Spatial transcriptome reveals histology-correlated immune signature learnt by deep learning attention mechanism on H&E-stained images for ovarian cancer prognosis by Chun Wai Ng, Kwong-Kwok Wong, Barrett C. Lawson, Sammy Ferri-Borgogno, Samuel C. Mok

“…Methods In this study, 773 WSIs of H&E-stained tumor sections from 335 patients with treatment naïve high-grade serous ovarian cancer who were included in The Cancer Genome Atlas (TCGA) Pan-Cancer study were used to train, and validate, and to test a ResNet101 CNN model modified with attention mechanism. …”
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The Prognostic Significance of TRs in Hepatocellular Carcinoma: Insights from TCGA and GEO Databases by Hao Zhou, Weijie Wang, Ruopeng Liang, Rongtao Zhu, Jiahui Cao, Chenguang Sun, Yuling Sun

“…Methods: This study utilized Kaplan-Meier analysis of TR expression profiles from The Cancer Genome Atlas (TCGA). Expression levels of TRs in HCC and immune single cells were assessed using datasets from the Gene Expression Omnibus (GEO) and TCGA, analyzed with R software. …”
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Crispant analysis in zebrafish as a tool for rapid functional screening of disease-causing genes for bone fragility by Sophie Debaenst, Tamara Jarayseh, Hanna De Saffel, Jan Willem Bek, Matthieu Boone, Ivan Josipovic, Pierre Kibleur, Ronald Y Kwon, Paul J Coucke, Andy Willaert

“…Six genes linked to severe recessive osteogenesis imperfecta (OI) and four associated with bone mineral density (BMD) from genome-wide association studies were analyzed using CRISPR/Cas9-based crispant screening in F0 mosaic founder zebrafish. …”
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Polymorphism of microsattelite loci within the grape germplasm collection maintained at the Dagestan Experiment Station of VIR by M. M. Agakhanov, V. A. Volkov, P. S. Ulianich, K. M. Abdullaev, E. N. Kislin

“…As for any other large germplasm collections, the problem of genetic identification of the accessions and their originality is critical for the ampelographical collection. Genome of Vitis vinifera L. contains many polymorphic microsatellite loci, their allele diversity could be used to reveal the genetic structure of the ex situ collection as well as for the identification of duplicates. …”
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The Immune Landscape of Hepatitis B Virus-Related Acute Liver Failure by Integration Analysis by Jiao Gong, Yaqiong Chen, Jing Cao, Yang Wang, Jiahao Chen, Danyang Li, Liuping Sha, Xinhua Li, Yutian Chong, Bo Hu

“…The enrichment scores of cell death gene sets from Kyoto Encyclopedia of Genes and Genomes (KEGG) were calculated by gene set variation analysis method, and a protein-protein interaction (PPI) network was constructed using Cytoscape. …”
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DHX37 Impacts Prognosis of Hepatocellular Carcinoma and Lung Adenocarcinoma through Immune Infiltration by Yanni Xu, Qiongchao Jiang, Hejun Liu, Xiaoyun Xiao, Dinghong Yang, Phei Er Saw, Baoming Luo

“…Coexpression genes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and fundamental regulators were performed via LinkedOmics. …”
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Modification of Gene Expression Involved in Alkaloid Production in Opium Poppy by VIGS Combined With Pretreatment of Macerozyme Enzyme by Deniz Ece Özcan, Deniz Köm, Ozan Doğan, Semiha Erişen, Selma Onarici

“…The combination of VIGS and enzymatic pretreatment provides a robust platform for targeted metabolic engineering, offering insights into the regulation of morphine biosynthesis and paving the way for advancements in pharmaceutical alkaloid production and functional genomics in medicinal plants.…”
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DETECTION OF CAMPYLOBACTER SPP. WITH REAL-TIME POLYMERASE CHAIN REACTION by G. S. Skitovich, K. V. Serova, N. B. Shadrova, O. V. Pruntova

“…The said method was used for testing 76 samples of raw materials of animal origin. Campylobacter spp. genome was detected in 18 samples. Obtained results showed that the optimized variant of real-time polymerase chain reaction based on 16S rRNA gene amplifi cation was a specifi c, sensitive, rapid, reproducible and accurate method for qualitative detection of Campylobacter spp. in samples of raw animal materials.…”
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The oncogenic roles of GPR176 in ovarian cancer: a molecular target for aggressiveness and gene therapy by Ning Yang, Wen-jing Yun, Zheng-guo Cui, Hua-chuan Zheng

“…Kyoto Encyclopaedia of Genes and Genomes analysis indicated that GPR176-related genes were involved in the ECM structural constituent and organisation and so on. …”
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RNA Sequencing Reveals the Differentially Expressed circRNAs between Stable and Unstable Carotid Atherosclerotic Plaques by Xueguang Lin, Ying Deng, Lujuan Ye, Bo Chen, Jindong Tong, Weijun Shi, Bo Wang, Bo Yu, Jingdong Tang

