Searching journal content for articles similar to Reiter et al. 33 (3): 346.

Displaying results 1-7 of 7

For checked items

view abstracts
download to citation manager

Select this article
Research: Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features
- J. Omar Yáñez-Cuna,
- Cosmas D. Arnold,
- Gerald Stampfel,
- Łukasz M. Boryń,
- Daniel Gerlach,
- Martina Rath,
- and Alexander Stark
Genome Res. July 2014 24: 1147-1156; Published in Advance April 8, 2014, doi:10.1101/gr.169243.113
...of functional enhancer sequences from three different Drosophila cell lines. We find that the enhancers display distinct cis-regulatory sequence signatures, which are predictive of the enhancers’ cell type-specific or broad activities. These signatures contain transcription factor motifs and a novel class...
OPEN ACCESS ARTICLE
Select this article
Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...a comprehensive APA atlas for 261 cell types across 19 porcine tissues based on single-nucleus RNA sequencing (snRNA-seq) data. This analysis reveals tissue- and cell type–specific patterns of APA. We find that many genes display a clear correlation between the average length of 3′ untranslated regions (3′ UTRs...
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
...biological contexts. Finally, biological analyses on PBMC data sets demonstrate PRISM-GRN's potential to facilitate the identification of cell type–specific or context-specific GRNs across broader real-world biological research applications. Overall, PRISM-GRN provides a novel paradigm for precise, robust...
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
...networks. Central genes in consensus networks are enriched for evolutionarily constrained genes and ubiquitous biological pathways, whereas context-specific central nodes include tissue-specific transcription factors. The increased statistical power from data aggregation facilitates the derivation...
OPEN ACCESS ARTICLE
Select this article
Research: Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations
- Ryne C. Ramaker,
- Andrew A. Hardigan,
- Say-Tar Goh,
- E. Christopher Partridge,
- Barbara Wold,
- Sara J. Cooper,
- and Richard M. Myers
Genome Res. July 2020 30: 939-950; Published in Advance July 2, 2020, doi:10.1101/gr.260463.119
...for markers of regulatory activity, such as initiating POLR2 binding, DNase I hypersensitivity, active histone marks, and strong activity in enhancer reporter assays conducted in transgenic mouse embryos. These studies also showed that context-specific HOT loci are generated in association with cell...
OPEN ACCESS ARTICLE
Select this article
Research: Interactions between pluripotency factors specify cis-regulation in embryonic stem cells
- Chris Fiore and
- Barak A. Cohen
Genome Res. June 2016 26: 778-786; Published in Advance April 15, 2016, doi:10.1101/gr.200733.115
...or flexible billboards? J Cell Biochem 94: 890–898. ↵Arnosti DN, Barolo S, Levine M, Small S. 1996. The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. Development 122: 205–214. ↵Bates DM, Watts DG. 1988. Nonlinear regression analysis and its applications. John Wiley & Sons, New York...
Select this article
Perspective: Linking RNA biology to lncRNAs
- Loyal A. Goff and
- John L. Rinn
Genome Res. October 2015 25: 1456-1465; doi:10.1101/gr.191122.115
...that the lncRNA locus is nonfunctional or dispensable (or highly context specific in function). As an example, for the well-conserved lncRNA C130071C03Rik (the mouse ortholog of human LINC00461), whole-gene ablation was found not to have a function (Oliver et al. 2014). Yet it is important to consider...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Reiter et al. 33 (3): 346.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: