Explanipedia

PlantScience.ai: An LLM-Powered Virtual Scientist for Plant Science Open

Haopeng Yu, Shasha Zhou, Mingyu Huang, Ling Ding, Yuxuan Chen , et al. · 2025

The accelerating growth of plant science literature presents a major challenge for researchers seeking to extract accurate, up-to-date knowledge from an increasingly fragmented and domain-specific corpus. General-purpose large language mod…

In vivo RNA structure influences the translation and stability of plant long non-coding RNAs Open

Qianli Dong, Bibo Yang, Wenqing Sun, Jie Liang, Qiang Xing , et al. · 2025

Long non-coding RNAs (lncRNAs) regulate numerous biological processes in plants, including development and stress responses. Although previous studies have mainly examined their sequences and transcriptional activity, other essential aspec…

Profiling RNA G‐Quadruplexes In vivo Open

Bibo Yang, Yiliang Ding, Yueying Zhang · 2025

RNA G‐quadruplexes (RG4s) are specific and complex tertiary structures that form in guanine‐rich regions of RNA and can be detected in vitro . A recently developed transcriptome‐wide technique, SHALiPE‐Seq, enables the assessment of RG4 fo…

Recessive epistasis of a synonymous mutation confers cucumber domestication through epitranscriptomic regulation Open

Tongxu Xin, Zheng Zhang, Yueying Zhang, Xutong Li, Shenhao Wang , et al. · 2025

Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization Open

Sebastian Balch, Zala Sekne, Elsa Franco-Echevarría, Patryk Ludzia, Rachael C. Kretsch , et al. · 2025

Telomerase ribonucleoprotein (RNP) synthesizes telomeric repeats at chromosome ends using a telomerase reverse transcriptase (TERT) and a telomerase RNA (hTR in humans). Previous structural work showed that human telomerase is typically mo…

Recessive epistasis of a synonymous mutation confers cucumber domestication through epitranscriptomic regulation Open

Tongxu Xin, Zheng Zhang, Yueying Zhang, Xutong Li, Shenhao Wang , et al. · 2025

Synonymous mutations, once known as "silent" mutations, are increasingly attracting the interest of biologists. Although they may affect transcriptional or post-transcriptional processes, their impact on biological traits remains under-inv…

A microsphere loaded with chondrocyte-targeting exosomes continuously deliver miR-148a for osteoarthritis therapy Open

Tao Yang, Haiwei Ma, Kechi Li, Jie Xiang, Jianxin Qiu , et al. · 2025

Due to the complex pathogenesis and limited treatment options, the clinical diagnosis and treatment of osteoarthritis (OA) remains extremely challenging. Umbilical cord derived mesenchymal stem cell-derived exosomes have low immunogenicity…

G-Quadruplexes Act as an On/Off Switch While i-Motifs Regulate Insulin Expression in Reporter Gene Assays Open

Dilek Guneri, Christopher J. Morris, Yiliang Ding, Timothy D. Craggs, Steven S. Smith , et al. · 2025

The insulin-linked polymorphic region (ILPR) is a variable number tandem repeat located in the promoter of the human insulin gene. This G-rich sequence can fold into four-stranded G-quadruplex DNA structures, while its complementary C-rich…

Unveiling the regulatory role of GRP7 in ABA signal-mediated mRNA translation efficiency regulation Open

Jing Zhang, Wenna Shao, Yongxin Xu, Fa’an Tian, Jinchao Chen , et al. · 2025

Abscisic acid (ABA) is a crucial phytohormone involved in plant growth and stress responses. While the transcriptional regulation triggered by ABA is well-documented, its effects on translational regulation have been less studied. Through …

An inflammation-associated lncRNA induces neuronal damage via mitochondrial dysfunction Open

Ane Olazagoitia‐Garmendia, Henar Rojas‐Márquez, Tim Trobisch, Cristina Moreno‐Castro, Ariadne Rodriguez Etxebarria , et al. · 2025

A Near-Field 30--40 Ghz Millimeter-Wave Phase Imaging Method for Non-Destructive Testing and Evaluation Open

Yiliang Ding, Xiaojun Xie, Dongjie Bi, Xifeng Li, Libiao Peng · 2025

An interpretable RNA foundation model for exploring functional RNA motifs in plants Open

Haopeng Yu, Heng Yang, Wenqing Sun, Zongyun Yan, Xiaofei Yang , et al. · 2024

Unveiling RNA structure-mediated regulations of RNA stability in wheat Open

Haidan Wu, Haopeng Yu, Yueying Zhang, Bibo Yang, Wenqing Sun , et al. · 2024

Despite the critical role of mRNA stability in post-transcriptional gene regulation, research on this topic in wheat, a vital agricultural crop, remains unclear. Our study investigated the mRNA decay landscape of durum wheat ( Triticum tur…

DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m6A reader YTHDF1 Open

Yuwei Zhang, Jieyu Zhao, Xiaona Chen, Yulong Qiao, Jinjin Kang , et al. · 2024

AtPRMT3-RPS2B promotes ribosome biogenesis and coordinates growth and cold adaptation trade-off Open

