Searching journal content for articles similar to Zhang et al. 36 (2): 361.

Displaying results 1-10 of 37

For checked items

view abstracts
download to citation manager

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
.... By integrating transcription factor (TF)–target gene relationships, chromatin accessibility, and genetic variation, this framework aims to elucidate the cell type–specific regulatory mechanisms underlying AD progression, link genetic risk variants to cis-regulatory elements and target genes, and prioritize...
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
...perform tasks of both GRN construction and causality prediction with different supervising strategies across broad biological research scenarios.ResultsThe framework of PRISM-GRNAs illustrated in Figure 1A, TFs bind to their specific target genes, thereby forming cell type–specific GRNs. In conjunction...
Select this article
Editorial: Innovations in computational biology: RECOMB 2024 Special Issue
- Jian Ma and
- Bonnie Berger
Genome Res. September 2024 34: vii-viii; doi:10.1101/gr.280036.124
...in this issue. Lal et al. (2024) present regLM, which uses autoregressive language models to design synthetic cis-regulatory elements. Li et al. (2024) propose the ANDES framework for improving gene set similarity analysis using a new gene embedding approach. Additionally, Iovino et al. (2024) introduce a novel...
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 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...primarily employed RNA sequencing(Jin et al. 2025), which, while 63 informative, does not fully elucidate the complex regulatory mechanisms underlying 64 transcriptional programs. Gene expression is regulated by cis-regulatory elements (CREs) in a 65 spatiotemporal manner through precise gene regulatory...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
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
...quintiles of network centrality (Supplemental Figs. S22 and S23; Supplemental Table S9). We observed that peripheral genes (Quintile 1) and central genes (Quintile 5) of consensus networks exhibited an excess overlap > 1 of eQTL-deficient genes (those which lacked significant cis-regulatory variants...
OPEN ACCESS ARTICLE
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
...from data generated by assays of single-cell RNA sequencing (scRNA-seq) and single-cell transposase-accessible chromatin sequencing (scATAC-seq). Most of these methods infer the relationships between TFs and target genes by estimating their interactions with cis-regulatory elements (CREs...
OPEN ACCESS ARTICLE
Select this article
Method: Ultrafast and scalable variant annotation and prioritization with big functional genomics data
- Dandan Huang,
- Xianfu Yi,
- Yao Zhou,
- Hongcheng Yao,
- Hang Xu,
- Jianhua Wang,
- Shijie Zhang,
- Wenyan Nong,
- Panwen Wang,
- Lei Shi,
- Chenghao Xuan,
- Miaoxin Li,
- Junwen Wang,
- Weidong Li,
- Hoi Shan Kwan,
- Pak Chung Sham,
- Kai Wang,
- and Mulin Jun Li
Genome Res. December 2020 30: 1789-1801; Published in Advance October 15, 2020, doi:10.1101/gr.267997.120
...type–specific, -wide DNA functional elements at high resolution. With the growing volume of functional annotation data and sequencing variants, existing variant annotation algorithms lack the efficiency and scalability to process big genomic data, particularly when annotating whole- sequencing variants...
Select this article
Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...expression, it also points to the need to model the role of trans effects. Gene expression is regulated by the interaction of cis regulatory elements with TFs. The activity of TFs, themselves, depends on their expression, which has its own regulatory logic. As such, faithfully modeling the role of trans...
OPEN ACCESS ARTICLE
Select this article
Research: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
- Amanda J. Lea,
- Julie Peng,
- and Julien F. Ayroles
Genome Res. October 2022 32: 1826-1839; Published in Advance October 13, 2022, doi:10.1101/gr.276430.121
...variation predicted individual responses at the transcriptional level. We found that diverse environmental perturbations induced diverse gene regulatory programs, whereas the genetic control of gene expression levels was more environmentally robust: at least 70% of ancestry effects on the transcriptome were...
OPEN ACCESS ARTICLE
Select this article
Research: Widespread contribution of transposable elements to the innovation of gene regulatory networks
- Vasavi Sundaram,
- Yong Cheng,
- Zhihai Ma,
- Daofeng Li,
- Xiaoyun Xing,
- Peter Edge,
- Michael P. Snyder,
- and Ting Wang
Genome Res. December 2014 24: 1963-1976; Published in Advance October 15, 2014, doi:10.1101/gr.168872.113
.... The large portion of mammalian s that TEs represent is thought to have provided raw material for the evolution of cis-regulatory elements (Feschotte 2008), possibly via binding site turnover or via spreading of binding sites when the TE transposes (Feschotte 2008). We have conducted here by far the most...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Zhang et al. 36 (2): 361.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: