Searching journal content for articles similar to Winstanley et al. 19 (1): 12.

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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
...to Mbp, retain much longer-range genomic information. Therefore, they can more easily distinguish intra-genomic repeats or highly similar strains, which supports the disambiguation of reads when determining the strain they stem from. Second, as per the basic properties of single-molecule sequencing...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
...such as arithmetic coding is used to convert the data into a compressed bitstream (Mahoney 2000). Following this line, “DeepZip” (Goyal et al. 2018) estimated the probabilities by processing genomic sequences with gated recurrent units (GRUs) and long short-term memory units (LSTMs). Mahoney (2005) introduced...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...algorithm tuning. Subsequently, the SHAP method was introduced to 93 assess the effects of genomic variants and generate effect distribution maps of SNPs at the 94 individual, site, and population levels. This study developed a comprehensive set of AI 95 prediction toolkits that integrate feature selection...
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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
.... briggsae strains and nine C. nigoni strains, including both reference strains. Through comparative pan-genomic analyses of both nematode species, we aim to identify the critical structural and genetic variations that drive intra- and interspecific evolution, ultimately leading to speciation...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...provides novel insights into the genomic regulatory landscape underlying antiviral 33 immunity in a farmed fish with a complex . 34 Introduction 35 The innate immune response to viral infection, which is mainly based on the type I interferon 36 (type I IFN) pathway is crucial to both disease progression...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...identify sequence variations relative to a reference . These genomic variations encompass a spectrum of sizes, from single-nucleotide variants (SNVs) and short insertions or deletions (indels, <50 bp) to SVs (≥50 bp). Thus, identifying the proper reference for long-read alignment is critical as it might...
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Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
- Laura E. Tibbs-Cortes,
- Tingting Guo,
- Carson M. Andorf,
- Xianran Li,
- and Jianming Yu
Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
...authors: xianran.li@usda.gov, jmyu@iastate.eduAbstractMaize phenotypes are plastic, determined by the complex interplay of genetics and environmental variables. Uncovering the genes responsible and understanding how their effects change across a large geographic region are challenging. In this study, we...
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Method: spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. February 3, 2026 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...and missing19 gene measurements, challenges that are further compounded by the higher cost20 of spatial data compared to traditional single-cell data. To overcome this chal-21 lenge, we introduce spRefine, a deep learning framework that leverages genomic22 language models to jointly denoise and impute spatial...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
..., these studies also highlight a critical challenge: Traditional methods to account for population structure struggle to capture this discrete, nonlinear population structure occurring within recent timescales. The nonlinear relationships and sparsity in the GRM introduced by rare variants can make rare variant...
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Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
- Romain Derelle,
- Johanna von Wachsmann,
- Tommi Mäklin,
- Joel Hellewell,
- Timothy Russell,
- Ajit Lalvani,
- Leonid Chindelevitch,
- Nicholas J. Croucher,
- Simon R. Harris,
- and John A. Lees
Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
...strands), excluding certain genomic regions or selecting a reference closely related to the strains of interest (Colquhoun et al. 2021). With typical mapping approaches, SNPs are totally missed when they occur in genomic regions that are either absent from or too dissimilar to the reference , a phenomenon...
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