Genome-wide association study on salt tolerance of core germplasm resources in watermelon by YUAN Gaopeng, ZHAO Yanlong, SUN Dexi, GAO Bowen, LI Weihua, SHI Mingkun, ZHANG Jingyu, ZHU Yingchun

“…This study aims to identify key candidate genes associated with salt tolerance in watermelon, thereby providing a crucial foundation for understanding the mechanisms underlying watermelon responses to salt stress and for the cultivation of new salt-tolerant varieties. …”
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Multi-omic biomarker panel in pancreatic cyst fluid and serum predicts patients at a high risk of pancreatic cancer development by Laura E. Kane, Gregory S. Mellotte, Eimear Mylod, Paul Dowling, Simone Marcone, Caitriona Scaife, Elaine M. Kenny, Michael Henry, Paula Meleady, Paul F. Ridgway, Finbar MacCarthy, Kevin C. Conlon, Barbara M. Ryan, Stephen G. Maher

“…Abstract Integration of multi-omic data for the purposes of biomarker discovery can provide novel and robust panels across multiple biological compartments. …”
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Moonlighting activity of threonine synthase in cyanobacterial cell death by Wonjae Kim, Yongjun Son, Yerim Park, Minkyung Kim, Reagan Lee, Keu Eun San Kim, Sung Jae Shin, Woojun Park

“…The production of α-ketobutyrate from threonine, both in vivo and in vitro, provided strong support for the role of ThrC as a threonine deaminase. …”
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Genome-Wide Identification of the <i>DOG1</i> Gene Family in Pepper (<i>Capsicum annuum</i>) and Its Expression Profiles During Seed Germination by Zhichao Zhao, Jingbo Sun, Feng Zhang, Chunjuan Dong

“…Taken together, these findings provide an extensive description of the <i>C. annuum DOG1</i> gene family and might facilitate further studies for elucidating their functions in seed germination.…”
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Large-scale integration of meta-QTL and genome-wide association study identifies genomic regions and candidate genes for photosynthetic efficiency traits in bread wheat by Ming Chen, Tao Chen, Letong Yun, Zhuo Che, Jingfu Ma, Binxue Kong, Jiangying Long, Chunhua Cheng, Kaiqi Guo, Peipei Zhang, Lijian Guo, Delong Yang

“…Integrating wheat genetic resources provides an opportunity to discover pivotal genomic regions and candidate genes (CGs) for photosynthetic efficiency traits in wheat. …”
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Multiomic analysis of monocyte-derived alveolar macrophages in idiopathic pulmonary fibrosis by Miaomiao Zhang, Jinghao Zhang, Haisheng Hu, Yuan Zhou, ZhiWei Lin, Hui Jing, Baoqing Sun

“…While scRNAseq analysis has proven valuable in the transcriptome profiling of Mo_AMs, the integration analysis of multi-omics may provide additional dimensions of understanding of these cellular populations. …”
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m6A-lncRNA landscape highlights reduced levels of m6A modification in glioblastoma as compared to low-grade glioma by Giedrius Steponaitis, Rugile Dragunaite, Rytis Stakaitis, Amit Sharma, Arimantas Tamasauskas, Daina Skiriute

“…Conclusions Overall, we provide evidence that m6A lncRNAs are strongly modulated in gliomas, representing biologically distinct subgroups. …”
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Using transcription modules to identify expression clusters perturbed in Williams-Beuren syndrome. by Charlotte N Henrichsen, Gábor Csárdi, Marie-Thérèse Zabot, Carmela Fusco, Sven Bergmann, Giuseppe Merla, Alexandre Reymond

“…However, little is known about the global dysregulations caused by the WBS deletion. We profiled the transcriptomes of skin fibroblasts from WBS patients and compared them to matched controls. …”
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A systems biology approach to understand temporal evolution of silver nanoparticle toxicity by Seung-Geun Park, Eunseo Lee, Hyun-Yi Kim, Tae Hyun Yoon

“…Through modeling the interplay between molecular responses and cell viability, the simulations provided a predictive temporal framework for advancing nanotoxicology research, providing insights into AgNPs-induced molecular disturbances, contributing to safety assessments.…”
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Integrative proteogenomic characterization of Wilms tumor by Cheng Cheng, Li Zhang, Xiaofeng Chang, Kai Chen, Tian He, Jia Shi, Fan Lv, Lijia Pan, Yangkun Wu, Qianqian Cheng, Dong Ren, Yongli Guo, Weiping Zhang, Huanmin Wang, Tieliu Shi, Jing Li, Xin Ni, Yeming Wu, Yaqiong Jin, Zhixiang Wu

“…To elucidate the molecular landscape of WT, we perform integrative proteomic, phosphoproteomic, transcriptomic, and whole-exome sequencing analyses of WT and normal kidney tissue adjacent to tumor. …”
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The de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging by Chun Zhou, Yun Wang, Yikun Huang, Yongpan An, Xian Fu, Daqian Yang, Yilin Wang, Jintao Zhang, Leslie A. Mitchell, Joel S. Bader, Yizhi Cai, Junbiao Dai, Jef D. Boeke, Zhiming Cai, Zhengwei Xie, Yue Shen, Weiren Huang

