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Method: OMA standalone: orthology inference among public and custom genomes and transcriptomes
- Adrian M. Altenhoff,
- Jeremy Levy,
- Magdalena Zarowiecki,
- Bartłomiej Tomiczek,
- Alex Warwick Vesztrocy,
- Daniel A. Dalquen,
- Steven Müller,
- Maximilian J. Telford,
- Natasha M. Glover,
- David Dylus,
- and Christophe Dessimoz
Genome Res. July 2019 29: 1152-1163; Published in Advance June 24, 2019, doi:10.1101/gr.243212.118
...OMA standalone: orthology inference among public and custom s and transcriptomes Adrian M. Altenhoff1,2,10, Jeremy Levy3,4,10, Magdalena Zarowiecki5, Bartłomiej Tomiczek4,6, Alex Warwick Vesztrocy1,4, Daniel A. Dalquen2, Steven Müller4, Maximilian J. Telford4, Natasha M. Glover1,7,8, David Dylus1...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
..., supplemental material, and publication date are at https://www..org/cgi/doi/10.1101/gr.281350.125. Freely available online through the Genome Research Open Access option. © 2026 Lang et al. This article, published inGenome Research, is available under a Creative Commons License (Attribution-NonCommercial 4...
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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
...- and short-read transcriptome data from multiple developmental stages and tissues across seven species. Using comparative genomics, expression profiles, phylogenetic analysis, and structural modeling, we trace MHC gene duplications and signatures of adaptive evolution, and identify putative classical...
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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
.... S11C). Considering the 80% sequence similarity and wide genomic distribution in both species, we hypothesize that the TCAST transposon-like element was present in the ancestral and gave rise to the 360-bp TCAST satDNA, the current major satellite of T. castaneum (Fig. 5A).The orthologous centromeric...
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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
..., Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, et al. 2022. The complete sequence of a human . Science 376: 44–53. doi:10.1126/science.abj6987 ↵Paten B, Novak AM, Eizenga JM, Garrison E. 2017. Genome graphs and the evolution of inference. Genome Res 27: 665–676. doi:10...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...+-enriched KZFPs among mammals (Supplemental Fig. S8A), and their human orthologs tend to be expressed in meiosis or in postmeiotic RSs (Supplemental Fig. S8B). To characterize these PS-enriched KZFPs, we first analyzed the binding preference of five PS-enriched KZFPs for which ChIP-seq data were available...
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Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
...analysis and have not been evaluated in the single-cell setting. For example, Sagittarius performs cross-species and cross-cell-line inference of bulk transcriptomic profiles through a transformer model (Woicik et al. 2023), and chronODE integrates bulk multiomics time-series data to model the temporal...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
....DiscussionThe 1kGP and HGDP were landmark efforts to increase the unrestricted public availability of genomic data from a geographically and ancestrally diverse set of individuals. These resources have been widely used across research efforts for decades, including as reference panels for ancestry inference...
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Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
...Sciences, University of Durham, Durham DH1 3LE, United Kingdom Corresponding author: nclark@pitt.eduAbstractEvolutionary rate covariation (ERC) is an established comparative genomics method that identifies sets of genes sharing patterns of sequence evolution, which suggests shared function. Whereas many...
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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
...left unaddressed in favor of computational performance. Prior research has shown that side channels in genomic analysis algorithms can be exploited to infer private genotypes, even when executed within a TEE (Brasser et al. 2017; Dokmai et al. 2021). TX-Phase eliminates all known timing and memory side...
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