Zhen Wang, Xiaofan Zhang, Chunyan Liu, Susan Duncan, Runlai Hang , et al. · 2024

The role of RNA structure in 3’ end processing in eukaryotes Open

Jin Xu, Susan Duncan, Yiliang Ding · 2024

Maturation of pre-mRNA into fully functional mRNA involves a series of highly coordinated steps that are essential for eukaryotic gene expression. RNA structure has been found to play regulatory roles in many of these steps, including clea…

iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning Open

Haopeng Yu, Li Fan, Bibo Yang, Yiman Qi, Dilek Guneri , et al. · 2024

DNA, beyond its canonical B-form double helix, adopts various alternative conformations, among which the i-motif, emerging in cytosine-rich sequences under acidic conditions, holds significant biological implications in transcription modul…

A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics Open

Yueying Zhang, Qianli Dong, Zhen Wang, Qinzhe Liu, Haopeng Yu , et al. · 2024

Prediction of DNA i-motifs via machine learning Open

Bibo Yang, Dilek Guneri, Haopeng Yu, Elisé P. Wright, Wenqian Chen , et al. · 2024

i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and …

Unveiling the regulatory role of GRP7 in ABA signal-mediated mRNA translation efficiency regulation Open

Jing Zhang, Yongxin Xu, Fa’an Tian, Chongsheng He, Xiang Yu , et al. · 2024

Abscisic acid (ABA) is a crucial phytohormone involved in plant growth and stress responses. Although ABA has been implicated in the regulation of translation efficiency in Arabidopsis thaliana , the underlying mechanism remains largely un…

Prediction of DNA i-Motifs Via Machine Learning Open

Bibo Yang, Dilek Guneri, Haopeng Yu, Elisé P. Wright, Wenqian Chen , et al. · 2023

i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and …

DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m6A/YTHDF1 Open

Yuwei Zhang, Jieyu Zhao, Xiaona Chen, Kaixin Lyu, Yiliang Ding , et al. · 2023

RNA structure constitutes a new layer of gene regulatory mechanisms. RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) is known to bind and u…

Editorial: Plant RNA structure Open

Huakun Zhang, Betty Chung, Zhiye Wang, Yiliang Ding · 2023

EDITORIAL article Front. Plant Sci., 26 May 2023Sec. Plant Cell Biology Volume 14 - 2023 | https://doi.org/10.3389/fpls.2023.1204600

Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection Open

Jun Xiao, Xuelei Lin, Yongxin Xu, Dongzhi Wang, Yiman Yang , et al. · 2023

Spike architecture largely affects grain number embraced, which is an important trait to optimize during wheat breeding process. In this study, we incorporated multi-omic data and investigated the genetic regulation of wheat spike developm…

3′ Untranslated Region Structural Elements in CYP24A1 Are Associated With Infantile Hypercalcemia Type 1 Open

Nicole Ball, Susan Duncan, Yueying Zhang, Rocky Payet, Isabelle Piec , et al. · 2023

Loss‐of‐function mutations in the CYP24A1 protein‐coding region causing reduced 25 hydroxyvitamin D (25OHD) and 1,25 dihydroxyvitamin D (1,25(OH) 2 D) catabolism have been observed in some cases of infantile hypercalcemia type 1 (HCINF1), …

Reference genes for quantitative Arabidopsis single molecule RNA fluorescencein situhybridization Open

Susan Duncan, Hans E. Johansson, Yiliang Ding · 2022

Subcellular mRNA quantities and spatial distributions are fundamental for driving gene regulatory programmes. Single molecule RNA fluorescence in situ hybridization (smFISH) uses fluorescent probes to label individual mRNA molecules, there…

Beyond transcription: compelling open questions in plant RNA biology Open

Pablo A. Manavella, Micaela A. Godoy Herz, Alberto R. Kornblihtt, Reed Sorenson, Leslie Sieburth , et al. · 2022

The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field bu…

Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection Open

Xuelei Lin, Yongxin Xu, Dongzhi Wang, Yiman Yang, Xiaoyu Zhang , et al. · 2022

The spike architecture of wheat plays a crucial role in determining grain number, making it a key trait to optimize in wheat breeding programs. In this study, through a multi-omic approach, we analyzed the transcriptome and epigenome profi…

RNA G-quadruplex structure contributes to cold adaptation in plants Open

Xiaofei Yang, Haopeng Yu, Susan Duncan, Yueying Zhang, Jitender Cheema , et al. · 2022

G4Atlas: a comprehensive transcriptome-wide G-quadruplex database Open

Haopeng Yu, Yiman Qi, Bibo Yang, Xiaofei Yang, Yiliang Ding · 2022

RNA G-quadruplex (rG4) is a vital RNA tertiary structure motif that involves the base pairs on both Hoogsteen and Watson-Crick faces of guanines. rG4 is of great importance in the post-transcriptional regulation of gene expression. Experim…

Yiliang Ding YOU? Author Swipe