Explanipedia

Biphasic control of the B cell transcriptome by mTORC1 and GSK3 Open

Jens Kalchschmidt, T. Kanno, Solji Park, Wendy du Bois, Yongbing Zhao , et al. · 2025

NaRaDa: A comprehensive nascent RNA database Open

Zhibiao Mai, Duo Li, Peng Tang, Chuanman Zhou, Yongbing Zhao , et al. · 2025

Nascent RNA-seq is pivotal for elucidating the dynamics and transcriptional regulation of enhancer RNA and protein-coding genes, and for revealing the regulatory linkages between enhancer-gene pairs in diverse physiological and pathologica…

3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network Open

Paweł Trzaskoma, Seolkyoung Jung, Aleksandra Pękowska, Christopher H. Bohrer, Xiang Wang , et al. · 2024

Discontinuous transcription is evolutionarily conserved and a fundamental feature of gene regulation; yet, the exact mechanisms underlying transcriptional bursting are unresolved. Analyses of bursting transcriptome-wide have focused on the…

A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification Open

Chunhong Liu, Hiroyuki Nagashima, Nilisha Fernando, Victor Bass, Jaanam Gopalakrishnan , et al. · 2024

TFSyntax: a database of transcription factors binding syntax in mammalian genomes Open

Yongbing Zhao · 2022

In mammals, transcriptional factors (TFs) drive gene expression by binding to regulatory elements in a cooperative manner. Deciphering the rules of such cooperation is crucial to obtain a full understanding of cellular homeostasis and deve…

Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data Open

Yongbing Zhao, Jinfeng Shao, Yan W. Asmann · 2022

Explainable artificial intelligence aims to interpret how machine learning models make decisions, and many model explainers have been developed in the computer vision field. However, understanding of the applicability of these model explai…

“Stripe” transcription factors provide accessibility to co-binding partners in mammalian genomes Open

Yongbing Zhao, Supriya V. Vartak, A. Conte, Xiang Wang, David A. Garcia , et al. · 2022

Mitochondrial hTERT rewires glucose metabolism to confer cancer chemoresistance by binding to MT-ND1 Open

Xinzhe Li, Xing Chang, Weichao Hu, Yongbing Zhao, Zhengguo Xu , et al. · 2022

Resistance to chemotherapy represents a bottleneck in clinical cancer treatment and demands urgent solutions. Dysfunction of glucose metabolism including the Warburg effect is an outstanding hallmark of aberrant cancer metabolism which rem…

Effects of Environmental and Pathological Hypoxia on Male Fertility Open

Zhibin Li, Sumin Wang, Chunli Gong, Yiyang Hu, Jiao Liu , et al. · 2021

Male infertility is a widespread health problem affecting approximately 6%–8% of the male population, and hypoxia may be a causative factor. In mammals, two types of hypoxia are known, including environmental and pathological hypoxia. Stud…

Long non‐coding small nucleolar RNA host genes in digestive cancers Open

Huan Yang, Zheng Jiang, Shuang Wang, Yongbing Zhao, Xiaomei Song , et al. · 2019

Although long noncoding RNAs (lncRNAs) do not have protein coding capacities, they are involved in the pathogenesis of many types of cancers, including hepatocellular carcinoma, cervical cancer, and gastric cancer. Notably, the roles of ln…

PADS Arsenal: a database of prokaryotic defense systems related genes Open

Yadong Zhang, Zhewen Zhang, Hao Zhang, Yongbing Zhao, Zaichao Zhang , et al. · 2019

Defense systems are vital weapons for prokaryotes to resist heterologous DNA and survive from the constant invasion of viruses, and they are widely used in biochemistry investigation and antimicrobial drug research. So far, numerous types …

Novel endoscopic treatment strategy for early esophageal cancer in cirrhotic patients with esophageal varices Open

Zhengguo Xu, Yongbing Zhao, Jin Yü, Jianying Bai, En Liu , et al. · 2019

The safety and efficacy of endoscopic submucosal dissection (ESD) and radiofrequency ablation for early esophageal cancer (EEC) in cirrhotic patients has not been thoroughly investigated to date. The present study aimed to establish a stan…

NucMap: a database of genome-wide nucleosome positioning map across species Open

Yongbing Zhao, Jinyue Wang, Liang Fang, Yanxia Liu, Qi Wang , et al. · 2018

This FAIRsharing record describes: NucMap is a database of genome-wide nucleosome positioning across multiple species. Based on raw sequence data from published studies, NucMap integrates, analyzes, and visualizes nucleosome positioning da…

PGAweb: A Web Server for Bacterial Pan-Genome Analysis Open

Xinyu Chen, Yadong Zhang, Zhewen Zhang, Yongbing Zhao, Chen Sun , et al. · 2018

An astronomical increase in microbial genome data in recent years has led to strong demand for bioinformatic tools for pan-genome analysis within and across species. Here, we present PGAweb, a user-friendly, web-based tool for bacterial pa…

PGAP-X: extension on pan-genome analysis pipeline Open

Yongbing Zhao, Chen Sun, Dongyu Zhao, Yadong Zhang, Yang You , et al. · 2018

MethBank 3.0: a database of DNA methylomes across a variety of species Open

Rujiao Li, Liang Fang, Mengwei Li, Dong Zou, Shixiang Sun , et al. · 2017

This FAIRsharing record describes: MethBank stores DNA methylome data across a variety of species. MethBank integrates consensus reference methylomes (CRMs) compiled from healthy human samples at different ages, single-base resolution meth…

FOXA1 defines cancer cell specificity Open

Gaihua Zhang, Yongbing Zhao, Yi Liu, Li-Pin Kao, Xiao Wang , et al. · 2016

Functional FOXA1 targeting is mostly unique to each of the four human cancer cell lines HepG2, LNCaP, MCF7, and T47D.

Foxa1 is essential for mammary duct formation Open

Yi Liu, Yongbing Zhao, Benjamin Skerry, Xiao Wang, Christelle Colin , et al. · 2016

Summary The transcription factor forkhead box protein A1 (FOXA1) plays a critical role in the proliferation of human breast cancer cells, particularly estrogen receptor alpha (ERα)‐positive luminal breast cancer cells. However, genetic stu…

The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng Open

Yongbing Zhao, Jinlong Yin, Haiyan Guo, Yuyu Zhang, Wen Xiao , et al. · 2015

Panax ginseng C.A. Meyer (P. ginseng) is an important medicinal plant and is often used in traditional Chinese medicine. With next generation sequencing (NGS) technology, we determined the complete chloroplast genome sequences for four Chi…

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