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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs Qiuhan Wen1,2, Zhen Wang1, Qi Bao1, Tianli Ding1, Haihan Zhang3, Jianbo Li4, Zhuang Liu5, Jieping Huang2 and Guoqiang Yi1,6,7 1Shenzhen Branch, Guangdong Laboratory of Lingnan...
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Research: 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 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...whenever a plausible alternative explanation (e.g., intramolecular secondary structure) existed. While this does not definitively rule out antisense pairing, we prioritized simpler, well-characterized mechanisms where multiple explanations were possible. Second, our reliance on poly(A)-selected RNA-seq...
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Method: Tree-based differential testing using inferential uncertainty for RNA-seq
- Noor Pratap Singh,
- Euphy Y. Wu,
- Jason Fan,
- Michael I. Love,
- and Rob Patro
Genome Res. October 2025 35: 2326-2338; Published in Advance August 21, 2025, doi:10.1101/gr.279981.124
...estimate the abundance of the features to be tested, with genes and transcripts being the most common features of interest for most RNA-seq analyses. A gene can express multiple isoforms or transcripts due to alternative splicing, where the transcripts can comprise an overlapping set of exons and thus...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...). For this approach, RNA-seq has been shown to overperform other forms of evidence, since this type of data is able to capture splice sites, exon, and alternative spliced exon boundaries (Yandell and Ence 2012). However, evidence-based methods have several downsides, one of them being the amount of data available...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...algorithms to accurately identify intronic polyadenylation 323 (IPA) events from bulk RNA-seq data. Unlike previous methods primarily focused on 3' UTR 324 alternative polyadenylation (APA), IPAseek robustly detects both composite and skipped IPA 325 isoforms, addressing challenges posed by complex splicing...
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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
...and AI Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: ajbattle@jhu.eduAbstractGene coexpression networks (GCNs) describe relationships among genes that maintain cellular identity and homeostasis. However, typical RNA-seq experiments often lack sufficient sample...
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Method: Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression
- Yipeng Gao,
- Lei Li,
- Christopher I. Amos,
- and Wei Li
Genome Res. October 2021 31: 1856-1866; Published in Advance May 25, 2021, doi:10.1101/gr.271346.120
...developed dynamic analysis of alternative polyadenylation from scRNA-seq (scDaPars), a bioinformatics algorithm for quantifying and recovering APA usage at the single-cell and single-gene resolution using standard scRNA-seq data. Because APA is reported to be regulated in a cell-state- or cell...
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Method: TransMeta simultaneously assembles multisample RNA-seq reads
- Ting Yu,
- Xiaoyu Zhao,
- and Guojun Li
Genome Res. July 2022 32: 1398-1407; Published in Advance July 20, 2022, doi:10.1101/gr.276434.121
..., -guided methods are more commonly used because they are usually more accurate (Shao and Kingsford 2017).Transcriptomic studies involve multiple samples. Constructing a consensus transcriptome from multiple samples is critical in an RNA-seq experiment for the subsequent quantification and differential...
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Method: BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
- Lars Gabriel,
- Tomáš Brůna,
- Katharina J. Hoff,
- Matthis Ebel,
- Alexandre Lomsadze,
- Mark Borodovsky,
- and Mario Stanke
Genome Res. May 2024 34: 769-777; Published in Advance June 12, 2024, doi:10.1101/gr.278090.123
...transcriptomes and proteomes vary across s, between genes, and even along a single gene. User-friendly and accurate annotation pipelines that can cope with such data heterogeneity are needed. The previously developed annotation pipelines BRAKER1 and BRAKER2 use RNA-seq or protein data, respectively, but not both...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...short-read RNA-seq as a modularized software that contains chimeric read extraction, fusion transcripts identification, expression quantification, gene fusion annotation, and interactive visualization. To benchmark existing tools, we collected or generated comprehensive simulation data sets to reflect...
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