COMPUTER ANALYSIS OF DATA ON GENE EXPRESSION IN BRAIN CELLS OBTAINED BY MICROARRAY TESTS AND HIGH-THROUGHPUT SEQUENCING by I. V. Medvedeva, O. V. Vishnevsky, N. S. Safronova, O. S. Kozhevnikova, M. A. Genaev, A. V. Kochetov, D. A. Afonnikov, Y. L. Orlov

Subjects: “…bioinformatics…”
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Identification and Validation of Pivotal Genes in Osteoarthritis Combined with WGCNA Analysis by Yang C, Chen X, Liu J, Wang W, Sun L, Xie Y, Chang Q

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Transcriptional Systems Vaccinology Approaches for Vaccine Adjuvant Profiling by Diogo Pellegrina, Heather L. Wilson, George K. Mutwiri, Mohamed Helmy

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Protocol for predicting the single-cell network-based gene activity landscape during human B cell development by Xin Huang, Xuetong Hou, Yizhen Li, Jun J. Yang, Jiyang Yu

Subjects: “…bioinformatics…”
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Exploring the Pharmacological Potential of Carrageenan Disaccharides as Antitumor Agents: An In Silico Approach by Ohana Leticia Tavares Silva, Monique Gabriela das Chagas Faustino Alves, Hugo Alexandre Oliveira Rocha

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A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases by Tesson, Florian, Planel, Rémi, Egorov, Artyom A, Georjon, Héloïse, Vaysset, Hugo, Brancotte, Bryan, Néron, Bertrand, Mordret, Ernest, Atkinson, Gemma Catherine, Bernheim, Aude, Cury, Jean

Subjects: “…Defense Systems, Phage, Antiphage, Bacteria, Bioinformatics…”
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Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink by Lejla Gul, Anna Julia Elias, Tanvi Tambaku, Marton Olbei, Emily Watters, Balazs Bohar, Dezso Modos, Matthew Madgwick, Tamas Korcsmaros

Subjects: “…Bioinformatics…”
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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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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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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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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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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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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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Identification of molecular characteristics in polycystic ovary syndrome using single-cell and transcriptome analysis by Xiaolin Zhu, Yanhua Han, Yuenan Feng, Yuanli Shan, Chang Liu, Kexin Wang, Xiaoke Li, Shidi Zhang, Yaguang Han

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