Rare Somatic MEN1 Gene Pathogenic Variant in a Patient Affected by Atypical Parathyroid Adenoma by Luigia Cinque, Flavia Pugliese, Celeste Clemente, Stefano Castellana, Maria Pia Leone, Danilo de Martino, Teresa Balsamo, Claudia Battista, Tommaso Biagini, Paolo Graziano, Marco Castori, Alfredo Scillitani, Vito Guarnieri

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Genomic and Drug Resistance Profile of Bovine Multidrug-Resistant <i>Escherichia coli</i> Isolated in Kazakhstan by Pavel G. Alexyuk, Andrey P. Bogoyavlenskiy, Yergali S. Moldakhanov, Kuralay S. Akanova, Adolat N. Manakbayeva, Timur Kerimov, Vladimir E. Berezin, Madina S. Alexyuk

“…Whole-genome sequencing, followed by bioinformatic processing and the annotation of genes of this strain, showed that the genome has a total length of 4,803,482 bp and contains 4986 genes, including 122 RNA genes. …”
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RKIP Suppresses Breast Cancer Metastasis to the Bone by Regulating Stroma-Associated Genes by Elena Bevilacqua, Casey A. Frankenberger, Marsha Rich Rosner

“…Experimental validation is followed by further bioinformatic analysis to establish the clinical significance of discoveries. …”
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The effects of the ketone body ?-hydroxybutyrate on the neuronal transcriptome by Zayn Cheema, Megan Chen, Dana Poon, Taara Reddy, John Vergis, Sinead O'Donovan

“…To assess the effect of BHB administration on the neuronal transcriptome, we reanalyzed a publicly available RNAseq dataset (GSE252513) using a bioinformatic “3-pod” approach. We conducted pathway analysis and identified leading edge genes using Gene Set Enrichment Analysis (GSEA) and conducted chemical perturbagen analysis using the iLINCS repository to identify drugs that are concordant and discordant with BHB administration. …”
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The Polymorphisms with Cataract Susceptibility Impair the EPHA2 Receptor Stability and Its Cytoprotective Function by Jin Yang, Dan Li, Qi Fan, Lei Cai, Xiaodi Qiu, Peng Zhou, Yi Lu

“…Despite accumulating evidence revealing susceptibility genes for age-related cataract, its pathophysiology leading to visual impairment at the cellular and molecular level remains poorly understood. Recent bioinformatic studies uncovered the association of two single nucleotide polymorphisms in human EPHA2, rs2291806 and rs1058371, with age-related cataract. …”
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Antibody Responses and the Vaccine Efficacy of Recombinant Glycosyltransferase and Nicastrin Against <i>Schistosoma japonicum</i> by Bowen Dong, Haoran Zhong, Danlin Zhu, Luobin Wu, Jinming Wang, Hao Li, Yamei Jin

“…Previous proteomic studies from our group revealed that the expression of <i>Schistosoma japonicum</i> glycosyltransferase and nicastrin as proteins was higher in single-sex males than mated males, suggesting their critical roles in parasite reproduction and their potential as vaccine candidates. In this study, bioinformatic tools were employed to analyze the structural and functional properties of these proteins, including their signal peptide regions, transmembrane domains, tertiary structures, and protein interaction networks. …”
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Phylogeography of the woolly mammoth (<i>Mammuthus primigenius</i>) in the Minusinsk Depression of southern Siberia in the Late Pleistocene by S. A. Modina, M. A. Kusliy, D. G. Malikov, A. S. Molodtseva

“…Within the framework of this effort, libraries for high-throughput sequencing of seven bone samples of woolly mammoths were obtained, two-round enrichment using biotinylated probes of modern mtDNA of Elephas maximus immobilised on magnetic microspheres and sequencing with subsequent bioinformatic analysis were carried out. Phylogenetic reconstructions showed the presence of all studied mammoths in clade I, which expanded its range. …”
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LPCAT3 regulates the proliferation and metastasis of serous ovarian cancer by modulating arachidonic acid by Fang Wen, Hongjian Ling, Rui Ran, Xinya Li, Houmei Wang, Qianfen Liu, Min Li, Tinghe Yu

“…Methods: LPCAT3 protein in ovarian cancer tissues was detected using bioinformatic and immunohistoche mical assays. Cell behaviors were observed after up- or down-regulating LPCAT3. …”
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Preliminary exploration of metagenomic sequencing for pathogenic identification in infectious uveitis by Jinxia Yu, Yane Gao, Hongsheng Bi, Youhua Zhang, Kai Tang, Dadong Guo, Xiaofeng Xie

“…Then, pathogenic microorganisms that cause uveitis were identified through bioinformatic analyses based on the sequencing data of MGS. …”
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Metabolic Blockade-Based Genome Mining of <i>Malbranchea circinata</i> SDU050: Discovery of Diverse Secondary Metabolites by Hu Yang, Xiaowei Luo, Zhuo Shang, Kunlong Li, Jian Cai, Yingying Chen, Longchao Xin, Jianhua Ju

“…This study reports the isolation and identification of four classes of secondary metabolites from wild-type <i>M. circinata</i> SDU050, alongside five additional metabolite classes, including three novel cytochalasins (<b>7</b>–<b>9</b>), obtained from a mutant strain through the metabolic blockade strategy. Furthermore, bioinformatic analysis of the BGC associated with the isocoumarin sclerin (<b>1</b>) enabled the deduction of its biosynthetic pathway based on gene function predictions. …”
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N-trans-Feruloyloctopamine Wakes Up BBC3, DDIT3, CDKN1A, and NOXA Signals to Accelerate HCC Cell Apoptosis by Bin Ma, Jing Li, Wen-Ke Yang, Mei-Gui Zhang, Xiao-Dong Xie, Zhong-Tian Bai

“…Real-time cell analyzer and flow cytometry data reveal that tumor cell proliferation and apoptosis were impacted by FO. DAVID bioinformatic data showed that most of the biological process GO terms are related to proliferation and apoptosis. …”
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Gut microbial profiles of patients with optic neuritis or myasthenia gravis by Tao Wu, Hanqiu Jiang, Chen Lin, Jingting Peng, Xiuyun Kong, Jie Yu, Jiawei Wang, Shilei Cui

“…Microbial genomic DNA was extracted, and the V3–V4 regions of bacterial 16S rRNA genes were amplified and sequenced. Bioinformatic analyses was performed to compare the alpha-diversity, beta-diversity, taxonomic assignments, and bacterial richness of the groups. …”
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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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Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes by Diana Samodova, Evelina Stankevic, Mathilde Sonne Søndergaard, Naiyu Hu, Tarunveer S. Ahluwalia, Daniel R. Witte, Daniel Belstrøm, Anniek Frederike Lubberding, Pratik D. Jagtap, Torben Hansen, Atul S. Deshmukh

“…Using state-of-the-art proteomics, over 4500 human and bacterial proteins were identified in a single 21-min run. Bioinformatic analysis revealed host signatures of altered immune-, lipid-, and glucose-metabolism regulatory systems, increased oxidative stress, and possible precancerous changes in T2D saliva. …”
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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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