Variational Approaches for Drug-Disease-Gene Links in Periodontal Inflammation by Pradeep Kumar Yadalam, Prabhu Manickam Natarajan, Musab Hamed Saeed, Carlos M. Ardila

“…Methods: Genes associated with Wnt-related periodontal inflammation were identified through comprehensive literature reviews and genomic databases. Their roles in various biological processes were evaluated using gene set enrichment analysis, employing tools like Enrichr, which integrates diverse gene sets from sources such as DSigDB, DisGeNET, and Lincs_l1000.drug. …”
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Isolation and Identification of Lipase-producing Actinobacteria from the Lut Desert of Iran by Samira Abedi-Dolatabadi, Moj Khaleghi, Sedigheh Ghasemzadeh, Azadeh Lohrasbi-Nejad, Arastoo Badoei Delfard

“…Actinobacteria, which are Gram-positive bacteria, have the largest genome size among bacteria and produce various secondary metabolites, including enzymes. …”
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Dicoumarol sensitizes hepatocellular carcinoma cells to ferroptosis induced by imidazole ketone erastin by Ziwei Yang, Ziwei Yang, Tixin Han, Ruibin Yang, Ruibin Yang, Yinuo Zhang, Yinuo Zhang, Yifei Qin, Yifei Qin, Yifei Qin, Jialu Hou, Jialu Hou, Fei Huo, Fei Huo, Zhuan Feng, Zhuan Feng, Yaxin Ding, Yaxin Ding, Jiali Yang, Jiali Yang, Gang Zhou, Gang Zhou, Shijie Wang, Shijie Wang, Xiaohang Xie, Xiaohang Xie, Peng Lin, Peng Lin, Zhi-Nan Chen, Zhi-Nan Chen, Jiao Wu, Jiao Wu

“…The intrinsic factors determining sensitivity to IKE-induced ferroptosis remain to be explored to improve its efficacy.MethodsBulk RNA-sequencing data from hepatocellular carcinoma (HCC) and normal liver tissues were collected from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. …”
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Killer-Cell Immunoglobulin-Like Receptors (KIR) in HIV-Exposed Infants in Cameroon by Kagoué Simeni Luc-Aimé, Yindom Louis-Marie, Loni Ekali Gabriel, Clauvis Kunkeng Yengo, F. Esemu Livo, Nguedia Jules Clement Assob

“…This may be partly due to differences in host immunogenetic factors in highly polymorphic regions of the human genome such as those encoding the killer-cell immunoglobulin-like receptor (KIR) molecules which modulate the activities of natural killer cells. …”
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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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RETRACTED ARTICLE: Single-cell omics and machine learning integration to develop a polyamine metabolism-based risk score model in breast cancer patients by Xiliang Zhang, Hanjie Guo, Xiaolong Li, Wei Tao, Xiaoqing Ma, Yuxing Zhang, Weidong Xiao

“…Data from The Cancer Genome Atlas, Gene Expression Omnibus, and Genotype-Tissue Expression identified 286 differentially expressed genes linked to polyamine pathways in breast cancer. …”
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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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Surveillance of tick-borne encephalitis virus foci in Slovakia: A seroprevalence study in ruminants combined with virus detection in ticks by Martina Ličková, Bronislava Víchová, Markéta Derdáková, Monika Sláviková, Sabína Fumačová Havlíková, Dana Zubriková, Diana Selyemová, Michal Chvostáč, Lucia Blaňarová, Viktória Čabanová, Veronika Vaňová, Lucia Šulejová, Jana Kerlik, Tomáš Szemes, Katarína Šoltys, Boris Klempa

“…Obtained full-length genome sequences revealed high genetic diversity and phylogenetic clustering with virus strains found across Europe. …”
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Physical activities and breast cancer: a Mendelian randomization study by Lishan Ding, Qingliang Chen, Hao Liang, Meng Shen, Ming Zheng, Zhaojun Li

“…Material and methods Genome-wide association studies utilizing data from the UK Biobank baseline were employed to analyze PA phenotypes, encompassing 460,376 participants. …”
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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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Analysis of marker substitutions in A/chicken/Astrakhan/2171-1/2020 H5N8 isolate of avian influenza virus recovered in the Astrakhan Oblast by N. G. Zinyakov, A. V. Andriyasov, Ye. V. Ovchinnikova, A. A. Kozlov, P. D. Zhestkov, D. B. Andreychuk, I. A. Chvala

“…Comparative analysis of genome segments using available databases showed that A/chicken/Astrakhan/2171-1/2020 H5N8 virus related to А/Н5 avian influenza virus isolates detected in the Russian Federation in 2016–2020. …”
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Construction and Investigation of MicroRNA-mRNA Regulatory Network of Gastric Cancer with Helicobacter pylori Infection by Ping Yang, Junjie Liu, Tianci Yang, Lei Zhang, Peiyou Gong, Boqing Li, Xiuzhi Zhou

“…We identified differentially expressed microRNAs (DEMs) and genes (DEGs) from the Gene Expression Omnibus (GEO) dataset, constructed microRNA-(miRNA-)mRNA expression networks, analyzed the function and signal pathway of cross-genes, analyzed the relations between cross-genes and GC prognosis with the Cancer Genome Atlas (TCGA) data, and verified the expression of cross-genes in patients with H. pylori infection. …”
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The cinnamyl alcohol dehydrogenase gene family is involved in the response to Fusarium oxysporum in resistant and susceptible flax genotypes by R. O. Novakovskiy, L. V. Povkhova, G. S. Krasnov, T. A. Rozhmina, A. A. Zhuchenko, L. P. Kudryavtseva, E. N. Pushkova, P. Kezimana, A. V. Kudryavtseva, A. A. Dmitriev, N. V. Melnikova

“…After filtering to exclude the F. oxysporum transcriptome, the remaining reads were mapped to the L. usitatissimum genome and quantified. Then, the expression levels of cinnamyl alcohol dehydrogenase (CAD) family genes, which are known to be involved in the response to F. oxysporum, were evaluated in resistant and susceptible flax genotypes. …”
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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 genetic associations and drug targets for mitochondrial proteins and schizophrenia risk by Wenxi Sun, Ping Sun, Jin Li, Qun Yang, Qing Tian, Shiting Yuan, Xueying Zhang, Peng Chen, Chuanwei Li, Xiaobin Zhang

“…We used summary data from a genome-wide association study (GWAS) of 66 mitochondria-associated proteins in 3,301 individuals from Europe, as well as a GWAS on the large, multi-ethnic ancestry of SCZ, involving 76,755 cases and 243,649 controls. …”
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PlantReg: the reconstruction of links between transcription factor regulatory networks and biological processes under their control by V. V. Lavrekha, N. A. Omelyanchuk, A. G. Bogomolov, E. V. Zemlyanskaya

“…The pleiotropic effect of a gene is due to its participation in numerous biological processes involved in different traits. A widespread use of genome-wide sequencing of transcripts and transcription factor (TF) binding regions has made the following tasks relevant: unveiling pleiotropic effects of TFs based on the functions of their target genes; compiling the lists of TFs that regulate biological processes of interest; and describing the ways of TF functioning (their primary and secondary targets, higher order targets, TF interactions in the process under study). …”
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Genetic evidence for the causal effect of clonal hematopoiesis on pulmonary arterial hypertension by Jia-Yong Qiu, Shen-Shen Huang, Chao Liu, Dong Ding, Yan-Hong Xu, Yi-Min Mao, Ya-Dong Yuan

“…Methods We utilized genetic variants associated with CH as instrumental variables, identified from two large genome-wide association studies (GWAS) involving 359,088 participants in the discovery cohort and 184,121 participants in the validation cohort, all of European descent. …”
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Urinary Uromodulin Levels and UMOD Variants in Black South Africans with Hypertension-Attributed Chronic Kidney Disease by Nolubabalo Unati Nqebelele, Caroline Dickens, Therese Dix-Peek, Raquel Duarte, Saraladevi Naicker

“…Patients with chronic kidney disease (CKD) have reduced urinary uromodulin levels secondary to tubular damage. Genome wide association studies identified significant single nucleotide polymorphism (SNP) associations with CKD at the uromodulin (UMOD) locus. …”
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