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Research: LTRs activated by Epstein-Barr virus–induced transformation of B cells alter the transcriptome
- Amy Leung,
- Candi Trac,
- Hiroyuki Kato,
- Kevin R. Costello,
- Zhaoxia Chen,
- Rama Natarajan,
- and Dustin E. Schones
Genome Res. December 2018 28: 1791-1798; Published in Advance October 31, 2018, doi:10.1101/gr.233585.117
...the noncanonical isoform of IRF5 (Babaian et al. 2016). We found that this isoform is expressed in both EBV-positive and EBV-negative B cell lymphoma cell lines tested by Babaian and colleagues (Babaian et al. 2016), indicating it is not unique to EBV transformation. We furthermore examined our RNA-sequencing...
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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
...of the Austrian Academy of Sciences, 1090 Vienna, Austria; 11Eric and Wendy Schmidt Center, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA Corresponding author: valentina.boeva@inf.ethz.chAbstractGene signature scoring is integral to single-cell RNA sequencing (scRNA-seq) data analysis...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Lê Cao
Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
..., Canberra 2601, Australia; 3Bioinformatics and Cellular Genomics, St Vincent’s Institute, Fitzroy, Victoria 3065, Australia Gene networks provide a fundamental framework for understanding the molecular mechanisms that govern gene expression. Advances in single-cell RNA sequencing (scRNA-seq) have enabled...
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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
...of the Special Issue on “Long-read DNA and RNA Sequencing Applications in Biology and Medicine,” following the success of Part 1. Due to the record number of submissions, we are thrilled to feature an additional 39 manuscripts showcasing the growing interest and groundbreaking science driven by long...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...to comprehensively map GRNs (Badia-i-Mompel et al. 2023). High-throughput RNA sequencing (RNA-seq), which enables -wide analysis of the cellular transcriptome on bulk cells (Ozsolak and Milos 2011), has revolutionized GRN inference by enabling the computational derivation of regulatory networks from gene expression...
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Method: Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated
- Sindri Emmanúel Antonsson and
- Páll Melsted
Genome Res. August 2025 35: 1832-1841; Published in Advance July 7, 2025, doi:10.1101/gr.279886.124
...Sindri Emmanúel Antonsson and Páll Melsted Faculty of Industrial Engineering, Mechanical Engineering, and Computer Science, University of Iceland, 102 Reykjavík, Iceland Corresponding author: pmelsted@hi.isAbstractAs the number of experiments that employ single-cell RNA sequencing (scRNA-seq) grows...
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Method: Restoring the potency of neutralizing antibody via guided hypermutation with hyper-antibody editor
- Yuhong Wang,
- Yuefeng Guo,
- Qiuyu Lu,
- Xinyi Liu,
- Haoqi Xu,
- Jiayi Chen,
- Ruiqi Pi,
- Shaopeng Yuan,
- Ziting Yang,
- Rusen Lu,
- Fei-Long Meng,
- Tingting Gan,
- and Jiazhi Hu
Genome Res. March 19, 2026 gr.281396.125; Published in Advance March 19, 2026, doi:10.1101/gr.281396.125
...4These authors contributed equally to this work: Yuhong Wang and Yuefeng Guo 17 *Corresponding author: Jiazhi Hu (hujz@pku.edu.cn) 18 19 2 Abstract 20 Somatic hypermutation (SHM) drives antibody affinity maturation in B cells. By mimicking this 21 process, guided hypermutation (GHM) tools employing...
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Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
- Gage S. Black,
- Xiaomeng Huang,
- Yi Qiao,
- Philip Moos,
- Deepa Sampath,
- Deborah M. Stephens,
- Jennifer A. Woyach,
- and Gabor T. Marth
Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
..., Columbus, Ohio 43210, USA ↵6 These authors contributed equally to this work. Corresponding author: gmarth@genetics.utah.eduAbstractBruton tyrosine kinase (BTK) inhibitors are effective for the treatment of chronic lymphocytic leukemia (CLL) due to BTK's role in B cell survival and proliferation. Treatment...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...short-read sequencing strategies to detect m6A are inherently limited to aggregate measurements and are incapable of quantification at an individual molecular level.In contrast, Oxford Nanopore Technologies (ONT) RNA sequencing enables direct detection of RNA modifications such as m6A with single...
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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
...a comprehensive APA atlas for 261 cell types across 19 porcine tissues based on single-nucleus RNA sequencing (snRNA-seq) data. This analysis reveals tissue- and cell type–specific patterns of APA. We find that many genes display a clear correlation between the average length of 3′ untranslated regions (3′ UTRs...

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