Searching journal content for articles similar to Foley et al. 29 (11): 1816.

Displaying results 1-10 of 6138

For checked items

view abstracts
download to citation manager

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
...Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson’s disease Kangli Wang,1 Weikun Xia,1 Yingli Gu,1 Songpeng Zu,1 Qian Yang,2 Maria Luisa Amaral,1 Yaozhi Wang,1 Allen Wang,2 Xiang-Dong Fu,3 William C. Mobley,4 and Bing Ren1...
OPEN ACCESS ARTICLE
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
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
...of growth (P < 5 × 10−9, GO:BP, g:Profiler) (Supplemental Table 9).Postduplication FIEs are distributed in a wider variety of genes, with less than half occurring in known cancer genesFewer FIEs were identified postduplication compared with preduplication (LUAD, 18.5%; LUSC, 30.8% of total FIEs), and less...
OPEN ACCESS ARTICLE
Select this article
Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...sample when performing sRNA-seq for dual profiling. In contrast, degradation bias (half-life analysis) and noise from housekeeping genes do not appear to have a significant effect upon or bias our approach. For the latter, Gene Ontology analysis identified tissue-specific pathways, reinforcing...
Select this article
Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
..., identify segmentally duplicated genes, and enable the phasing of reads (Logsdon et al. 2020). The phasing specifically allows for the assignment of haplotypes to pathogenic variants, enhancing diagnostic utility. LRS advancements enable the simultaneous measurement of DNAm profiles alongside genetic data...
OPEN ACCESS ARTICLE
Select this article
Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...in tissue sections. PCL-seq offers a more cost-effective and adaptable approach. We demonstrate its compatibility with both conventional fresh-frozen tissue sections and FFPE sections of mouse embryos. Moreover, PCL-seq achieves subcellular resolution, enabling the profiling of gene expression in distinct...
Select this article
Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
- Joshua Lee,
- Elizabeth A. Snell,
- Joanne Brown,
- Charlotte E. Booth,
- Rosamonde E. Banks,
- Daniel J. Turner,
- Naveen S. Vasudev,
- and Dimitris Lagos
Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
...in their gene expression levels (Fig. 1F; Supplemental Fig. S2). Overall, while PCS provided greater sequencing depth, our data demonstrated that both methods can capture a diverse range of transcripts from archival clinical samples, yielding highly concordant gene expression profiles.Differential gene...
OPEN ACCESS ARTICLE
Select this article
Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
- Stephanie M. Zimmerman,
- Robin Fropf,
- Bridget R. Kulasekara,
- Maddy Griswold,
- Oliver Appelbe,
- Arya Bahrami,
- Rich Boykin,
- Derek L. Buhr,
- Kit Fuhrman,
- Margaret L. Hoang,
- Quoc Huynh,
- Lesley Isgur,
- Andrew Klock,
- Alecksandr Kutchma,
- Alexa E. Lasley,
- Yan Liang,
- Jill McKay-Fleisch,
- Jeffrey S. Nelson,
- Karen Nguyen,
- Erin Piazza,
- Aric Rininger,
- Daniel R. Zollinger,
- Michael Rhodes,
- and Joseph M. Beechem
Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
..., preserving the spatial and morphological context of gene expression. Here, we describe expanding the chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed...
OPEN ACCESS ARTICLE
Select this article
Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...temporal patterns of TE expansion. Importantly, we uncover 50 robust coevolutionary signatures between 90 KZFPs and specific TE k-mer clusters, notably 51 involving 32 KZFPs that target Bovidae-specific LTR/ERVK clusters. Furthermore, 52 Bovinae-specific TEs impact gene structure by exonizing 14 genes...
- Abstract
- Full Text (PDF)
ACCEPTED MANUSCRIPT
Select this article
Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...and Koreski 2017) and are poorly captured by standard RNA-seq, making RNAPIIS5P profiling especially suitable for assessing their transcriptional regulation. Direct comparison of 40-day-old versus 15-day-old tissues shows widespread loss of RNAPIIS5P at most genes, accompanied by orders-of-magnitude higher...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Foley et al. 29 (11): 1816.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: