WNT3A promotes the cementogenic differentiation of dental pulp stem cells through the FOXO1 signaling pathway by Dongmei Cheng, Yang Bao, Xue Wang, Haidong Xiang, Tianyuan Guo, Yong Du, Zhiyong Zhang, Han Guo

“…Results Differentially expressed genes (DEGs) associated with DPSC cementogenic differentiation were predominantly enriched in crucial pathways such as the signaling pathway, cell apoptosis, and Wnt signaling pathway. Bioinformatics analysis confirmed WNT3A as a pivotal biomarker for DPSC cementogenic differentiation, and WNT3A was highly expressed in the cementogenic differentiation group. …”
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Deciphering the multifaceted mechanism of Shuang Huang Lian in treating upper respiratory tract infections: A metabolomics-based network pharmacology approach by Gang Xu, Akshay Suresh Patil, Ruhan Wei, Dan Liu, Aimin Zhou, Yan Xu

“…Key cheminformatics and bioinformatics platforms and databases, including ADMETlab, SEA, PASS, Super-Pred, SwissTargetPrediction, PharmMapper, and GeneCards, were used to predict the drug-like properties of active SHL components and identify protein targets shared between the active SHL components and the URTI-related disease genes. …”
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Single-cell transcriptomes of dissecting the intra-tumoral heterogeneity of breast cancer microenvironment by Peixian Chen, Kaifeng Liang, Xiaofan Mao, Qiuyuan Wu, Zhiyan Chen, Yabin Jin, Kairong Lin, Tiancheng He, Shuqing Yang, Huiqi Huang, Guolin Ye, Juntao Gao, Dan Zhou, Zhihao Zeng

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Identification of prognostic biomarker of non-small cell lung cancer based on mitochondrial permeability transition-driven necrosis-related genes and determination of anti-tumor ef... by Zhifei Ma, Wen Chen, Aiping Zhang, Xiaokang Shen, Lin Zheng

“…RT-qPCR confirmed that expression levels of three genes in tissues or cells were consistent with the results of bioinformatics analysis. Finally, ARL14 knockdown inhibited the malignant phenotype of NSCLC cells. …”
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Embracing Generative Artificial Intelligence in Clinical Research and Beyond by Henry P. Foote, MD, Chuan Hong, PhD, Mohd Anwar, PhD, Maria Borentain, MD, Kevin Bugin, PhD, Nancy Dreyer, PhD, MPH, Josh Fessel, MD, PhD, Nitender Goyal, MD, Morgan Hanger, MPP, Adrian F. Hernandez, MD, Christoph P. Hornik, MD, PhD, MPH, Jennifer G. Jackman, PhD, MBA, Alistair C. Lindsay, MD, MPH, DPhil, Michael E. Matheny, MD, Kerem Ozer, MD, Jan Seidel, PhD, Norman Stockbridge, MD, PhD, Peter J. Embi, MD, Christopher J. Lindsell, PhD

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Observational research in epidemic settings: a roadmap to reform by Marc Lipsitch, Nicholas Evans, Alexandra L Phelan, Stephany N Duda, Annette Rid, Colin J Carlson, Jennifer B Rosen, Natalie E Dean, John Barugahare, Maya B Mathur, Emily E Ricotta, Fausto A Bustos Carrillo, Samuel Angelli-Nichols, Adia Benton, Emma Chang-Rabley, Lisa Federer, Mary-Margaret A Fill, Elizabeth C LeRoy, Natalie M Linton, Lauren Sauer, Sheena G Sullivan, Mackenzie Zendt

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RETRACTED ARTICLE: NR3C2 affects the proliferation and invasiveness of colon cancer cells through the Wnt/β-Catenin signaling pathway by Ke Nie, Zhong-Jiang He, Ling-Jun Kong

“…The relative role of NR3C2 were further predicted through bioinformatics methods and receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value of NR3C2 in colon cancer. …”
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Comprehensive analysis of α2,3-sialyltransferases as prognostic biomarkers and immunotherapy targets in kidney renal clear cell carcinoma by Yuli Jian, Kangkang Yang, Jinjing Li, Ling Tang, Guang Zeng, Xiaoxin Sun, Xiao Yu, Abdullah Al-danakh, Qiwei Chen, Deyong Yang, Shujing Wang

“…In the study, through systematic bioinformatics analysis and experimental verification, we demonstrated that ST3Gal5 expression was elevated in tumor tissues of KIRC patients, correlating with poor prognosis, and ST3Gal1 was downregulated and associated with a better prognosis. …”
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Integrated analyses uncover new features of atypical memory B cells and novel targets for intervention by Fuli Fan, Shubei Liu, Bin Wang, Xiaojian Song, Wei Wang

“…Functional characterization of AMB was performed with bioinformatics and CyTOF-based phenotyping. Alternation of AMB in systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and Sjögren's syndrome (SjS) was evaluated via bioinformatic approaches. …”
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Identification of HOXA9 methylation as an epigenetic biomarker predicting prognosis and guiding treatment choice in acute myeloid leukemia by Fei Xie, Ting-juan Zhang, Xin-long Zhang, Zi-jun Xu, Liang Qiao, Yun Wang, Yang-jing Zhao, Jun Qian, Jing-dong Zhou