“…Abstract In the era of synthetic biology, design, construction, and utilization of synthetic chromosomes with unique features provide a strategy to study complex cellular processes such as aging. …”
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Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper by Hongji Yang, Guorong Yu, Zhidong Lv, Tonghui Li, Xi Wang, Ying Fu, Zhangsheng Zhu, Guangjun Guo, Hang He, Ming Wang, Guochen Qin, Feng Liu, Zhenhui Zhong, Yan Xue

“…Conclusions We demonstrate that variations in the REs may contribute to more diversified and agronomically desired phenotypes. Our study provides a foundation not only for studying gene regulation, but also for targeted genetic and epigenetic manipulation for pepper improvement.…”
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Aberrant epigenome in iPSC‐derived dopaminergic neurons from Parkinson's disease patients by Rubén Fernández‐Santiago, Iria Carballo‐Carbajal, Giancarlo Castellano, Roger Torrent, Yvonne Richaud, Adriana Sánchez‐Danés, Roser Vilarrasa‐Blasi, Alex Sánchez‐Pla, José Luis Mosquera, Jordi Soriano, José López‐Barneo, Josep M Canals, Jordi Alberch, Ángel Raya, Miquel Vila, Antonella Consiglio, José I Martín‐Subero, Mario Ezquerra, Eduardo Tolosa

“…Using a patient‐specific iPSC‐based DAn model, our study provides the first evidence that epigenetic deregulation is associated with monogenic and sporadic PD.…”
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Genome-wide identification of the Medicago sativa L. MYB family and its transcriptional dynamics during pollen development by Zhenfei Yan, Yaqi Feng, Qi Yan, Pan Xu, Fan Wu, Caibin Zhang, Jiyu Zhang

“…Conclusions This study provides a comprehensive understanding of MsMYBs in alfalfa and elucidates their potential roles and expression patterns in pollen development.…”
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Cell‐Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis by Zhaoxu Gao, Yanning Su, Guanzhong Jiao, Zhiying Lou, Le Chang, Renbo Yu, Chao Xu, Xue Han, Zejia Wang, Jian Li, Xing Wang Deng, Hang He

“…To date, analyses of miRNAs‐induced transcriptome remodeling are at the whole plant or tissue levels. …”
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Sperm‐Derived CircRNA‐1572 Regulates Embryogenesis and Zygotic Genome Activation by Targeting CCNB2 via Bta‐miR‐2478‐L‐2 by Yanfang Wu, Yaochang Wei, Yuelin Li, Yiming Dou, YongQiang Yang, Hanghang Liu, Xiaoyan Wang, Zheng Wang, Jianmin Su, Yong Zhang, Yongsheng Wang

“…This study identify circRNA‐1572, a sperm‐derived circRNA deliver into oocytes during fertilization, through whole‐transcriptome sequencing of porcine metaphase II (MII) oocytes, purified mature sperm, and in vitro fertilized pronuclear (PN) embryos. …”
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Additional far-red light promotes adventitious rooting of double-root-cutting grafted watermelon seedlings by Xue Wu, Xiaoyan Zhang, Yaya Wang, Cuinan Wu, Yudong Sun, Yi Zhang, Yongran Ji, Encai Bao, Liru Xia, Zhonghua Bian, Kai Cao

“…The findings of this study demonstrated a practicable way to shorten the healing period of graftings and improve the quality of grafted watermelon seedlings, which will provide a theoretical basis for the speeding development of industrialized seedlings production.…”
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The transcription factor PbbHLH164 is destabilized by PbRAD23C/D.1 and mediates ethylene biosynthesis during pear fruit ripening by ZhiHua Guo, Hong Liu, SiQi Zheng, KaiJie Qi, ZhiHua Xie, XuePing Wang, YeMei Hong, YanBo Cui, Xiaoxiang Liu, Chao Gu, Shao-Ling Zhang

“…Herein, a new basic helix-loop-helix transcription factor, PbbHLH164, was identified based on the transcriptome analysis of different developing and ripening fruits of two pear cultivars ‘Sucui No. 1’ and ‘Cuiguan’. …”
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Development and validation of a deep learning-based pathomics signature for prognosis and chemotherapy benefits in colorectal cancer: a retrospective multicenter cohort study by Shenghan Lou, Yanming Huang, Fenqi Du, Jingmin Xue, Genshen Mo, Hao Li, Zhanjiang Yu, Yuanchun Li, Hang Wang, Yuze Huang, Haonan Xie, Wenjie Song, Xinyue Zhang, Huiying Li, Chun Lou, Peng Han, Peng Han, Peng Han

“…An interpretable multi-instance learning model was developed to construct PSCRC, with SHapley Additive exPlanations (SHAP) and gradient-weighted class activation mapping (Grad-CAM) for the improvement of model interpretability and the identification of critical histopathological features, respectively. The transcriptomic data was provided by The Cancer Genome Atlas (TCGA) and integrated to investigate the biological mechanisms underpinning PSCRC.ResultsThe results demonstrated that PSCRC was proven to be an independent prognostic indicator for both overall and disease-free survival. …”
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Single-cell sequencing in diabetic retinopathy: progress and prospects by Tianshu Yang, Ningzhi Zhang, Ning Yang

“…Single-cell RNA sequencing overcomes this limitation by providing transcriptomic data at the individual cell level and distinguishing novel cell subtypes, developmental trajectories, and intercellular communications. …”
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