Identification and expression analysis of the ZF-HD gene family in castor by XU Xingyuan, HUANG Fenglan, ZHANG Chunlan, ZHU Mengyang, CUI Zhiyu, LIU Peng

“…[Methods] Based on the whole genome data of castor, ZF-HD genes were identified, and bioinformatics and expression analysis under abiotic stress were carried out. …”
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Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in color... by Xiaoyu Qin, Wenjuan Xu, Jinxiu Wu, Ming Li

“…We integrated scRNA-seq data from four Gene Expression Omnibus (GEO) samples and performed Weighted gene correlation network analysis (WGCNA) based on 587 the Cancer Genome Atlas (TCGA) colorectal cancer samples to uncover NK cell-related genes. …”
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Intercellular communication is crucial in the regulation of healthy aging via exosomes by Huifang Sun, Tengyuan Xia, Shuting Ma, Tao Lv, Yuhong Li

“…The hallmarks of aging encompass a variety of molecular categories (genomic, telomeric, and epigenetic), organelles (proteostasis, autophagy, and mitochondria), cellular components (including stem cells), systems (such as intercellular communication and chronic inflammation), and environmental factors (dysbiosis and nutrient sensing). …”
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A cross-tissue transcriptome-wide association study identified susceptibility genes for age-related macular degeneration by Hongfan Yang, Haofei Huang, Kunlin Pu

“…Multi-marker Analysis of Genomic Annotation (MAGMA) was employed to validate results and identify reliable susceptibility genes, followed by summary data-based Mendelian randomization (SMR) and colocalization analyses to explore causal associations. …”
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Subgenome asymmetry of gibberellins-related genes plays important roles in regulating rapid growth of bamboos by Ling Mao, Cen Guo, Liang-Zhong Niu, Yu-Jiao Wang, Guihua Jin, Yi-Zhou Yang, Ke-Cheng Qian, Yang Yang, Xuemei Zhang, Peng-Fei Ma, De-Zhu Li, Zhen-Hua Guo

“…However, the genetic basis and evolution of this trait are poorly understood. Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels, we integrated morphological, physiological, and transcriptomic datasets to investigate rapid growth. …”
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Unlocking precision medicine: clinical applications of integrating health records, genetics, and immunology through artificial intelligence by Yi-Ming Chen, Tzu-Hung Hsiao, Ching-Heng Lin, Yang C. Fann

“…Machine learning models excel at identifying high-risk patients, predicting disease activity, and optimizing therapeutic strategies based on clinical, genomic, and immunological profiles. Deep learning techniques have significantly advanced variant calling, pathogenicity prediction, splicing analysis, and MHC-peptide binding predictions in genetics. …”
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Development of animal models to study aggressive thyroid cancers by Shovan Dutta, Jeffrey A Knauf

“…Recent studies exploring the genomic landscape of advanced thyroid cancer have identified several cooperating mutations, which are secondary genetic alterations that work alongside driver mutations to promote thyroid tumor progression. …”
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SARS-CoV-2 Remained Airborne for a Prolonged Time in a Lockdown Confined Space by Xinyue Li, Xiao Qi, Jianxin Ma, Yang Pan, Tian Tian, Yue Zhang, Zhen Li, Wenjing Li, Lingli Sun, Lu Zhang, Zheng Zhang, Quanyi Wang, Maosheng Yao

“…The traveler did not have any contacts with the two employees; however, genome sequencing showed that SARS-CoV-2 variants from three patients and two environmental surface samples belonged to 20B viral clade, sharing a nucleic acid identity of more than 99.9%. …”
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Tumor-initiating and metastasis-initiating cells of clear-cell renal cell carcinoma by Dinh-Xuan Pham, Tien Hsu

“…A majority of ccRCC is characterized by the loss of the von Hippel-Lindau (VHL) tumor suppressor gene function. Recent advances in genome analyses of ccRCC indicate that in ccRCC, tumor-initiating cells (TICs) and metastasis-initiating cells (MICs) are two distinct groups of progenitors. …”
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Manipulation of seed coat content for increasing oil content via modulating BnaMYB52 in Brassica napus by Jiang Ye, Xiaowei Wu, Xiang Li, Yuting Zhang, Yuqing Li, Hui Zhang, Jie Chen, Yuyan Xiang, Yefan Xia, Hu Zhao, Zengdong Tan, Liang Guo, Xuan Yao

“…However, the genetic and molecular mechanisms of how seed coat development affects seed oil content (SOC) remains less studied. Through genome-wide association studies in Brassica napus accessions, we identify BnaA09.MYB52 transcription factor as a candidate gene underlying ZS11_qSCC.A09. …”
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Isolation and characterization of a highly pathogenic strain of Vibrio harveyi EFL-2201 from pearl gentian grouper by Biao Yuan, Zhixia Zhuang, Xiaoru Wang, Huabin Huang, Qingpi Yan

