Genome assembly of <i>Vitis rotundifolia</i> Michx. using third-generation sequencing (Oxford Nanopore Technologies) by M. M. Agakhanov, E. A. Grigoreva, E. K. Potokina, P. S. Ulianich, Y. V. Ukhatova

“…Stage 4 included not only de novo sequencing, but also the analysis of the available bioinformatic data, thus minimizing errors and increasing precision during the assembly of the studied genome. …”
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Exosomal miR-543 Inhibits the Proliferation of Ovarian Cancer by Targeting IGF2 by Shupei Zhang, Diling Pan, Shaoyu Zhang, Qiumei Wu, Lan Zhen, Shihuang Liu, Jingjing Chen, Rong Lin, Qiuhua Hong, Xiangqin Zheng, Huan Yi

“…Differentially expressed microRNAs in exosomes derived from OvCa cell lines were identified by bioinformatic analysis and verified by RT-PCR. Cell proliferation ability was estimated by clonogenic and 5-ethynyl-2′-deoxyuridine assays in vitro and in vivo. …”
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Prospects for mineral biofortification of wheat: classical breeding and agronomy by I. N. Leonova, E. V. Ageeva, V. K. Shumny

“…The new markers obtained from wheat genome sequencing and application of bioinformatic methods (GWAS, meta-QTL analysis) has expanded our knowledge on the traits that determine the grain mineral concentration and has identified the key gene candidates. …”
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The search for microRNAs potentially involved in the selfrenewal maintaining of laboratory rat pluripotent stem cells by V. V. Sherstyuk, S. P. Medvedev, M. T. Ri, Y. V. Vyatkin, O. V. Saik, D. N. Shtokalo, S. M. Zakian

“…We analyzed the expression of miRNAs in rat embryonic stem cells, induced pluripotent stem cells and embryonic fibroblasts using bioinformatic methods and data obtained with next generation sequencing. …”
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THE ORIGIN OF SYNAPTONEMAL COMPLEX PROTEINS. SEARCH FOR RELATED PROTEINS IN PROTEOMES OF ALGAE, LOWER FUNGI, MOSSES, AND PROTOZOANS by T. M. Grishaeva, Yu. F. Bogdanov

“…Proteins similar to known proteins of the synaptonemal complexes (SCs) of seven species of higher eukaryotes, from budding yeast to mouse, which are used as models for studying meiosis, have been sought by bioinformatical methods. In the proteomes of green and brown algae, mosses, a number of lowest fungi, Euglenozoa, Apicomplexa, and some other unicellular eukaryotes, proteins containing the HORMA domain show the greatest similarity to SC proteins of the model organisms. …”
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16S rRNA metabarcoding applied to the microbiome of insect products (novel food): a comparative analysis of three reference databases by Gabriele Spatola, Alice Giusti, Laura Gasperetti, Roberta Nuvoloni, Alessandra Dalmasso, Francesco Chiesa, Andrea Armani

“…The process involves a "dry-lab" phase where NGS data are processed through bioinformatic pipelines, which finally rely on taxonomic unit assignment against reference databases to assign them at order, genus, and species levels. …”
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GENE EXPRESSION AND mRNA SECONDARY STRUCTURES IN DIFFERENT Mycoplasma SPECIES by V. S. Sokolov, V. A. Likhoshvai, Yu. G. Matushkun

“…Microorganisms that feed on humans and pets are particularly interesting. In this work, bioinformatical analysis of 62 Mycoplasma strains is performed. …”
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Molecular anti-tumorigenic mechanism of Radix Polygoni Multiflori-derived exosome-like nanoparticles by Mingqing Yang, Lining Xu, Weiyu Wang

“…RNA sequencing and qPCR experiments were performed, and the results of bioinformatic analyses revealed that RPM-ELNs could globally regulate expression levels of numerous genes associated with cancer and the cell cycle. …”
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circRNA Expression Profile in Dental Pulp Stem Cells during Odontogenic Differentiation by Ming Chen, Yeqing Yang, Junkai Zeng, Zilong Deng, Buling Wu

“…This study reported 187 circRNAs that were differentially expressed in hDPSCs during odontogenic differentiation. Bioinformatic analysis of the expression data suggested that circRNA-miRNA-mRNA networks might act as a crucial mechanism for hDPSC odontogenic differentiation, providing a theoretical foundation for the study of pulp regeneration regulation by circRNAs.…”
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Exploring the role of oxidative stress in carotid atherosclerosis: insights from transcriptomic data and single-cell sequencing combined with machine learning by Yiqin Yang, Mei Dong

“…It is closely related to oxidative stress and immune inflammation. This bioinformatic study was conducted to identify key oxidative stress-related genes and key immune cell infiltration involved in the formation, progression, and stabilization of plaques and investigate the relationship between them. …”
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Propofol Regulates ER Stress to Inhibit Tumour Growth and Sensitize Osteosarcoma to Doxorubicin by Hua Wei, Xinhui Du, Huaping Zhao, Peipei Sun, Jianjun Yang