“…Importantly, AML patients with HOXA9 hypomethylation may profit from transplantation, whereas AML patients with HOXA9 hypermethylation could not, suggesting that HOXA9 methylation may be used to guide therapeutic selection between transplantation and chemotherapy. Bioinformatics analysis demonstrated the association of HOXA9 expression with diverse leukemia-related genes (HOXAs, SOSTDC1, MEG3, miR-10a, miR-381 and miR-193b) and signaling pathways (PI3K-Akt signaling) in AML. …”
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In silico evaluation of missense SNPs in cancer-associated Cystatin A protein and their potential to disrupt Cathepsin B interaction by Shafaat Hossain, Omar Hamza Bin Manjur, Mst Sharmin Sultana Shimu, Tamanna Sultana, Mustafizur Rahman Naim, Shahariar Siddique, Abdullah Al Mamun, Md Miftaur Rahman, Md Abu Saleh, Md Rakibul Hasan, Tania Rahman

“…In this study, eight bioinformatics tools (SIFT, PolyPhen-2, PROVEAN, P-Mut, MutPred2, SNAP2, SNPs & GO, and PHD-SNP) were implemented to analyze non-synonymous SNPs from the dbSNP database. …”
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Identifying the Latitude and Longitude of ATMs in ATM Networks by Niloofar Haghjoo, Mohammad rahmati, Ali Zare Mirakabad

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MUC5B modulation of early oral biofilm glucose metabolism by Carolina Robertsson, Carolina Robertsson, Julia Davies, Gunnel Svensäter, Anders Bay Nord, Niclas Norrström, Claes Wickström

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The dual anti-inflammatory and anticoagulant effects of Jianpi Huashi Tongluo prescription on Rheumatoid Arthritis through inhibiting the activation of the PI3K/AKT signaling pathw... by Fanfan Wang, Fanfan Wang, Jian Liu

“…Secondly, an adjuvant-induced arthritis rat model was established to directly observe the anti-inflammatory and anticoagulant effects of XFC in vivo. Furthermore, bioinformatics and network pharmacology techniques were applied to decipher the major active components and their targets of XFC. …”
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RETRACTED ARTICLE: A prospective diagnostic model for breast cancer utilizing machine learning to examine the molecular immune infiltrate in HSPB6 by Lizhe Wang, Yu Wang, Yueyang Li, Li Zhou, Sihan Liu, Yongyi Cao, Yuzhi Li, Shenting Liu, Jiahui Du, Jin Wang, Ting Zhu

“…The objective of this research was to perform bioinformatics analyses on breast cancer-related datasets to gain a comprehensive understanding of the molecular mechanisms at play and to identify key genes associated with the disease. …”
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Positional embeddings and zero-shot learning using BERT for molecular-property prediction by Medard Edmund Mswahili, JunHa Hwang, Jagath C. Rajapakse, Kyuri Jo, Young-Seob Jeong

“…The study highlights the robustness of the BERT model in predicting chemical properties and its potential applications in cheminformatics and bioinformatics.…”
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High trophic similarity between non-native common carp and gibel carp in Turkish freshwaters: Implications for management by Sadi Aksu, Özgür Emiroğlu, Paride Balzani, J. Robert Britton, Esengül Köse, Irmak Kurtul, Sercan Başkurt, Oğuzcan Mol, Emre Çınar, Phillip J. Haubrock, Pinar Oztopcu-Vatan, Ali Serhan Tarkan

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The Multifaceted Roles of Myrrha in the Treatment of Breast Cancer: Potential Therapeutic Targets and Promises by Anwar Shams MD, MSc, PhD, Abdullah Ahmed Alzahrani, Taghreed A Ayash MSc, PhD, Shadi Tamur MD, FRCPC, FAAP, Majed AL-Mourgi MD, FRCS, FCCP, FACS

“…Results: Combining the results of network pharmacology with other bioinformatics databases suggests that myrrh’s active components exert anti-cancer effects by regulating genes involved in breast cancer pathogenesis, particularly PTGS2, EGFR, ESR2, MMP2, and JUN. …”
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Autism common variants associated with white matter alterations at birth: cross-sectional fixel-based analyses of 221 European term-born neonates from the developing human connecto... by Hai Le, Alexandra F. Bonthrone, Alena Uus, Daphna Fenchel, Alexandra Lautarescu, Konstantina Dimitrakopoulou, A. David Edwards, Joseph V. Hajnal, Serena J. Counsell, Lucilio Cordero-Grande, Daan Christiaens, Dafnis Batalle, Maximilian Pietsch, Anthony N. Price, Hamel Patel, Charles Curtis, Harriet Cullen, Maria Deprez, Jacques-Donald Tournier

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Standardization and validation of a novel reverse transcriptase polymerase chain reaction method for detecting virulent strains of the infectious bursal disease virus by Vladimir Longa-Bobadilla, Phillip Ormeño-Vásquez, Manuel Criollo-Orozco, Luis Tataje-Lavanda, Katherine Huamán-Gutierrez, Ángela Montalván, Mirko Zimic, Manolo Fernández-Sanchez, Manolo Fernández-Díaz

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