Searching journal content for articles similar to Huang et al. 29 (4): 657.

Displaying results 1-9 of 9

For checked items

view abstracts
download to citation manager

Select this article
Research: Epigenetic characterization of pseudogenes across human tissues
- Yunzhe Jiang,
- Beatrice Borsari,
- and Mark Gerstein
Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
...whether pseudogene expression mirrors that of their parent protein-coding genes across tissues. Cross-tissue co-expression analysis revealed that processed pseudogenes display significantly lower correlation with their parent genes than unprocessed pseudogenes (Wilcoxon rank-sum test, p-value = 4...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes
- Alexandra J. Scott,
- Colby Chiang,
- and Ira M. Hall
Genome Res. December 2021 31: 2249-2257; Published in Advance September 20, 2021, doi:10.1101/gr.275488.121
..., including nonreference insertions that were not detected in our prior GTEx study. It has been proposed that MEIs may have broad effects on gene expression owing to their ability to disrupt genes, promote epigenetic gene silencing, and serve as alternate promoters (Chuong et al. 2017; Payer and Burns 2019...
OPEN ACCESS ARTICLE
Select this article
Research: Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
- Khang Ma and
- Rinki Ratnapriya
Genome Res. October 2025 35: 2143-2157; Published in Advance August 26, 2025, doi:10.1101/gr.280554.125
....Molecular signatures of retina and brain microgliaTo gain deeper insight into the similarities and differences between microglia in the retina and brain at the molecular level, we examined global gene expression profiles using correlation heatmaps. For these analyses, we obtained the average gene expression for all...
Select this article
Methods: Inferring causal relationships among different histone modifications and gene expression
- Hong Yu,
- Shanshan Zhu,
- Bing Zhou,
- Huiling Xue,
- and Jing-Dong J. Han
Genome Res. August 2008 18: 1314-1324; Published in Advance June 18, 2008, doi:10.1101/gr.073080.107
...to gene silencing, H3K4me3 to gene activation and the effect of bivalent modification of both H3K4me3 and H3K27me3, but also identified many other relationships that may predict new epigenetic interactions important in epigenetic gene regulation. Our automated inference method, which is potentially...
Select this article
Research: Enhancer–silencer transitions in the human genome
- Di Huang and
- Ivan Ovcharenko
Genome Res. March 2022 32: 437-448; Published in Advance February 1, 2022, doi:10.1101/gr.275992.121
...). These results are consistent with the silencer function of DFREs in T cells and the enhancer function of DFREs in hESCs. On the other hand, CTCF ChIP-seq TFBSs show no consistent correlation with either highly or lowly expressed genes in both cell types (Supplemental Fig. S16), supporting a functional...
OPEN ACCESS ARTICLE
Select this article
Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
..., and kidney across mammals, as well as in Gallus gallus and in the lizard Anolis carolinensis. This is accompanied by elevated expression of TCA cycle enzymes and reduction in hypoxia response genes, suggesting a conserved cross-tissue metabolic switch after birth/hatching. Analysis of about 70 known...
Select this article
Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
..., saliva, and buccal mucosa) and correlate it to phenotypic outcomes. This reveals a strong correlation between X inactivation skew and disease presentation, confirming the value in performing this assay and its potential as a way to prioritize patients for early intervention, such as gene therapy...
Select this article
Resource: RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse
- Catherine M. Farrell,
- Tamara Goldfarb,
- Sanjida H. Rangwala,
- Alexander Astashyn,
- Olga D. Ermolaeva,
- Vichet Hem,
- Kenneth S. Katz,
- Vamsi K. Kodali,
- Frank Ludwig,
- Craig L. Wallin,
- Kim D. Pruitt,
- and Terence D. Murphy
Genome Res. January 2022 32: 175-188; Published in Advance December 7, 2021, doi:10.1101/gr.275819.121
...to other research fields, most notably to bioclinical research that relies on annotation for personal genomics or disease-associated variant interpretation (Perenthaler et al. 2019). Gene regulatory elements are the most abundantly studied among the nongenic element types, and their epigenetic signatures...
Select this article
Research: Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters
- Shrutii Sarda,
- Avinash Das,
- Charles Vinson,
- and Sridhar Hannenhalli
Genome Res. April 2017 27: 553-566; Published in Advance February 21, 2017, doi:10.1101/gr.212050.116
..., likely due to the narrow expression breadth (i.e., tissue specificity) of MethExp genes. To distinguish between the alternative scenarios of promoter misannotation and unsuspected context-specific distal promoter usage, we carried out two specific analyses. First, we performed a locusspecific cross-tissue...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Huang et al. 29 (4): 657.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: