RETRACTED ARTICLE: Single-cell omics and machine learning integration to develop a polyamine metabolism-based risk score model in breast cancer patients by Xiliang Zhang, Hanjie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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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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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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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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Activin levels correlate with lymphocytic infiltration in epithelial ovarian cancer by Elizabeth T. Evans, Emily F. Page, Alex Seok Choi, Zainab Shonibare, Andrea G. Kahn, Rebecca C. Arend, Karthikeyan Mythreye

“…Immune gene expression profile was further explored within the TCGA‐OV cohort derived from The Cancer Genome Atlas (TCGA). Immunohistochemical analysis was performed to evaluate activin A and T‐cell markers CD8 and FoxP3 at the protein level. …”
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Clinical Utility of Combined Tissue and Plasma Next-Generation Sequencing in Patients With Advanced, Treatment-Naïve NSCLC by Helena Bote-de Cabo, MD, Marco Siringo, MD, Esther Conde, MD, PhD, Susana Hernández, PhD, Fernando López-Ríos, MD, PhD, Alicia Castelo-Loureiro, MD, Esther García-Lorenzo, MD, Javier Baena, MD-PhD, Mercedes Herrera, MD, Ana Belén Enguita, MD, Yolanda Ruano, PhD, Jon Zugazagoitia, MD, PhD, Luis Paz-Ares, MD, PhD

“…Methods: We retrospectively collected clinical and genomic data from 275 patients with treatment-naïve advanced NSCLC who had undergone plasma-based NGS at diagnosis in our institution. …”
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Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypan... by Peylhard, Moana, Berthier, David, Dayo, Guiguigbaza-Kossigan, Chantal, Isabelle, Sylla, Souleymane, Nidelet, Sabine, Dubois, Emeric, Martin, Guillaume, Sempéré, Guilhem, Flori, Laurence, Thévenon, Sophie

“…To this end, whole blood genome-wide transcriptome of three trypanotolerant taurine breeds (N’Dama, Lagune and Baoulé), one susceptible zebu (Zebu Fulani) and one African taurine x zebu admixed breed (Borgou) were profiled by RNA sequencing at four time points, one before and three during infection. …”
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Integrating microplastic research in sustainable agriculture: Challenges and future directions for food production by Marcelo Illanes, María-Trinidad Toro, Mauricio Schoebitz, Nelson Zapata, Diego A. Moreno, María Dolores López-Belchí

“…Currently, the application of omics technologies, including genomics, transcriptomics, and metabolomics, offers novel insights into molecular mechanisms that enable the identification of specific biomarkers associated with MP exposure. …”
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Writers, readers, and erasers of N6-Methyladenosine (m6A) methylomes in oilseed rape: identification, molecular evolution, and expression profiling by Chaofan Shan, Kui Dong, Dongyu Wen, Ziyi Ye, Fei Hu, Meryem Zekraoui, Jun Cao

“…During the course of evolution, whole genome duplication (WGD) and segmental duplication were the primary drivers of the expansion of m6A-related gene families. …”
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Domestication of different varieties in the cheese-making fungus Geotrichum candidum by Bennetot, Bastien, Vernadet, Jean-Philippe, Perkins, Vincent, Hautefeuille, Sophie, Rodríguez de la Vega, Ricardo C., O’Donnell, Samuel, Snirc, Alodie, Grondin, Cécile, Lessard, Marie-Hélène, Peron, Anne-Claire, Labrie, Steve, Landaud, Sophie, Giraud, Tatiana, Ropars, Jeanne

“…Geotrichum candidum is a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. …”
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Eucalyptus grandis WRKY genes provide insight into the role of arbuscular mycorrhizal symbiosis in defense against Ralstonia solanacearum by Jianlang Zhang, Xinzhu Yang, Chunyu Huo, Xinyi Fan, Qiutong Liu, Zhihong Liu, Yu Su, Zujing Chen, Zujing Chen

“…IntroductionWRKY transcription factors are essential for plant growth, health, and responses to biotic and abiotic stress.MethodsIn this study, we performed a deep in silico characterization of the WRKY gene family in the genome of Eucalyptus grandis. We also analyzed the expression profiles of these genes upon colonization by the arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis (Ri) and infection with the bacterial pathogen Ralstonia solanacearum (Rs).ResultsA total of 117 EgWRKYs were identified. …”
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Investigating the miRNA-mRNA interactome of human trabecular meshwork cells treated with TGF-β1 provides insights into the pathogenesis of pseudoexfoliation glaucoma. by Anton W Roodnat, Chelsey Doyle, Breedge Callaghan, Karen Lester, Megan Henry, Carl Sheridan, Declan J McKenna, Colin E Willoughby, Sarah D Atkinson

“…This is the first study to present a genome-wide microRNA-mRNA regulatory network for human trabecular meshwork cells treated with TGF-β1 and may serve to generate unbiased hypotheses about regulatory functions and mRNA targets of miRNAs in pseudoexfoliation glaucoma and may help to develop miRNA-based therapeutics.…”
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The Role of Phosphatidylethanolamine-N-methyltransferase (PEMT) Gene rs12449964 Polymorphism in the Development of Acute Pancreatitis and its Complications by T. A. Samgina, Yu. E. Azarova, Yu. V. Kanishchev, V. A. Lazarenko, P. M. Nazarenko, A. V. Polonikov

“…The average age of patients and healthy individuals was 48.9 ± 13.1 and 47.89 ± 12.1 years, respectively. Genomic DNA was isolated by a standard phenol-chloroform extraction method. …”
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Genetic evidence for the liver-brain axis: lipid metabolism and neurodegenerative disease risk by Zeyu Wang, Zixiao Yin, Guangyong Sun, Dong Zhang, Jianguo Zhang

“…The research incorporated UK Biobank genomic data to examine associations between genetic variants and lipid metabolism parameters. …”
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Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR by Ahtisham Fazeel Abbasi, Muhammad Nabeel Asim, Andreas Dengel

“…This groundbreaking technology holds immense potential for the development of targeted therapies for a wide range of diseases, including cancers, genetic disorders, and hereditary diseases. CRISPR-Cas9 based genome editing is a multi-step process such as designing a precise gRNA, selecting the appropriate Cas protein, and thoroughly evaluating both on-target and off-target activity of the Cas9-gRNA complex. …”
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Exploring the Causal Relationship and Molecular Mechanisms Between Fasting Insulin and Androgenetic Alopecia: A Mendelian Randomization Study with Bioinformatics Analysis by Ding X, Bai Z, Wang W, Gu Y, Li Z, Fan Y

“…In this study, a Mendelian randomization (MR) analysis was utilized to discover the causal associations between FI and AGA.Methods: Genome-wide association study (GWAS) data for FI and AGA were retrieved, and bidirectional MR analysis was conducted. …”
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Degradation and ultrastructural changes of resin-based pit and fissure sealants under simulated chewing conditions by Pimduean Sivavong, Ekamon Mahapoka, Anucharte Srijunbarl, Thawanrat Singthong, Thanchanok Suriyapongprapai, Soranun Chantarangsu, Murali Srinivasan, Thantrira Porntaveetus, Dusit Nantanapiboon

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A Bidirectional Mendelian Randomization Study Investigating the Causal Relationship Between Ankylosing Spondylitis and Chronic Obstructive Pulmonary Disease by Pan D, Dai X, Li P, Xue L

“…The analysis utilized publicly available statistics on AS and COPD from the Genome-wide Association Study (GWAS). The primary MR method employed was Inverse-Variance Weighting (IVW), supplemented by additional MR methods such as weighted median, MR-Egger, simple mode, and weighted mode. …”
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