Searching journal content for articles similar to Rahman Hera et al. 33 (7): 1061.

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Research: Epigenetic characterization of pseudogenes across human tissues
- Yunzhe Jiang,
- Beatrice Borsari,
- and Mark Gerstein
Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
...characterization of promoter epigenetic activity across 26 human tissues (Supplemental Table S2). In addition to this epigenetic characterization, we included further promoter properties by analyzing guanine-cytosine (GC) content, evolutionary conservation, and mutation spectra based on single nucleotide variant...
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Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- Lianne B Cohen,
- Tamara Hadzic,
- Caitlin Sauer,
- Julia R Gibbs,
- and Zeba Wunderlich
Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
...these pathways, which are conserved not only 73 across insects, but also in mammals (Dushay and Eldon 1998; Yu et al. 2022). 74 75 To identify immune regulated enhancers wide, we used STARR-seq (Self Transcribing 76 Active Regulatory-Region sequencing) (Arnold et al. 2013; Muerdter et al. 2015). This high-77...
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Research: A transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...source of dsRNA is cotranscription of sense and antisense strands of the same genomic region. Binding of these complementary, naturally occurring, antisense transcripts (NATs) results in a perfect RNA duplex, which may be targeted by ADARs. To explore the scope of ADAR editing of NAT-derived dsRNA, we...
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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
...SNVs in specific genomic contexts, suggesting that the observed rate increase in ART-derived mice is a general -wide phenomenon. Together, our findings show that ART is moderately mutagenic in house mice and motivate future work to define the procedure(s) associated with this increased mutational vulnerability...
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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
...area indicates the 95% confidence interval of the sampling noise, inferred from bootstrapping. The mean value is indicated by the dotted line. The detailed metrics are shown in the insets. (C) TL distribution of strain AHG, using data from O'Donnell et al. (2023) (Exp #1) and from a new sequencing (Exp...
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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
...of G4s locations in the human viruses’ s (Lavezzo et al. 2018); and Plant-GQ harbors G4s across 195 plants (Ge et al. 2019). Genome-wide G4-seq-based detection of G4s was performed in 19 organisms (Chambers et al. 2015; Marsico et al. 2019) and rG4-seq maps in the s of Pseudomonas aeruginosa...
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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
...genes.Calculating the ERC for each pair of orthologous genes across a phylogeny allows for the generation of an evolutionarily derived cofunctional map of the cell, which in turn can be used to predict functional relationships and interactions (Goh et al. 2000; Pazos and Valencia 2001; Ramani...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...frequency at TCG (0.00788; shown in red) is a significant outlier relative to other contexts and lies outside the 95% confidence interval of the predicted value based on its CPD frequency (0.00235 ± 0.00539). (G) Same as panel F, except mutation frequency is derived from published whole- sequencing data...
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Research: Proteome-wide structural analysis quantifies structural conservation across distant species
- Shijie Zhang,
- Teng Zhang,
- and Yuan Fu
Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
...at this phylogenetic distance highlights the importance of using structural comparison approaches to explore the relationship between organisms across different domains of life.Here, we present the first attempt to make a global structural-based comparison of the protein-coding genes from the three model organisms...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...) to scan s for sequences representing protein-coding intervals, with AUGUSTUS (Stanke and Waack 2003) being the most widely used example. Recent implementations of this approach, such as BRAKER1 (Hoff et al. 2016) and BRAKER2 (Brůna et al. 2021) wrap optimized implementations of AUGUSTUS, using protein...

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