Searching journal content for articles similar to Prabhakar et al. 16 (7): 855.

Displaying results 1-10 of 321

For checked items

view abstracts
download to citation manager

Select this article
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
.... S6A), which explains why negative genes were mistakenly predicted as positive genes. For TNs (Supplemental Fig. S6B), we observe a linear distribution of the four chromatin signals, with DNase and H3K27ac signals close to zero. Similarly, FNs also show a linear distribution of the chromatin signals...
OPEN ACCESS ARTICLE
Select this article
Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...) and tissues (Fig. 3D–G). We find that in promoters the proportion of TEs in open chromatin decreases toward a transcription start site (TSS) and the gene body, probably reflecting increased purifying selection pressure (less tolerance for TE insertions) inside the gene body.Furthermore, we find that close...
Select this article
Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...functional TE-derived cis-regulatory elements.Helitrons have been extensively reported on the promoter of other eukaryotic species (Gupta et al. 2005; Cultrone et al. 2007; Thomas et al. 2014; Huang et al. 2016), in which a few cases of embedded TFBSs were reported (Carareto et al. 2014; Batista et al. 2019...
Select this article
Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...how the phylogenetic information in the multiassembly graph compares to what is known about species relationships from SNP studies of the Lake Malawi cichlid radiation (Malinsky et al. 2018). Overall, the pan graph closely reflected the expected interspecies relationships based on the prevailing...
OPEN ACCESS ARTICLE
Select this article
Research: Local sequence features that influence AP-1 cis-regulatory activity
- Hemangi G. Chaudhari and
- Barak A. Cohen
Genome Res. February 2018 28: 171-181; Published in Advance January 5, 2018, doi:10.1101/gr.226530.117
...toward the mean as the sequences got shorter, HIGH and LOW sequences as short as 50 bp retained distinct activities (Wilcoxon test, P = 1.86 × 10−9) (Fig. 1E). This result suggests that most of the sequence features that are necessary for high activity of AP-1 sites reside close to the AP-1 core motifs...
Select this article
Research: Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf
- Charles Y. Feigin,
- Axel H. Newton,
- and Andrew J. Pask
Genome Res. October 2019 29: 1648-1658; Published in Advance September 18, 2019, doi:10.1101/gr.244251.118
...based on protein-coding genes in close proximity (significance of enrichment tests are reported in Supplemental Tables). Two background sets were used in GREAT analyses. The first, corresponding to the whole , was used to ensure sufficient sensitivity to detect small enrichments of relevant ontology...
Select this article
Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
...regulation.In addition to chromatin loops that involve enhancers, we also observed several promoter–promoter 3D interactions between genes that are upregulated by estrogen. This finding goes along with our observation that estrogen upregulated genes cluster in close proximity within the more than expected...
Select this article
Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...SETDB1 through an intermediary cofactor, TRIM28, which is absent in zebrafish. However, two close relatives of TRIM28, namely, TRIM24 and TRIM33, are present in zebrafish and have been shown to silence endogenous retroviruses in mice (Boudinot et al. 2011; Margalit et al. 2020). Furthermore, structural...
OPEN ACCESS ARTICLE
Select this article
Research: Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period
- Juan J. Tena,
- Cristina González-Aguilera,
- Ana Fernández-Miñán,
- Javier Vázquez-Marín,
- Helena Parra-Acero,
- Joe W. Cross,
- Peter W.J. Rigby,
- Jaime J. Carvajal,
- Joachim Wittbrodt,
- José L. Gómez-Skarmeta,
- and Juan R. Martínez-Morales
Genome Res. July 2014 24: 1075-1085; Published in Advance April 7, 2014, doi:10.1101/gr.163915.113
...zebrafish and medaka pharyngula embryos morphologically and molecularly. We have examined both their transcriptomes and predictive epigenetic marks for conserved active enhancers during the phylotypic window. Whereas in closely related vertebrates, the high overall similarity masks the identification...
Select this article
Research: Accumulation and ineffective silencing of transposable elements on an avian W Chromosome
- Vera M. Warmuth,
- Matthias H. Weissensteiner,
- and Jochen B.W. Wolf
Genome Res. April 2022 32: 671-681; Published in Advance February 11, 2022, doi:10.1101/gr.275465.121
...using Oxford Nanopore Technologies (ONT) long-read sequencing (1.12 Gb total size and 9.3 Mb contig N50 after filtering; see Methods). We then combined a sex-specific coverage-based approach with synteny information from the W Chromosome of the closely related New Caledonian crow (Corvus moneduloides...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Prabhakar et al. 16 (7): 855.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: