A Case Study Identified a New Mutation in the TTN Gene for Inherited Hypertrophic Cardiomyopathy by Dong J, Liu M, Chen Q, Zha L

“…Candidate variants obtained by WES were verified using Sanger sequencing, pathogenic mutation screening was conducted among family members, and the mutations were systematically analyzed using bioinformatics.Results: WES revealed a novel heterozygous missense mutation, c.20233 C>T (p.R6745C), located in exon 80 of the HCM-related gene TTN, which may be a pathogenic mutation in the family. …”
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Ddx21 mutant peptide is an effective neoantigen in prophylactic lung cancer vaccines and activates long-term anti-tumor immunity by Zhe Zhang, Yimeng Xia, Yimeng Xia, Zhihong Wang, Yaxing Sun, Dan Pu, Yijia He, Ruixian Liu, Yanru Zhang, Yan Liu, Junzhi Yu, Shiyang Ning, Baisui Feng, Yaohe Wang, Na Wang

“…MethodsTo investigate the fundamental reason for the difference between KPL 160302S and KPL 160424S vaccines, we employed bioinformatics methods and immune related experiments to explore the effects and mechanisms of the screened neoantigens. …”
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Integrative genomic analyses combined with molecular dynamics simulations reveal the impact of deleterious mutations of Bcl-2 gene on the apoptotic machinery and implications in ca... by Ghazi Elamin, Ghazi Elamin, Zhichao Zhang, Depika Dwarka, Kabange Kasumbwe, John Mellem, Nompumelelo P. Mkhwanazi, Paradise Madlala, Paradise Madlala, Mahmoud E. S. Soliman

“…Therefore, this study explores the association between SNPs in Bcl-2 and the structural, functional, protein-protein interactions (PPIs), drug binding and dynamic characteristics.MethodsComprehensive cross-validated bioinformatics tools and molecular dynamics (MD) simulations. …”
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Single-Cell RNA Sequencing Reveals LEF1-Driven Wnt Pathway Activation as a Shared Oncogenic Program in Hepatoblastoma and Medulloblastoma by Christophe Desterke, Yuanji Fu, Jenny Bonifacio-Mundaca, Claudia Monge, Pascal Pineau, Jorge Mata-Garrido, Raquel Francés

“…Both tumor types can exhibit genetic alterations that affect the β-catenin and Wnt pathways; (2) Materials and Methods: This study used bioinformatics and integrative analysis of multi-omics data at both the tumor and single-cell levels to investigate two distinct pediatric tumors: medulloblastoma and hepatoblastoma; (3) Results: The cross-transcriptome analysis revealed a commonly regulated expression signature between hepatoblastoma and medulloblastoma tumors. …”
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Diagnostic Value of Glycosylated Extracellular Vesicle microRNAs in Gastric Cancer by Wang S, Ma C, Ren Z, Zhang Y, Hao K, Liu C, Xu L, He S, Zhang J

“…The signatures were screened in a discovery cohort of GC patients (n=55) and non-disease controls (n=46) using an integrated process, including high-throughput sequencing technology, screening using a complete bioinformatics algorithm, validation using RT-qPCR, and evaluation by constructing a diagnostic model. …”
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FadA antigen of Fusobacterium nucleatum: implications for ceRNA network in colorectal cancer and adenomatous polyps progression by Sama Rezasoltani, Elahe Shams, Moein Piroozkhah, Yaser Aidi, Mehdi Azizmohammad Looha, Parmida Bagheri, Roudabeh Behzadi Andouhjerdi, Amir Sadeghi, Leili Rejali, Ehsan Nazemalhosseini-Mojarad

“…According to our previous study to identify shared MicroRNA-Interaction-Targets (MITs) between ANXA2 and LINC00460, TargetScanHuman (V7.2) and miRDB databases have been used respectively. The Bioinformatics and Evolutionary Genomics web tool was employed to intersect the sets of shared microRNAs and their common targets. …”
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Exosome-mediated delivery of miR-9 induces cancer-associated fibroblast-like properties in human breast fibroblasts by Sara Baroni, S Romero-Cordoba, I Plantamura, M Dugo, E D’Ippolito, A Cataldo, G Cosentino, V Angeloni, A Rossini, M G Daidone, M V Iorio

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The necroptosis-related lncRNA ENSG00000253385.1 promotes the progression of esophageal squamous cell carcinoma by targeting the miR-16-2-3p/VDAC1 axis by Xiaoyang Duan, Jian Shi, Ran Hou, Yajie Huang, Chunyan Wang, Huazhen Du

“…The binding sites between miR-16-2-3p and lncRNA ENSG00000253385.1 or voltage-dependent anion channel 1 (VDAC1) were predicted by bioinformatics database and confirmed by dual luciferase reporter gene assay. …”
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Advances and Challenges in Antiviral Development for Respiratory Viruses by Luis Adrián De Jesús-González, Moisés León-Juárez, Flor Itzel Lira-Hernández, Bruno Rivas-Santiago, Manuel Adrián Velázquez-Cervantes, Iridiana Monserrat Méndez-Delgado, Daniela Itzel Macías-Guerrero, Jonathan Hernández-Castillo, Ximena Hernández-Rodríguez, Daniela Nahomi Calderón-Sandate, Willy Salvador Mata-Martínez, José Manuel Reyes-Ruíz, Juan Fidel Osuna-Ramos, Ana Cristina García-Herrera

