The study of organelle DNA variability in alloplasmic barley lines in the NGS era by M. G. Siniauskaya, A. M. Makarevich, I. M. Goloenko, V. S. Pankratov, A. D. Liaudanski, N. G. Danilenko, N. V. Lukhanina, A. M. Shimkevich, O. G. Davydenko

“…Organelle DNA samples were prepared from a set of 12 alloplasmic barley lines with different cytoplasms of Hordeum vulgare ssp. spontaneum and H. vulgare ssp. vulgare, as well as from their paternal varieties. A bioinformatic approach for analysis of NGS data obtained on an organellar DNA mix has been developed and verified. …”
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Progress in plant genome sequencing: research directions by M. K. Bragina, D. A. Afonnikov, E. A. Salina

“…New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. …”
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A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor by Olga Kuźmycz, Aleksandra Kowalczyk, Aleksandra Bolanowska, Anna Drozdzowska, Jakub Lach, Jakub Lach, Wiktoria Wierzbińska, Wiktoria Wierzbińska, Tomasz Kluz, Tomasz Kluz, Paweł Stączek

“…The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. …”
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First report of hypoplastic left heart syndrome in 3p- syndrome and review of candidate genes by Ana Kalise Böttcher, Monique Banik Siqueira, Natasha Malgarezi, Marcela Rodrigues Nunes, Rafaella Mergener, Luisa Pigatto Kalil, Patrícia Trevisan, Paulo Ricardo Gazzola Zen

“…Case description: The diagnosis was made by karyotyping, followed by a literature investigation and in silico bioinformatic analysis about the possible candidate genes associated with congenital heart defects or hypoplastic left heart syndrome in 3p- syndrome. …”
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Gene Expression Profiling of the Sciatic Nerve in Streptozotocin-Induced Diabetic Rats with Peripheral Neuropathy by Yiji Tu, Zenggan Chen, Feng Zhang, Zhenglin Di, Junhui Zhang, Li Cai

“…Microarray was performed on the sciatic nerve tissues from control rats and DPN rats at then6th week after diabetes induction, and differentially expressed genes (DEGs) between them were identified and applied for further bioinformatic analyses. Results. Experimental DPN rats were successfully constructed, presenting significantly decreased withdrawal threshold and motor nerve conduction velocity, and typical histological changes in the sciatic nerve. 597 DEGs (186 up- and 411 downregulated) were identified in DPN rats. …”
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ENO1 promotes PDAC progression by inhibiting CD8+ T cell infiltration through upregulating PD-L1 expression via HIF-1α signaling by Aziguli Tulamaiti, Shu-Yu Xiao, Yan Yang, Musitaba Mutailifu, Xia-Qing Li, Shi-Qi Yin, Hong-Tai Ma, Hong-Fei Yao, Lin-Li Yao, Li-Peng Hu, Jun Li, Shu-Heng Jiang, Zhi-Gang Zhang, Yan-Miao Huo, Dong-Xue Li, Xue-Li Zhang

“…Here, we investigated the role of ENO1 in modulating the PDAC microenvironment.Using bioinformatic analyses, we demonstrated that ENO1 was highly expressed in PDAC patients, which was related to a poor prognosis. …”
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Altered expression of miRNA profile in peripheral blood mononuclear cells following the third dose of inactivated COVID-19 vaccine by Guanguan Qiu, Ruoyang Zhang, Huifeng Qian, Ruoqiong Huang, Jie Xia, Ruoxi Zang, Zhenkai Le, Qiang Shu, Jianguo Xu, Guoping Zheng, Jiangmei Wang

“…Our results validated the differential expression of miR-25-5p, miR-34c-3p, and miR-206 post-booster, with a significant correlation to the receptor binding domain (RBD)-specific antibody. Bioinformatic analysis suggested that miR-25-5p, miR-34c-3p, and miR-206 may target multiple pathways involved in immune regulation and inflammation. …”
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Oncogenic RIT1 mutations confer ferroptosis vulnerability in lung adenocarcinoma by Ruilan Ma, Dian Yang, Peng Wang, Ziyi Zhang, Xuehong Zhang, Jialiang Song, Han Liu, Shuyan Liu, Yingqiu Zhang, Lijuan Zou

