Molecular mechanisms of autism as a form of synaptic dysfunction by E. A. Trifonova, T. M. Khlebodarova, N. E. Gruntenko

“…Genetic screening has identified hundreds of mutations and other genetic variations associated with autism, and bioinformatic analysis of signaling pathways and gene networks has led to understanding that many of these mutational changes are involved in the functioning of synapses. …”
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DPSCs Protect Architectural Integrity and Alleviate Intervertebral Disc Degeneration by Regulating Nucleus Pulposus Immune Status by Xiwen Dong, Fanqi Hu, Jing Yi, Yuning Zhang, Chao Liu, Panpan Geng, Han Duan, Chu-Tse Wu, Xuesong Zhang, Hua Wang

“…To understand the biological effects of dental pulp stem cells (DPSCs) on nucleus pulposus (NP) cells, we carried out RNA sequencing, bioinformatic analysis which unveiled gene expression differences, and pathway variation in primarily isolated patients’ NP cells after treatment with DPSCs supernatant. …”
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LAMB1 downregulation suppresses glioma progression by inhibiting aerobic glycolysis through regulation of the NF-κB/HK2 axis by Zhenxiang Zhao, Haiying Liu, Yingzi Liu, Junpeng Wen, Jiangwei Yuan

“…Western blotting was conducted to monitor the expression of HK1, HK2, PDHA, and PKM. Bioinformatic analysis was employed to investigate the downstream mechanism of LAMB1. …”
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In silico analysis of mitochondrial DNA genes: implication for conservation of Tor putitora (Hamilton, 1822) by Kushal Thakur, Deepika Sharma, Ankita Sharma, Amit Kumar Sharma, Danish Mahajan, Bhavna Brar, Hishani Kumari, Sandeep Kumar, Madhu Bala, Sunil Kumar, Rakesh Kumar

“…The present study aimed to examine the haplotypic diversity, genetic variation and population structure of T. putitora isolates using COI and Cyt b gene sequences submitted in GenBank. Bioinformatic analysis was carried out using 106 COI and 183 Cyt b gene sequences as well as 2 reference genome sequences. …”
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EXO1 is a key gene for lung-resident memory T cells and has diagnostic and predictive values for lung adenocarcinoma by Zhuoqi Li, Xiaoyan Lin, Yuanhui Yang, Mei Tian, Lu Zhang, Fujing Huang, Xiao Wen, Zhigang Wei, Yuan Tian

“…In this study, the RNA expression, DNA methylation, CNV, somatic mutation data of EXO1, and the corresponding patients’ clinical information from publicly available databases were analyzed using bioinformatic methods. The results were validated through immunohistochemical staining of EXO1 in LUAD samples. …”
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Metabolomic characterisation of the glioblastoma invasive margin reveals a region-specific signature by James Wood, Stuart J. Smith, Marcos Castellanos-Uribe, Anbarasu Lourdusamy, Sean T. May, David A. Barrett, Richard G. Grundy, Dong-Hyun Kim, Ruman Rahman

“…This proof-of-principle study assesses intratumour heterogeneity through mass spectrometry-based metabolite profiling of multi-region biopsies. Bioinformatic interpretation of the GBM metabolome has highlighted the invasive region to be biologically distinct compared to tumour core and revealed putative drug-targetable metabolic pathways associated with purine and pyrimidine metabolism.…”
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Identification of Functional Modules and Key Pathways Associated with Innervation in Graft Bone—CGRP Regulates the Differentiation of Bone Marrow Mesenchymal Stem Cells via p38 MAP... by Ziqian Wu, Xudong Wang, Jingcun Shi, Anand Gupta, Yuhan Zhang, Bingqing Zhang, Yang Cao, Lei Wang

“…In parallel, we established protein–protein interaction networks to screen functional modules. Based on bioinformatic results, we validated in vitro the osteogenic differentiation potential of rat bone marrow mesenchymal stem cells (BMMSCs) after calcitonin gene-related peptide (CGRP) stimulation and the expression of p38 MAPK and Wnt6/β-catenin pathways during osteogenesis. …”
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DNA metabarcoding technology for the identification of the fecal microbiome in patients with chronic stress by Abraham Eudes Pérez Urruchi, Lucy Eliana Ramírez Elizalde, Flor de María Zapata Cornejo, María Luisa Matalinares Calvet, Miluska Vanessa Baylon Cuba, Fredy Fabian Dominguez

“…Next Generation Illumina genetic sequencing targeting the 16S rDNA gene was then performed, followed by bioinformatic analysis using QUIME II software. The results, at the psychological test level, 20 people with chronic stress were diagnosed, on the other hand, at the metabarcoding level, specifically at the Gender level, the Asteroleplasma bacteria present only in the 20 healthy patients was molecularly identified. …”
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A Robust Metatranscriptomic Technology for Population-Scale Studies of Diet, Gut Microbiome, and Human Health by Andrew Hatch, James Horne, Ryan Toma, Brittany L. Twibell, Kalie M. Somerville, Benjamin Pelle, Kinga P. Canfield, Matvey Genkin, Guruduth Banavar, Ally Perlina, Helen Messier, Niels Klitgord, Momchilo Vuyisich

“…Stool metatranscriptomic analysis offers a comprehensive functional view of the gut microbiome, but despite its usefulness, it has rarely been used in clinical studies due to its complexity, cost, and bioinformatic challenges. This method has also received criticism due to potential intrasample variability, rapid changes, and RNA degradation. …”
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Emodin Ameliorates Intestinal Dysfunction by Maintaining Intestinal Barrier Integrity and Modulating the Microbiota in Septic Mice by Mina Zhang, Bo Lian, Rui Zhang, Yuhong Guo, Jingxia Zhao, Shasha He, Yunjing Bai, Ning Wang, Yan Lin, Xuerui Wang, Qingquan Liu, Xiaolong Xu