“…In addition, innovative approaches such as inhibiting host cellular proteins to reduce viral resistance and repurposing existing drugs are explored, using advanced bioinformatics tools that optimize the identification of antiviral candidates. …”
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First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale by Ivan Tsers, Ekaterina Marenina, Azat Meshcherov, Olga Petrova, Olga Gogoleva, Alexander Tkachenko, Natalia Gogoleva, Yuri Gogolev, Evgenii Potapenko, Olga Muraeva, Mira Ponomareva, Viktor Korzun, Vladimir Gorshkov

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CtBP1 is essential for epigenetic silencing of μ-opioid receptor genes in the dorsal root ganglion in spinal nerve ligation-induced neuropathic pain by Cheng-Yuan Lai, Ming-Chun Hsieh, Chou-Ming Yeh, Tzer-Bin Lin, Dylan Chou, Hsueh-Hsiao Wang, Kuan-Hung Lin, Jen-Kun Cheng, Po-Sheng Yang, Hsien-Yu Peng

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GPR137-RAB8A activation promotes ovarian cancer development via the Hedgehog pathway by Chao Tang, Lin Li, Chongying Zhu, Qiang Xu, Zihao An, Shouying Xu, Chao Lin

“…Methods Human ovarian tissue specimens, RNA sequencing, GEPIA database and bioinformatics analyses were used to analyze the gene correlation, and to identify and validate potential downstream candidates. …”
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Insights Into Causal Effects of Genetically Proxied Lipids and Lipid‐Modifying Drug Targets on Cardiometabolic Diseases by Liwan Fu, Qin Liu, Hong Cheng, Xiaoyuan Zhao, Jingfan Xiong, Jie Mi

“…Comprehensive analyses including colocalization, mediation, and bioinformatics were conducted to validate the results and investigate potential mediators and mechanisms. …”
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miRNA-541-5p regulates myocardial ischemia–reperfusion injury by targeting ferroptosis by ZhiYu Zhao, BoXia Li, DianWei Cheng, YuFang Leng

“…In addition, ADAM 7, FNIP 2, HOXD 10, HCCS and STK 3 were preliminarily identified as potential candidate target genes for miRNA-541-5p by bioinformatics analysis. Among them, ADAM7 emerges as the most suitable potential target gene based on the selection criteria. …”
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Expression and delivery of HA1-M2e antigen using an innovative attenuated Salmonella–mediated delivery system confers promising protection against H9N2 avian influenza challenge by Ram Prasad Aganja, In-Shik Kim, Hyun-Jin Tae, John Hwa Lee

“…It demonstrated a safety profile with lower induction of inflammatory cytokines than the wild-type strain. Bioinformatics tools predicted that the HA1 and M2e sequences, which were designed as consensus sequences of South Korean strains (2000–2021), would have high antigenicity and favorable structures. …”
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circICMT upregulates and suppresses the malignant behavior of bladder cancer by Xin Luo, FangMei Xie, Guoqiang Qin, Ge Zou, Xu Lu, Chaofeng Zhang, Zeping Han, Ying Zhao, Xiaoyu Song, WenFeng Luo, Yongsheng Li, JinHua He, Jian Shen

“…Overexpression of circICMT can inhibit cell migration, proliferation and colony formation ability, while knockdown of circICMT promotes the malignant phenotype of bladder cancer cells. Bioinformatics predictions have found that circICMT can bind to a variety of miRNAs and RBPs and may form a complex regulatory network to regulate the progression of bladder cancer. …”
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Discovery of anti-Ebola virus multi-target inhibitors from traditional Chinese medicine database using molecular screening, biophysical investigation, and binding free energy calcu... by Abbas Khan, Abrar Mohammad Sayaf, Anwar Mohammad, Fahad M. Alshabrmi, Tarek Benameur, Dong-Qing Wei, Kar Kheng Yeoh, Abdelali Agouni

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Revealing the role of natural killer cells in ankylosing spondylitis: identifying diagnostic biomarkers and therapeutic targets by Yuling Chen, Yan Li, Yuan Xu, Qing Lv, Yuanchun Ye, Jieruo Gu

“…This study integrated bioinformatics methods with experimental validation to explore the role of natural killer (NK) cells in AS.Methods Two microarray datasets, GSE25101 and GSE73754, were selected, and the scRNA-seq data were obtained from GSE194315 and Liu’s research. …”
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Exploring the Mechanism of Skeletal Muscle in a Tacrolimus-Induced Posttransplantation Diabetes Mellitus Model on Gene Expression Profiles by Chenlei Zheng, Cheng Wang, Tan Zhang, Ding Li, Xiao-feng Ni, Jian-Hu Lin, Linxiao Sun, Bicheng Chen

“…This study explored the molecular mechanism of muscle atrophy in a tacrolimus-induced PTDM model by bioinformatics analyses. We identified 275 DEGs and identified significant biomarkers for predicting the development and progression of tacrolimus-induced PTDM.…”
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Detection and characterization of bovine hepacivirus in cattle and sheep from Hulunbuir, northeastern China by Jingge Ma, Jingge Ma, Zhiwei Wei, Liang Li, Wei Wang, Ziyan Liu, Ziyan Liu, Ning Liu, Feng Wei, Xiangyu Zheng, Zedong Wang

“…BovHepV-positive samples were confirmed using semi-nested PCR with primers designed based on the obtained viral sequences. Comprehensive bioinformatics analyses were employed to assess sequence similarity, phylogenetic evolution, and recombination of the obtained viral strains.ResultsA total of 988 serum samples from sheep (520) and cattle (468) were collected from 12 administrative districts in Hulunbuir from June to August, 2022. …”
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