“…Functional evaluation of the DE circRNAs was conducted via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Results. …”
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SLC25A38 is required for mitochondrial pyridoxal 5’-phosphate (PLP) accumulation by Izabella A. Pena, Jeffrey S. Shi, Sarah M. Chang, Jason Yang, Samuel Block, Charles H. Adelmann, Heather R. Keys, Preston Ge, Shveta Bathla, Isabella H. Witham, Grzegorz Sienski, Angus C. Nairn, David M. Sabatini, Caroline A. Lewis, Nora Kory, Matthew G. Vander Heiden, Myriam Heiman

“…In this study, we used a genome-wide CRISPR interference screen in erythroleukemia cells and organellar metabolomics to identify the mitochondrial inner membrane protein SLC25A38 as a regulator of mitochondrial pyridoxal 5’-phosphate. …”
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Using spectrometric analysis for indirect estimation of 146S component concentration while measuring FMDV RNA amount by M. I. Doronin, D. V. Mikhalishin, N. Ye. Kamalova, A. V. Borisov

“…As expected, no FMDV genome or 146S particles were detected in the negative control sample.…”
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Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase by Hyun Gyu Lim, Ye Gao, Kevin Rychel, Cameron Lamoureux, Xuwen A. Lou, Bernhard O. Palsson

“…This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria.IMPORTANCENutrient limitations are critical environmental perturbations in bacterial physiology. …”
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Associations between sleep traits and colorectal cancer: a mendelian randomization analysis by Xiangyue Meng, Enshuo Fan, Dan Lv, Yongjing Yang, Shixin Liu

“…Publicly accessible GWAS (Genome-Wide Association Study) data were used to identify these variants to investigate the putative causal relationships between sleep traits and CRC. …”
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The association between primary frozen shoulder and serum lipids may be overestimated: evidence based on retrospective observational studies and Mendelian randomization by Yongchao Zhang, Wenhao Fan, Yichang Wang, Tengjing Dong, Deding Liu, Yiming Shao

“…Genetic variants for the serum lipids and frozen shoulder were then extracted from large-scale genome-wide association studies. Causal effects were assessed using Inverse variance weighting (IVW), Weighted median, MR-Egger, simple and weighted models in MR analysis.ResultsThe analysis showed that after excluding patients with diabetes and thyroid dysfunction, the serum lipids (TC, TG, HDL, and LDL) in the primary frozen shoulder group were no different from those of normal individuals. …”
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Intersection of rare pathogenic variants from TCGA in the All of Us Research Program v6 by Blaine A. Bates, Kylee E. Bates, Spencer A. Boris, Colin Wessman, David Stone, Justin Bryan, Mary F. Davis, Matthew H. Bailey

“…Summary: Using rare cancer predisposition alleles derived from The Cancer Genome Atlas (TCGA) and high cancer prevalence (14% of participants) in All of Us (version 6), we assessed the impact of these rare alleles on cancer occurrence in six broad groups of genetic similarity provided by All of Us: African/African American (AFR), Admixed American/Latino (AMR), East Asian (EAS), European (EUR), Middle Eastern (MID), or South Asian (SAS). …”
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Chromatin environment-dependent effects of DOT1L on gene expression in male germ cells by Manon Coulée, Alberto de la Iglesia, Mélina Blanco, Clara Gobé, Clémentine Lapoujade, Côme Ialy-Radio, Lucia Alvarez-Gonzalez, Guillaume Meurice, Aurora Ruiz-Herrera, Pierre Fouchet, Julie Cocquet, Laïla El Khattabi

“…This coincides with a significant increase in DOT1L expression at this stage and a genome-wide acquisition of H3K79me2, particularly on the sex chromosomes. …”
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The effect of coagulation traits on the risk of retinal vein occlusion: a mendelian randomization study by Chaoyi Yuan, Chao He, Ling Zuo, Baoxing Liu, Hui Qi

“…This study aims to investigate the potential causal relationship between coagulation traits and the risk of RVO by analyzing publicly available genome-wide association study (GWAS) summary statistics. …”
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Exploring the bidirectional causality between neuroticism and frailty: a Mendelian randomization analysis by Yuhang Xing, Rui Pu, Mengdie Fu, Zhikang Wang, Zhen Wang, Xiaopeng Shang, Guoli Yang, Zhiwei Jiang

“…Methods The neuroticism genome-wide association study (GWAS) data from the UK Biobank contained twelve neuroticism-related traits with 489,212 participants. …”
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Feature Selection in Cancer Classification: Utilizing Explainable Artificial Intelligence to Uncover Influential Genes in Machine Learning Models by Matheus Dalmolin, Karolayne S. Azevedo, Luísa C. de Souza, Caroline B. de Farias, Martina Lichtenfels, Marcelo A. C. Fernandes

“…Gene expression data from RNA-seq, extracted from The Cancer Genome Atlas (TCGA), were used to train ML models, including decision trees (DTs), random forest (RF), and XGBoost (XGB), which achieved accuracies of 98.69%, 99.82%, and 99.37%, respectively. …”
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