Study on the Correlation between Interleukin-27 and CXCL10 in Pulmonary Tuberculosis by Jiahui Fan, Yefeng Yang, Liang Wang, Xiaoqian Shang, Li Zhang, Hu Sun, Yujie Ma, Ying Li, Jing Wang, Xiumin Ma

“…To investigate the correlation between interleukin-27 and CXCL10 and other cytokines in pulmonary tuberculosis and to further explore the related miRNAs through bioinformatics. Methods. Collect the lesion tissue and peripheral blood of pulmonary tuberculosis patients and the peripheral blood of healthy controls. …”
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Frugivore Traits Predict Plant–Frugivore Interactions Using Generalized Joint Attribute Modeling by Laurel R. Yohe, Leith B. Leiser‐Miller, Zofia A. Kaliszewska, Susan R. Whitehead, Sharlene E. Santana, Liliana M. Dávalos

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Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy by Lanlan Tang, Wei Zhang, Yang Zhang, Wenjun Deng, Mingyi Zhao

“…We conducted a meticulous bioinformatics analysis leveraging expression data of 226 PANRGs obtained from previous studies, as well as clinical data from AML patients derived from the HOVON database. …”
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Cell Differentiation Trajectory Predicts Prognosis and Immunotherapeutic Response in Clear Cell Renal Cell Carcinoma by Jin Xu, Xi Chen, Yinyu Chen, Qiushuang Wang, Yingliang Jin, Huashuo Zhao

“…In this study, we explored the differentiation status of ccRCC cells and its significance in prognosis and immunotherapeutic response through bioinformatics. We characterized distinct differentiation states and differentiation-related genes (DRGs) in ccRCC cells through single cell RNA sequencing (scRNA-seq) analysis. …”
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GNG2 inhibits brain metastases from colorectal cancer via PI3K/AKT/mTOR signaling pathway by Chenhua Luo, ZhiMing Xiao, WenLong Yang

“…This study identifies GNG2 as a key regulator in metastatic colorectal cancer (mCRC) through bioinformatics analysis and experimental validation. Functional enrichment analyses reveal that GNG2 is related to the PI3K/AKT/mTOR signaling pathway and cell cycle regulation. …”
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Fenofibrate Exerts Antitumor Effects in Colon Cancer via Regulation of DNMT1 and CDKN2A by Rui Kong, Nan Wang, Wei Han, Wen Bao, Jie Lu

“…Recently, the potential role of PPARA in other pathological conditions, such as cancers, has been recognized. Here, using bioinformatics analysis, we found that PPARA was expressed at relatively low levels in pancancers, and Kaplan-Meier analyses revealed that high PPARA protein expression was correlated with better survival of patients with colon cancer. …”
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Immunoinformatic Analysis of Calcium-Dependent Protein Kinase 7 (CDPK7) Showed Potential Targets for Toxoplasma gondii Vaccine by Ali Taghipour, Sanaz Tavakoli, Mohamad Sabaghan, Masoud Foroutan, Hamidreza Majidiani, Shahrzad Soltani, Milad Badri, Ali Dalir Ghaffari, Sheyda Soltani

“…Apicomplexan parasites, including Toxoplasma gondii (T. gondii), express different types of calcium-dependent protein kinases (CDPKs), which perform a variety of functions, including attacking and exiting the host cells. In the current bioinformatics study, we have used several web servers to predict the basic features and specifications of the CDPK7 protein. …”
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Bio-primed machine learning to enhance discovery of relevant biomarkers by David M. Henke, Alexander Renwick, Joseph R. Zoeller, Jitendra K. Meena, Nicholas J. Neill, Elizabeth A. Bowling, Kristen L. Meerbrey, Thomas F. Westbrook, Lukas M. Simon

“…Traditional statistical methods often fall short in this context, necessitating novel computational approaches that harness the full potential of big data in bioinformatics. Here, we introduce a novel machine learning approach extending the Least Absolute Shrinkage and Selection Operator (LASSO) regression framework to incorporate biological knowledge, such as protein-protein interaction databases, into the regularization process. …”
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A Hybrid Approach for Modular Neural Network Design Using Intercriteria Analysis and Intuitionistic Fuzzy Logic by Sotir Sotirov, Evdokia Sotirova, Vassia Atanassova, Krassimir Atanassov, Oscar Castillo, Patricia Melin, Todor Petkov, Stanimir Surchev

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On the current and future potential of simulations based on directed acyclic graphs by Lutz P. Breitling, Anca D. Dragomir, Chongyang Duan, George Luta

