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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
...and explore the cross-tissue communication beyond HPG axis. The results further enrich the duck regulatory variant resource, deepen our understanding of the genetic regulation of egg production, and broaden our insight into the systemic regulation of reproductive traits in poultry...
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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
...in the early 2000s, has enabled rapid 39 and affordable quantification of gene expression. Since then, substantial research efforts have been 40 dedicated to developing statistical network inference methods that leverage associations in gene 41 expression (coexpression) to decipher gene regulation (Huynh...
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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
...hub genes which were enriched for gastrulation (GO:0007369, P = 5.9 × 10−4) and circulatory system development (GO:0072359, P = 6.2 × 10−3) (Supplemental File 3).Genes with high network centrality are proximal to variants enriched for complex trait heritabilityPrevious work by Kim et al. (2019...
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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
...equally to this work. Corresponding author: johnq@hsph.harvard.eduAbstractGene regulatory networks (GRNs) are effective tools for inferring complex interactions between molecules that regulate biological processes and hence can provide insights into drivers of biological systems. Inferring coexpression...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...mechanisms remain unclear. To investigate the relationship between protein 3D structure and phenotype, we predict the 3D structures of 795,649 proteins from 26 maize (Zea mays L.) inbred lines using AlphaFold2. Population genetics analysis of these protein 3D structures reveal that buried residues held...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...breeds are endangered under the pressure of purebreds or crossbreds that meet the demand of changing farming systems and breeding objectives (Reist-Marti et al. 2003). To adapt to those challenges, many countries joined efforts to increase the diverse range of animal genetic resources. Therefore, tools...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...of Zimmermann et al. (2020), who associated metabolic potential of members of the C. elegans microbiome with specific traits, but extends this idea by considering the response of specific coexpression networks in the worm as molecular phenotypes. This established a first global map of more than 2800 metabolic...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...Systems Biology of Signal Transduction, German Cancer 15 Research Center (DKFZ), 69120 Heidelberg, Germany 16 8 These authors contributed equally. Either author can be listed first. 17 * Correspondence: falk.butter@fli.de (FB) 18 19 Abstract 20 A tightly regulated DNA damage response is critical...
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Method: Genetics-driven risk predictions leveraging the Mendelian randomization framework
- Daniel Sens,
- Liubov Shilova,
- Ludwig Gräf,
- Maria Grebenshchikova,
- Bjoern M. Eskofier,
- and Francesco Paolo Casale
Genome Res. September 2024 34: 1276-1285; Published in Advance September 27, 2024, doi:10.1101/gr.279252.124
...GWAS summary statistics for T2D (Mahajan et al. 2018). As input risk factors, we used 37 traits previously linked to diabetes risk (Edlitz and Segal 2022), including metabolic, anthropometric, and cardiovascular metrics (Fig. 4A). We used 6077 independent genetic variants associated with at least one...
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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 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...reveal a highly significant association between endoderm HCNEs and genes encoding DNA-binding and gene regulatory proteins, including HMG domain-containing and chromatin binding factors. Notably, however, the endodermHCNEs appear to show a greater enrichment of such genes compared with all HCNEs...

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