Searching journal content for articles similar to Kukurba et al. 26 (6): 768.

Displaying results 1-10 of 1011

For checked items

view abstracts
download to citation manager

Select this article
Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...PMods). We additionally show that rs344131, located within a regulatory enhancer region of SHROOM3, demonstrates allele-specific effects on enhancer activity and thus impacts expression levels of the associated SHROOM3 allele harboring any rare coding variant. Our findings also suggest that CePMods may serve...
Select this article
Research: Variation in the fitness impact of translationally optimal codons among animals
- Florian Bénitière,
- Tristan Lefébure,
- and Laurent Duret
Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
...are the primary factor driving the observed variation in codon usage across species.NSPs can vary within the of a given species and impact codon usage accordingly. In Homo sapiens, the per gene GC3 and GCi are highly correlated (Spearman's correlation coefficient, rho = 0.83, P < 10−16), whereas this correlation...
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
...by the standing genetic variation and the effects of selection. A synthetic regulatory genomic approach is uniquely able to uncover novel biology, and these new technologies will move the field toward consideration of regulatory function at a locus scale.Recent work applying synthetic regulatory genomics has...
Select this article
Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...moderate and low impact, respectively, and the remaining 6.4% were rated high impact (Fig. 4B). Our results thus suggest that improved gene coverage facilitates detection of functionally relevant variation.We identified 17,446 LoF variants using T2T-CHM13, an increase from GRCh37 and GRCh38 (Table 1...
OPEN ACCESS ARTICLE
Select this article
Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
..., and cells maintain higher levels of MYH6.Lastly, we identified cardiomyopathy-associated genetic variants within R3 (Supplemental Fig. S11A). This underscores the impact of genetic variation on complex human traits. Allelic imbalance of disease-related genes has been observed in patients with hypertrophic...
OPEN ACCESS ARTICLE
Select this article
Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...and transcriptomic levels, along with their regulatory effects on structural variations (SVs) and gene expression. Functional validation is performed using dual-luciferase assays and cell-based experiments. Our findings reveal that integrated HBV sequences form long concatemers, mediating inter- and intrachromosomal...
Select this article
Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...the complementary nature of multilayer regulatory features in capturing phenotypic variation in complex traits. Among all features contributing to the integrated model, GRIN3A expression, as well as the 3′ end usage of COL17A1 in the shell gland, exhibited the highest importance scores (Fig. 2D). These two genes...
Select this article
Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...on the array (Dover et al. 1993; Elder and Turner 1995; Lower et al. 2018). Untangling patterns of concerted evolution on tandem arrays experiencing different forces requires a comprehensive map of genetic variation spanning such clusters.The cluster of highly conserved histone genes on Chromosome arm 2L...
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
...and cell types. Our investigations revealed that the SNP rs323354626, located within the 3′ UTR of the CD47 gene, markedly impacts gene expression, underscoring the pivotal role of 3′ UTR variations in the regulatory mechanisms of genes. Additionally, this locus demonstrated significant associations...
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
...between genetic and epigenetic effects. As the field of genomics works toward characterizing human genetic diversity and its impacts on regulatory function, multiplexed assays such as this will be an important tool to maximize the breadth of sequence variation that can be investigated and contribute...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Kukurba et al. 26 (6): 768.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: