Searching journal content for articles similar to Vockley et al. 25 (8): 1206.

Displaying results 1-10 of 27

For checked items

view abstracts
download to citation manager

Select this article
Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...in evolutionary biology and biomedicine is to understand the complex interactions between genetic variants, the epi, and gene expression. However, the causal relationships between these factors remain poorly understood. mSTARR-seq, a methylation-sensitive massively parallel reporter assay, is capable...
OPEN ACCESS ARTICLE
Select this article
Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...this mechanism is disrupted in human pathologies.In the hematopoietic system, inter-individual phenotypic variation has been associated with thousands of independent variants in noncoding regions of the . What distinguishes individuals who can successfully adapt to stressors from those who cannot? Prior work has...
Select this article
Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...variants require experimental validation by separation from linked variants. To this end, massively parallel reporter assays (MPRAs) represent a high-throughput solution for experimental validation, compared to luciferase or EMSA assays, because several thousand sequences can be tested for regulatory...
Select this article
Method: Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change
- Pejman Mohammadi,
- Stephane E. Castel,
- Andrew A. Brown,
- and Tuuli Lappalainen
Genome Res. November 2017 27: 1872-1884; Published in Advance October 11, 2017, doi:10.1101/gr.216747.116
..., and it is a valuable approach for investigating novel aspects of eQTL data sets. [Supplemental material is available for this article.] Noncoding genetic variation affecting gene regulation and other cellular phenotypes has a key role in phenotypic variation and disease susceptibility (Albert and Kruglyak 2015). One...
OPEN ACCESS ARTICLE
Select this article
Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...(circRNAs), a class of long noncoding RNAs, are known to be enriched in mammalian neural tissues. Although a wide range of dysregulation of gene expression in autism spectrum disorder (ASD) have been reported, the role of circRNAs in ASD remains largely unknown. Here, we performed -wide circ...
OPEN ACCESS ARTICLE
Select this article
Research: Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network
- Nicolas Chassaing,
- Erica E. Davis,
- Kelly L. McKnight,
- Adrienne R. Niederriter,
- Alexandre Causse,
- Véronique David,
- Annaïck Desmaison,
- Sophie Lamarre,
- Catherine Vincent-Delorme,
- Laurent Pasquier,
- Christine Coubes,
- Didier Lacombe,
- Massimiliano Rossi,
- Jean-Louis Dufier,
- Helene Dollfus,
- Josseline Kaplan,
- Nicholas Katsanis,
- Heather C. Etchevers,
- Stanislas Faguer,
- and Patrick Calvas
Genome Res. April 2016 26: 474-485; Published in Advance February 18, 2016, doi:10.1101/gr.196048.115
...1 We selected 407 candidate genes (Supplemental Table 1) involved in ocular development for targeted exon liquid capture followedby massively parallel sequencing.We screened 22 unrelated individuals with ODA and mutation negative for SOX2, OTX2, RAX, and VSX2 and two positive control individuals...
Select this article
Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...equally to this work. Corresponding author: sgillett@cornellcollege.eduAbstractGenome-wide association studies (GWASs) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. Here...
Select this article
Research: Functional characterization of enhancer activity during a long terminal repeat's evolution
- Alan Y. Du,
- Xiaoyu Zhuo,
- Vasavi Sundaram,
- Nicholas O. Jensen,
- Hemangi G. Chaudhari,
- Nancy L. Saccone,
- Barak A. Cohen,
- and Ting Wang
Genome Res. October 2022 32: 1840-1851; Published in Advance October 3, 2022, doi:10.1101/gr.276863.122
...regulatory activity has evolved. We systematically tested the human LTR18A subfamily for regulatory activity using massively parallel reporter assay (MPRA) and found AP-1- and CEBP-related binding motifs as drivers of enhancer activity. Functional analysis of evolutionarily reconstructed ancestral sequences...
OPEN ACCESS ARTICLE
Select this article
Method: Cross-species analysis of enhancer logic using deep learning
- Liesbeth Minnoye,
- Ibrahim Ihsan Taskiran,
- David Mauduit,
- Maurizio Fazio,
- Linde Van Aerschot,
- Gert Hulselmans,
- Valerie Christiaens,
- Samira Makhzami,
- Monika Seltenhammer,
- Panagiotis Karras,
- Aline Primot,
- Edouard Cadieu,
- Ellen van Rooijen,
- Jean-Christophe Marine,
- Giorgia Egidy,
- Ghanem-Elias Ghanem,
- Leonard Zon,
- Jasper Wouters,
- and Stein Aerts
Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
...identity. A better understanding of how enhancers work will improve the interpretation of noncoding variation and empower the generation of cell type–specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable...
OPEN ACCESS ARTICLE
Select this article
Research: RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing
- Heidi Dvinge,
- Jamie Guenthoer,
- Peggy L. Porter,
- and Robert K. Bradley
Genome Res. October 2019 29: 1591-1604; Published in Advance August 21, 2019, doi:10.1101/gr.246678.118
...reflect their biological role. Core components of the spliceosome can play regulatory, in addition to basal, roles. Even if a particular core spliceosomal protein is required for splicing to occur, developmental stage–specific or tissue-specific variation in its expression level can confer a regulatory...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Vockley et al. 25 (8): 1206.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: