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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
...typical divergence thresholds used to define species, strain, and lineage boundaries. (Right) Recall when requiring exact matches of the middle base, with inset showing recall over the within-lineage range.SKA1 has the option, through ska merge, to invert the keys and values in the merged dictionary...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...cell-types, reveals lineage and stage-specific 17 IPA signatures, with lymphoid cells exhibiting higher IPA site usage than myeloid cells. Temporal 18 profiling during megakaryocyte differentiation uncovers dynamic, gene-specific IPA regulation 19 linked to functional pathways including peroxisomal...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...-kB in three mammalian lineages. Our comparative analyses of RELA binding, together with epigenetic and transcriptional profiles, revealed conserved and lineage-specific TE subfamilies that are likely to participate in mammalian NF-kB regulatory networks. Given the active enhancer features and proximity...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...analyses. Overall, our JS divergence approach provides a single, biologically agnostic measure for effectively quantifying differences in COPs.Nucleosome and TF changes can be simultaneously quantified from COPsAfter using JS divergence to summarize chromatin differences in a biologically agnostic way, we...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
.... (E) Mapping quality (MAPQ) distributions of Hi-C reads whose paired mates contained rDNA subtype-specific or non-subtype-specific 31-mers, categorized by the nuclear haplotype they mapped against.Detailed analyses of sequencing reads revealed two major rDNA subtypes (1 and 2) supported by substantial...
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Method: ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
- Xiran Liu,
- Lorin Crawford,
- and Sohini Ramachandran
Genome Res. December 2025 35: 2691-2700; Published in Advance November 19, 2025, doi:10.1101/gr.280440.125
..., or nonprioritized—among multiple traits based on their regularized effects. Clustering applied to our neural network shrinkage results also produces consistently higher precision and recall for distinguishing gene-level associations in simulations. We demonstrate the application of ML-MAGES on association analyses...
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Research: Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
- John S. Sproul,
- Scott Hotaling,
- Jacqueline Heckenhauer,
- Ashlyn Powell,
- Dez Marshall,
- Amanda M. Larracuente,
- Joanna L. Kelley,
- Steffen U. Pauls,
- and Paul B. Frandsen
Genome Res. October 2023 33: 1708-1717; Published in Advance September 22, 2023, doi:10.1101/gr.277387.122
...Analyses of 600+ insect s reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges John S. Sproul1,2,3,12, Scott Hotaling4,5,12, Jacqueline Heckenhauer6,7,12, Ashlyn Powell8, Dez Marshall2, Amanda M. Larracuente3, Joanna L. Kelley4,9, Steffen U. Pauls6...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...(Marques et al. 2005; Shi and Su 2012; Zhang and Long 2014). Brain transcriptomic analysis has revealed that upregulated genes early in human development are enriched with primate-specific genes, particularly within the human-specific prefrontal cortex (Zhang et al. 2011). The recruitment of new genes...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses reveal significant variation in gene content and structure across Blastocystis. Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...of these analyses yielded the same trend observed -wide using sequence divergence from consensus sequences: The Ty1/copia LTR retrotransposons (n = 135) overlapping piCs are significantly younger than nonoverlapping ones, whereas Tc1/mariner (n = 89) DNA transposons show no such bias (Fig. 4E).To examine whether...

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