Searching journal content for articles similar to Lægreid et al. 13 (5): 965.

Displaying results 1-10 of 279

For checked items

view abstracts
download to citation manager

Select this article
Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
..., such as known patterns of driver mutual exclusivity (Bokhari et al. 2020). Biological pathways can provide insights into the timing of driver events in a tumor cohort by mapping predicted pathogenic mutations to genes in KEGG pathways (Kanehisa et al. 2019) and estimating the order in which hallmark pathways...
OPEN ACCESS ARTICLE
Select this article
Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
...of recapitulating female-/male-biased patterns in each sex-matched time point and cell type. (B) Similar to in A, pairwise comparison of Sunbear prediction and the nearest neighbor baseline in ranking escape genes to be more female-biased than all other genes on the X Chromosome. (C,D) Predicted temporal sex...
OPEN ACCESS ARTICLE
Select this article
Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
.... We found that the patterns of early/late replication reproduced the RT timing data obtained with standard Repli-seq (Fig. 3B). Finally, PARTAGE total-nuclear RNA-seq reproduced the transcriptome of the HepG2 cells obtained from separate RNA-seq analysis (Fig. 3). To display global trends in gene...
OPEN ACCESS ARTICLE
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
...rate. (3) Identify SEs and typical enhancers (TEs) based on distal H3K27ac peaks. (ROSE) ranked order of super-enhancers, (TSSs) transcription start sites. (4) Analysis of enriched TF motifs on SEs. (5) Using hierarchical clustering to reveal temporal patterns of SEs. (6) Construct gene regulatory...
Select this article
Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...database and differentially expressed genes to calculate the enrichment score (ES). The ES reflects the drug's potential to reverse the observed gene expression patterns within the given network.To construct the cell type–specific regulatory atlas, we performed comprehensive bioinformatics analyses...
OPEN ACCESS ARTICLE
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
...been proposed as a key pathological feature of neurodegeneration (Dean et al. 2016). Furthermore, our analysis revealed distinct temporal patterns of gene expression during aging. For example, myelination-related gene expression decreased in early aging, whereas changes in genes related to cell...
OPEN ACCESS ARTICLE
Select this article
Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...The grasshopper reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution Xinghua Li1,2, Judith E. Mank3 and Liping Ban1 1Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University...
Select this article
Method: Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
- Yingxin Lin,
- Tung-Yu Wu,
- Xi Chen,
- Sheng Wan,
- Brian Chao,
- Jingxue Xin,
- Jean Y.H. Yang,
- Wing H. Wong,
- and Y.X. Rachel Wang
Genome Res. January 2024 34: 119-133; Published in Advance December 15, 2023, doi:10.1101/gr.277960.123
...of cell representations to their measured features (genes and peaks). We formulate a trajectory prediction problem using the estimated transition probabilities from OT and use gradient-based saliency mapping (Ciortan and Defrance 2021; Yang et al. 2021) to identify genes and peaks that are potentially...
OPEN ACCESS ARTICLE
Select this article
Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...difference in seud-1/sult-1’s expression was at 48 h (Fig. 4F), essentially in the middle of the critical window, whereas nag-1 was differentially expressed at 72 h (Fig. 4G). This temporal pattern, as well as the absence of other differentially expressed mouth-form genes, suggests that seud-1/sult-1...
OPEN ACCESS ARTICLE
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
...,154 cells from all samples passing quality control (QC) for both RNA-seq and ATAC-seq were integrated, clustered, and annotated into 14 cell types (Fig. 2A; Supplemental Fig. S1A). The clustering distinguished nuclei of different cell types by their global pattern of gene expression (for the full list...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Lægreid et al. 13 (5): 965.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: