured, different approaches are appropriate...
  3. Editorial: Innovations in computational biology: RECOMB 2024 Special Issue
    • Jian Ma and
    • Bonnie Berger
    Genome Res. September 2024 34: vii-viii; doi:10.1101/gr.280036.124
    ...†µ Burch M , Bose A , Dexter G , Parida L , Drineas P . 2024 . Matrix sketching framework for linear mixed models in association studies . Genome Res (this issue) 34 : 1304 – 1311 . doi: 10.1101/gr.279230.124 ↵ Chandra G , Gibney D , Jain C . 2024 . Haplotype-aware sequence alignment to pan graphs...
  4. Method: Spatial Cellular Networks from omics data with SpaCeNet
    • Stefan Schrod,
    • Niklas Lück,
    • Robert Lohmayer,
    • Stefan Solbrig,
    • Dennis Völkl,
    • Tina Wipfler,
    • Katherine H. Shutta,
    • Marouen Ben Guebila,
    • Andreas Schäfer,
    • Tim Beißbarth,
    • Helena U. Zacharias,
    • Peter J. Oefner,
    • John Quackenbush,
    • and Michael Altenbuchinger
    Genome Res. September 2024 34: 1371-1383; Published in Advance September 4, 2024, doi:10.1101/gr.279125.124
    ....We used SpaCeNet to estimate a global, intracellular network (the precision matrix Ω) and a network of spatial molecular interactions (the spatial-interaction parameters Δρ(·)), where we set L = 3 and split the data into four equally sized batches of which three served for model building and one for model...
  5. Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
    • Zhengcao Li,
    • Xiaohong Liu,
    • Chen Wang,
    • Zhenyang Li,
    • Bo Jiang,
    • Ruifeng Zhang,
    • Lu Tong,
    • Youping Qu,
    • Sheng He,
    • Haifan Chen,
    • Yafei Mao,
    • Qingnan Li,
    • Torsten Pook,
    • Yu Wu,
    • Yanjun Zan,
    • Hui Zhang,
    • Lu Li,
    • Keying Wen,
    • and Yaosheng Chen
    Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
    ...are exclusively present in Chinese pigs and European pigs, respectively, which may have significant effects on the genetic activity of corresponding genes and phenotype differentiation (Fig. 5D; Supplemental Fig. S9), for example, a PRE insertion located in 3′ UTR of gene MMP2 (matrix metallopeptidase 2) (Fig. 5E...
    OPEN ACCESS ARTICLE
  6. Resource: Fast model-based estimation of ancestry in unrelated individuals
    • David H. Alexander,
    • John Novembre,
    • and Kenneth Lange
    Genome Res. September 2009 19: 1655-1664; Published in Advance July 31, 2009, doi:10.1101/gr.094052.109
    ...coefficient matrix Q and the population allele frequency matrix F. Each update of Q itself involves sequential quadratic programming, a generalization of Newton’s method suitable for constrained optimization. Finally, we accelerate convergence of block relaxation by a novel quasiNewton method. Once point...
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