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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...). To corroborate the observation, we investigated histone post-translational modifications (PTMs) by mass spectrometry (Johnson et al. 2004; Scheid et al. 2022), which confirmed an approximately eight- to 10-times-lower level of H3K9me2 but similar H3K9me1 levels in Spirodela relative to Arabidopsis (Supplemental...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...interactions of living organisms, and developing precise techniques to detect genomic differences between species. Nevertheless, the increase in biological data also necessitates algorithmic advances to capture the most useful information.As species evolve and diverge, they acquire new traits. This leads...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...with neither occupied CTCF motifs nor ChromHMM state annotations linked with enhancer/promoter activity.Epigenomic pileup analysisAs hundreds or thousands of stripes may be called, we sought to analyze our findings at a mass scale, so the aggregate epigenomic pileup analysis visualizes context sequence...
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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...for the detection of many novel variants, especially in the previously unresolved regions. They also found that their novel reference reduces the number of false-positive calls mainly in protein-coding genes, and they highlight the increased sensitivity for detection of rare variants and singletons (Aganezov et al...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...capacity. The animals can replace any part of their body when dissected into multiple fragments. Each part usually regrows into a new organism within 2–3 days (Fujisawa 2003; Tomczyk et al. 2015), as demonstrated in the most extreme case from a fragment of only 1% of the body mass (Shimizu et al. 1993...
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Method: Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA
- Han Shu,
- Jing Chen,
- Chang Xu,
- Jialu Hu,
- Yongtian Wang,
- Jiajie Peng,
- Qinghua Jiang,
- Xuequn Shang,
- and Tao Wang
Genome Res. October 2025 35: 2285-2299; Published in Advance August 14, 2025, doi:10.1101/gr.280584.125
...framework for multiple ST analysis tasks, including spatial domain detection and cell cycle identification. Although these methods have successfully analyzed individual slices, they remain limited to two-dimensional (2D) analyses owing to their single-slice focus.As the availability of SO data derived from...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...with the form count ∼ cohort using the MASS package in R (Venables and Ripley 2002). dnSNV counts were modeled as a negative binomial random variable with a log link function, rather than a Poisson random variable, as preliminary exploration of the count data revealed mild overdispersion (mean = 19.4, variance...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...the sequence of the underlying repeat unit. Although several methods exist, they often exhibit low accuracy when the repeat unit length increases or the number of copies is low. Furthermore, methods capable of handling highly mutated sequences remain scarce, highlighting a significant opportunity...
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Research: Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage
- Emily Lowry,
- Yiqing Wang,
- Tal Dagan,
- and Amir Mitchell
Genome Res. August 2024 34: 1154-1164; Published in Advance August 16, 2024, doi:10.1101/gr.279517.124
...; Pleguezuelos-Manzano et al. 2020). This enrichment is attributed to the particularly narrow minor groove of these sequences, which promotes colibactin binding (Dziubańska-Kusibab et al. 2020). Recent work has found that a colibactin-associated mutational signature is detected in 5%–10% of colorectal cancers...
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Research: Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini
- Chan Hyun Na,
- Mustafa A. Barbhuiya,
- Min-Sik Kim,
- Steven Verbruggen,
- Stephen M. Eacker,
- Olga Pletnikova,
- Juan C. Troncoso,
- Marc K. Halushka,
- Gerben Menschaert,
- Christopher M. Overall,
- and Akhilesh Pandey
Genome Res. January 2018 28: 25-36; Published in Advance November 21, 2017, doi:10.1101/gr.226050.117
...the corresponding N-terminal peptide generated by tryptic digest is too large (38 amino acids) for mass spectrometric detection. Also, the majority of N-terminal peptides mapped within a single nucleotide of the TISs predicted by ribosome profiling data.View larger version: In this window In a new window Figure 4...

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