Searching journal content for articles similar to Yu et al. 32 (7): 1398.

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Method: Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads
- Netanya Keil,
- Carolina Monzó,
- Lauren McIntyre,
- and Ana Conesa
Genome Res. April 2025 35: 987-998; Published in Advance March 3, 2025, doi:10.1101/gr.280021.124
...control metrics, repurposed in SQANTI-reads, are highly effective for assessing the homogeneity in a lrRNA-seq multisample experiment, identifying read quality control failures, and detecting outliers. Additionally, we have added new metrics that provide insights into the potential utility and discovery...
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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
...of reads that can map equally well to shared regions of sequence between transcripts. This quantification uncertainty, in turn, can impact the quality and robustness of differential analysis using transcripts as features. mehenDi provides a different approach to tackle this problem for RNA-seq data...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...tools reveals that MotifScope can identify a greater number of motifs and more accurately represent the underlying repeat sequences. Moreover, MotifScope has been specifically designed to enable motif composition comparisons across assemblies of different individuals, as well as across long-read...
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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
...Evaluation of strategies for evidence-driven annotation using long-read RNA-seq Alejandro Paniagua1,2,6, Cristina Agustín-García1,6, Francisco J. Pardo-Palacios1, Thomas Brown3,4, Maite De Maria5, Nancy D. Denslow5, Camila J. Mazzoni3,4 and Ana Conesa1 1Institute for Integrative Systems Biology...
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Method: A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data
- Mengyuan Zhao,
- Jiawei Li,
- Xiaoyi Liu,
- Ke Ma,
- Jijun Tang,
- and Fei Guo
Genome Res. July 2024 34: 1036-1051; Published in Advance August 12, 2024, doi:10.1101/gr.278439.123
....In single-cell transcriptome sequencing, high-resolution quantification of gene expression profiles provides insights into cellular heterogeneity and the molecular underpinnings of tissue phenotype variations (Kalucka et al. 2020; Argelaguet et al. 2021). Analyzing cell type composition using scRNA-seq...
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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
...). To evaluate the feasibility of using 10x snRNA-seq data for detecting APA events, we first analyzed gene body coverage across different tissues and cell types. The results showed that 10x snRNA-seq reads were concentrated near the 3′-end regions of genes (Fig. 1A), enabling reliable detection of 3′ UTR...
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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 the NCBI Sequence Read Archive (SRA; https://www.ncbi.nlm.nih.gov/sra) (Kodama et al. 2012; Katz et al. 2022).Public RNA-seq data resources such as recount3 offer an unprecedented opportunity to improve GCN inference but also present major challenges due to heterogeneity in sample preparation, sequencing...
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Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
...with CTAT-LR-Fusion by combining LRS and short-read sequencing, improving the detection of clinically relevant gene fusions in cancer. Keil et al. (2025) introduce SQANTI-reads, a quality assessment framework for multisample long-read RNA-seq experiments, identifying under-annotated genes and novel...
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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
...extrinsic and intrinsic evidence. Extrinsic evidence is extracted from transcripts and cross-species homologous proteins. RNA-seq reads offer direct evidence on introns and, if assembled, on a gene structure. Protein sequences from related s can be used to identify regions of a that encode proteins...
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Method: Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network
- Xingyan Liu,
- Qunlun Shen,
- and Shihua Zhang
Genome Res. January 2023 33: 96-111; Published in Advance December 16, 2022, doi:10.1101/gr.276868.122
...equally to this work. Corresponding author: zsh@amss.ac.cnAbstractCross-species comparative analyses of single-cell RNA sequencing (scRNA-seq) data allow us to explore, at single-cell resolution, the origins of the cellular diversity and evolutionary mechanisms that shape cellular form and function. Cell...

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