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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Implication of fibroblast growth factor 7 in ovarian cancer metastases and patient survival by Laura F. Mortan, Laura F. Mortan, Brooke A. Meelheim, Justin Garland, Justin Garland, Jacqueline A. Bohn, Zitha Redempta Isingizwe, Doris M. Benbrook, Doris M. Benbrook

“…Associated cell types and pathways were explored with bioinformatics. FGF7 protein was measured using capillary-based immunoassays or ELISA in mouse and clinical specimens. …”
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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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Predictors and Outcomes of Hematoma Expansion and Neurological Decline in Intracerebral Hemorrhage: A Multisite Mobile Stroke Unit Study by Asish K. Gulati, Tianwen Ma, Isaiah Rolle, Ryan Peterson, Bianca Pirlog, Justine Chen, Megan Heckathorn, Jonathan Ratcliff, Nicolas Bianchi, Carol Fleming, Michael Frankel, James Grotta, Ritvij Bowry, Stephanie Parker, William Hicks, Digvijaya Navalkele

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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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Inflammatory bowel disease increases the risk of pancreatitis: a two-sample bidirectional Mendelian randomization analysis by Li-Hui Fang, Jia-Qi Zhang, Jin-Ke Huang, Xu-Dong Tang

“…Four independent summary statistics of pancreatitis from the the European Bioinformatics Institute (EMBL-EBI, 10,630 AP cases and 844,679 controls, 1,424 CP cases and 476,104 controls) and FinnGen Consortium (8,446 AP cases, 4,820 CP cases and 437,418 controls) were used for bidirectional MR analyses and sensitivity analysis. …”
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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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Bindarit attenuates neuroinflammation after subarachnoid hemorrhage by regulating the CCL2/CCR2/NF-κB pathway by Yanting Yao, Qiaowei Wu, Kaikun Yuan, Pei Wu, Chao Xu, Zhiyong Ji, Weishi Xu, Hongli Yu, Anyu Xu, Yanchen Liu, Huaizhang Shi

“…Methods: Pre-processed RNA-seq transcriptome datasets GSE79416 from the Gene Expression Omnibus (GEO) database were analyzed to identify genes differentially expressed between mice with SAH and control mice using bioinformatics methods. Bindarit, a CCL2 inhibitor, was administered intraperitoneally one hour after SAH. …”
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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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EIF4A3-induced circ_0022382 promotes breast cancer cell progression through the let-7a-5p/PI3K/AKT/mTOR signaling pathway and SLC7A11 axis by Wei Liu, Wei Liu, Jun Zhang, Jiawen Zhang, Yu Ye, Jianqin Zhu, Qiwen Yu, Tao Li, Tao Li, Xiaochun Sun, Huabiao Chen, Huabiao Chen

“…In this study, we explored the impacts of circRNAs on the progression of breast cancer cells.MethodsUsing bioinformatics analysis, we screened out one up-regulated circRNA in breast cancer, and its function and regulatory mechanisms were confirmed by quantitative real-time PCR, cell counting kit-8 experiment, migration assay, dual luciferase reporter assay, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, cell immunofluorescence, clone formation assay, scratch wound healing experiment, RNA immunoprecipitation and subcutaneous tumor-bearing experiments.ResultsCirc_0022382 was highly expressed in breast cancer cell lines MDA-MB-231, MCF-7 as well as breast cancer tissues, and promoted the proliferative and migratory capacity of breast cancer cells. …”
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Phylogenetic inferences reveal multiple intra- and interhost genetic diversity among bat rabies viruses circulating in northeastern Brazil by Larissa Leão F. de Sousa, Mariana Dias Guilardi, Junior Olimpio Martins, Bruna Stefanie S. Alves, Luiz Henrique S. Tibo, Patrícia da Silva-Antunes, Gustavo Cabral-Miranda, Débora Bellini Caldeira, Paulo Eduardo Brandão, Fabrício Souza Campos, Luiz Mário R. Janini, Ricardo Durães-Carvalho

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Relationship between CTF1 gene expression and prognosis and tumor immune microenvironment in glioma by Hongqing Cai, Shen Tian, Angsi Liu, Guanchao Xie, Hongsheng Zhang, Xiaogang Wu, Jinghai Wan, Sai Li

“…Methods We initially assessed the expression of CTF1, a member of the IL-6 family, in glioma, using bioinformatics tools and publicly available databases. …”
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Overexpression of miR-21-5p as a potential pathogenesis marker for ovarian endometriosis by Mohamed Mahmoud, Amr Ahmed WalyEldeen, Mohamed A. Samie, Ahmed M. Sadek, Sayed Elakhras, Mohamed Samir, Osama Ahmed, Rasha Mohamed Samir Sayed, Ahmed Abdelaziz Baiomy, Sherif Abdelaziz Ibrahim, Hebatallah Hassan

“…A significant overexpression of miR-21-5p in ovarian endometrioma was further independently verified by qPCR. Using bioinformatics tools, Gene Ontology Kyoto Encyclopedia of Genes and Genomes pathways, and protein–protein interactions, we identified differentially expressed genes and several pathways regulated by miR-21-5p that may contribute to endometriosis progression. …”
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