“…Nuclear factors including NF-κB and AP-1 were further identified as downstream effectors of JNK2. Bioinformatic analysis based on 16s rRNA gene sequencing illustrated that emodin treatment significantly increased the alpha- and beta-diversity of gut microbiota in septic mice. …”
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Global biogeography of N₂-fixing microbes: <i>nifH</i> amplicon database and analytics workflow by M. Morando, J. D. Magasin, S. Cheung, S. Cheung, M. M. Mills, J. P. Zehr, K. A. Turk-Kubo

“…To address these knowledge gaps, a bioinformatic workflow was designed that standardizes the processing of <i>nifH</i> amplicon datasets originating from high-throughput sequencing (HTS). …”
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Proteomic Analysis Reveals Growth Inhibition of Coriolus versicolor by Methanol Extracts of Cinnamomum camphora Xylem by Quan Li, Xiangyang Li, Hui Lin

“…To understand the antifungal mechanisms of Coriolus versicolor inhibition with methanol extracts of C. camphora xylem, the protein profiles of C. versicolor were analyzed using 2-DE followed by MALDI-TOF/MS and bioinformatic analyses. The results showed that 41 protein spots were obviously changed among the 366-385 protein spots of C. versicolor treated with methanol extracts of C. camphora xylem. …”
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Isovitexin targets SIRT3 to prevent steroid-induced osteonecrosis of the femoral head by modulating mitophagy-mediated ferroptosis by Yinuo Fan, Zhiwen Chen, Haixing Wang, Mengyu Jiang, Hongduo Lu, Yangwenxiang Wei, Yunhao Hu, Liang Mo, Yuhao Liu, Chi Zhou, Wei He, Zhenqiu Chen

“…In this study, we analyzed clinical samples obtained from SIONFH patients using proteomic and bioinformatic approaches. We found an imbalance in mitochondrial homeostasis and ferroptosis-induced impairment of osteogenic capacity in SIONFH. …”
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CD63 Promotes Hemocyte-Mediated Phagocytosis in the Clam, Paphia undulata by Mingjia Yu, Shanjun Yang, Hongxia Sun, Qiang Xia

“…The complete cDNA of Pu-CD63 is 1,738 bp in length with an open reading frame (ORF) of 849 bp, encoding a 282 amino acid protein with four putative hydrophobic transmembrane helixes. Bioinformatic analysis revealed that Pu-CD63 contains one putative YXXØ consensus motif of “110-YVII-113” and one N-glycosylation site “155-NGT-157” within the large extracellular loop (LEL) region, supporting its conserved function in plasma membrane and endosomal/lysosomal trafficking. …”
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LINC00707 Regulates miR-382-5p/VEGFA Pathway to Enhance Cervical Cancer Progression by Hua Guo, Jing Li, Furong Fan, Ping Zhou

“…In addition, the action of LINC00707 in cervical cancer cells was studied using bioinformatic tools and luciferase reporter experiment. …”
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Comprehensive Analysis of Gene Signatures of m6ARNA Methylation Regulators in Lung Adenocarcinoma and Development of a Risk Scoring System by Chundi Gao, Huayao Li, Wenzhe Ma, Qiming Zhang, Cun Liu, Lijuan Liu, Jing Zhuang, Changgang Sun

“…Overall, our findings revealed an important role of M6A methylation regulators in LUAD, and our risk scoring system involving these regulators might help to screen groups at high risk for LUAD and provide important theoretical bioinformatic support for evaluating the prognosis of such patients.…”
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Identification of mitochondrial carrier homolog 2 as an important therapeutic target of castration-resistant prostate cancer by Yankui Liu, Anjie Chen, Yufan Wu, Jiang Ni, Rong Wang, Yong Mao, Ning Sun, Yuanyuan Mi

“…Abstract We here investigate the expression of the mitochondrial carrier homolog 2 (MTCH2) and its potential function in castration-resistant prostate cancer (CRPC). Bioinformatic analyses reveal that MTCH2 overexpression is associated with critical clinical parameters of prostate cancer. …”
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Translational regulation of PKD1 by evolutionarily conserved upstream open reading frames by Lei Chen, Xia Gao, Xiangshen Liu, Ye Zhu, Dong Wang

“…In this study, we investigated the effects of uORFs and uORF-affecting variants by combining bioinformatic analyses, luciferase reporter assays, RT-qPCR and immunoblotting experiments. …”
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OGT-mediated O-GlcNAcylation regulates macrophage polarization in heart failure via targeting IRF1 by Guoqiang Jing, Yuhong Ma

“…Underlying mechanism was analyzed using bioinformatic analysis, co-immunoprecipitation (co-IP), IP, and western blotting. …”
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MetaboLINK is a novel algorithm for unveiling cell-specific metabolic pathways in longitudinal datasets by Jared Lichtarge, Gerarda Cappuccio, Gerarda Cappuccio, Soumya Pati, Soumya Pati, Alfred Kwabena Dei-Ampeh, Alfred Kwabena Dei-Ampeh, Senghong Sing, Senghong Sing, Senghong Sing, LiHua Ma, Zhandong Liu, Zhandong Liu, Mirjana Maletic-Savatic, Mirjana Maletic-Savatic, Mirjana Maletic-Savatic

“…IntroductionIn the rapidly advancing field of ‘omics research, there is an increasing demand for sophisticated bioinformatic tools to enable efficient and consistent data analysis. …”
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