Searching journal content for articles similar to Clark et al. 22 (4): 714.

Displaying results 1-10 of 77

For checked items

view abstracts
download to citation manager

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
...by the ovary (Supplemental Table S4). In contrast to gene expression, the number of significantly associated AS and 3′APA events were relatively limited, with only two AS and six 3′APA events identified (Fig. 2A; Supplemental Table S4). Functional enrichment analysis revealed an overrepresentation...
Select this article
Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...target expression variation and covariation, but these observations have been limited to a few microRNAs. Here we systematically study microRNA alternative functions in mouse embryonic stem cells (mESCs) by genetically deleting Drosha, leading to global loss of microRNAs. We apply complementary single...
OPEN ACCESS ARTICLE
Select this article
Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
.... 2012. Evolutionary rate covariation reveals shared functionality and coexpression of genes. Genome Res 22: 714–720. doi:10.1101/gr.132647.111 ↵Clark NL, Alani E, Aquadro CF. 2013. Evolutionary rate covariation in meiotic proteins results from fluctuating evolutionary pressure in yeasts and mammals...
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
...framework to describe gene-gene relationships and are comprised of nodes that represent genes and edges linking coexpressed genes (Stuart et al. 2003). A comprehensive catalog of gene coexpression relationships has the potential to characterize genes with unknown functions (Schlitt et al. 2003), identify...
OPEN ACCESS ARTICLE
Select this article
Method: Debiased personalized gene coexpression networks for population-scale scRNA-seq data
- Shan Lu and
- Sunduz Keles
Genome Res. June 9, 2023 gr.277363.122; Published in Advance June 9, 2023, doi:10.1101/gr.277363.122
...and controls uniquely reveals coexpression modules of innate immune response with distinct coexpression levels between the diagnoses. Dozer represents an important advance in estimating personalized coexpression networks from scRNA-seq data. Introduction The advent of single-cell RNA sequencing (scRNA-seq) has...
ACCEPTED MANUSCRIPT
Select this article
Method: Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus
- Bharat Panwar,
- Benjamin J. Schmiedel,
- Shu Liang,
- Brandie White,
- Enrique Rodriguez,
- Kenneth Kalunian,
- Andrew J. McKnight,
- Rachel Soloff,
- Gregory Seumois,
- Pandurangan Vijayanand,
- and Ferhat Ay
Genome Res. April 2021 31: 659-676; Published in Advance March 5, 2021, doi:10.1101/gr.265249.120
...-by-association” principle (Chu et al. 1998), suggesting genes with coordinated changes in expression are more likely to be involved in similar biological functions. Therefore, we used weighted gene coexpression network analysis (WGCNA) to generate a network from classical monocyte gene expression profiles of 64 SLE donors...
Select this article
Research: A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize
- Mélisande Blein-Nicolas,
- Sandra Sylvia Negro,
- Thierry Balliau,
- Claude Welcker,
- Llorenç Cabrera-Bosquet,
- Stéphane Dimitri Nicolas,
- Alain Charcosset,
- and Michel Zivy
Genome Res. November 2020 30: 1593-1604; Published in Advance October 15, 2020, doi:10.1101/gr.255224.119
..., and genomic data acquired from 254 maize hybrids grown under two watering conditions. Using association genetics and protein coexpression analysis, we detected more than 22,000 pQTLs across the two conditions and confidently identified 15 loci with potential pleiotropic effects on the proteome. We showed...
Select this article
Research: Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue
- Aarthi Venkat,
- Maximillian J. Carlino,
- Betty R. Lawton,
- Manju L. Prasad,
- Matthew Amodio,
- Courtney E. Gibson,
- Caroline J. Zeiss,
- Scott E. Youlten,
- Smita Krishnaswamy,
- and Diane S. Krause
Genome Res. June 2024 34: 837-850; Published in Advance July 8, 2024, doi:10.1101/gr.278215.123
...primate parathyroid cells and use coimmunostaining to reveal high levels of RARRES2 protein (also known as chemerin) in PTH-expressing cells, which could indicate that RARRES2 plays an unrecognized role in parathyroid endocrine function. The data obtained are the first single-cell RNA transcriptome...
Select this article
Resource: Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types
- Peng Xu and
- Bin Zhang
Genome Res. October 2023 33: 1806-1817; Published in Advance October 31, 2023, doi:10.1101/gr.278063.123
...al. 2021; Xu et al. 2022). By applying MEGENA to all major cancer types within the TCGA cohort, we comprehensively characterized coexpression networks and prognostic modules in cancers and revealed the multiomic regulatory mechanisms related to cancer prognosis. We also shared all the networks...
OPEN ACCESS ARTICLE
Select this article
Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...as a function of the 1D genomic distance (Fig. 3C). It can be seen that the tumor samples display large decay rates in the megabase scale, and the comparison between normal and cancerous CTG distance matrices suggests the loss of specific long-range interactions in colon cancer, as revealed by Figure 3C...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Clark et al. 22 (4): 714.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: