Searching journal content for articles similar to Shivakumar and Langmead.

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  1. Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
    • Yidi Deng,
    • Jiadong Mao,
    • Jarny Choi,
    • and Kim-Anh Lê Cao
    Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
    ...improves computational efficiency and stabilizes coexpression estimates, mitigating challenges posed by small sample sizes in KNN regression and the inherent noise and sparsity of scRNA-seq data. Beyond coexpression, NNet supports scalable downstream analyses, including (i) clustering and aggregating cell...
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  2. Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
    • Qinhu Zhang,
    • Siguo Wang,
    • Zhipeng Li,
    • Wenzheng Bao,
    • Wenjian Liu,
    • and De-Shuang Huang
    Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
    ....To demonstrate the flexible scalability of ScPGE, we performed a series of experiments by modifying the number of epigenomic tracks, the number of cCREs, and the structure of ScPGE: (i) scalability of epigenomic tracks (Fig. 2C)—we find that ScPGE using 13 epigenomic tracks performs better than ScPGE using four...
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  3. Method: Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains
    • Hang Zhang,
    • Yi Zhang,
    • Kai Ming Ting,
    • Jie Zhang,
    • and Qiuran Zhao
    Genome Res. February 2025 35: 355-367; Published in Advance February 5, 2025, doi:10.1101/gr.278983.124
    ...types of clusters. The limitation of k-means clustering is well studied; that is, it can only find clusters of globular shapes because each cluster is represented with an average vector (Aggarwal 2015). Although density-based methods (Ester et al. 1996; Rodriguez and Laio 2014) can detect arbitrary...
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  4. Method: Scalable summary-statistics-based heritability estimation method with individual genotype level accuracy
    • Moonseong Jeong,
    • Ali Pazokitoroudi,
    • Zhengtong Liu,
    • and Sriram Sankararaman
    Genome Res. September 2024 34: 1286-1293; Published in Advance July 22, 2024, doi:10.1101/gr.279207.124
    ...heritability is then defined as the proportion of genetic variance over total phenotypic variance, .One approach to estimating the variance components is to find the maximum likelihood estimator (MLE) and its variants, such as restricted maximum likelihood (REML) estimators (Yang et al. 2011; Loh et al. 2015b...
    OPEN ACCESS ARTICLE
  5. Method: A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits
    • Boyang Fu,
    • Prateek Anand,
    • Aakarsh Anand,
    • Joel Mefford,
    • and Sriram Sankararaman
    Genome Res. September 2024 34: 1294-1303; Published in Advance August 29, 2024, doi:10.1101/gr.279140.124
    ...interpretability. We propose QuadKAST, a scalable algorithm focused on testing pairwise interaction effects (quadratic effects) within small to medium-sized sets of genetic variants (window size ≤100) on a trait and provide quantified interpretation of these effects. Comprehensive simulations show that Quad...
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  6. Method: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
    • Yunheng Han and
    • Erin K. Molloy
    Genome Res. July 2023 33: 1042-1052; Published in Advance May 17, 2023, doi:10.1101/gr.277629.122
    ...that offers accuracy and scalability under these challenging scenarios. TREE-QMC builds upon weighted Quartet Max Cut, which takes weighted quartets as input and then constructs a species tree in a divide-and-conquer fashion, at each step forming a graph and seeking its max cut. The wQMC method has been...
  7. Method: A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings
    • Louxin Zhang,
    • Niloufar Abhari,
    • Caroline Colijn,
    • and Yufeng Wu
    Genome Res. July 2023 33: 1053-1060; Published in Advance May 22, 2023, doi:10.1101/gr.277669.123
    ...(Mirzaei and Wu 2015) have been developed. All of these methods reconstruct a tree–child network with the smallest HN. Some of the methods insert reticulate edges or use other editing operations to search a network in the network space. Others reduce the tree–child network reconstruction problem to finding...
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  8. Method: Scalable and model-free detection of spatial patterns and colocalization
    • Qi Liu,
    • Chih-Yuan Hsu,
    • and Yu Shyr
    Genome Res. September 2022 32: 1736-1745; Published in Advance September 9, 2022, doi:10.1101/gr.276851.122
    ...-scale spatial omics studies. Analyzing simulation and a variety of spatially resolved transcriptomics data showed that SpaGene is more powerful and scalable than existing methods. Spatial expression patterns identified by SpaGene reconstruct unobserved tissue structures. SpaGene also successfully discovers...
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  9. 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...
  10. Method: Ultrafast and scalable variant annotation and prioritization with big functional genomics data
    • Dandan Huang,
    • Xianfu Yi,
    • Yao Zhou,
    • Hongcheng Yao,
    • Hang Xu,
    • Jianhua Wang,
    • Shijie Zhang,
    • Wenyan Nong,
    • Panwen Wang,
    • Lei Shi,
    • Chenghao Xuan,
    • Miaoxin Li,
    • Junwen Wang,
    • Weidong Li,
    • Hoi Shan Kwan,
    • Pak Chung Sham,
    • Kai Wang,
    • and Mulin Jun Li
    Genome Res. December 2020 30: 1789-1801; Published in Advance October 15, 2020, doi:10.1101/gr.267997.120
    ...type–specific, -wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole- sequencing variants...
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