Integrating single-cell RNA-Seq and bulk RNA-Seq data to explore the key role of fatty acid metabolism in hepatocellular carcinoma by Hua Dai, Xin Tao, Yuansen Shu, Fanrong Liu, Xiaoping Cheng, Xiushen Li, Bairui Shu, Hongcheng Luo, XuXiang Chen, Zhaorui Cheng

“…Data procurement encompassed transcriptomic and clinical datasets from HCC patients, sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) repositories. …”
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Detection of CRISPR‒Cas and type I R–M systems in Klebsiella pneumoniae of human and animal origins and their relationship to antibiotic resistance and virulence by Xue Li, Ling Wang, Jinghuan Lin, Yingjuan Gu, Zhihua Liu, Jing Hu

“…In this study, the whole genomes of 520 strains of K. pneumoniae from GenBank, including 325 from humans and 195 from animals, were collected for CRISPR‒Cas systems and type I R-M systems, virulence genes, antibiotic resistance genes, and multilocus sequence typing detection. …”
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NALCN expression is down-regulated and associated with immune infiltration in gastric cancer by Xuewei Li, Xuewei Li, Na Wu, Chen Wang, Beibei Pei, Xiaoyan Ma, Jun Xie, Jun Xie, Wenhui Yang

“…Data obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were utilized to investigate the correlation between NALCN expression and immune cell infiltration in GC. …”
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Identification of biomarkers for the diagnosis of type 2 diabetes mellitus with metabolic associated fatty liver disease by bioinformatics analysis and experimental validation by Guiling Wu, Guiling Wu, Sihui Wu, Sihui Wu, Tian Xiong, Tian Xiong, Tian Xiong, You Yao, You Yao, Yu Qiu, Yu Qiu, Yu Qiu, Liheng Meng, Cuihong Chen, Xi Yang, Xi Yang, Xi Yang, Xinghuan Liang, Yingfen Qin

“…We utilised protein–protein interactions (PPIs), Gene Ontology, and the Kyoto Encyclopedia of Genes and Genomes to identify T2DM-associated MAFLD genes and potential mechanisms. …”
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High-throughput methylation sequencing reveals novel biomarkers for the early detection of renal cell carcinoma by Wenhao Guo, Weiwu Chen, Jie Zhang, Mingzhe Li, Hongyuan Huang, Qian Wang, Xiaoyi Fei, Jian Huang, Tongning Zheng, Haobo Fan, Yunfei Wang, Hongcang Gu, Guoqing Ding, Yicheng Chen

“…Using a training set from The Cancer Genome Atlas (TCGA) dataset of 443 early-stage RCC tumors and matched normal tissues, we applied LASSO regression and identified 23 methylation signatures. …”
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Association between chronic obstructive pulmonary disease and osteoporosis: Mendelian randomization combined with bibliometric analysis by Fangjun Yang, Huaming Wang, Miaomiao Liu, Shengtai Pei, Xiaoming Qiu

“…These BMD measurements were derived primarily from a genome-wide association study (GWAS) and summary statistics from the International Genetic Factors Consortium for Osteoporosis (GEFOS). …”
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Identification of potential druggable targets for endometriosis through Mendelian randomization analysis by Peng Chen, Xin Wei, Xiao-Ke Li, Yi-Hang Zhou, Yi-Hang Zhou, Qi-Fang Liu, Ling Ou-Yang

“…This study aimed to identify both cerebrospinal fluid (CSF) and plasma protein markers as promising therapeutic targets for EM.MethodsWe utilized Mendelian randomization (MR) analysis to explore potential disease-causing proteins, utilizing genetic datasets from genome-wide association studies (GWAS) and protein quantitative trait loci (pQTL) analyses. …”
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EHMT2‐mediated R‐loop formation promotes the malignant progression of prostate cancer via activating Aurora B by Yuyang Zhang, Mingqin Su, Yiming Chen, Li Cui, Wei Xia, Renfang Xu, Dong Xue, Xiansheng Zhang, Xingliang Feng

“…Methods Bioinformatic analyses were conducted to identify genes overexpressed in PCa tissues using The Cancer Genome Atlas (TCGA) and GEO datasets. Western blotting and immunohistochemistry assays were applied to determine the expression levels of euchromatic histone lysine methyltransferase 2 (EHMT2), pT232‐Aurora B and Cullin 3 (CUL3). …”
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Construction of the bromodomain-containing protein-associated prognostic model in triple-negative breast cancer by Wei Chen, Yushuai Yu, Chenxi Wang, Zirong Jiang, Xiewei Huang, Yidan Lin, Hongjing Han, Qing Wang, Hui Zhang

“…Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and protein-protein interaction (PPI) network analysis were conducted to investigate active pathways and molecular interactions. …”
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Assessment of Antibiotic Resistance Among Isolates of <i>Klebsiella</i> spp. and <i>Raoultella</i> spp. in Wildlife and Their Environment from Portugal: A Positive Epidemiologic Ou... by Carolina Sabença, Rani de la Rivière, Paulo Barros, João Alexandre Cabral, Roberto Sargo, Luís Sousa, Maria de Lurdes Enes Dapkevicius, Filipe Silva, Filipa Lopes, Ana Carolina Abrantes, Madalena Vieira-Pinto, Manuela Caniça, Gilberto Igrejas, Carmen Torres, Patrícia Poeta

