LINC00707 Regulates miR-382-5p/VEGFA Pathway to Enhance Cervical Cancer Progression by Hua Guo, Jing Li, Furong Fan, Ping Zhou

“…In addition, the action of LINC00707 in cervical cancer cells was studied using bioinformatic tools and luciferase reporter experiment. …”
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Comprehensive Analysis of Gene Signatures of m6ARNA Methylation Regulators in Lung Adenocarcinoma and Development of a Risk Scoring System by Chundi Gao, Huayao Li, Wenzhe Ma, Qiming Zhang, Cun Liu, Lijuan Liu, Jing Zhuang, Changgang Sun

“…Overall, our findings revealed an important role of M6A methylation regulators in LUAD, and our risk scoring system involving these regulators might help to screen groups at high risk for LUAD and provide important theoretical bioinformatic support for evaluating the prognosis of such patients.…”
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Identification of mitochondrial carrier homolog 2 as an important therapeutic target of castration-resistant prostate cancer by Yankui Liu, Anjie Chen, Yufan Wu, Jiang Ni, Rong Wang, Yong Mao, Ning Sun, Yuanyuan Mi

“…Abstract We here investigate the expression of the mitochondrial carrier homolog 2 (MTCH2) and its potential function in castration-resistant prostate cancer (CRPC). Bioinformatic analyses reveal that MTCH2 overexpression is associated with critical clinical parameters of prostate cancer. …”
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Translational regulation of PKD1 by evolutionarily conserved upstream open reading frames by Lei Chen, Xia Gao, Xiangshen Liu, Ye Zhu, Dong Wang

“…In this study, we investigated the effects of uORFs and uORF-affecting variants by combining bioinformatic analyses, luciferase reporter assays, RT-qPCR and immunoblotting experiments. …”
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Comprehensive analysis of cuproptosis-related genes in immune infiltration and development of a novel diagnostic model for acute kidney injury by Yajing Li, Yingxue Ding

“…Nomogram and DCA further confirmed the accuracy of the model in predicting the risk of AKI.Conclusion This study elucidated the role of cuproptosis in AKI and revealed the association between CRGs and infiltrated immune cells through comprehensive bioinformatic techniques. The six-gene cuproptosis-related signature exhibited remarkable predictive efficiency for AKI.…”
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In Vitro and In Silico Analysis of Bergenia ciliata and Mimosa pudica for Inhibition of α-Amylase by Mahesh Bohara, Sajani Ghaju, Kabita Sharma, Surya Kant Kalauni, Karan Khadayat

“…The biological potential of the reported phytochemicals was also assessed by using bioinformatic tools. Furthermore, the active phytochemicals from these plants were docked with human pancreatic α-amylase to study their inhibitory activities to this enzyme. …”
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Transcriptomic-Based Identification of miR-125a Novel Targets in Human Hepatocarcinoma Cells by Ilenia De Leo, Nicola Mosca, Mariaceleste Pezzullo, Danila Valletta, Francesco Manfrevola, Vincenza Grazia Mele, Rosanna Chianese, Aniello Russo, Nicoletta Potenza

“…The merging of down-regulated genes with results from bioinformatic predictive tools yielded a number of candidate direct targets that were further experimentally validated by luciferase-based reporter assays. …”
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OMIC Technologies and Vaccine Development: From the Identification of Vulnerable Individuals to the Formulation of Invulnerable Vaccines by Nicola Cotugno, Alessandra Ruggiero, Veronica Santilli, Emma Concetta Manno, Salvatore Rocca, Sonia Zicari, Donato Amodio, Manuela Colucci, Paolo Rossi, Ofer Levy, Federico Martinon-Torres, Andrew J. Pollard, Paolo Palma

“…Finally, we will discuss how system biology “OMICs” data can be used to design bioinformatic tools to predict the vaccination outcome providing genetic and molecular “signatures” of protective immune response. …”
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Placental Vimentin Expression in Preeclampsia and Gestational Diabetes Mellitus by Fırat Asir, Suleyman Cemil Oglak, Tugcan Korak, Fatih Tas, Mehmet Yilmaz, Fikri Erdemci, Firat Sahin, Hayat Ayaz, Emine Zeynep Yilmaz, Gokhan Bolluk

“…Vimentin expression was generally recorded as negative in placental villi, fibrinoid substances, and connective tissue cells in the GDM group. Bioinformatic analysis showed that the AGE-RAGE signaling pathway and cancer-related pathways were mainly observed in Vimentin-associated pathways, which finally activate inflammatory pathways in both preeclampsia and GDM. …”
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Proteomic Profiling and Functional Analysis of B Cell-Derived Exosomes upon Pneumocystis Infection by Dan Ma, Qian-Yu Zhang, Heng-Mo Rong, Kan Zhai, Zhao-Hui Tong

“…In this study, using tandem mass tag-based quantitative proteomics coupled with bioinformatic analysis, we attempted to characterize exosomes derived from B lymphocytes in response to PCP. …”
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Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer’s Disease Mutations by Alejandro Soto-Ospina, Pedronel Araque Marín, Gabriel de Jesús Bedoya, Andrés Villegas Lanau

