Searching journal content for articles similar to Chen et al. 33 (4): 541.

Displaying results 1-10 of 5566

For checked items

view abstracts
download to citation manager

Select this article
Method: Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
- Lin Li,
- Xianbin Su,
- and Ze-Guang Han
Genome Res. October 2025 35: 2300-2315; Published in Advance August 21, 2025, doi:10.1101/gr.279689.124
...genes exhibited distinct region-specific patterns (Supplemental Fig. S14E). We applied DeCEP to identify the DeCEP states of the spots corresponding to the two most spatially dependent gene programs mentioned earlier. Our analysis revealed that the DeCEP states were consistent with the changes observed...
Select this article
Research: Transcriptional programs mediating neuronal toxicity and altered glial–neuronal signaling in a Drosophila knock-in tauopathy model
- Hassan Bukhari,
- Vanitha Nithianandam,
- Rachel A. Battaglia,
- Anthony Cicalo,
- Souvarish Sarkar,
- Aram Comjean,
- Yanhui Hu,
- Matthew J. Leventhal,
- Xianjun Dong,
- and Mel B. Feany
Genome Res. April 2024 34: 590-605; Published in Advance April 10, 2024, doi:10.1101/gr.278576.123
...signaling pathways, including glial–neuronal signaling, were broadly dysregulated as were brain region and cell type–specific protein interaction networks and gene regulatory programs. In summary, we present here a genetic model of tauopathy that faithfully recapitulates the genetic context and phenotypic...
OPEN ACCESS ARTICLE
Select this article
Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
OPEN ACCESS ARTICLE
Select this article
Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...to markedly differing degrees. Notably, the degree of knockdown was not strongly correlated with the number of DEGs identified or the expression level of the target itself in this system (Supplemental Fig. S1E,F), nor were the effects correlated with modifier expression in neurons isolated from mouse brains...
Select this article
Research: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123
...138672; 4Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 169857; 5Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599; 6Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593...
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
...). We annotated six distinct brain cell types, including astrocytes, endothelial cells, excitatory neurons, inhibitory neurons, microglia, and oligodendrocytes using cell type–specific markers from published studies (Supplemental Tables S2, S3; Supplemental Fig. S3; Haney et al. 2024). Next, we...
Select this article
Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...Corresponding authors: twang@wustl.edu, gzhao@wustl.eduAbstractFollowing amputation, zebrafish regenerate their injured caudal fin through lineage-restricted reprogramming. Although previous studies have charted various genetic and epigenetic dimensions of this process, the intricate gene regulatory programs...
OPEN ACCESS ARTICLE
Select this article
Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...stressors can contribute to the onset and progression of neurological and psychiatric diseases (Walker et al. 2019; Aygün et al. 2021; Jerber et al. 2021; Schumann et al. 2023; Emani et al. 2024; Wen et al. 2024).Brain cells, especially neurons, are highly sensitive to environmental perturbations like...
OPEN ACCESS ARTICLE
Select this article
Resource: Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury
- Qiuyun Yang,
- Lingxuan Zhang,
- Manrui Li,
- Yang Xu,
- Xiaogang Chen,
- Ruixuan Yuan,
- Xiaofeng Ou,
- Min He,
- Miao Liao,
- Lin Zhang,
- Hao Dai,
- Meili Lv,
- Xiaoqi Xie,
- Weibo Liang,
- and Xiameng Chen
Genome Res. October 2023 33: 1818-1832; Published in Advance September 20, 2023, doi:10.1101/gr.277881.123
...and suppressing neuronal lineage differentiation. Targeting Tcf7l1 represents a potential direction in regenerative medicine for brain injury.View larger version: In this window In a new window Figure 7. Suppressing Tcf7l1 promotes neuronal differentiation of the SVZ NSCs after mTBI. (A, top) Schematic diagram...
Select this article
Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...), and gene retrocopy variants (Zhang et al. 2021; Zhang and Tautz 2022). This made the house mouse an ideal system to directly trace the origin and pattern of alternative isoforms in natural populations.Here, we use mice brains as the source tissue for the transcriptome analysis. The brain harbors...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Chen et al. 33 (4): 541.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: