Searching journal content for articles similar to Jakt et al. 11 (1): 112.

Displaying results 1-10 of 1331

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
...mutation cluster or hotspot (35% of cases; significance level of 5%). The majority of cases in which mutations were not clustered occurred in tumor-suppressor genes (TP53, PTEN, and VHL) (Supplemental Note 1; Supplemental Fig. 14), which acquire loss-of-function variants across a larger proportion of sites...
OPEN ACCESS ARTICLE
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
...target genes for positive TF-regulators by assessing the correlation between motif activity and gene expression, as well as the linkage score for each gene–TF pair (Supplemental Table S7). We selected several TFs specific to microglia (SPI1, IRF1, and CEBPB) (Fig. 5A), excitatory neurons (JUN, JUND, FOSB...
OPEN ACCESS ARTICLE
Select this article
Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...PGE accurately discovers some crucial TF motifs within prioritized cCREs and reveals the different regulatory types of these cCREs.Cell type–specific gene expression patterns are primarily determined through complex interactions between cis-regulatory elements (CREs) and transcriptional factors, playing...
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. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...of an age-associated DAC adjacent to the Lrig1 gene in microglia is shown in Figure 3C. We further performed clustering analysis to group DACs, followed by motif and functional enrichment analysis. Notably, a DAC group downregulated during late aging in oligodendrocyte was enriched for motifs of the SOX...
OPEN ACCESS ARTICLE
Select this article
Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
...graph https://github.com/adamewing/methylartist. The command used to generate Figure 4 and Supplemental Figure S18 is shown below: methylartist locus –b <IN_BAM1>,<IN_BAM2> -i chr16:88532537-88536321 –g –-plot_coverage <IN_BAM1>,<IN_BAM2> –-labelgenes –-genes ZFPM1 –-motif CG –-phased...
OPEN ACCESS ARTICLE
Select this article
Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...assess PRISM-GRN's capabilities, we analyzed the A549 data set by clustering genes using the Leiden algorithm (Traag et al. 2019) and visualizing the clusters with UMAP, based on both gene expression data and the embeddings of zGRN derived from the causal prediction task. As shown in Figure 6A...
Select this article
Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...sequence is functional, the reporter gene is expressed/induced and the cellular concentration of the gene product is measured (Smale 2010).TF binding predictionTFs bind DNA in a sequence-specific manner based on motifs, with each binding site having a consensus sequence that indicates prerequisites...
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
...). Differential analysis was performed using a paired two-tailed DESeq2 test. (C,D) Gene Ontology enrichment analysis for differentially expressed genes increasing (C) or decreasing (D) in expression. Select terms are displayed. (E) The top five unique TF motifs for repressed or activated ATAC peaks. (F...
OPEN ACCESS ARTICLE
Select this article
Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...that form in nucleic acids have known roles in regulating gene expression and include G-quadruplexes (G4s), intercalated motifs (iMs), and R-loops (RLs). In this paper, we used the computational tools G4-iM Grinder and QmRLFS-finder to predict the formation of each of these structures throughout the lnc...
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
...to the number of studies, samples, and median PCs regressed for incremental data aggregation are provided in Supplemental Table S2. Additionally, we assessed the recapitulation of known biological pathways by computing the F1-score of finding canonical gene-gene relationships compiled from KEGG (Kanehisa...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Jakt et al. 11 (1): 112.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: