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Corrigendum: Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- Juan L. Mateo,
- Debbie L.C. van den Berg,
- Maximilian Haeussler,
- Daniela Drechsel,
- Zachary B. Gaber,
- Diogo S. Castro,
- Paul Robson,
- Q. Richard Lu,
- Gregory E. Crawford,
- Paul Flicek,
- Laurence Ettwiller,
- Joachim Wittbrodt,
- François Guillemot,
- and Ben Martynoga
Genome Res. November 2016 26: 1626; doi:10.1101/gr.216044.116
....116 Corrigendum 1626 Genome Research www..org Juan L. Mateo , Debbie L.C. van den Berg , Maximilian Haeussler , Daniela Drechsel , Zachary B. Gaber , Diogo S. Castro , Paul Robson , Q. Richard Lu , Gregory E. Crawford , Paul Flicek , Laurence Ettwiller , Joachim Wittbrodt , François Guillemot and Ben Martynoga...
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Research: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- Juan L. Mateo,
- Debbie L.C. van den Berg,
- Maximilian Haeussler,
- Daniela Drechsel,
- Zachary B. Gaber,
- Diogo S. Castro,
- Paul Robson,
- Q. Richard Lu,
- Gregory E. Crawford,
- Paul Flicek,
- Laurence Ettwiller,
- Joachim Wittbrodt,
- François Guillemot,
- and Ben Martynoga
Genome Res. January 2015 25: 41-56; Published in Advance October 7, 2014, doi:10.1101/gr.173435.114
...@gmail.com, juan.mateo@cos.uni-heidelberg.deAbstractThe gene regulatory network (GRN) that supports neural stem cell (NS cell) self-renewal has so far been poorly characterized. Knowledge of the central transcription factors (TFs), the noncoding gene regulatory regions that they bind to, and the genes whose...
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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
...neural networks with transformers. Compared with current state-of-the-art models, ScPGE exhibits superior performance in predicting gene expression and yields higher accuracy in identifying active enhancer–gene interactions through attention mechanisms. By comprehensively analyzing ScPGE's predictions...
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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
..., and interpretable exploration of causal GRNs with prior knowledge and multi-omics data.Gene regulatory networks (GRNs), which encapsulate the complex interactions among transcription factors (TFs), target genes, and various regulatory elements, constitute the core machinery of gene regulation (Levine and Davidson...
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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
...associated with cCREs and AD GWAS data across diverse cellular populations.Cell type–specific TF regulatory network in AD progressionTo gain further insight into TF-mediated gene regulation across AD progression, we constructed cell type–specific positive TF regulatory networks. We identified candidate...
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Research: Epigenetic characterization of pseudogenes across human tissues
- Yunzhe Jiang,
- Beatrice Borsari,
- and Mark Gerstein
Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
...for transcribed pseudogenes, lncRNAs and protein-coding genes, and used this resource to interrogate pseudogene regulation across human tissues. Mining this dataset, we identified distinct regulatory patterns not only between protein-coding genes and pseudogenes, but also among different pseudogene biotypes...
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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
...by adult P. pacificus with teeth colored for ease of visualization. (B) A gene-regulatory network for mouth-form development with St-promoting genes colored in blue and Eu-promoting genes in red. Genes in black may regulate the development of both morphs. (C) Experimental design for developmental...
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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
...In a new window Figure 3. Mapping and characterization of regulatory variants. (A) Proportions of molGenes with different numbers of independent molQTL. From left to right, the panels show the proportions for eGenes, sGenes, and apaGenes across tissues. Bars of different colors represent molGenes...
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Corrigendum: Corrigendum: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. February 2026 36: 432; doi:10.1101/gr.281294.125
...Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.281294.125 ;36/2/432 ;gr.281294.125 432 gr.281294.125 Corrigendum Corrigendum Corrigenda Corrigendum Corrigendum Razavi-Mohseni Milad Huang Weitai Guo Yu A. Shigaki Dustin Ho Shamaine Wei Ting Tan Patrick Skanderup Anders J...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...are largely unknown. Here, we profile -wide changes to gene expression and chromatin structure in cardiomyocytes derived from human pluripotent stem cells. We identify and characterize a gene regulatory element essential for regulating MYH6 expression, which encodes human fetal myosin. Using chromatin...
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