Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species by Kristopher J. L. Irizarry, Doug Bryant, Jordan Kalish, Curtis Eng, Peggy L. Schmidt, Gini Barrett, Margaret C. Barr

“…Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.…”
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A telomere-related signature for predicting prognosis and assessing immune microenvironment in osteosarcoma by Shihao Li, Lina Zhang, Haiyang Zhang

“…Subsequently, we analyzed the prognostic value, functional annotation, immune microenvironment, and cell communication patterns of the telomere-related signature in osteosarcoma via comprehensive bioinformatics analyses. Cell proliferation was analyzed using the CCK-8 assay, and cell migration and invasion capabilities were evaluated using the Transwell assay.ResultsBased on the SP110, HHAT, TUBB, MORC4, TERT, PPARG, MAP3K5, PAGE5, MAP7, and CAMK1G, a telomere-related signature was built in osteosarcoma patients. …”
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ATP-Binding Cassette Genes Genotype and Expression: A Potential Association with Pancreatic Cancer Development and Chemoresistance? by Li Pang, Beverly Word, Joshua Xu, Honggang Wang, George Hammons, Shiew-Mei Huang, Beverly Lyn-Cook

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Inosine monophosphate dehydrogenase 2 (IMPDH2) modulates response to therapy and chemo-resistance in triple negative breast cancer by Tatiane da Silva Fernandes, Bryan M. Gillard, Tao Dai, Jeffrey C. Martin, Kanita A. Chaudhry, Scott M. Dugas, Alyssa A. Fisher, Pia Sharma, RongRong Wu, Kristopher M. Attwood, Subhamoy Dasgupta, Kazuaki Takabe, Spencer R. Rosario, Anna Bianchi-Smiraglia

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Core-genome guided novel therapeutic targets identification and chimeric vaccine designing against Rickettsia rickettsii by Fizza Arshad, Asifa Sarfraz, Muhammad Shehroz, Umar Nishan, Asia Perveen, Riaz Ullah, Mohamed A. Ibrahim, Mohibullah Shah

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Development of immune-derived molecular markers for preeclampsia based on multiple machine learning algorithms by Zhichao Wang, Long Cheng, Guanghui Li, Huiyan Cheng

“…The contribution of immune dysregulation to PE is not fully understood, highlighting the need to explore molecular markers and their relationship with immune infiltration to potentially inform therapeutic strategies. We used bioinformatics tools to analyze gene expression data from the Gene Expression Omnibus (GEO) database using the GEOquery package in R. …”
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Combining Microarray Technology and Molecular Epidemiology to Identify Genes Associated with Invasive Group B Streptococcus by Lixin Zhang, Usha Reddi, Usha Srinivasan, Sheng Li, Stephanie M. Borchardt, Parvathy Pillai, Puja Mehta, Anne N. Styka, Joan DeBusscher, Carl F. Marrs, Betsy Foxman

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Retinitis Pigmentosa with EYS Mutations Is the Most Prevalent Inherited Retinal Dystrophy in Japanese Populations by Yuuki Arai, Akiko Maeda, Yasuhiko Hirami, Chie Ishigami, Shinji Kosugi, Michiko Mandai, Yasuo Kurimoto, Masayo Takahashi

“…For segregation analyses, 63 of their family members were employed. Bioinformatics data from 1,208 Japanese individuals were used as controls. …”
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Exploring the mechanism of Schisandra rubriflora in the treatment of polycystic ovary syndrome based on network pharmacology and molecular docking by Zhengyan Dou, Qingxian Li, Jing Zhang, Xin Zhang

“…Results A total of 14 bioactive ingredients of S. rubriflora and 26 potential therapeutic targets of S. rubriflora in PCOS treatment were obtained. Bioinformatics analyses suggested that the mechanisms of S. rubriflora in treating PCOS were related to IL-17 signaling pathway and TNF signaling pathway. …”
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Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing. by Lance D Eckerle, Michelle M Becker, Rebecca A Halpin, Kelvin Li, Eli Venter, Xiaotao Lu, Sana Scherbakova, Rachel L Graham, Ralph S Baric, Timothy B Stockwell, David J Spiro, Mark R Denison

“…The results define a novel genetic and bioinformatics model for introduction and identification of multi-allelic mutations in replication competent viruses that will be powerful tools for testing the effects of decreased fidelity and increased quasispecies diversity on viral replication, pathogenesis, and evolution.…”
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ACTN1 promotes cell invasion, migration, and EMT in thyroid cancer and is associated with immune infiltration by Song Chen, Xue Luo, Wentai Wang, Xing-hong Chen, Ning Ma, Xue-yin Zhu, Tian Zhou, Qing-jun Gao, Dai-wei Zhao

