Analysis of Microarray-Identified Genes and MicroRNAs Associated with Idiopathic Pulmonary Fibrosis by Lichao Fan, Xiaoting Yu, Ziling Huang, Shaoqiang Zheng, Yongxin Zhou, Hanjing Lv, Yu Zeng, Jin-Fu Xu, Xuyou Zhu, Xianghua Yi

“…Differentially expressed miRNAs (DE-miRNAs)/genes (DEGs) were screened with GEO2R, and their associations with IPF were analyzed by comprehensive bioinformatic analyses. A total of 45 DE-microRNAs were identified between IPF and control tissues, whereas 67 common DEGs were determined to exhibit the same expression trends in all three microarrays. …”
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Landscape analysis of m6A modification reveals the dysfunction of bone metabolism in osteoporosis mice by Lifeng Zheng, Chao Lan, Xinyue Gao, An Zhu, Yaoqing Chen, Jinluan Lin, Sunjie Yan, Ximei Shen

“…This study aimed to explore the relationship between OP and RNA m6A methylation, investigating its underlying mechanisms through comprehensive bioinformatic analysis and experimental validation. The mRNA sequencing (mRNA-seq) and methylated RNA immunoprecipitation sequencing (MeRIP-seq) were performed on control mice as well as ovariectomized mice to discover differentially expressed genes (DEGs) and m6A regulators in OP. …”
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Characterization and phylogenetic analysis of the chloroplast genome of endangered Impatiens chishuiensis by LAN Wenxiang, MO Qing, HUANG Haiquan, HUANG Meijuan

“…[Methods] Based on the chloroplast genome sequence of I. chishuiensis, an endemic species in China, the assembly, annotation, gene characterization, sequence repetition and phylogenetic analysis of chloroplast genome were performed by bioinformatic softwares. [Results] (1) The chloroplast genome of I. chishuiensis has a typical tetrameric structure with a total GC content of 37% and a length of 152 892 bp. …”
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TMT-based quantitative proteomics reveals the genetic mechanisms of secondary hair follicle development in fine-wool sheep. by Li-Xia Qiu, Qian Yu, Hua-Qian Zhou, Wen-Hua Fan, Jing-Jing Zheng, Yong-Lin Yang, Wen-Zhe Zhang, Xin Cao, Hua Yang

“…We found that the density of secondary hair follicles and the secondary hair follicles/primary hair follicles ratio increased from 85 to 105 gestational days. Bioinformatic analysis identified 238, 35, and 348 differentially expressed proteins in the respective comparison periods. …”
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Prospects for marker-associated selection in tomato <i>Solanum lycopersicum</i> L. by A. B. Shcherban

“…Recently, due to modern technologies of sequencing, SNP-genotyping, the development of new bioinformatic approaches, it has become possible to establish genetic cascades determining the biochemical composition of tomato fruits, to identify key genes that can be used in the future for marker-associated selection of nutritional value. …”
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Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis by Michal Motyka, Dominik Kusy, Matej Bocek, Renata Bilkova, Ladislav Bocak

“…We suggest that focused field research and subsequent laboratory and bioinformatic workflow steps would substantially accelerate the inventorying of any hyperdiverse tropical group with several thousand species. …”
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COEX-Seq: Convert a Variety of Measurements of Gene Expression in RNA-Seq by Sang Cheol Kim, Donghyeon Yu, Seong Beom Cho

“…To solve this problem, we have developed a web-based application using Shiny, COEX-seq (Convert a Variety of Measurements of Gene Expression in RNA-Seq) that easily converts data in a variety of measurement formats of gene expression used in most bioinformatic tools for RNA-Seq. It provides a workflow that includes loading data set, selecting measurement formats of gene expression, and identifying gene names. …”
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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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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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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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Predicted Cold Shock Proteins from the Extremophilic Bacterium Deinococcus maricopensis and Related Deinococcus Species by Michael J. LaGier

“…The primary aim of this study was to test whether a representative, desert-dwelling Deinococcus, Deinococcus maricopensis, encodes Csps as part of its genome. Bioinformatic approaches were used to identify a Csp from D. maricopensis LB-34. …”
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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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