“…Doxorubicin sensitivity was increased after propofol treatment compared with the control group (p<0.05). Bioinformatic analysis showed significant functional enrichment in ER stress response after propofol treatment. …”
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Differentially localizing isoforms of the migraine component calcitonin gene-related peptide (CGRP), in the mouse trigeminal ganglion: βCGRP is translated but, unlike αCGRP, not so... by Sofia Lyng Wæver, Kristian Agmund Haanes

“…We further categorized the localization patterns of CGRP in neuronal cell bodies in the TG and found using bioinformatic analyses that differences in localization might be explained by intracellular peptide sorting. …”
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Endothelial Cells Potentially Participate in the Metastasis of Triple-Negative Breast Cancer by Yanfei Ma, Yanghong Li, Pengwei Guo, Jingjie Zhao, Qiang Qin, Jiajia Wang, Zhengfang Liang, Dalong Wei, Zechen Wang, Jiajia Shen, Siyuan He, Qianli Tang, Guanming Lu, Guiling Shi, Lingzhang Meng

“…In this study, freshly isolated triple-negative breast cancer biopsied cells obtained from consenting patients were subjected to flow cytometry and bioinformatic analysis to identify three endothelial cell subclusters: EC (ATP1B3), EC (HSPA1B), and EC (KRT7) in the tumor microenvironment. …”
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Mining the Prognostic Value of HNRNPAB and Its Function in Breast Carcinoma by Yun Cao, Wei Zhang, Yi-Ting Jin, Qiang Zou

“…In the present study, bioinformatic analysis identified HNRNPAB as the only commonly upregulated HNRNP in BC. …”
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Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements by Anastasia Gulyaeva, Lei Liu, Sanzhima Garmaeva, Marloes Kruk, Rinse K. Weersma, Hermie J. M. Harmsen, Alexandra Zhernakova

“…Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. …”
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Genome-wide identification of short-chain dehydrogenases/reductases genes and functional characterization of ApSDR53C2 in melanin biosynthesis in Arthrinium phaeospermum by Jiao Liao, Yisi Wang, Han Liu, Sijia Liu, Peng Yan, Hang Chen, Shujiang Li, Shujiang Li

“…We have characterized the SDR family of A. pheospermum bioinformatically. Candidate ApSDRs screened by transcriptome sequencing were compared by qPCR experiments to obtain key ApSDRs that may play an important role in infestation and adversity resistance. …”
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Genome-Wide Approach Identifies Natural Large-Fragment Deletion in ASFV Strains Circulating in Italy During 2023 by Claudia Torresi, Roberta Biccheri, Cesare Cammà, Carmina Gallardo, Maurilia Marcacci, Simona Zoppi, Barbara Secondini, Caterina Riverso, Alejandro Soler, Cristina Casciari, Michela Pela, Elisabetta Rossi, Claudia Pellegrini, Carmen Iscaro, Francesco Feliziani, Monica Giammarioli

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A select inhibitor of MORC2 encapsulated by chimeric membranecoated DNA nanocage target alleviation TNBC progression by Xiaohan Su, Yunbo Luo, Yali Wang, Peng Qu, Jun Liu, Shiqi Han, Cui Ma, Shishan Deng, Qi Liang, Xiaowei Qi, Panke Cheng, Lingmi Hou

“…Triple-negative breast cancer (TNBC) is the most malignant type of breast cancer and lacks effective targeted therapeutic drugs, resulting in a high recurrence rate and worse outcome. In this study, bioinformatic analysis and a series of experiments demonstrated that MOCR2 was highly expressed in TNBC and closely associated with poor prognosis, indicating that MOCR2 may be a potential therapeutic target for TNBC. …”
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Exploratory analysis of molecular traits of the mitochondrial DNA of leafcutting ants to infer taxonomic characters towards an integrative taxonomy by Perpetua Ndubuisi Onyinyechi, Natália Martins Travenzoli, Maykon Passos Cristiano, Danon Clemes Cardoso

“…., 2020, Atta Fabricius, 1804 and Acromyrmex Mayr, 1865 as models to evaluate a mitochondrial genome fragment regularly applied in phylogenetic and evolutionary studies. Bioinformatic analysis revealed shared structural evidence between species that can serve as diagnostic characters, distinguishing them from other species and supporting the classification of the three genera of leafcutting ants. …”
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Transcriptional Profiling at High Temporal Resolution Reveals Robust Immune/Inflammatory Responses during Rat Sciatic Nerve Recovery by Lingyan Xing, Qiong Cheng, Guangbin Zha, Sheng Yi

“…We found that immune/inflammatory reactions not only occur in the acute injury but also remained activated over two weeks after injury. Detailed bioinformatic studies suggested that multiple immune/inflammatory pathways, including agranulocyte adhesion and diapedesis, granulocyte adhesion and diapedesis, IL-6 signaling, and IL-10 signaling, were sustained activated during nerve degeneration and regeneration. …”
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