“…In vitro assays indicated that the conditions during the outbreak were conducive to the proliferation, motility, biofilm formation, and chemotaxis of EFL-2201. Whole-genome sequencing of the strain revealed that mechanisms related to adhesion, secretion, toxins, and invasion significantly contributed to its pathogenicity. …”
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Insights into the molecular mechanisms and nanoparticle-based therapies for gastric cancer: A review by Smarika Chauhan, Eswar Marcharla, Sneha Hariharan, Saranya Vinayagam, Thanigaivel Sundaram, Priya SD, Swamynathan Ganesan, Maximilian Lackner

“…This review aims to explore the role of nanoparticles in the prognosis and diagnosis of gastric cancer. We have analysed genomic pathways linked with gastric carcinoma and explored the utilisation of nanoparticles for multimodal imaging techniques, precise drug delivery and efficient therapeutic approaches. …”
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Expression of cell-wall related genes is highly variable and correlates with sepal morphology by Hartasánchez, Diego A., Kiss, Annamaria, Battu, Virginie, Soraru, Charline, Delgado-Vaquera, Abigail, Massinon, Florian, Brasó-Vives, Marina, Mollier, Corentin, Martin-Magniette, Marie-Laure, Boudaoud, Arezki, Monéger, Françoise

“…We produced a dataset composed of morphological parameters and genome-wide transcriptome obtained from 27 individual sepals from wild-type plants with nearly identical genetic backgrounds, environment, and developmental stage. …”
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Beyond the Comfort Zone: Strenuous Sports as a Preventive Tactic Against Benign Prostatic Hyperplasia by Wei Zhang, Gang Li, Chengya Hao, Aijun Cheng

“…The study utilizes single nucleotide polymorphisms (SNPs) associated with strenuous sports obtained from published genome-wide association studies (GWAS), alongside summarized genetic data related to benign prostatic hyperplasia (BPH) from published GWAS. …”
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The genetic architecture of local adaptation in a cline by Laroche, Fabien, Lenormand, Thomas

“…It has been repeatedly proposed that the localization of these genes in the genome may not be random, but could be an evolved feature. …”
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Unlocking biological complexity: the role of machine learning in integrative multi-omics by Ravindra Kumar, Rajrani Ruhel, Andre J. van Wijnen

“…Integrative multi-omics approaches use multi-layered datasets such as genomic, transcriptomic, proteomic, and metabolomic data to understand biological processes much more comprehensively compared to the single-omics analysis and to provide a comprehensive view of cellular and molecular processes. …”
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A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolution by Shizhou Yu, Jufen Wan, Jufen Wan, Tenghang Xu, Tenghang Xu, Jie Zhang, Linggai Cao, Jie Liu, Hongfeng Liu, Xueliang Ren, Zhixiao Yang

“…In this study, we collected 599 tobacco RNA-seq datasets from 35 projects. 207,689 transcripts were identified in this study, of which 35,519 were annotated in the reference genome, while 172,170 transcripts were newly annotated. …”
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Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans. by Tammie Bishop, Kah Weng Lau, Andrew C R Epstein, Stuart K Kim, Min Jiang, Delia O'Rourke, Christopher W Pugh, Jonathan M Gleadle, Martin S Taylor, Jonathan Hodgkin, Peter J Ratcliffe

“…However, persisting differential gene expression in hif-1 versus hif-1; vhl-1 double mutant worms clearly distinguished HIF-1-independent effects of VHL-1 inactivation. Genomic clustering, predicted functional similarities, and a common pattern of dysregulation in both vhl-1 worms and a set of mutants (dpy-18, let-268, gon-1, mig-17, and unc-6), with different defects in extracellular matrix formation, suggest that dysregulation of these genes reflects a discrete HIF-1-independent function of VHL-1 that is connected with extracellular matrix function.…”
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Replication-IDentifier links epigenetic and metabolic pathways to the replication stress response by Sophie C. van der Horst, Leonie Kollenstart, Amandine Batté, Sander Keizer, Kees Vreeken, Praveen Pandey, Andrei Chabes, Haico van Attikum

“…Here, we develop Replication-IDentifier (Repli-ID), which allows for genome-wide identification of regulators of DNA replication in Saccharomyces cerevisiae. …”
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The autophagy component LC3 regulates lymphocyte adhesion via LFA1 transport in response to outside-in signaling by Naoyuki Kondo, Yuko Mimori-Kiyosue, Keizo Tokuhiro, Giuseppe Pezzotti, Tatsuo Kinashi

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