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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
..., Katneni U, Jankowska KI, Meyer D, Kimchi-Sarfaty C. 2023. In silico methods for predicting functional synonymous variants. Genome Biol 24: 126. doi:10.1186/s13059-023-02966-1 ↵Liu Y. 2020. A code within the genetic code: codon usage regulates co-translational protein folding. Cell Commun Signal 18: 145...
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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
...in the strength of selection occurred along the long branches separating MHC-I-like1 and MHC-I-like2 from other sequences in MHC-I phylogeny, and (ii) whether the number and location of codons under positive/purifying selection differ among the three categories of genes.There was evidence of selection relaxation...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...sign of overfitting (Fig. 4I). These findings show that AlphaFold-predicted structures can help validate clustering quality. However, direct integration of AlphaFold predictions into clustering is challenging due to the inherent sequence uncertainty of short 50-mers, as reflected by their Shannon...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...disomy (UPD) of specific chromosomes or chromosomal regions (i.e., mice that inherit two maternal copies and no paternal copies, or vice versa, of a chromosome or part of a chromosome) have helped further define the genomic regions involved in this phenomenon. These studies identified several genomic...
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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
...on homomorphic encryption provide a valuable alternative with strong security guarantees (Kim et al. 2021; Gürsoy et al. 2022), they are less computationally flexible than TEEs, often resulting in notable accuracy loss owing to the algorithmic simplifications needed for practical runtimes (Dokmai et al. 2021...
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Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...-cell short-read gene expression data is used to cluster the cells, based on the conventional analysis pipeline for scRNA-seq. The transcript usage and mutation/deletion information are then aligned with the single-cell gene expression data. The bridge connecting these data sets is the shared cell barcodes...
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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
...they ranged between 65.15% and 95.87% (Supplemental Fig. 1). For both computational methodologies, we observe high concordance between the experimentally validated and computationally derived G4s across all examined model organisms. Next, we scanned the 108,459 organismal reference s for G4s using the regex...
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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
...that these arrays are embedded in conserved genomic regions, with >90% similarity in the 10-kb flanking regions (Supplemental Fig. S15). However, the PCA showed species-specific clustering of repeats (Fig. 6A), suggesting that the ∼40-kb array was present in the common ancestor but diverged through gene conversion...
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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
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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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
...of related species. Note that the gray branch is a separate background branch because it denotes the branch when the potential nuclear genomic integration took place.Selection analysis on isolated dcNUMT genes imply noncanonical NUMT integrations and “missing” mitochondrial sWe first conducted a codon...

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