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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 Le Cao
Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...1Scalable cell-specific coexpression networks for granular regulatory 2 pattern discovery with NeighbourNet 3 Yidi Deng1,2, Jiadong Mao1,† & Jarny Choi3,† & Kim-Anh Lê Cao1,*,† 4 1Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, 5 3010, Australia 6...
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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
...Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs Qiuhan Wen1,2, Zhen Wang1, Qi Bao1, Tianli Ding1, Haihan Zhang3, Jianbo Li4, Zhuang Liu5, Jieping Huang2 and Guoqiang Yi1,6,7 1Shenzhen Branch, Guangdong Laboratory of Lingnan...
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Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...expectations for when differential gene expression should matter. Here, we collated existing data into a gene-regulatory network (GRN) and performed developmental transcriptomics across different environmental conditions, genetic backgrounds, and mutants to assess the regulatory logic of mouth-form plasticity...
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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
...primary analysis concerns the recapitulation of individual, direct gene-gene edges through graphical lasso, which we expected to be heavily impacted by sample size, we also performed a limited evaluation of the effects of data aggregation with weighted gene coexpression network analysis (WGCNA...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...Generation and analysis of a mouse multitissue annotation atlas Matthew Adams1 and Christopher Vollmers2 1Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA; 2Department of Biomolecular Engineering, University...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...1 Functional genomics analysis of developing zebrafish and human endoderm reveals 1 highly conserved cis-regulatory modules acting during vertebrate organogenesis 2 3 Daniela M. Riley1,†, Randa Elsayed1,†, Mark D. Walsh2,†, Simaran Johal2, Ying Lin3,4, Harry 4 Walton1, Till Bretschneider5, Sascha...
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Method: Bayesian inference of sample-specific coexpression networks
- Enakshi Saha,
- Viola Fanfani,
- Panagiotis Mandros,
- Marouen Ben Guebila,
- Jonas Fischer,
- Katherine H. Shutta,
- Dawn L. DeMeo,
- Camila M. Lopes-Ramos,
- and John Quackenbush
Genome Res. September 2024 34: 1397-1410; Published in Advance August 12, 2024, doi:10.1101/gr.279117.124
..., right panel). Nevertheless, BONOBO performed at least comparably to, and sometimes even better than, the other methods in all the tests we performed using yeast data.Finally, we wanted to understand what BONOBO's sample-specific coexpression networks can reveal about how a TF KO affects the overall...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...for genomic data. Integrated into diverse architectures such as convoluted neural networks (CNNs), long short-term memory (LSTM), dilated CNNs, and transformers, ConvNeXt V2 blocks consistently improve performance, leading to similar prediction accuracy across these different model types. This reveals...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...between genetic variants and environmental stressors is key to understanding the mechanisms underlying neurological diseases. In this study, we use human brain organoids to explore how varying oxygen levels expose context-dependent gene regulatory effects. By subjecting a genetically diverse panel of 21...
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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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