MetArea: a software package for analysis of the mutually exclusive occurrence in pairs of motifs of transcription factor binding sites based on ChIP-seq data by V. G. Levitsky, A. V. Tsukanov, T. I. Merkulova

“…ChIP-seq technology, which is based on chromatin immunoprecipitation (ChIP), allows mapping a set of genomic loci (peaks) containing binding sites (BS) for the investigated (target) transcription factor (TF). …”
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Standardization and validation of a novel reverse transcriptase polymerase chain reaction method for detecting virulent strains of the infectious bursal disease virus by Vladimir Longa-Bobadilla, Phillip Ormeño-Vásquez, Manuel Criollo-Orozco, Luis Tataje-Lavanda, Katherine Huamán-Gutierrez, Ángela Montalván, Mirko Zimic, Manolo Fernández-Sanchez, Manolo Fernández-Díaz

“…For many years, the development of molecular techniques for either diagnostic purposes or surveillance of the appearance of new pathogenic strains has mainly focused on targeting the VP2 genomic region. However, due to the constant necessity for the discrimination between already prevalent vaccine strains and new pathogenic strains of this virus, it becomes imperative to have an immediate molecular method targeting a consensus sequence to achieve this task using field samples to reduce costs. …”
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Los olvidados: Non-BRCA variants associated with Hereditary breast cancer in Mexican population by Dione Aguilar, María Lourdes Garza-Rodríguez, Carolina Elizabeth Muñiz-Garza, Fernando Alcorta Nuñez, Cynthia Mayte Villarreal-Garza, Oscar Vidal-Gutiérrez, Diana Cristina Pérez-Ibave, Carlos Horacio Burciaga-Flores

“…Methods This multicentric study included 1285 patients with HBOC diagnosis from four oncologic centers in northeast Mexico from 2016 to 2023. Genomic and clinical data were analyzed based on multi-gene panel results and electronic records of the medical geneticist consultation. …”
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Overcoming the Silencing of Doxycycline-Inducible Promoters in hiPSC-derived Cardiomyocytes [version 1; peer review: 1 approved, 2 approved with reservations] by Michelle Guichardaz, Elisa Balmas, Alessandro Bertero, Sveva Bottini

“…The doxycycline (dox)-inducible OPTi-OX system, which integrates the Tet-On 3G transactivator and dox-responsive transgene at the hROSA26 and AAVS1 genomic safe harbors (GSHs), respectively, offers a promising solution. …”
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Revealing the core suppression effects of various Di (2-ethylhexyl) phthalate exposure on early meiosis progression in postnatal male mice via single-cell RNA sequencing by Baoquan Han, Lei Hua, Shuai Yu, Wei Ge, Cong Huang, Yu Tian, Chunxiao Li, Jiamao Yan, Tian Qiao, Jiachen Guo, Dongliang Lu, Bin Wang, Diya Cai, Yunqi Zhang, Shaolin Liang, Jianjuan Zhao, Qi Hou, Wei Shen, Zhongyi Sun

“…The transcriptomic changes in testicular cells of postnatal male rodents following DEHP exposure were meticulously analyzed using 10X Genomics single-cell RNA sequencing in this study. …”
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Effect of Acetyl tributyl citrate on bone metabolism based on network toxicology and molecular docking technology by Xuan Lin, Kun Lin, Yue Lai, Qingping Peng, Miao Xu, Yiting Xu, Jialin Yang, Huan Liu, Jianlin Shen

“…In-depth Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, conducted within the Metascape database, revealed that the core targets of ATBC’s influence on bone metabolism are predominantly concentrated within vital signaling cascades, including thyroid hormone signaling, FOXO signaling, glucagon signaling, AMPK signaling, insulin signaling, adipocytokine signaling, and Notch signaling pathways. …”
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Evaluating the Association Between Methylenetetrahydrofolate Reductase (Rs1801131 and Rs1801133) Gene Polymorphisms and Severity of Coronary Lesions in Patients With STEMI and NSTE... by Behnam Nazarzadeh, Saeedeh sadat Ghazanfari, Farzaneh Karimi, Seyed ali Moezibady, Fatemeh Salmani, Kazem Dastjerdi, Hamidreza Mohammadi