“…This study aimed to explore the expression and biological function of ACTN1 in THCA. Bioinformatics analysis revealed that ACTN1 was significantly upregulated in THCA and was associated with tumor size, extraglandular invasion, lymph node and distant metastasis, patient prognosis, and immune cell infiltration. qRT-PCR, immunohistochemistry, and western blotting verified the high expression of ACTN1 in the PTC samples. …”
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Enhancing Agricultural Disease Detection: A Multi‐Model Deep Learning Novel Approach by Muhammad Khalid Hamid, Said Khalid Shah, Ghassan Husnain, Yazeed Yasin Ghadi, Shahab Ahmad Al Maaytah, Ayman Qahmash

“…ABSTRACT Artificial intelligence, especially deep learning, has attracted significant interest in bioinformatics, with prominent applications in precision agriculture. …”
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The Long Noncoding RNA Gm9866/Nuclear Factor-κB Axis Promotes Macrophage Polarization by Xiaomin Liao, Xianxian Ruan, Xiubing Chen, Biaolin Zheng, Xianbin Wu, Zhejun Deng, Zhe Yang, Feng Wang, Shanyu Qin, Haixing Jiang

“…Long noncoding RNA Gm9866 was found to be closely related to macrophage polarization through bioinformatics analysis. In this study, by conducting real-time polymerase chain reaction analysis, it was observed that long noncoding RNA Gm9866 expression significantly increased after treatment with interleukin-4 but significantly decreased after treatment with lipopolysaccharide. …”
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Perilipin2-dependent lipid droplets accumulation promotes metastasis of oral squamous cell carcinoma via epithelial-mesenchymal transition by Jiayu Zhang, Jianmin Peng, Siyu Wang, Li Wang, Yutong Sun, Juan Xia, Bin Cheng, Qinchao Hu

“…Possible mechanisms of these biological effects were clarified by detecting the levels of epithelial-mesenchymal transition (EMT) markers and phosphatidylinositol 3-kinase (PI3K) pathway proteins as well as conducting various bioinformatics analyses. The results indicated that PA/OA promoted the migration and invasion of OSCC cells and induced PLIN2-dependent LDs accumulation in vitro. …”
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Redesigning error control in cross-linking mass spectrometry enables more robust and sensitive protein-protein interaction studies by Boris Bogdanow, Max Ruwolt, Julia Ruta, Lars Mühlberg, Cong Wang, Wen-feng Zeng, Arne Elofsson, Fan Liu

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Detection of colorectal‐cancer‐associated bacterial taxa in fecal samples using next‐generation sequencing and 19 newly established qPCR assays by Thulasika Senthakumaran, Tone M. Tannæs, Aina E. F. Moen, Stephan A. Brackmann, David Jahanlu, Trine B. Rounge, Vahid Bemanian, Hege S. Tunsjø

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Identification of Pseudoperonospora cubensis RxLR Effector Genes via Genome Sequencing by Rahel Dinsa Guta, Marc Semunyana, Saima Arif, Inyong Jeong, Sun Ha Kim, Jiyoung Min, Sang-Keun Oh

“…In this study, we sequenced the genome of the P. cubensis isolate CNU-OTH and identified RxLR effector genes using bioinformatics tools. A total of 45 RxLR effector genes were identified from the genome of P. cubensis. …”
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Prediction of circRNA-miRNA Associations Based on Network Embedding by Wei Lan, Mingrui Zhu, Qingfeng Chen, Jianwei Chen, Jin Ye, Jin Liu, Wei Peng, Shirui Pan

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Genome-wide identification and expression analysis of GRAS transcription factors under cold stress in diploid and triploid Eucalyptus by Jiannan Liu, Hao Chen, Chenhe Li, Kang Du, Jun Yang

“…This study conducted a bioinformatics analysis of Eucalyptus grandis GRAS family and investigated the expression patterns of GRAS genes in different ploidy Eucalyptus under cold treatment. …”
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Exploring the link between soil health and crop productivity by Yingying Xing, Xiukang Wang, Adnan Mustafa

“…By utilizing state-of-the-art bioinformatics, we offer an in-depth exploration of rhizosphere microbial communities, emphasizing the functions of phosphate-solubilizing and nitrogen-fixing bacteria in promoting vital nutrient cycles. …”
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