Searching journal content for articles similar to Inoue et al. 28 (5): 766.3.

Displaying results 1-10 of 6116

For checked items

view abstracts
download to citation manager

Select this article
Research: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
- Fumitaka Inoue,
- Martin Kircher,
- Beth Martin,
- Gregory M. Cooper,
- Daniela M. Witten,
- Michael T. McManus,
- Nadav Ahituv,
- and Jay Shendure
Genome Res. January 2017 27: 38-52; Published in Advance November 9, 2016, doi:10.1101/gr.212092.116
...the functional activities of 2236 candidate liver enhancers in an episomal versus a chromosomally integrated context. We find that the activities of chromosomally integrated sequences are substantially different from the activities of the identical sequences assayed on episomes, and furthermore are correlated...
Select this article
Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
..., requires efficient computational detection methods due to experimental limitations. Although machine learning predictors have been proposed, their performance could be enhanced through systematic optimization of feature encoding schemes. Here, we propose EnDeep4mC, a dual-adaptive framework integrating...
OPEN ACCESS ARTICLE
Select this article
Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...at equal molarity (Supplemental Fig. S1B), minimizing experimental complexity and ligation bias. In contrast, fully modeling GC-content for 50-mers would require 450 permutations, which is impractical. By systematically analyzing GC-content, MFE, and 3D features, we reveal how specific RNA structural...
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
...).Beyond biological relevance, it is also important to distinguish between methods that study the steady state of the cell versus those that introduce experimental perturbations for comparative analysis. Some techniques rely on genetic modifications to reveal functional differences. Gain-of-function approaches...
OPEN ACCESS ARTICLE
Select this article
Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...the spatial and temporal dynamics of enhancer–promoter interactions. Understanding how enhancers interact with promoters will deepen our understanding of the regulation of gene expression and the molecular underpinnings of transcriptional control.Gene expression programs are encoded by cis-regulatory elements...
Select this article
Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...regulatory mechanisms in IGN using these data sets to define diverse chromatin states in the germline , reveal intra- and inter-chromosomal patterns of histone modifications and chromatin accessibility, and identify chromatin states that are unique to the germline relative to the soma. Germline...
OPEN ACCESS ARTICLE
Select this article
Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...and its potential target gene during myogenesis. Our findings reveal the dynamic regulatory features of SEs in skeletal muscle development and provide a general integrative framework for identifying critical enhancers underlying the formation of complex traits.Skeletal muscle, which constitutes nearly...
Select this article
Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...) (Fig. 2G). These findings suggest that regions with extensive intraspecific divergence among C. nigoni strains substantially contribute to the interspecific divergence between these two species.Gene-based pan analysis reveals disproportionate expansions of dispensable gene families between C. nigoni...
Select this article
Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...STARR-seq) (Vanhille et al. 2015) to identify enhancers active during early brain development. The CapSTARR-seq method is a plasmid-based, in vitro approach for large-scale validation of enhancer regions (Vanhille et al. 2015). We leveraged several PsychENCODE data sets, including data from the prefrontal cortex (PFC...
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. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...analysis revealed that transcription factors such as CTCF, BORIS, TCF3, and PRDM15 may serve as key regulators (Supplemental Fig. S9B). Tcf3 encodes a member of the E protein family of helix-loop-helix transcription factors and plays a role in macrophage activation and inflammatory induction (Benayoun et...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Inoue et al. 28 (5): 766.3.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: