Searching journal content for articles similar to Chassaing et al. 26 (4): 474.

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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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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. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...decisions is achieved during normal development. Furthermore, to understand the basis for developmental disorders, it will be necessary to decipher gene regulatory networks (GRNs) underpinning normal development. Zebrafish is an excellent model organism for dissecting gene regulatory control of cell fate...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...101800576 and LOC101790890 in the shell gland, of LOC119713219 in the ovary, and of GLP2R in the spleen is causally linked to declining egg production at peak laying. Last, we delineate a cross-tissue regulatory landscape underlying duck egg production and identify liver-derived modules, particularly Liver...
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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 Lê Cao
Genome Res. April 2026 36: 785-801; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...regulation. To enhance the interpretability of coexpression networks, we extend NNet to annotate TF–target coexpression by leveraging prior knowledge of gene regulation and signaling interactions. This approach helps us discern active gene regulation from confounding effects. In addition to identifying...
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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
...of the important contributors, just matching the function of the cCRE labeled as pELS, CTCF-bound.DiscussionDeciphering the relationships between cis-regulatory elements and target gene expression has been a long-standing unsolved problem in molecular biology. To address this problem, some quantitative models have...
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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...). Similarly to the predictions on the Sox2 data set, the sum of predicted accessibility of all five enhancers (Supplemental Table S2) presented a good correlation to experimentally measured Hba expression (Fig. 1D).We then investigated predictive performance for individual TF recognition sequences identified...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...-seq and ChIP-seq datasets allows demarcation of genomic regions 499 with putative functional involvement in the early antiviral response. However, further 500 20 experimental validation, such as knockout or knock-in studies targeting the identified 501 regulatory elements, will be essential to confirm...
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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...Enrichment Analysis) that were shared by three or 236 more samples from smokers. Using GREAT (McLean et al. 2010) , these loci were 237 mapped to 49 putative distal regulatory target genes. Pathway enrichment analysis 238 revealed that six of the top ten enriched pathways (q < 0.05) were immune-related, 239...
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Research: Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes
- Shuai Sun,
- Christian Rödelsperger,
- and Ralf J. Sommer
Genome Res. September 2021 31: 1590-1601; Published in Advance July 22, 2021, doi:10.1101/gr.275303.121
...have a single tooth and are strict bacterial feeders, whereas “eurystomatous” (Eu) animals have two teeth and can additionally feed on fungi and other nematodes by predation (Ragsdale et al. 2013). By now, the gene regulatory network controlling mouth-form plasticity has been identified...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...with WT CRX functions when both alleles are present, leading to the severe dominant photoreceptor deficits in developing mouse retinas. Here, we extend our multiomics approach to further elucidate the consequences of E80A and K88N mutations on CRX regulatory activities in developing photoreceptors. We...
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