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Method: MCHelper automatically curates transposable element libraries across eukaryotic species
- Simon Orozco-Arias,
- Pío Sierra,
- Richard Durbin,
- and Josefa González
Genome Res. December 2024 34: 2256-2268; Published in Advance December 9, 2024, doi:10.1101/gr.278821.123
...inputs: the raw library, the assembly, and the BUSCO gene set. As such, this tool can be easily integrated into any automatic pipeline to annotate TEs.DiscussionWe have shown that MCHelper increases TE libraries accuracy and completeness, producing longer and unfragmented TE annotations across eukaryotic...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...functional molecules. The biological function of a given protein is dictated by the arrangement of the atoms and functional groups in its three-dimensional (3D) structure. Therefore, variation in protein 3D structure is an essential source of information to explain how coding sequence variants impact gene...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...-base resolution methylation levels for individual CpG sites across the . These resources also annotate hypomethylated regions commonly linked to gene promoters, as well as allele-specific methylation patterns relevant to genomic imprinting. Notable examples include MethBase (Song et al. 2013), MethBank (Zhang et...
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Method: Memory-bound k-mer selection for large and evolutionarily diverse reference libraries
- Ali Osman Berk Şapcı and
- Siavash Mirarab
Genome Res. September 2024 34: 1455-1467; Published in Advance August 29, 2024, doi:10.1101/gr.279339.124
...ultra-large genomic reference sets (e.g., Parks et al. 2018; McDonald et al. 2024), often used with marker genes (Asnicar et al. 2020; Balaban et al. 2024). Using these data sets with k-mers-based methods, however, runs into a mundane but key limitation—the memory needed to use these s as reference...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...for the cerebellum (Fig. 1B), heart (Fig. 1C), and kidney (Fig. 1D). The correlation between gene expression levels from the RNA-seq and sRNA-seq libraries was highest in brain (R2 = 0.76) and cerebellum (R2 = 0.62).View larger version: In this window In a new window Figure 1. Comparison of the expression levels...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...al. 2015) and reformatted to follow the naming conventions of panEDTA. The curated Arabidopsis library was provided to panEDTA with the “‐‐curatedlib” parameter.This study utilized previously generated assemblies of the 26 maize NAM founder lines (Hufford et al. 2021), and their assemblies and gene...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...at different times during the 4sU labeling period. Moreover, peak identification can be computationally challenging for genes with low read coverage or uneven nascent transcription profiles, limiting the number of analyzable genes. Additionally, the 10- to 40-min time windows used in DRB/TTchem-seq restrict...
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Method: Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries
- Matthew Wiens,
- Hossein Farahani,
- R. Wilder Scott,
- T. Michael Underhill,
- and Ali Bashashati
Genome Res. August 2024 34: 1196-1210; Published in Advance August 15, 2024, doi:10.1101/gr.277066.122
..., this is not because of differences in expression levels, as the gene on which the edit is located (Htra1) is expressed in all involved clusters.Overall, this constitutes evidence that RNA-editing events may be seen in Chromium scRNA-seq libraries and used to infer heterogeneous presentation of RNA editing. Although...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...profiles of P. pacificus nematodes in response to diverse microbiota and used them to test the hypothesis that the adaptation to novel microbiota might be facilitated by the evolution of novel genes (Athanasouli et al. 2023). This revealed evidence that novel genes might be preferentially integrated...
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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
.... Recently, systematic evaluation of the impact of CREs on gene expression has become possible with CRISPR perturbations (Fulco et al. 2019), but only a small subset of CREs can be evaluated in the . Meanwhile, the evaluation is restricted to a small number of cell types. Due to its high cost...
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