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Method: Balancing gene ontology annotation specificity in protein function prediction based on the protein sequence large graph
- Jiangyi Shao,
- Shutao Chen,
- Ziwen Wang,
- Zixu Chen,
- and Bin Liu
Genome Res. April 15, 2026 gr.280816.125; Published in Advance April 15, 2026, doi:10.1101/gr.280816.125
...all three ontology categories. As illustrated in Fig. 133 1A, proteins annotated with low-specificity GO terms form densely connected clusters, 134 whereas proteins annotated with high-specificity terms are sparsely represented: a 135 pattern consistent across CC, MF, and BP. This uneven annotation...
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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
...the APGs. MHC-I genes exhibit lineage-specific duplications and signs of concerted evolution, resulting in poorly resolved phylogenies. In contrast, MHC-II genes are more conserved and exhibit extensive trans-species polymorphism. Expression and polymorphism patterns identify putative nonclassical MHC...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
..., particularly for unsupervised cellular state annotation based on maximum signature score values. However, this application requires robust and comparable score distributions across diverse signatures and experimental conditions. Our systematic evaluation of established scoring methodologies—Seurat, SCANPY...
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Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- Marjan Farahbod,
- Aboud Diab,
- Paul Sud,
- Meenakshi S. Kagda,
- Ian Whaling,
- Mehdi Foroozandeh,
- Ishan Goel,
- Habib Daneshpajouh,
- Benjamin Hitz,
- J. Michael Cherry,
- and Maxwell W. Libbrecht
Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
...integrative summary of such data sets. Here, we present the ENCODE4 Catalog of Segway Annotations, a set of sample-specific -wide chromatin state annotations of 234 human biosamples inferred from 1,794 genomics experiments. This catalog identifies genomic elements, accurately captures cell type...
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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...to modifiable risk factors, such as tobacco exposure and alcohol consumption(Bray et 42 al. 2024; Sung et al. 2021; Chen et al. 2024; Johnson et al. 2020). However, the molecular 43 mechanisms by which these exogenous factors induce genomic instability remain unclear. 44 Early symptoms of LSCC are often...
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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
...patterns in NUMT abundance between mammals and birds, we investigated the phylogenetic distribution of NUMTs. Established species phylogenies for mammals and birds (Kumar et al. 2017; https://timetree.org) were used to reconstruct NUMT counts as a phylogenetic trait through a Bayesian approach implemented...
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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
...within lineages. Beyond insects, we use this large, diverse data set to highlight the opportunities and obstacles for investigating RE dynamics in biodiversity studies with an emphasis on RE annotation bottlenecks. We conclude by describing the ways in which the biodiversity genomics community can...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...cell types into NK cells. These errors followed a common pattern: either splitting a single major cell type into several incorrect annotations or merging multiple cell types into one. CAMUS can capture such common-pattern errors in misannotations, as they inherently conflict with the underlying...
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Method: Robust chromatin state annotation
- Mehdi Foroozandeh Shahraki,
- Marjan Farahbod,
- and Maxwell W. Libbrecht
Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
...; for review, see Libbrecht et al. 2021). They take a collection of epigenomic assay data sets from a given cell type or tissue as input and partition the into segments with similar patterns in the input data sets. The output is an annotation that assigns a label to each genomic position. These algorithms use...
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Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
..., Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Corresponding author: borodovsky@gatech.eduAbstractLarge-scale genomic initiatives, such as the Earth BioGenome Project, require efficient methods for eukaryotic annotation. Here we present an automatic gene finder, GeneMark-ETP, integrating...
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