Searching journal content for articles similar to Horsfield et al. 33 (9): 1622.

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  1. Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
    • Enzo Battistella,
    • Anant Maheshwari,
    • Barış Ekim,
    • Bonnie Berger,
    • and Victoria Popic
    Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
    ...-020-01413-2 ↵Browning SR, Browning BL. 2007. Rapid and accurate haplotype phasing and missing-data inference for whole- association studies by use of localized haplotype clustering. Am J Hum Genet 81: 1084–1097. doi:10.1086/521987 ↵Browning SR, Browning BL. 2011. Haplotype phasing: existing methods and new developments...
  2. Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
    • Wenhai Zhang,
    • Yuansheng Liu,
    • Guangyi Li,
    • Jialu Xu,
    • Enlian Chen,
    • Alexander Schönhuth,
    • and Xiao Luo
    Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
    ...the sequence correlations among these s, potentially introducing ambiguity and biases in metagenomic profiling. Here, we present PanTax, a pan graph-based taxonomic profiler that overcomes the shortcomings of sequence-based approaches, because pan graphs possess the capability to depict the full range...
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  3. Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
    • Samuel T. Horsfield,
    • Basil C.T. Fok,
    • Yuhan Fu,
    • Paul Turner,
    • John A. Lees,
    • and Nicholas J. Croucher
    Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
    ...increase the enrichment of CBL sequences.Graph-based alignment facilitates the discovery of novel CBLWe investigated whether GNASTy's graph representation of CBL variation would enable it to discover and enrich novel CBL variants more accurately than conventional NAS. To evaluate this, we tested whether...
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  4. Method: Pangenome-based genome inference using integer programming
    • Ghanshyam Chandra,
    • Md Helal Hossen,
    • Stephan Scholz,
    • Alexander T. Dilthey,
    • Daniel Gibney,
    • and Chirag Jain
    Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
    ...as either a cyclic or acyclic directed graph in which the vertices are labeled with sequences. Paths in this graph spell the reference haplotype sequences and their recombinations. The graph-based representation is flexible enough to incorporate SNPs, indels, large structural variants (SVs), nested variants...
  5. Method: Accurate short-read alignment through r-index-based pangenome indexing
    • Rahul Varki,
    • Massimiliano Rossi,
    • Eddie Ferro,
    • Marco Oliva,
    • Erik Garrison,
    • Ben Langmead,
    • and Christina Boucher
    Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
    ...regions across multiple s. Common regions in the pan are collapsed into single nodes and single edges, making the representation efficient for pans with a lot of shared DNA. For collections of highly repetitive s, graphs can efficiently compress the pan. However, there are downsides to graph-based pan...
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  6. Method: Graph-based self-supervised learning for repeat detection in metagenomic assembly
    • Ali Azizpour,
    • Advait Balaji,
    • Todd J. Treangen,
    • and Santiago Segarra
    Genome Res. September 2024 34: 1468-1476; Published in Advance July 19, 2024, doi:10.1101/gr.279136.124
    ...the sequencing process before constructing the contig graph and are used in Steps 3 and 5. In addition, we incorporate four graph-based features that are widely used in the literature: betweenness centrality, k-core value, degree, and clustering coefficient. Previous studies have emphasized the significance...
  7. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...the populations of the two nematodes, driving their incompatibilities, remain elusive.Here we performed a comparative pan analysis across populations of C. briggsae and C. nigoni to elucidate the genomic divergences underlying their speciation. We generated high-quality assemblies and annotations for seven C...
  8. Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
    • Qunlun Shen,
    • Shuqin Zhang,
    • and Shihua Zhang
    Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
    ...Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS Qunlun Shen1,2, Shuqin Zhang1,3 and Shihua Zhang2,4,5 1School of Mathematical Sciences, Fudan University, Shanghai 200433, China; 2State Key Laboratory of Mathematical Sciences, Academy...
  9. Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
    • Zepu Miao and
    • Jia-Xing Yue
    Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
    ...-by-side visualization between the graph-based pan representation and the conventional primary linear reference –based feature annotations, therefore seamlessly bridging the graph and linear genomic contexts. To further demonstrate its functionality and scalability, we applied VRPG to the cutting-edge yeast and human...
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  10. Method: Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
    • Juri Kuronen,
    • Samuel T. Horsfield,
    • Anna K. Pöntinen,
    • Sudaraka Mallawaarachchi,
    • Sergio Arredondo-Alonso,
    • Harry Thorpe,
    • Rebecca A. Gladstone,
    • Rob J.L. Willems,
    • Stephen D. Bentley,
    • Nicholas J. Croucher,
    • Johan Pensar,
    • John A. Lees,
    • Gerry Tonkin-Hill,
    • and Jukka Corander
    Genome Res. July 2024 34: 1081-1088; Published in Advance August 12, 2024, doi:10.1101/gr.278485.123
    ...from the large cluster driven by LD on the left side of both plots, can be interpreted as strong signals of coselection or epistasis. The green points in A, driven by gaps in alignment with the reference , would be represented as unitig-presence and -absence patterns in the graph-based approach...
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