Searching journal content for articles similar to Parey et al. 33 (9): 1513.

Displaying results 1-10 of 6006

For checked items

view abstracts
download to citation manager

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
...of nine blood-related traits from the 42 independent traits (Crohn's disease, rheumatoid arthritis, ulcerative colitis, eosinophil count, platelet count, red blood cell count, red blood cell width, white blood cell count, and eczema) (Supplemental Table S16). As with the consensus networks, tissue-specific...
OPEN ACCESS ARTICLE
Select this article
Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...to decipher tissue-specific codes of gene regulation for individual and groups of TFs using available single-cell gene expression data in both species. Studying key conserved factors in worm and fly greatly will enhance analysis, interpretation, and the broader relevance of data gathered in ENCODE and other...
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 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...CRMs, though understanding of this is currently 74 lacking. 75 76 4 While the importance and complete range of functions of HCNEs remain to be fully 77 understood, many have been shown to direct tissue-specific gene expression consistent with 78 them acting as enhancers (Nelson and Wardle 2013...
- Abstract
- Full Text (PDF)
ACCEPTED MANUSCRIPT
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
...and its potential target gene during myogenesis. Our findings reveal the dynamic regulatory features of SEs in skeletal muscle development and provide a general integrative framework for identifying critical enhancers underlying the formation of complex traits.Skeletal muscle, which constitutes nearly...
Select this article
Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...(Amante et al. 2020), we hypothesized that coexpression could influence tissue-specific profiles and tested this by focusing on the correlation between host and nested genes expression. This also tested the model whereby there is a steric hindrance between two RNA polymerases transcribing in the same...
OPEN ACCESS ARTICLE
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
...enriched in metabolic processes and protein kinase activity, whereas genes with tissue-specific expression or AS in the spleen were significantly enriched in multiple immune-related processes (Supplemental Fig. S1C,D).Multilayer regulatory features enhance the predictive power of egg productionWe conducted...
Select this article
Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...of samples owing to expense and throughput considerations (Orchard et al. 2021; Wang et al. 2022b; Zhang et al. 2022; Chapman et al. 2023; Travisano et al. 2023; Zhu et al. 2023), the ability to model the regulatory circuits within each of thousands of cells nonetheless provides high statistical power...
Select this article
Method: A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures
- Shulin Mao,
- Jiayu Su,
- Longteng Wang,
- Xiaochen Bo,
- Cheng Li,
- and Hebing Chen
Genome Res. August 2023 33: 1381-1394; Published in Advance July 31, 2023, doi:10.1101/gr.277491.122
...of known aging-associated genes to enhance the robustness and the interpretability of feature selection (Methods; Supplemental Figs. S6, S7A,B). Based on this method, we generated tissue-specific aging gene sets for downstream analysis (Supplemental Table S1).View larger version: In this window In a new...
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 complex traits. The predominance of TUTR-APA genes in various tissues enhances the diversity of gene expression (Mittleman et al. 2020). The proportion of ALE-APA was relatively lower, possibly because it can cause significant changes in protein sequence and function (Dubbury et al. 2018). Our tissue-specific...
Select this article
Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...brain organoids to hypoxic and hyperoxic conditions, we identify hundreds of gene regulatory changes that are undetectable under baseline conditions, with 148 trait-associated genes showing regulatory effects only in response to oxygen stress. To capture more nuanced transcriptional patterns, we employ...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Parey et al. 33 (9): 1513.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: