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Method: Evaluation of N⁶-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes
- Brian M. Debo,
- Benjamin J. Mallory,
- and Andrew B. Stergachis
Genome Res. March 2023 33: 427-434; Published in Advance February 14, 2023, doi:10.1101/gr.276696.122
...-MTase results in the clustering of m6A-modified bases within regulatory elements and internucleosomal linker regions (Stergachis et al. 2020), a pattern that mirrors the distribution of validated endogenous m6A in eukaryotes (Kong et al. 2022). We then tested 12 commercial anti-DNA-m6A antibodies against...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...a cluster on the right arm of Chr IV (Fig. 6B). Although the genomic regions surrounding this gene cluster show lower conservation (i.e., reduced phyloP scores) than those flanking Cni-neib-1, the syntenic genes bordering both regions remain conserved (Fig. 6B). This conservation suggests that the fbxn...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...for downstream TFBS analysis, allowing the 142 identification of key regulatory motifs involved in the antiviral response. 143 To further characterise the genomic distribution of ATAC-seq and H3K27ac peaks, we 144 annotated consensus peaks relative to gene features and transcription start sites (TSS). The 145...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease Yunxiao Ren1,2, Ming Hu3,4, Yang E. Li5, Andrew A. Pieper6,7,8,9,10,11, Jeffrey Cummings12 and Feixiong Cheng1,2,4,13 1Cleveland Clinic Genome Center, Cleveland Clinic Research...
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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
.... More specialized tools for this approach include the Peak Browser at ChIP Atlas (Oki et al. 2018) or browsing ChIPBase (Huang et al. 2023), which is especially strong for ncRNAs but can also be used for mRNA genes. The Eukaryotic Promoter Database ExPASy has the useful Mass Genome Annotation Archive...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...Medhat Mahmoud1,4, Daniel P. Agustinho1,4 and Fritz J. Sedlazeck1,2,3 1Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; 3Department of Computer Science, Rice...
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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
...of the paerucumarin biosynthesis gene cluster showed the strongest and most consistent effect (Supplemental Fig. S4). Closer examination of the presence of these genes in our data set revealed that these orthologs are exclusively present in some strains of the genus Serratia. Because the paerucumarin gene cluster has...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...by chromatin looping (Fullwood et al. 2009).Although ESR1 occupies several thousand genomic sites, the number of genes actively regulated in response to E2 is substantially lower (Chen et al. 2021; Piryaei et al. 2022, 2023). One proposed explanation is that the DNA-receptor-ligand complex exhibits allosteric...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...to ggRibo, GWIPS-viz plots Ribo-seq reads in a single color, which hinders the intuitive interpretation of reading frames (Supplemental Fig. S2B). Although RiboCrypt offers color-coded reading frames in the “gene” view, the reading frame is assigned based on the genomic sequence, and therefore...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...with a high number of connections or hubs (Pastor-Satorras et al. 2003; Chou et al. 2014; Oh et al. 2015). Because eukaryotic transcriptional networks typically consist of a subset of genes, often transcription factors, that regulate many downstream target genes (Albert 2005), we chose specific values...
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