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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...and reverse strands in each genomic bin and observed highly biased distributions when comparing the relative enrichment between the two strands across the (Fig. 6A–C; Supplemental Fig. 11). These biases reflect a preference for G4s in the leading strand and a dearth in the lagging strand. At individual phyla...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...understood. Here, we use comparative genomics, expression across multiple ontogenetic stages and tissues, as well as polymorphism data to investigate MHC evolution in newts. Contrary to earlier suggestions of a massively expanded MHC in salamanders, we find that the core MHC region remains relatively compact...
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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
...directly from ONT sequencing reads. It is highly versatile, as it can be applied to any S. cerevisiae sequencing data set without any particular telomere enrichment step, enabling the investigation of TL distribution diversity across numerous strains.TL distributions are highly diverse across S. cerevisiae...
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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
...GENE (CZI Cell Science Program et al. 2025), and the Human Cell Atlas (Regev et al. 2017). Similarly, integrating spatial transcriptomics (ST) data sets, which contain both spatial coordinates and gene expression, enables comparative analysis across samples, technologies, and conditions, revealing cellular...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
..., with an example plot of each showing the regulatory activity (normalized DNA and RNA counts) and ASE (the ratio of reference allele to total counts, i.e., allelic imbalance) present in each replicate. (C) Fisher's exact test for enrichment in ChromHMM genomic annotations comparing ASE sites (combined across...
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Method: Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation
- Yang Zhou,
- Qiongyu Sheng,
- Jing Qi,
- Jiao Hua,
- Bo Yang,
- Lei Wan,
- and Shuilin Jin
Genome Res. May 2023 33: 750-762; Published in Advance June 12, 2023, doi:10.1101/gr.277522.122
...various scenarios to show the capability of identifying condition-specific cell subpopulations across multiple heterogeneous data sets.ResultsscInt uniformly learns the contrastive biological variation for data integrationscInt aims to integrate multiple scRNA-seq data sets that may be generated from...
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Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...contribute to genomic diversification driven by the acquisition of adaptive elements across species.An intriguing possibility for the acquisition of novel, genetically adapted elements is the transfer of organelle DNA (Popadin et al. 2022; Butenko et al. 2024). In many eukaryotic species, organelles...
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Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
- Matthew M. Hong,
- David Froelicher,
- Ricky Magner,
- Victoria Popic,
- Bonnie Berger,
- and Hyunghoon Cho
Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
...-Relate on the UK Biobank and All of Us data sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.Collaborative studies that aim...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...copies mapped on the 10 T. freemani chromosomes, fLG2-fLGX, in the Tfree1.0 assembly. The number of annotated copies is color-coded according to the color scale. (C) UpSet plot showing the number of the T. freemani satDNAs with annotated genes, transposable elements (TEs), and/or satDNAs within 10-kb...
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Method: Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
- Hongyu Zheng,
- Hirak Sarkar,
- and Benjamin J. Raphael
Genome Res. December 2025 35: 2734-2743; Published in Advance November 17, 2025, doi:10.1101/gr.280555.125
...) to construct a latent gene expression matrix from the views obtained by the two SRT technologies. We demonstrate the effectiveness of SIID on both simulated and two paired Xenium-Visium data sets by evaluating the imputed gene expression and the inferred cell type mixtures. On paired 10x Genomics Xenium...
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