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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
...and consequently, yielding better visualizations.View larger version: In this window In a new window Figure 5. Metrics for assessing LD structure and inter-SNP correlation. (A) Average correlation versus genomic distance for real (blue) and simulated (orange) genotypes. We select multiple reference SNPs and plot...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
.... simulans (accession AB055959 [Tsunemoto and Matsuo 2001]), the aligned portion of the sequences differ by ∼6.7% without indels or by about 9.2% when indels are included.Linkage disequilibrium (LD) in the histone locusTo measure LD across the histone locus, we used data from the Zambian lines from...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...(Horton et al. 2023). Direct STR genotyping at a scale is thus valuable; STRs cannot always be imputed using SNVs (Gymrek et al. 2016; Saini et al. 2018), as SNV–STR linkage disequilibrium (LD) is lower than SNV–SNV pair LD (Willems et al. 2014; Press et al. 2018). Examination of STR variation...
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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
...for graphs. Bioinformatics 37: i460–i467. doi:10.1093/bioinformatics/btab302 ↵Letcher B, Hunt M, Iqbal Z. 2021. Gramtools enables multiscale variation analysis with graphs. Genome Biol 22: 259. doi:10.1186/s13059-021-02474-0 ↵Li H. 2022. Sample graphs and sequences for testing sequence-to-graph alignment...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...the new s, we show that gars have the slowest rates of genomic structural and sequence evolution of all vertebrates. In species of the two living gar genera Atractosteus and Lepisosteus, 83.35% of the s remain identical even though they diverged over 100 million years ago. Genome size variation among gars...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...does not contain the RYR3 PE.This analysis simultaneously allowed us to discover TRs directly regulating splicing. We adjusted the P-values of all ANOVA tests of each gene using the Bonferroni method and selected the minimum P-value in each gene to ensure the inter-independence of inputs...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...-quality genomic data, phylogenomic methods, and phylogeny-aware statistical inference, our study aimed to shed light on the nuanced consequences of the interplay between defense systems and MGEs on bacterial evolution across timescales.ResultsAssociation between defense systems and MGE abundance is MGE and taxon...
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Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...–Whitney U test reveals significant differences in SynScore distribution between the splice site consensus (SSC) regions and internal exons, with sSNVs located at SSC regions showing higher SynScores, indicating a higher pathogenic potential. Furthermore, spatial clustering analysis using InterPro (Blum et...
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Method: Unified integration of spatial transcriptomics across platforms with LLOKI
- Ellie Haber,
- Ajinkya Deshpande,
- Jian Ma,
- and Spencer Krieger
Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
...spatial organization and dynamics across diverse contexts in health and disease (Hu et al. 2024). Although batch integration has been extensively studied in scRNA-seq (Argelaguet et al. 2021), ST presents unique challenges. A key difficulty is variation in gene panels across samples, even within the same...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...-read assemblies of Lake Malawi haplochromine cichlids. This graph intuitively represents complex and nested variation between the s and reveals that the SV landscape is dominated by large insertions, many exclusive to individual assemblies. The graph incorporates a substantial amount of extra sequence across...
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