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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
...embedding; and the orange square represents the cell types provided by reference data set. (F) The output of scHGR includes automatic cell annotation and differential expression gene (DEG) analysis based on propagation weight, revealing novel cell subtypes with biological significance and Gene Ontology (GO...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
....Subsequently, we estimated the percentage conservation of genes for each sample based on the path they traversed through the graph. This calculation was performed for a set of 20,785 (86.9%) genes on the A. calliptera–backboned graph, which were located outside overly complex bubbles and had spanning coverage from...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...subclasses within two GABAergic (GABA) classes, eleven subclasses within three glutamatergic (Glut) classes, as well as one specific subclass of dopaminergic (Dopa) class. We validated our annotations by examining the expression of representative marker genes (Supplemental Fig. S3). The number of cells per...
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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
...the direction-specific predictive power of each method and ensures that all models are evaluated under comparable conditions. As demonstrated in Supplemental Table S5, PRISM-GRN consistently outperforms both SCENIC+ and its base methods, GENIE3 and GRNBoost2, in recovering directed TF–gene interactions across...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...were normalized by the mean of the pre-exercise samples. (C) Network plot reveals the cell-type-specific target genes (blue) of PPARD (orange) identified by the integrated regulatory circuit analysis. Selected GO terms enriched in the target genes are annotated below. (D,E) Log2 fold-change (log2FC...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
..., cldnh was highly expressed in EM, MET, and the two unannotated cell clusters (Fig. 1C). The majority of cell-type annotations were supported by both marker gene expression and the marker gene promoter region accessibility (Fig. 1C,D). Each cell type was also characterized by specifically expressed genes...
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Method: A best-match approach for gene set analyses in embedding spaces
- Lechuan Li,
- Ruth Dannenfelser,
- Charlie Cruz,
- and Vicky Yao
Genome Res. September 2024 34: 1421-1433; Published in Advance September 4, 2024, doi:10.1101/gr.279141.124
...biological processes (Greene et al. 2015). Leveraging the directed acyclic graph structure of the ontology, we propagate gene annotations from child terms to parent terms based on annotated “is a” and “part of” relationships; parent terms thus also contain genes that participate in more specific (child term...
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Method: Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
- Yingxin Lin,
- Tung-Yu Wu,
- Xi Chen,
- Sheng Wan,
- Brian Chao,
- Jingxue Xin,
- Jean Y.H. Yang,
- Wing H. Wong,
- and Y.X. Rachel Wang
Genome Res. January 2024 34: 119-133; Published in Advance December 15, 2023, doi:10.1101/gr.277960.123
...of cell representations to their measured features (genes and peaks). We formulate a trajectory prediction problem using the estimated transition probabilities from OT and use gradient-based saliency mapping (Ciortan and Defrance 2021; Yang et al. 2021) to identify genes and peaks that are potentially...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
..., conduct a -wide analysis to assess the functions of dynamically expressed tsRNAs. Our results show that the predicted target genes are highly enriched in biological processes specific to this stage of development including metamorphosis. We further show that tsRNA action is required for successful...
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Research: Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation
- Montgomery Blencowe,
- Xuqi Chen,
- Yutian Zhao,
- Yuichiro Itoh,
- Caden N. McQuillen,
- Yanjie Han,
- Benjamin L. Shou,
- Rebecca McClusky,
- Karen Reue,
- Arthur P. Arnold,
- and Xia Yang
Genome Res. May 2022 32: 807-824; Published in Advance April 8, 2022, doi:10.1101/gr.275965.121
...specificity was prominent, with a major impact of estradiol on adipose tissue gene regulation and of testosterone on the liver transcriptome. The networks affected by the three sex-biasing factors include development, immunity and metabolism, and tissue-specific regulators were identified for these networks...
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