“…The angiographical characteristics of CAD were defined by the SYNTAX score. Genomic DNA was isolated from peripheral blood and genotyped for rs1801131 and rs1801133 using the TaqMan real‐time PCR method. …”
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Exploring the multi-targeted mechanism of Saikosaponin A in prostate cancer treatment: a network pharmacology and molecular docking approach by Genbao Zhu, Genbao Zhu, Genbao Zhu, Zhiming Jiang, Niuping Zhu, Niuping Zhu, Donghui Wang, Donghui Wang, Tianpeng Guo, Tianpeng Guo, Yiqing Meng, Yiqing Meng, Yi Zhu, Yi Zhu, Kemeng Tan, Mengxue Hu, Heng Tang, Xuannian Wang, Xuannian Wang

“…Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to elucidate associated biological functions and signaling pathways. …”
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Identification of Critical Signature in Post‐Traumatic Stress Disorder Using Bioinformatics Analysis and in Vitro Analyses by Lifen Liu, Yang Liu, Rui Li, Yue Teng, Shuyang Zhao, Jinhong Chen, Changjiang Li, Xinyu Hu, Lin Sun

“…Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for functional annotation and enrichment analysis, respectively. …”
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A survey of the Sli gene in wild and cultivated potato by Mercedes Ames, Andy Hamernik, William Behling, David S. Douches, Dennis A. Halterman, Paul C. Bethke

“…DNA sequence alignment and phylogenetic trees based on genomic and protein sequences show that there are two highly conserved groups of Sli sequences. …”
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Molecular Detection of Panton Valentine Leukocidin Toxin in Clinical Isolates of Staphylococcus aureus from Kiambu County, Kenya by Sani Iliya, Jonathan Mwangi, Ronald Maathai, Mary Muriuki, Christopher Wainaina

“…The detection of PVL toxins was performed by amplification of genomic DNA and by reverse hybridization that identifies PVL genes using Geno Type MRSA kit. …”
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Mutation in the COL2A1 gene is associated with acetabular dysplasia by Miaomiao Xin, Xin Guan, Xin Guan, Jiangfei Yang, Yi Li, Zhentao Man, Hongsheng Sun, Min Fu

“…BackgroundDevelopmental dysplasia of the hip (DDH) is one of the most common developmental disorders worldwide, caused by a combination of genetic and environmental factors.MethodsTo investigate the genetic etiology of DDH in a proband (a 27-year-old male), we reviewed the patient’s clinical data and collected peripheral blood samples from the proband and his parents. Genomic DNA was extracted, and polymerase chain reaction (PCR) amplification was performed. …”
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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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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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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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Different DNA Loidy Patterns for the Differentiation of Common Subtypes of Renal Tumors by Guorong Li, Michèle Cottier, Odile Sabido, Anne Gentil-Perret, Claude Lambert, Christian Genin, Jacques Tostain

“…DNA ploidy is viewed as a marker of gross genomic aberrations. The aim of this study is to evaluate the DNA ploidy in the common subtypes of renal tumors to increase our understanding of renal tumor biology and to broaden clinical application of DNA ploidy. …”
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Analysis of Bacterial Diversity in Different Heavy Oil Wells of a Reservoir in South Oman with Alkaline pH by Biji Shibulal, Saif N. Al-Bahry, Yahya M. Al-Wahaibi, Abdulkadir E. Elshafie, Ali S. Al-Bemani, Sanket J. Joshi

“…Molecular approaches like proteomic and genomic characterization of the isolates are replacing the traditional method of identification with systemic classification. …”
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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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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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