Searching journal content for articles similar to Nikaido et al. 23 (10): 1740.

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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
...SVs landscape 29 and reveals a significant positive correlation between somatic deletion burden and smoking 30 intensity. Furthermore, a high-frequency somatic simple repeat expansion is identified in 31 28/39 (71.79%) of LSCC patients, which upregulates the expression of genes TP53BP2 and 32 FBXO28...
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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: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
.... 2024). Their genomic features, particularly the presence of eukaryotic signature proteins (ESPs), provide insights into the steps leading to eukaryotic cellular complexity. Recent phylogenetic analyses place eukaryotes within Asgard archaea (Spang et al. 2015; Zaremba-Niedzwiedzka et al. 2017), most...
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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
...haplotype sequence as a mosaic of the reference haplotypes, to compute the transition probabilities over the phased genotypes between adjacent genomic segments, representing the current belief over the target phases. These probabilities are then used to sample a new pair of phased haplotype estimates...
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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
...in a traditional sense. Instead, the signatures of selection may reflect broader genomic processes, such as linkage to functional genomic regions under selection or historical constraints on these sequences prior to their nuclear integration.To test selection on dcNUMTs, we divided our data set into (1) single...
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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
...at Austin, Dell Pediatric Research Institute, Austin, Texas 78723, USA; 9Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 1516, Cyprus; 10Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus...
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Resource: Lignature provides a curated resource of ligand induced transcriptomic signatures for signaling inference
- Ying Xin,
- Md Amanullah,
- Cheng Qian,
- Chingmo Zhou,
- and Jiang Qian
Genome Res. April 8, 2026 gr.281287.125; Published in Advance April 8, 2026, doi:10.1101/gr.281287.125
...Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 Cold Spring Harbor Laboratory Press 10.1101/gr.281287.125 ;gr.281287.125v1 ;gr.281287.125 gr.281287.125 gr.281287.125 Resource Resource Resources Lignature for signaling inference The Johns Hopkins University School of Medicine...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...with the up- and downregulation of genes and use these signatures to reveal regulatory mechanisms previously unexplored in expression-based studies. Finally, we demonstrate that chromatin features are predictive of transcriptional activity, and we leverage these features to reconstruct chromatin...
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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
...Analyses of 600+ insect s reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges John S. Sproul1,2,3,12, Scott Hotaling4,5,12, Jacqueline Heckenhauer6,7,12, Ashlyn Powell8, Dez Marshall2, Amanda M. Larracuente3, Joanna L. Kelley4,9, Steffen U. Pauls6...
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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
...the transcription start site (TSS) and transcription end site (TES) of human genes and that the sequence pattern of CPD deamination shows strong similarity to the COSMIC signature 7 mutation pattern that occurs in melanoma and other skin cancers (Jin et al. 2021). Although these results revealed a promising...
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