Modern Bioinformatics Solutions Used for Genetic Data Analysis by Ya. A. Kibirev, A. V. Kuznetsovskiy, S. G. Isupov, I. V. Darmov

Subjects: “…bioinformatics…”
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CATS: a bioinformatic tool for automated Cas9 nucleases activity comparison in clinically relevant contexts by Ettore Rocchi, Ettore Rocchi, Federico Magnani, Federico Magnani, Gastone Castellani, Gastone Castellani, Antonio Carusillo, Martina Tarozzi, Martina Tarozzi

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Modern Hardware and Software Solutions for Whole-Genome Sequencing, Prospects of Their Implementation in the Practice of Nuclear, Chemical and Biological Protection Troops of the A... by A. A. Petrov, A. V. Kazantsev, E. A. Kovalchuk, M. Yu. Pavlyukov, A. V. Sapkulov, D. A. Kutaev, S. V. Borisevich

“…For the successful use of NGS by units of the RCB protection troops of the Armed Forces of the Russian Federation, it is necessary to solve the main problem, which is the development of domestic hardware, appropriate bioinformatics tools and databases certified in accordance with the established procedure for functioning offiine without connecting to the Internet.…”
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«Okun-2» software-computing complex for calculating the mutational profile of samples of the sequenced whole genomes of mycobacteria tuberculosis by M. V. Sprindzuk, L. P. Titov, V. V. Slizen, A. E. Skryahin, E. M. Skryahina, O. M. Zalutskaya, A. P. Konchits

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Identifying pyroptosis- and inflammation-related genes in spinal cord injury based on bioinformatics analysis by Xiang-Xia, Kai-xuan Li, Qiu-Wei Li, Zuo-Meng Wu, Ruo-Cheng Guo, Cai-Liang Shen

“…This study utilized bioinformatics methods to identify pyroptosis-related genes (PRGs) and investigate their roles in inflammatory responses. …”
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Bioinformatics screening of therapeutic targets in chemoresistance human colon cancer HCT8 cell line by Zohreh Jahanafrooz

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Identification and verification of XDH genes in ROS induced oxidative stress response of osteoarthritis based on bioinformatics analysis by Chengze Qiu, Zhiyong Zhang, Haocheng Wang, Na Liu, Ruixin Li, Zhiheng Wei, Benjie Wang, Nan Zhang

“…Abstract The purpose of this study was to search for genes related to ros induced oxidative stress in osteoarthritis(OA) cartilage through bioinformatics analysis, and to verify the expression of related genes in articular cartilage of OA patients. …”
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THE SNP-MED SYSTEM FOR ANALYSIS OF THE EFFECT OF SINGLE-NUCLEOTIDE POLYMORPHISMS ON THE FUNCTION OF GENES ASSOCIATED WITH SOCIALLY SIGNIFICANT DISEASES by N. L. Podkolodnyy, D. A. Afonnikov, Yu. Yu. Vaskin, L. O. Bryzgalov, V. A. Ivanisenko, P. S. Demenkov, M. P. Ponomarenko, D. A. Rasskazov, K. V. Gunbin, I. V. Protsyuk, I. Yu. Shutov, P. N. Leontyev, M. Yu. Fursov, N. P. Bondar, E. V. Antontseva, T. I. Merkulova, N. A. Kolchanov

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Expression analysis of plasma extracellular vesicle associated candidate MiRNAs in endometriosis using integrative bioinformatics and experiential data by Samaneh Alsadat Sadati, Zahra Chekini, Faezeh Shekari, Maryam Hafezi, Azadeh Ghaheri, Maryam Shahhoseini, Ashraf Moini, Reza Aflatonian, Mehdi Totonchi, Parvaneh Afsharian

“…In order to identify candidate miRNAs, a comprehensive search was performed in PubMed database using the search terms “micro-RNA” and “endometriosis”. Then, bioinformatics analysis was performed utilizing the miRTarBase database, Enrichr, and relevant software. …”
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Bioinformatics Analysis and Functional Verification of Phytoene Synthase Gene <i>Pj</i>PSY1 of <i>Panax japonicus</i> C. A. Meyer by Tingting Tang, Rui Jin, Xilun Huang, E Liang, Lai Zhang

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Computational identification of promising genetic markers associated with molecular mechanisms of reduced rice resistance to <i>Rhizoctonia solani</i> under excess nitrogen fertili... by E. A. Antropova, A. R. Volyanskaya, A. V. Adamovskaya, P. S. Demenkov, I. V. Yatsyk, T. V. Ivanisenko, Y. L. Orlov, Ch. Haoyu, M. Chen, V. A. Ivanisenko

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A Comprehensive Joint Learning System to Detect Skin Cancer by Lubna Riaz, Hafiz Muhammad Qadir, Ghulam Ali, Mubashir Ali, Muhammad Ahsan Raza, Anca D. Jurcut, Jehad Ali

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Gene Surfing: An efficient and versatile tool for targeted enzyme mining in metagenomics by Tong Xu, Danyang Huang, Tingting Huang, Yuxin Wang, Wanqiu Chen, Shijunyin Chen, Yurong Qian, Haitao Yue

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Cloning, sequence and expression analysis of two SOC1 genes from Anthurium by MA Guangying, ZHU Kaiyuan, SHI Xiaohua, ZOU Qingcheng, LIU Huichun, ZHAN Jing, TIAN Danqing

“…Preliminary analysis of their characteristics, structure, and potential function were performed through bioinformatics software, combined with multiple sequence alignment and phylogenetic tree construction. …”
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Multi-omics analysis of the effects of pla2g4a on the prognosis of various cancers and its experimental validation in breast cancer cell lines by Yao Qian, Quan Yuan, Hao Yu, Rongjie Ye, Ming Niu, Feng Liu

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Use ATCCfinder to identify commercially available American Type Culture Collection strains based on sequence queries by Samuel I. Koehler, Earl A. Middlebrook, Blake T. Hovde, Erik R. Hanschen

“…Here we present the software ATCCfinder (GitHub: https://github.com/lanl/ATCCfinder, Zenodo: https://doi.org/10.5281/zenodo.15178103), utilizing ATCC application interface software (API) to generate query-able databases from ATCC genome resources. …”
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GNGT1 is a potential prognostic and immunologic biomarker in gastric cancer by Xuchong Huang, Juan Lin, Jian Wang, Weifeng Yang, Wenquan Ou, Xing Huang, Jiahua Chen, Zixing Zhang, Xiaohua Wu

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GeneRiskCalc: a web-based tool for genetic risk association analysis in case–control studies by Amrit Sudershan, Kuljeet Singh, Parvinder Kumar

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PuMA: PubMed gene/cell type-relation Atlas by Lucas Bickmann, Sarah Sandmann, Carolin Walter, Julian Varghese

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Increasing pathogenic germline variant diagnosis rates in precision medicine: current best practices and future opportunities by Sonam Dukda, Manoharan Kumar, Andrew Calcino, Ulf Schmitz, Matt A. Field

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