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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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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
.... To this end, we present a cross–data set cell type annotation methodology with a universal reference data and method selection strategy (CAMUS) to achieve highly accurate and efficient annotations. We demonstrate the advantages of CAMUS by conducting comprehensive analyses on 672 pairs of cross-species scRNA-seq...
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Resource: A single-cell transcriptome atlas of the maturing zebrafish telencephalon
- Shristi Pandey,
- Anna J. Moyer,
- and Summer B. Thyme
Genome Res. April 2023 33: 658-671; Published in Advance April 18, 2023, doi:10.1101/gr.277278.122
.... 2018). Such detailed single-cell RNA-seq data sets can support cross-species comparisons (Hashikawa et al. 2020) and functional studies with discovered cell types (Stednitz et al. 2018; Ncube et al. 2022). Therefore, a more detailed survey of the neuronal cell types in the pallium and subpallium...
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Method: Cross-species analysis of enhancer logic using deep learning
- Liesbeth Minnoye,
- Ibrahim Ihsan Taskiran,
- David Mauduit,
- Maurizio Fazio,
- Linde Van Aerschot,
- Gert Hulselmans,
- Valerie Christiaens,
- Samira Makhzami,
- Monika Seltenhammer,
- Panagiotis Karras,
- Aline Primot,
- Edouard Cadieu,
- Ellen van Rooijen,
- Jean-Christophe Marine,
- Giorgia Egidy,
- Ghanem-Elias Ghanem,
- Leonard Zon,
- Jasper Wouters,
- and Stein Aerts
Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
...identity. A better understanding of how enhancers work will improve the interpretation of noncoding variation and empower the generation of cell type–specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable...
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Research: Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants
- Juan Deng,
- Ya-Jing Liu,
- Wen-Tian Wei,
- Qi-Xuan Huang,
- Li-Ping Zhao,
- Ling-Yun Luo,
- Qi Zhu,
- Lin Zhang,
- Yuan Chen,
- Yan-Ling Ren,
- Shan-Gang Jia,
- Yu-Luan Lin,
- Ji Yang,
- Feng-Hua Lv,
- Hong-Ping Zhang,
- Feng-E Li,
- Li Li,
- and Meng-Hua Li
Genome Res. October 2023 33: 1690-1707; Published in Advance October 26, 2023, doi:10.1101/gr.278239.123
...and specific cell types (Cheng et al. 2019). Rumen epithelial single-cell atlases of cattle and sheep obtained with scRNA-seq have been reported (Gao et al. 2021; Wu et al. 2022; Xue et al. 2022; Yuan et al. 2022). However, a comprehensive developmental cell atlas and a metagenomic characteristic map...
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Research: Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface
- Mihaela Pavličev,
- Günter P. Wagner,
- Arun Rajendra Chavan,
- Kathryn Owens,
- Jamie Maziarz,
- Caitlin Dunn-Fletcher,
- Suhas G. Kallapur,
- Louis Muglia,
- and Helen Jones
Genome Res. March 2017 27: 349-361; Published in Advance February 7, 2017, doi:10.1101/gr.207597.116
...) are reflected in heterogeneous placental structure, encompassing many distinct cell types. Placental cell fate is determined in early eutherian development, as the outer layer of the blastocyst, the trophectoderm, is the precursor of placental tissue. Enveloped by the trophectoderm is the inner cell mass, which...
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Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
...projection and cross-time alignment (Tong et al. 2020; Huguet et al. 2022; Zhang et al. 2024a). Graph-based methods, such as GraphFP (Jiang et al. 2022), perform dynamic inference on top of cell graphs. However, most of these existing methods are focused on a single data modality (e.g., single-cell RNA-seq...
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Resource: High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration
- Zihe Li,
- Ziyu Xu,
- Lei Zhu,
- Tao Qin,
- Jinrui Ma,
- Zhanying Feng,
- Huishan Yue,
- Qing Guan,
- Botong Zhou,
- Ge Han,
- Guokun Zhang,
- Chunyi Li,
- Shuaijun Jia,
- Qiang Qiu,
- Dingjun Hao,
- Yong Wang,
- and Wen Wang
Genome Res. January 2025 35: 188-201; Published in Advance November 14, 2024, doi:10.1101/gr.279448.124
...and their specific TGs from single-cell RNA-seq data (Fig. 4A).View larger version: In this window In a new window Figure 4. cTOP models cell programs in antler regeneration. (A) cTOP couples cell expression modules and TF combinatory modules under the PECA regulatory network to model cellular regulatory programs...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33...
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Method: Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome
- Dachang Dang,
- Shao-Wu Zhang,
- Ran Duan,
- and Shihua Zhang
Genome Res. March 2023 33: 386-400; Published in Advance March 9, 2023, doi:10.1101/gr.277187.122
...frequency matrix built from all single cells, whereas the regions belonging to NWBs might act as dynamic boundaries among single cells and correspond to some weaker boundaries in the proximity frequency matrix (Supplemental Fig. S22F). These results reflected the high heterogeneity of topological domains...

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