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Method: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data
- Cameron Park,
- Shouvik Mani,
- Nicolas Beltran-Velez,
- Katie Maurer,
- Teddy Huang,
- Shuqiang Li,
- Satyen Gohil,
- Kenneth J. Livak,
- David A. Knowles,
- Catherine J. Wu,
- and Elham Azizi
Genome Res. September 2024 34: 1384-1396; Published in Advance September 5, 2024, doi:10.1101/gr.279126.124
...on databases compiled from limited contexts. We introduce DIISCO, a Bayesian framework designed to characterize the temporal dynamics of cellular interactions using single-cell RNA-sequencing data from multiple time points. Our method utilizes structured Gaussian process regression to unveil time...
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Method: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
- Shuai Guo,
- Xiaoqian Liu,
- Xuesen Cheng,
- Yujie Jiang,
- Shuangxi Ji,
- Qingnan Liang,
- Andrew Koval,
- Yumei Li,
- Leah A. Owen,
- Ivana K. Kim,
- Ana Aparicio,
- Sanghoon Lee,
- Anil K. Sood,
- Scott Kopetz,
- John Paul Shen,
- John N. Weinstein,
- Margaret M. DeAngelis,
- Rui Chen,
- and Wenyi Wang
Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
...Department of Statistics, University of California at Riverside, Riverside, CA 92521, USA; ↵16Division of Ophthalmology, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Corresponding author: wwang7@mdanderson.orgAbstractBulk deconvolution with single-cell...
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Editorial: New frontiers in single-cell genomics
- Nicholas E. Navin,
- Orit Rozenblatt-Rosen,
- and Nancy R. Zhang
Genome Res. October 2021 31: ix-x; doi:10.1101/gr.276129.121
...densities . Genome Res (this issue) 31 : 1843 – 1855 . doi: 10.1101/gr.271288.120 ↵ Nieto P , Elosua-Bayes M , Trincado JL , Marchese D , Massoni-Badosa R , Salvany M , Henriques A , Nieto J , Aguilar-Fernández S , Mereu E , et al. 2021 . A single-cell tumor immune atlas for precision oncology . Genome Res...
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Method: Iterative epigenomic analyses in the same single cell
- Hidetaka Ohnuki,
- David J. Venzon,
- Alexei Lobanov,
- and Giovanna Tosato
Genome Res. October 2021 31: 1819-1830; Published in Advance February 24, 2021, doi:10.1101/gr.269068.120
...single-cell epigenomic techniques for detection of active histone marks display a “precision” of 53% (Drop-ChIP; H3K4me3) (Rotem et al. 2015), 50% (scChIC-seq; H3K4me3) (Ku et al. 2019), and 60% (ACT-seq; H3K4me3) (Carter et al. 2019). Therefore, REpi-seq detection of H3K27ac has a high degree...
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Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
- Joshua Lee,
- Elizabeth A. Snell,
- Joanne Brown,
- Charlotte E. Booth,
- Rosamonde E. Banks,
- Daniel J. Turner,
- Naveen S. Vasudev,
- and Dimitris Lagos
Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
...Kingdom ↵6 Present address: Enhanc3D Genomics Ltd., Cambridge CB4 0DS, UK Corresponding author: dimitris.lagos@york.ac.ukAbstractThe use of long-read direct RNA sequencing (DRS) and PCR cDNA sequencing (PCS) in clinical oncology remains limited, with no direct comparison between the two methods. We used...
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Method: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
- Jean Fan,
- Hae-Ock Lee,
- Soohyun Lee,
- Da-eun Ryu,
- Semin Lee,
- Catherine Xue,
- Seok Jin Kim,
- Kihyun Kim,
- Nikolaos Barkas,
- Peter J. Park,
- Woong-Yang Park,
- and Peter V. Kharchenko
Genome Res. August 2018 28: 1217-1227; Published in Advance June 13, 2018, doi:10.1101/gr.228080.117
...auto prep system, in the same way as MM cells. Variants were called separately on the individual cell (instead of joint calling) for a fair comparison to bulk data, which was also separately fed to the same variant calling pipeline. Later, to match precision, single-cell variants that occurred in only...
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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
...level to better understand its regulatory roles in traits of economic importance and further genetic breeding.To expand the pig single-cell atlas with posttranscriptional regulatory insights, we aimed to construct a comprehensive APA atlas across major tissue types and investigate the cell type...
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Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
...Corresponding author: twang@wustl.eduAbstractRecent studies have shown that the noncoding can produce unannotated proteins as antigens that induce immune response. One major source of this activity is the aberrant epigenetic reactivation of transposable elements (TEs). In tumors, TEs often provide cryptic...
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Research: Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
- David E. Symer,
- Keiko Akagi,
- Heather M. Geiger,
- Yang Song,
- Gaiyun Li,
- Anne-Katrin Emde,
- Weihong Xiao,
- Bo Jiang,
- André Corvelo,
- Nora C. Toussaint,
- Jingfeng Li,
- Amit Agrawal,
- Enver Ozer,
- Adel K. El-Naggar,
- Zoe Du,
- Jitesh B. Shewale,
- Birgit Stache-Crain,
- Mark Zucker,
- Nicolas Robine,
- Kevin R. Coombes,
- and Maura L. Gillison
Genome Res. January 2022 32: 55-70; Published in Advance December 13, 2021, doi:10.1101/gr.275911.121
..., Kevin R. Coombes8 and Maura L. Gillison2 1Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; 2Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; 3New York Genome...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...), and more recently, (spatial) single-cell sequencing approaches (Moncada et al. 2020; Ma and Zhou 2022). Recent advances in organoid models represent a transformative development in cancer research. Organoids, cultured in vitro, retain self-renewal and self-organizing capabilities that mimic the structure...
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