Evaluation of 16s Long Read Metabarcoding for Characterizing the Microbiome and Salmonella Contamination of Retail Poultry Meat by Zachary Tobar, Katie Y. Lee, Megan E. Gaa, Bryshal P. Moore, Xunde Li, Maurice E. Pitesky

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Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques by Jiazhang Cai, Shushan Wu, Huimin Cheng, Wenxuan Zhong, Guo-Cheng Yuan, Ping Ma

Subjects: “…bioinformatics…”
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Investigating novel Streptomyces bacteriophage endolysins as potential antimicrobial agents by Jindanuch Maneekul, Amanda Chiaha, Rachel Hughes, Faith Labry, Joshua Saito, Matthew Almendares, Brenda N. Banda, Leslie Lopez, Nyeomi McGaskey, Melizza Miranda, Jenil Rana, Brandon R. Zadeh, Lee E. Hughes

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A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for Membrane Proteins by Teresa Milano, Sebastiana Angelaccio, Angela Tramonti, Martino Luigi Di Salvo, Roberto Contestabile, Stefano Pascarella

“…The results reported represent a framework for rational design of experiments and for bioinformatics analysis of other MocR subgroups.…”
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Comprehensive bioinformatics analysis identifies metabolic and immune-related diagnostic biomarkers shared between diabetes and COPD using multi-omics and machine learning by Qianqian Liang, Yide Wang, Zheng Li, Zheng Li, Zheng Li, Zheng Li

“…Finally, the 4 shared biomarkers were validated in single-cell sequencing data, clinical samples, and animal models, and their expression changes were consistent with the results of bioinformatic analysis.ConclusionsThrough comprehensive bioinformatics analysis, we revealed the potential connection between diabetes and COPD, providing a theoretical basis for exploring the common regulatory genes.…”
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Bioinformatics Analysis of miRNAs Targeting TRAF5 in DLBCL Involving in NF-κB Signaling Pathway and Affecting the Apoptosis and Signal Transduction by Chunyao Li, Lanshan Huang, Yongqin Wen, Muhua Yi, Min Gao

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Letter to the editor, “exploring salivary gene expression clusters: A bioinformatics approach for advanced diagnosis and prognosis in head and neck squamous cell carcinoma” by Geetha Shanmugam

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A Panel of Three MicroRNA Signatures as a Potential Biomarker for CRC Screening Based on Stages and Functional Prediction Using Bioinformatic Analysis by Syarah Syamimi Mohamed, Azmir Ahmad, Nurul Syakima Ab Mutalib, Tengku Ahmad Damitri Al-Astani Tengku Din, Md Salzihan Md Salleh, Andee Dzulkarnaen Zakaria, Zaidi Zakaria

“…Therefore, this study aims to identify the significantly deregulated miRNAs in CRC tumorigenesis. (2) Methods: Three upregulated miRNAs (hsa-miR-20a-5p, hsa-miR-21-5p, and hsa-miR210-3p) from 14 significant differentially expressed miRNAs (DEMs) were chosen from microarray profiling to be validated in plasma. Bioinformatics analyses showed that these miRNAs generally contributed to tumorigenesis, but only hsa-miR-20a-5p and hsa-miR-21-5p were specifically linked to CRC. …”
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Integrated analysis of bioinformatics, mendelian randomization, and experimental validation reveals novel diagnostic and therapeutic targets for osteoarthritis: progesterone as a potential therapeutic agent by Ziyu Weng, Chenzhong Wang, Bo Liu, Yi Yang, Yueqi Zhang, Chi Zhang

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A bioinformatic search for correspondence between differentially expressed genes of domestic versus wild animals and orthologous human genes altering reproductive potential by M. P. Ponomarenko, I. V. Chadaeva, P. M. Ponomarenko, A. G. Bogomolov, D. Yu. Oshchepkov, E. B. Sharypova, V. V. Suslov, A. V. Osadchuk, L. V. Osadchuk, Yu. G. Matushkin

“…In our previous study, we created a bioinformatic model of human self-domestication syndrome using differentially expressed genes (DEGs; of domestic animals versus their wild congeners) orthologous to the human genes (mainly, nervous-system genes) whose changes in expression affect reproductive potential, i.e., growth of the number of humans in the absence of restrictions caused by limiting factors. …”
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Synthesis, In vitro antimicrobial activity, and In silico bioinformatical approach of xanthone-fatty acid esters against Staphylococcus aureus, Escherichia coli, and Candida albicans by Yehezkiel Steven Kurniawan, Ervan Yudha, Jumina, Harno Dwi Pranowo, Eti Nurwening Sholikhah

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Structural bioinformatic study of human mitochondrial respiratory integral membrane megacomplex and its AlphaFold 3 predicted water-soluble QTY megacomplex analog by Edward Chen, Shuguang Zhang

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Bioinformatics Based Drug Repurposing Approach for Breast and Gynecological Cancers: RECQL4/FAM13C Genes Address Common Hub Genes and Drugs by Gizem Ayna Duran

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Expression and Clinical Significance of DAP3 in Breast Cancer and Effect of Bruceine D on Expression of DAP3:Analysis Based on Data-mining from Bioinformatics by Wenlong WANG, Qingzhi KONG, Hongda LU, Qingdong XIANG, Dianlei LIU

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Differential regulation of apoptosis-related genes during long-term culture and differentiation of canine adipose-derived stem cells - a functional bioinformatical analysis by Maurycy Jankowski, Maurycy Jankowski, Maurycy Jankowski, Katarzyna Stefańska, Michał Suchodolski, Claudia Dompe, Claudia Dompe, Grzegorz Wąsiatycz, Bartosz Kempisty, Bartosz Kempisty, Bartosz Kempisty, Bartosz Kempisty, Michał Nowicki, Magdalena Roszak

“…RNA sequencing (RNA-seq) and bioinformatical analysis were performed to obtain comprehensive transcriptomic data. …”
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A novel machine learning-based immune prognostic signature for improving clinical outcomes and guiding therapy in colorectal cancer: an integrated bioinformatics and experimental study by Yuanchun Zhao, Dexu Xun, Jiajia Chen, Xin Qi

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Author’s Response to Peer Reviews of “Identifying Safeguards Disabled by Epstein-Barr Virus Infections in Genomes From Patients With Breast Cancer: Chromosomal Bioinformatics Analysis” by Bernard Friedenson

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Golgi scaffold protein PAQR11 in pan-cancer landscape: A comprehensive bioinformatics exploration of expression patterns, prognostic significance, and potential immunological function by Zhu Liu, Zhi-Qiang Ling

“…Methods: We conducted a comprehensive bioinformatics analysis using publicly available pan-cancer datasets from TCGA, GEO, UALCAN, TIMER, GEPIA2, KM plotter, and TISIDB. …”
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Bioinformatics Analysis for Identifying Differentially Expressed MicroRNAs Derived from Plasma Exosomes Associated with Radiotherapy Resistance in Non-Small-Cell Lung Cancer by Lirong Zeng, Guilin Zeng, Zhong Ye

“…High-throughput sequencing and bioinformatics analysis were used to compare the DEmiRs between the three groups. …”
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Integrative genetics and multiomics analysis reveal mechanisms and therapeutic targets in vitiligo highlighting JAK STAT pathway regulation of CTSS by Zi-yue Dong, Ming-jie He, Yong-kai Yu, Fang Wang, Peng-yuan Zhao, De-long Ran, De-shuang Fu, Qing He, Run-ping Yang, Jiang-an Zhang

Subjects: “…Bioinformatics…”
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