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Novel transcripts of EMT driving the malignant transformation of oral submucous fibrosis by Smitha Sammith Shetty, Kanaka Sai Ram Padam, Mohit Sharma, Adarsh Kudva, Pratik Patel, Raghu Radhakrishnan

“…The curated EMT genes were correlated with functional cancer states and subjected to clustering to identify candidate genes. Integration of bioinformatics and proteomics led to the discovery of the EMT genes MMP9, SPARC, and ITGA5 as novel candidates. …”
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Genomic Variability among Field Isolates and Laboratory-Adapted Strains of Leptospira borgpetersenii Serovar Hardjo by Alejandro Llanes, Carlos Mario Restrepo, Pablo Riesgo-Ferreiro, Sreekumari Rajeev

“…In addition, the bioinformatics methodology used in this study for variant calling can be useful to other groups working with nonmodel prokaryotic organisms such as Leptospira species.…”
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HAVCR1 Affects the MEK/ERK Pathway in Gastric Adenocarcinomas and Influences Tumor Progression and Patient Outcome by Ji Xue, Ying Li, Jianfeng Yi, Hong Jiang

“…We first determined the expression of HAVCR1 in GAC tissues compared with normal gastric tissues based on the Cancer Genome Atlas (TCGA) database using bioinformatics analysis methods. Then, we assessed the biological function of HAVCR1 in GAC cells using quantitative real-time reverse transcription-PCR (qRT-PCR), western blot, cell counting kit-8- (CCK-) 8, colony formation assay, wound healing assay, and transwell assay. …”
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lncRNA PAPPA-AS1 Induces the Development of Hypertrophic Scar by Upregulating TLR4 through Interacting with TAF15 by Pengju Fan, Yongjie Wang, Jingjing Li, Man Fang

“…In the present study, the regulatory effect of lncRNA PAPPA-AS1 on the Toll-like receptor 4 (TLR4) signal pathway, as well as the molecular mechanism, was investigated. Bioinformatics analysis was utilized to screen the differentially expressed lncRNAs in HTS tissues. …”
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Clustering Pattern and Functional Effect of SNPs in Human miRNA Seed Regions by Sha He, Haiyan Ou, Cunyou Zhao, Jian Zhang

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Advances in antiviral strategies targeting mosquito-borne viruses: cellular, viral, and immune-related approaches by Ayyaz Khan, Zakirullah, Shahid Wahab, Seong-Tshool Hong

“…Additionally, it explores immunomodulatory therapies to enhance antiviral responses and emphasizes the potential of drug repurposing, bioinformatics, artificial intelligence, and deep learning in identifying novel antiviral candidates. …”
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The Potential Diagnostic Value of Immune-Related Genes in Interstitial Fibrosis and Tubular Atrophy after Kidney Transplantation by Bin Yang, Dike Shi, Yahong Chen, Yi Zhu

“…The aim of this study was to reveal new diagnostic markers of IF/TA based on bioinformatics analysis. Methods. Raw data of IF/TA samples after kidney transplantation and control samples after kidney transplantation were extracted from the Gene Expression Omnibus (GEO) database (GSE76882 and GSE120495 datasets), and genes that were differentially expressed between the two groups (DEGs) were screened. …”
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Transcription Factor FXR Activates DHRS9 to Inhibit the Cell Oxidative Phosphorylation and Suppress Colon Cancer Progression by Jinlai Zhao, Yigang Wang, Yang Wang, Jianchao Gao, Haichao Yang, Xiaotang Wu, Hua Li

“…The downstream target gene of FXR was predicted by bioinformatics analysis and found to be associated with cellular oxidative phosphorylation. …”
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A pan-cancer analysis of MARCH8: molecular characteristics, clinical relevance, and immuno-oncology features by Zihan Quan, Songqing Fan, Hongmei Zheng, Yue Ning, Yang Yang

“…We investigated the role of MARCH8 expression in clinical relevance, prognosis, tumor immune microenvironment, immune checkpoint (ICP) with a series of bioinformatics tools and methods, such as TISIDB database, ESTIMATE, and CIBERSORT method. …”
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Upregulation of PGC-1α Attenuates Oxygen-Glucose Deprivation-Induced Hippocampal Neuronal Injury by Bin Han, Hui Zhao, Xingji Gong, Jinping Sun, Song Chi, Tao Liu, Anmu Xie

“…Our results showed that mitochondrial membrane potentials were increased and ROS production was decreased in PGC-1α overexpressing cells, which increased cell viability. The further bioinformatics analysis from ChIP-Seq data indicated that PGC-1α may participate in the regulation of apoptosis, autophagy, and mitophagy pathways in HT-22 cells. …”
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