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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
...the versatility of NNet through three case studies and its utility in facilitating the identification of fine-grained regulatory signals pertinent to specific cell states or transitions.In the first case study of TF activity inference, we performed a proof-of-concept analysis on NNet coexpression. By comparing TF...
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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 cis-regulatory DNA elements (CREs), we pinpoint 141 ADNC-associated genes. Using gene set enrichment analysis (GSEA) and network proximity analysis, we further identify nine candidate repurposable drugs that were associated with these ADNC-related genes. In summary, this cell type–specific multiomic...
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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
...to perform comprehensive motif analysis on DNA sequences, to discover TF motifs from these TPs. The most relevant discovered motifs were matched against HOCOMOCO V11 (Kulakovskiy et al. 2018) using TOMTOM (Gupta et al. 2007). As shown in Figure 6A, we identified a series of important TF motifs...
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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
...cell populations. An analysis of HCNEs within CRMs acting in specific germ layers and tissues across disparate vertebrate species is therefore generally lacking.Identification of tissue-specific CRMs and their key operative TFs is pivotal to understanding how gene regulatory control of cell fate...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...opportunities for researchers to delve into the functional, regulatory, and evolutionary origin of G4 DNA, using the plethora of available complete organismal s.ResultsIdentification of potential G4-forming sequences in organismal s across the tree of lifeWe examined 108,459 organismal reference s spanning...
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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
...used to map 51 open chromatin and histone modifications across the , enabling the identification of 52 putative regulatory elements. While these assays are powerful, they have limitations, 53 including the potential for false positives (regions that are accessible but not functionally 54 active...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
..., offering insights into the regulatory mechanisms underlying gene expression (Clark et al. 2017). In particular, DNA methylation has proven valuable in cancer research, in which it uncovers intratumoral heterogeneity and aids in the discovery of early diagnostic biomarkers and personalized therapeutic...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...a regulatory axis connecting epigenetic 23 state and IPA. This finding aligns with emerging evidence that DNA methylation modulates 24 2 alternative polyadenylation via CTCF-mediated chromatin looping. Thus, IPAseek provides a 25 platform to characterize IPA across physiological systems and disease contexts...
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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
...to comprehensively map GRNs (Badia-i-Mompel et al. 2023). High-throughput RNA sequencing (RNA-seq), which enables -wide analysis of the cellular transcriptome on bulk cells (Ozsolak and Milos 2011), has revolutionized GRN inference by enabling the computational derivation of regulatory networks from gene expression...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
..., this is the most comprehensive resource of its kind. This data set contains three modification types: 4mC, 5mC, and 6mA. The 4mC modification data are integrated from data sets established in Hyb4mC (Liang et al. 2022), iDNA-MS (Lv et al. 2020), and DeepTorrent (Liu et al. 2021a). All collected 4mC sequences (41...
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