Searching journal content for articles similar to Dutta et al. 33 (3): 314.

Displaying results 1-10 of 4409

For checked items

view abstracts
download to citation manager

Select this article
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. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...rewiring from a stemness-associated state (meta-network 1) to erythrocyte-autonomous programs (meta-network 2), indicating an abrupt transcriptional transition. (D) Continuous tracking of GATA gene (GATA1 and GATA2) regulatory dynamics during erythropoiesis. (D1) tracks changes in connectivity (log node...
OPEN ACCESS ARTICLE
Select this article
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
...key regulatory genes and understand their functional significance, we additionally calculated betweenness centrality, a critical metric that quantifies a node's importance in a network by measuring how frequently it appears on the shortest paths between other nodes. The top 25 genes, all of which...
Select this article
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
...of existing methodologies to decipher complex network structures. The architecture of GRNs, both globally or locally, is crucial in complex biological systems, revealing essential nodes (e.g., highly interconnected TFs) and regulatory modules and elucidating how GRNs adapt to intercellular variations...
OPEN ACCESS ARTICLE
Select this article
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
...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 and behavior (Figiel et al. 2021). Large clutch sizes, ex utero development, and the availability of well...
Select this article
Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
.... As illustrated above, our data enable broad correlation studies with any RNAPII-associated factor, opening avenues to discover novel regulators of elongation, including factors whose effects may be gene-specific or context-dependent. We expect our method will be a powerful tool for identifying novel regulatory...
OPEN ACCESS ARTICLE
Select this article
Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...: In this window In a new window Figure 5. Potential trait-affecting regulatory network mediated by candidate critical enhancers. Lavender nodes represent TFs, pink nodes represent candidate critical enhancers, and light blue nodes represent target genes. The size of each node is proportional to its degree...
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...as beta-catenin) drives the expression of target genes from regulatory regions bound by TCF/LEF transcription factors. Gene regulation, however, entails the interplay between sequence information and 3D structure, yet the impact of Wnt signaling on structure has been poorly explored. Here, we investigate...
OPEN ACCESS ARTICLE
Select this article
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
...the relevance of inferred network features, such as node centrality, to known regulatory roles and their enrichment for complex trait heritability using stratified LD score regression (S-LDSC) (Finucane et al. 2015). In summary, our study seeks to provide a carefully annotated RNA-seq data set, outline best...
OPEN ACCESS ARTICLE
Select this article
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
.... Domain-adaptive neural networks improve cross-species prediction of transcription factor binding. Genome Res 32: 512–523. doi:10.1101/gr.275394.121 ↵de Boer CG, Taipale J. 2024. Hold out the : a roadmap to solving the cis-regulatory code. Nature 625: 41–50. doi:10.1038/s41586-023-06661-w ↵Dey KK, van de...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Dutta et al. 33 (3): 314.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: