Searching journal content for articles similar to Newman et al. 27 (11): 1807.

Displaying results 1-10 of 6188

For checked items

view abstracts
download to citation manager

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
...prevalent, whereas ALE-APA was less frequent. Tissues such as spleen, testis, and adipose exhibited the highest APA gene counts, consistent with previous findings (Hong et al. 2020; Li et al. 2021). In contrast, kidney, skeletal muscle, and colon had fewer APA events, indicating high tissue specificity (Fig...
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
...-specific networks. Central genes in consensus networks are enriched for evolutionarily constrained genes and ubiquitous biological pathways, whereas context-specific central nodes include tissue-specific transcription factors. The increased statistical power from data aggregation facilitates the derivation...
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
...molecular phenotypes are independently regulated in terms of expression patterns. Additionally, sample clustering based on these three molecular phenotypes recapitulated tissue types (Fig. 1C). We detected 3325 genes with tissue-specific expression and 946 AS events with tissue-specific splicing, but we...
Select this article
Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...processed ∼5 million R2C2 reads and produced annotations that, although certainly not complete, contained at least one isoform for most genes expressed in that tissue. Further, these tissue-specific annotations contained information on how highly these isoforms were expressed.In addition to creating...
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: 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
...that host/nested organization could play a role in tissue-specific regulation of expression.View larger version: In this window In a new window Figure 4. Host and nested gene expression profiles and tissue specificity. (A) Distribution of the expression of all, host, and nested genes for the biotypes...
OPEN ACCESS ARTICLE
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
...version: In this window In a new window Figure 1. Schematic illustration of SCALE and the study design. We designed SCALE to select interpretable aging-related genes and quantify tissue-specific transcriptomic aging in a robust and easily generalizable manner. SCALE starts with a core set of manually...
OPEN ACCESS ARTICLE
Select this article
Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...in neurons is well established, yet few studies have examined activity-dependent alternative splicing. Alternative splicing regulates >95% of genes and is essential to diverse neuronal functions, including synapse development and calcium channel diversity. Alternative splicing is regulated by the expression...
Select this article
Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
.... 2007; Turpin et al. 2016). Thus, a deeper understanding of these resistance mechanisms remains a critical challenge in overcoming and managing breast cancer tumors expressing HER2.Alternative splicing, a fundamental post-transcriptional process in eukaryotic gene expression, allows a single gene locus...
Select this article
Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...). Statistical modeling showed no significant compositional changes with age after correcting for multiple tests.View larger version: In this window In a new window Figure 2. Profiling of age-associated gene expression variations across substantia nigra cell subclasses. (A) UMAP representation of all nuclei...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Newman et al. 27 (11): 1807.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: