Identification of Differentially Expressed Genes and Signaling Pathways in Acute Myocardial Infarction Based on Integrated Bioinformatics Analysis by Da-Qiu Chen, Xiang-Sheng Kong, Xue-Bin Shen, Mao-Zhi Huang, Jian-Ping Zheng, Jing Sun, Shang-Hua Xu

“…These DEGs were performed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses by using Clusterprofiler package. …”
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Resistance to viruses of potato: current status and prospects by S. S. Makarova, V. V. Makarov, M. E. Taliansky, N. O. Kalinina

“…Recently developed new genome editing technologies with the potential to be a powerful tool for gene design open up broad opportunities for development of next-generation resistance genes. …”
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Transcriptomic Response of Arabidopsis thaliana to Pseudomonas syringae Infection: An In Silico Approach by Amir Ghaffar Shahriari, Mohamad Hamed Ghodoum Parizipour, Yaser Biniaz, Aminallah Tahmasebi, Fatemeh Gholizadeh

“…A total number of 22 biological pathways were significantly enriched with up-/down-regulated differentially expressed genes (DEGs) in the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Also, 39 TFs of A. thaliana were altered during the bacterial infection. …”
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Identification of genetic mechanisms of non-isolated auditory neuropathy with various phenotypes in Chinese families by Yang Cao, Xiaolong Zhang, Lan Lan, Danyang Li, Jin Li, Linyi Xie, Fen Xiong, Lan Yu, Xiaonan Wu, Hongyang Wang, Qiuju Wang

“…Pathogenicity was assessed following American College of Medical Genetics and Genomics guidelines. Genes associated with non-isolated AN were summarized from prior reports, and functional enrichment analysis was conducted using Gene Ontology databases. …”
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Assessment of prognosis and responsiveness to immunotherapy in colorectal cancer patients based on the level of immune cell infiltration by Kaili Liao, Minqi Zhu, Lei Guo, Zijun Gao, Jinting Cheng, Bing Sun, Yihui Qian, Bingying Lin, Jingyan Zhang, Tingyi Qian, Yixin Jiang, Yanmei Xu, Qionghui Zhong, Xiaozhong Wang

“…ObjectiveTo build a new prognostic risk assessment model based on immune cell co-expression networks for predicting overall survival and evaluating the efficacy of immunotherapy for colon cancer patients.MethodsThe Cancer Genome Atlas (TCGA) database was used to obtain mRNA expression profiling data, clinical information, and somatic mutation data from colorectal cancer patients. …”
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Genotyping-by-sequencing derived SNP markers reveal genetic diversity and population structure of Dactylis glomerata germplasm by Muhammad Tanveer Altaf, Pablo Federico Cavagnaro, Kağan Kökten, Amjad Ali, Andres Morales, Andres Morales, Muhammed Tatar, Mehmet Bedir, Muhammad Azhar Nadeem, Muhammad Aasim, Nafiz Çeliktaş, Sheikh Mansoor, Faheem Shehzad Baloch, Faheem Shehzad Baloch

“…The majority of the genetic variation (85.8%) was observed within clusters, with minimal differentiation among clusters (FST = 0.007). Genome-wide association studies (GWAS) identified significant marker-trait associations for dry biomass weight, a critical agronomic trait, with markers DArT-100715788, DArT-101043591, and DArT-101171265 and DArT-101090822 located on Chromosomes 1, 6, and 7 respectively. …”
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High-Resolution Melting Analysis to Detect Antimicrobial Resistance Determinants in South African Neisseria gonorrhoeae Clinical Isolates and Specimens by Nireshni Mitchev, Ravesh Singh, Veron Ramsuran, Arshad Ismail, Mushal Allam, Stanford Kwenda, Florah Mnyameni, Nigel Garrett, Khine Swe Swe-Han, Abraham J. Niehaus, Koleka P. Mlisana

“…Real-time PCR and high-resolution melting analysis were used to detect porA pseudogene (species-specific marker) and resistance-associated targets. Whole-genome sequencing was used as the gold standard for the presence of point mutations. …”
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Taxonomic refinement of Bacillus thuringiensis by Nagham Shiekh Suliman, Reza Talaei-Hassanloui, Hamid Abachi, Sadegh Zarei, Ebrahim Osdaghi

“…By October 2023, whole genome sequences (WGS) of 885 bacterial strains were labeled as B. thuringiensis in the NCBI GenBank database. …”
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Ganciclovir Resistance-Linked Mutations in the HCMV <i>UL97</i> Gene: Sanger Sequencing Analysis in Samples from Transplant Recipients at a Tertiary Hospital in Southern Brazil by Anna Caroline Avila da Rocha, Grazielle Motta Rodrigues, Alessandra Helena da Silva Hellwig, Dariane Castro Pereira, Fabiana Caroline Zempulski Volpato, Afonso Luís Barth, Fernanda de-Paris

“…<b>Background/Objectives:</b> Human cytomegalovirus (HCMV) DNAemia remains a significant concern for transplant recipients, largely due to mutations in the viral genome that may lead to antiviral-resistant strains. …”
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Cooperation Between <i>Rhodococcus qinshengii</i> and <i>Rhodococcus erythropolis</i> for Carbendazim Degradation by Roosivelt Solano-Rodríguez, Fortunata Santoyo-Tepole, Mario Figueroa, Voleta Larios-Serrato, Nora Ruiz-Ordaz, Abigail Pérez-Valdespino, Everardo Curiel-Quesada

