Searching journal content for articles similar to Siahpirani et al. 32 (7): 1367.

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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
...125 transcriptional program. Aggregating TFs according to their learned module yields meta-TF–target 126 CSNs with only a few meta-TFs. 127 Signalling inference In parallel, we incorporate prior knowledge by mapping observed coex- 128 pression edges to curated regulatory and signalling interaction...
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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
...data (Pratapa et al. 2020). Initial methods primarily rely on correlation or mutual information to infer regulatory interactions. For instance, weighted gene coexpression network analysis (WGCNA) (Langfelder and Horvath 2008) clusters coexpressed genes into modules to construct gene associations...
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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
...of genes examined, a potential solution to increase statistical power by reducing network complexity has been to utilize methods such as WGCNA that infer modules or groups of coexpressed genes that are regulated by one or more transcription factors rather than individual gene interactions (Segal et al...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...Lactobacillus can enhance learning and memory (Zhang et al. 2022a) and modify 75 the sugar sensitivity of honey bees (Zheng et al. 2017; Zhang et al. 2022b). Gut microbiota 76 can also affect the amount of host neurotransmitters (Zhang et al. 2022b) and modulate the 77 social network (Liberti et al. 2022...
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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
...and multimodal profiles across time, and extrapolate single-cell profiles in a missing modality. We apply Sunbear to reveal sex-biased transcription during mouse embryonic development and predict dynamic relationships between epigenetic priming and transcription for cells in which multimodal profiles...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...–specific TFs in regulating key genes associated with AD progression, linking transcriptional changes to genetic risk loci and highlighting potential mechanisms underlying disease pathology.View larger version: In this window In a new window Figure 5. Cell type–specific TF regulatory network. (A) TF regulatory...
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Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
- Chuanyuan Wang and
- Zhi-Ping Liu
Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
....The transcriptional state of a cell is intricately controlled by a gene regulatory network (GRN) comprising numerous transcription factors (TFs) and their target genes. Coordinating with other regulatory elements, GRNs modulate the cell's phenotype, identity, and function in a dynamic and specific manner (Levine...
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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...@eitech.edu.cnAbstractDeciphering the relationships between cis-regulatory elements (CREs) and target gene expression has been a long-standing unsolved problem in molecular biology, and the dynamics of CREs in different cell types make this problem more challenging. To address this challenge, we propose a scalable computational framework...
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Research: Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus
- William R. Thomas,
- Cecilia Baldoni,
- Yuanyuan Zeng,
- David Carlson,
- Julie Holm-Jacobsen,
- Marion Muturi,
- Dominik von Elverfeldt,
- Tue B. Bennike,
- Dina K.N. Dechmann,
- John Nieland,
- Angelique P. Corthals,
- and Liliana M. Dávalos
Genome Res. January 2026 36: 61-70; Published in Advance November 4, 2025, doi:10.1101/gr.280639.125
...budget with glucose to maintain their active winter lifestyle.To examine metabolic dynamics and regulatory changes throughout Dehnel's phenomenon, and its potential parallels to other wintering strategies, we conducted a multiomic analysis of S. araneus across seasonal time points that match...
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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
...to mediate 57 consistent phenotypic outcomes there must also be consistent regulation of such genes by 58 cis-regulatory modules (CRMs). CRMs consist of clusters of transcription factor binding sites 59 (TFBSs) that regulate the expression of target genes through collective or competitive binding 60...
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