“…Extended-spectrum β-lactamase (ESBL) production was tested by the double-disc synergy test, and one ESBL-producing <i>K. pneumoniae</i> isolate was screened by PCR and whole-genome sequencing. Biofilm production was analyzed using the microtiter plate method. …”
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An exceptionally rare case of a diffuse midline glioma with concomitant H3.1 K27M and G34R mutations in the HIST1H3C (H3C3) gene by Zita Reisz, Rita Pereira, Smitha Nevis, Alan Mackay, Leena Bhaw, Yura Grabovska, Ross Laxton, Valeria Molinari, Anna Burford, Barnaby Clark, Cristina Bleil, Bassel Zebian, Erika Pace, Annette Weiser, Fernando Carceller, Lynley Marshall, Andrew King, Istvan Bodi, Safa Al-Sarraj, Chris Jones, Matthew Clarke

“…Further molecular studies (whole exome, whole genome sequencing) revealed concurrent H3.1 K27M and G34R mutations (clonal, in the same reads) of H3C3, FGF11 and PIK3CA somatic variants, and a pathogenic germline NBN variant. …”
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Association between sex steroid hormones and α-klotho: Results from the NHANES 2013-2016 and Mendelian randomization study by Andong Guo, Pengcheng Chen, Jishuang Cao, Chenrui Wu, Sentai Ding

“…Then, utilizing summary data from genome-wide association studies (GWAS), a bidirectional two-sample Mendelian randomization (MR) was conducted to assess the causal relationship between sex steroid hormones and α-Klotho. …”
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Glioma Image-Level and Slide-Level Gene Predictor (GLISP) for Molecular Diagnosis and Predicting Genetic Events of Adult Diffuse Glioma by Minh-Khang Le, Masataka Kawai, Kenta Masui, Takashi Komori, Takakazu Kawamata, Yoshihiro Muragaki, Tomohiro Inoue, Ippei Tahara, Kazunari Kasai, Tetsuo Kondo

“…In this study, the Cancer Genome Atlas whole-slide images (WSIs) were used to train the model. …”
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Genetic Biomarkers and Circulating White Blood Cells in Osteoarthritis: A Bioinformatics and Mendelian Randomization Analysis by Yimin Pan, Xiaoshun Sun, Jun Tan, Chao Deng, Changwu Wu, Georg Osterhoff, Nikolas Schopow

“…Data sources encompassed the largest genome-wide analysis for OA and a comprehensive GWAS summary for circulating WBC counts. …”
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Impaired hippocampal neurogenesis associated with regulatory ceRNA network in a mouse model of postoperative cognitive dysfunction by Jingrun Lin, Xiaoqiu Zhu, Xuan Li, Yu Hong, Yaohui Liang, Siqi Chen, Chenzhuo Feng, Lin Cao

“…Hippocampal mRNA expression was analyzed using Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment. …”
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Studying a collection of common-wheat varieties for leaf rust resistance, crop yield and grain quality in the environmental conditions of Novosibirsk region by L. P. Sochalova, V. A. Aparina, N. I. Boyko, E. V. Zuev, E. V. Morozova, E. V. Musinov, N. A. Vinichenko, I. N. Leonova, V. V. Piskarev

“…Varieties Tuleevskaya and Altayskaya 110 with Lr9 in their genomes are recommended for the development of resistance gene-pyramided genotypes. …”
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Characteristics and multi-omics analysis of spontaneous spondyloarthritis in non-human primates: Case report by Lei Cai, Qing Lv, Ronghua Ma, Wei Liu, Yalun Guan, Zhongqiang Huang, Qingyu Liu, Yunfeng Li, Shuhua Liu, Ge Li, Yu Zhang

“…Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on these co-expressed genes and proteins, indicating a predominant enrichment in the IL-17 signaling pathway, with S100A8 and S100A9 identified as the core proteins. …”
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Ethanolamine-induced assembly of microcompartments is required for Fusobacterium nucleatum virulence by Dana S. Franklin, Yi-Wei Chen, Yimin Chen, Manuel Wittchen, Angela Agnew, Alexis Luu, Julian P. Whitelegge, Z. Hong Zhou, Andreas Tauch, Asis Das, Hung Ton-That

“…Here we investigated the molecular assembly, regulation, and function of BMCs in Fusobacterium nucleatum—a Gram-negative oral pathobiont that is associated with adverse pregnancy outcomes. The F. nucleatum genome harbors a conserved ethanolamine utilization (eut) locus with 21 genes that encode several putative BMC shell proteins and a two-component signal transduction system (TCS), in addition to the enzymes for ethanolamine transport and catabolism. …”
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A gut-derived Streptococcus salivarius produces the novel nisin variant designated nisin G and inhibits Fusobacterium nucleatum in a model of the human distal colon microbiome by Garreth W. Lawrence, Enriqueta Garcia-Gutierrez, A. Kate O’Mahony, Calum J. Walsh, Paula M. O'Connor, Máire Begley, Caitriona M. Guinane, Paul D. Cotter

“…Screening for gut-derived strains that exhibit anti-F. nucleatum activity in vitro revealed Streptococcus salivarius DPC6487 as a strain of interest. Whole-genome sequencing of S. salivarius DPC6487 identified a nisin operon with a novel structural variant designated nisin G. …”
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Biology-Informed inverse problems for insect pests detection using pheromone sensors by Malou, Thibault, Parisey, Nicolas, Adamczyk-Chauvat, Katarzyna, Vergu, Elisabeta, Laroche, Béatrice, Calatayud, Paul-André, Lucas, Philippe, Labarthe, Simon

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