“…Sequencing analysis of genomes of both strains revealed the presence of <i>cbm</i>A, the gene coding for the enzyme that hydrolyses carbendazim to produce 2-aminobenzimidazole (2-AB). …”
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Enhanced membrane protein production in HEK293T cells via ATF4 gene knockout: A CRISPR-Cas9 mediated approach by Byung-Jo Choi, Ba Reum Kim, Ho Joong Choi, Ok-Hee Kim, Say-June Kim

“…Comparative evaluations were conducted using all-in-one and two-vector systems. Genome sequencing and membrane protein productivity of ATF4-KO cells were compared to wild-type cells using next-generation sequencing (NGS) and a membrane protein isolation kit, respectively. …”
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Drought Adaptation and Responses of Stipa krylovii Vary Among Different Regions: Evidence From Growth, Physiology, and RNA‐Seq Transcriptome Analysis by Ziqing Gong, Zehang Qu, Yulin Liu, Tao Wang, Baijie Fan, Anzhi Ren, Yubao Gao, Nianxi Zhao

“…By Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis on gene expressions of individuals from each treatment, unique enriched pathways were found under heavy drought. (2) The decrease in the number of tillers with the increasing drought was much lower for individuals from the western region than those from the other two regions. …”
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Causal association between matrix metalloproteinases and diabetic neuropathy: a two-sample Mendelian randomization study by Chao Bai, Chao Bai, Wenwen Yang, Guangwei Qi, Liuyu Yang, Qingrui Wu, Jieguang Peng, Ning Wang, Tao Liu

“…The objective of this research is to investigate the casual relationship between MMPs and DN through two-sample Mendelian randomization (MR).MethodsData for this investigation were derived from genome-wide association studies (GWAS) of MMPs and DN. …”
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Causal association among smoking, bitter beverage consumption, and risk of osteoporosis: a two-sample mendelian randomization-based study by Yanqian Wu, Jianqian Chao, Min Bao, Na Zhang, Leixia Wang

“…Methods Publicly available genome-wide association study summary data were analyzed using MR methods. …”
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Recombinant short TNF-BD protein from smallpox virus is pharmacologically active in an experimental septic shock model by I. P. Gileva, S. N. Yakubitskiy, I. V. Kolosova, S. N. Shchelkunov

“…Throughout evolution, anthropogenic Variola virus (VARV) has developed effective mechanisms to overcome human defense reactions. The viral genome encodes soluble proteins imitating the structure of cellular cytokine receptors. …”
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Transcriptomic reprogramming and epigenetic regulation underlying pollination-dependent and auxin-induced fruit set in tomato by Xiaohan Li, Xiaohan Li, Xiaohan Li, Bing He, Anis Djari, Pierre Frasse, Elie Maza, Farid Regad, Julien Pirrello, Guojian Hu, Guojian Hu, Guojian Hu, Guojian Hu, Mondher Bouzayen

“…Notably, this developmental process can also proceed in the absence of flower fertilization, although it remains unclear whether pollination-dependent and pollination-independent fruit sets undergo similar transcriptomic reprogramming. Genome-wide transcriptomic profiling of the flower-to-fruit transition, either pollination-induced or triggered by auxin treatment, shows that both types of triggers modulate the expression of a common large set of genes primarily expressed in maternal tissues. …”
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Comparative analysis of the DNA isolated from thyme leaves using different methods by I. V. Bulavin, O. A. Grebennikova, V. A. Brailko, S. A. Feskov, I. V. Mitrofanova

“…Among the tested kits and methods, CTAB + 2% PVP provided thyme DNA suitable for PCR and, presumably, for genome library preparation. The low cost of reagents for this technique makes it applicable for future mass analysis of plant material.…”
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Combination of inflammatory proteins in serum can be used to diagnose papillary thyroid carcinoma with lymph node metastasis by Yongqin Pan, Guanghao Wang, Delin Chen, Zhihui Wu, Yimwing Kei, Mingxi Xu

“…Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis were used to analyze the potential regulatory pathways. …”
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Drug Efficacy Recommendation System of Glioblastoma (GBM) Using Deep Learning by Sajid Naveed, Mujtaba Husnain, Ali Samad, Amna Ikram, Hina Afreen, Ghulam Gilanie, Najah Alsubaie

“…Therefore, drug efficacy recommendation systems are very useful in the treatment of various types of cancers. The Genomics of Drug Sensitivity in Cancer (GDSC) database was used as the primary data source, containing 135,242 cell line-drug interactions, inhibitory concentration of cancer drug for more than 800 cancer cell lines. …”
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The potential mechanism of Isodon suzhouensis against COVID-19 via EGFR/TLR4 pathways by Hong Duan, Wei Wang, Shu Li, Han Li, Ghulam Jilany Khan, Yong Ma, Fawang Liu, Kefeng Zhai, Henggui Hu, Zhaojun Wei

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched 582 function targets and 87 target proteins pathways, respectively. …”
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