Searching journal content for articles similar to Sproul et al. 33 (10): 1708.

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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
...aimed at capturing the evolutionary history within families (Hubley et al. 2016; Carey et al. 2021). In the era of high-throughput sequencing-based functional genomics analysis, however, repetitive elements have presented a challenge. Since repeat elements, as the name suggests, are highly repetitive...
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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
..., demonstrating that gigantism does not scale proportionally in this region. Our finding also challenges the model of coevolution between a single classical MHC-Ia gene and antigen processing genes (APGs), revealing instead several polymorphic and highly expressed putative MHC-Ia located at varying distances from...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...) to assemble the recalcitrant repetitive regions of the and developed a new framework to reveal the detailed pattern of structural variation in repeat clusters. Using a comprehensive map of variation within the histone and Stellate clusters, we explore patterns of variation that empower us to comment...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...have the potential of discarding real biological TD from less abundant transcripts or those present in sample-specific conditions. Therefore, developing accurate algorithms to identify TD represents a new and important challenge for the computational biology and RNA communities.Genome annotation...
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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
...associated with patient survival and treatment resistance, accurate cell annotation is essential for identifying clinically relevant populations. Our analyses across nine healthy and cancer scRNA-seq data sets, covering diverse gene signatures and experimental conditions, revealed that established scoring...
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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
...with lengths that greatly exceed typical sequencing fragment sizes. When applied to data from the 1000 Genomes Project, ScatTR detects potential large TR expansions that other methods missed, highlighting its ability to better characterize -wide TR variation.Tandem repeats (TRs) are consecutively repeated...
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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
...DNAs with a lower proportion (<0.02%) revealed a distinct signal only on one chromosome pair (Supplemental Fig. S3D–F), which is generally consistent with the in silico analysis. In terms of monomer repetitiveness, 71 satDNAs were found exclusively in arrays of five or more consecutive repeats, whereas...
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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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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
...-value > 0.1). As there are few experimentally validated genomic elements, it is challenging to precisely measure the accuracy of annotations. Thus, to quantitatively assess these annotations, we evaluated their efficacy towards understanding tissue-specific gene regulation by performing three analyses...
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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
...epigenetic activity in hundreds of cell and tissue types. Chromatin state annotations produced by segmentation and annotation (SAGA) methods have emerged as the predominant way to summarize these epigenomic data sets in order to annotate the . These chromatin state annotations are essential for many genomic...
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