“…From a theoretical analysis, a preliminary bioinformatic study is made to find the phosphorylation patterns in the protein and the hydropathic index according to the polarity and chemical environment. …”
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Methods of yeast genome editing by A. S. Rozanov, V. N. Shlyahtun, L. A. Tekutieva, O. M. Son, S. V. Sizova, S. E. Peltek

“…Many high­throughput methods were developed in the second decade of the XXI century, including those used in genomics, transcriptomics, proteomics, metabolomics, interactomics, etc. Modern bioinformatic databases now allow one to rapidly process the increasing flow of information and model cellular processes. …”
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Microcephalic osteodysplastic primordial dwarfism type II in four Indian children with PCNT variants by Amit Singh, Mahak Garg, Mohammed Shariq, Preeti Khetarpal, Inusha Panigrahi

“…Data were analyzed using standard bioinformatic algorithms and possible causal variants identified. …”
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Dataset for comparative analysis of precision metagenomics and traditional methods in urinary tract infection diagnosticsNCBI by Rob E. Carpenter, Sadia Almas, Vaibhav K. Tamrakar, Rahul Sharma

“…The dataset includes 47 urine samples, each analyzed by microbial culture, PCR, and precision metagenomics, followed by bioinformatic classification using the Explify® platform. precision metagenomics identified significantly more uropathogens (62 distinct organisms) compared to PCR (19 organisms) and microbial culture (13 organisms), with 98 % of samples testing positive for polymicrobial infections via precision metagenomics. …”
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Structure and Expression Analyses of SVA Elements in Relation to Functional Genes by Yun-Jeong Kwon, Yuri Choi, Jungwoo Eo, Yu-Na Noh, Jeong-An Gim, Yi-Deun Jung, Ja-Rang Lee, Heui-Soo Kim

“…SINE-VNTR-Alu (SVA) elements are present in hominoid primates and are divided into 6 subfamilies (SVA-A to SVA-F) and active in the human population. Using a bioinformatic tool, 22 SVA element-associated genes are identified in the human genome. …”
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lncRNA HHIP-AS1 Promotes the Osteogenic Differentiation Potential and Inhibits the Migration Ability of Periodontal Ligament Stem Cells by Qianyi Qin, Haoqing Yang, Chen Zhang, Xiao Han, Jing Guo, Zhipeng Fan, Jie Guo

“…In addition, the RNA sequencing data showed that 356 mRNAs and 14 lncRNAs were upregulated, including receptor tyrosine kinase-like orphan receptor 2 and nuclear-enriched abundant transcript 1, while 185 mRNAs and 6 lncRNAs were downregulated, including fibroblast growth factor 5 and LINC00973, in HHIP-AS1-depleted PDLSCs. Bioinformatic analysis revealed several biological processes and signaling pathways related to HHIP-AS1 functions, including the PI3K-Akt signaling pathway and JAK-STAT signaling pathway. …”
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Extracellular Vesicle-Loaded Oncogenic lncRNA NEAT1 from Adipose-Derived Mesenchymal Stem Cells Confers Gemcitabine Resistance in Pancreatic Cancer via miR-491-5p/Snail/SOCS3 Axis by Rongxiang Wu, Zhan Su, Le Zhao, Ruifeng Pei, Yiren Ding, Deqiang Li, Shuo Zhu, Lu Xu, Wei Zhao, Wuyuan Zhou

“…The binding affinity among NEAT1, miR-491-5p, and Snail was identified through bioinformatic analysis and experimental validation. NEAT1 competitively bound to miR-491-5p to elevate Snail expression and diminish SOCS3 expression. …”
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CRIP1 inhibits cutaneous melanoma progression through TFAM-mediated mitochondrial biogenesis by Jianqiang Wu, Lixia Chen, Peijun Wen

“…However, the biological function and underlying mechanisms of CRIP1 in melanoma progression are largely unknown. Bioinformatic prediction of CRIP1 expression in melanoma and its association with clinical parameters and prognosis of patients. …”
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Alternative splicing expands the antiviral IFITM repertoire in Chinese rufous horseshoe bats. by Nelly S C Mak, Jingyan Liu, Dan Zhang, Jordan Taylor, Xiaomeng Li, Kazi Rahman, Feiyu Chen, Siddhartha A K Datta, Kin Kui Lai, Zhengli Shi, Nigel Temperton, Aaron T Irving, Alex A Compton, Richard D Sloan

“…In parallel with human IFITM1-3, bat IFITM isoforms localize to distinct sites of virus entry which influences their antiviral potency. Further bioinformatic analysis of IFITM repertoires in 206 mammals reveals that alternative splicing is a recurring strategy for IFITM diversification, albeit less widely adopted than gene duplication. …”
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Tumor mutational burden quantification from targeted gene panels: major advancements and challenges by Sara Gandini, Laura Fancello, Pier Giuseppe Pelicci, Luca Mazzarella

“…Moreover, we highlight how various experimental, platform-related or methodological variables, as well as bioinformatic pipelines, influence panel-based TMB quantification. …”
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