“…Therefore, further investigation on RIT1 will facilitate future development of targeted therapies. Our bioinformatic analysis revealed that RIT1 alterations in lung cancer predicted poor survivals but differed from its RAS paralogs by showing largely amplification and mutation. …”
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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

“…Design: The design was bioinformatic analysis combined with experimental study. …”
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CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics by Young-Kyu Park, Tae-Wook Kang, Su-Jin Baek, Kwon-Il Kim, Seon-Young Kim, Doheon Lee, Yong Sung Kim

“…This report presents a new web-accessible bioinformatic tool, called CaGe, a cancer genome annotation system for the assessment of candidates of cancer genes from HGT-based cancer genomics. …”
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The Systematic Analysis of Exercise Mechanism in Human Diseases by Lei Pu, Peng Sun

“…Finally, 3 upregulated hub genes (VEGFA, POMC, and NRAS) and 3 downregulated hub genes (HRAS, NCOR1, and CAV1) were identified through the PPI network. Conclusions. The bioinformatic analysis of samples before and after exercise provides key pathways and genes related to exercise to regulate various diseases, which confirms that exercise has an important influence on the treatment of many diseases.…”
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Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes by Biigba Yakubu, Edwin Moses Appiah, Andrews Frimpong Adu

“…As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. …”
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Establishment and Validation of a Gene Signature-Based Prognostic Model to Improve Survival Prediction in Adrenocortical Carcinoma Patients by Xiaoqin Ge, Zhenzhen Liu, Xuehua Jiao, Xueyan Yin, Xiujie Wang, Gengxu Li

“…Using a series of bioinformatic and statistical approaches, a gene-expression signature was established and validated in two independent cohorts. …”
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Involvement of circRNAs in Proinflammatory Cytokines-Mediated β-Cell Dysfunction by Zhen Wang, Chao Deng, Ying Zheng

“…MicroRNA target prediction software and multiple bioinformatic approaches were used to predict the targeting genes of circRNAs and analyze possible functions of the circRNAs. …”
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Overexpression of PAX8-AS1 Inhibits Malignant Phenotypes of Papillary Thyroid Carcinoma Cells via miR-96-5p/PKN2 Axis by Ping Zhou, Tongdao Xu, Hao Hu, Fei Hua

“…The expression of genes was detected by qRT-PCR. The bioinformatic analysis and luciferase reporter assay were used to confirm the binding relationship of PAX8-AS1 to miR-96-5p, and the targeting relationship of miR-96-5p to PKN2 was also predicted. …”
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Problems with studying directional natural selection in humans by S. V. Mikhailova

“…The review describes the main methods for assessing directional selection in human populations. These include bioinformatic analysis of DNA sequences via detection of linkage disequilibrium and of deviations from the random distribution of frequencies of genetic variants, demographic and anthropometric studies based on a search for a correlation between fertility and phenotypic traits, genome-wide association studies on fertility along with genetic loci and polygenic risk scores, and a comparison of allele frequencies between generations (in modern samples and in those obtained from burials). …”
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Gut microbial alteration in chronic spontaneous urticaria unresponsive to second generation antihistamines and its correlation with disease characteristics‐ a cross‐sectional case‐... by Indrashis Podder, David Pesqué, Nerea Carrón, Pedro Iñaki González Torres, Ramon M. Pujol, Ana M. Giménez‐Arnau

“…Clinico‐demographic profile, laboratory investigations and stool analysis were conducted in all study participants. 16S RNA gene sequencing and DNA isolation was performed for all stool samples, followed by bioinformatic analysis. Results The CSU patients (mean age 39.5 ± 9.3, M:F 1:4) and healthy controls (mean age 35 ± 13, M:F 1:2) were statistically comparable. …”
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Theoretical Study of Sphingomyelinases from <i>Entamoeba histolytica</i> and <i>Trichomonas vaginalis</i> Sheds Light on the Evolution of Enzymes Needed for Survival and Colonizati... by Fátima Berenice Ramírez-Montiel, Sairy Yarely Andrade-Guillen, Ana Laura Medina-Nieto, Ángeles Rangel-Serrano, José A. Martínez-Álvarez, Javier de la Mora, Naurú Idalia Vargas-Maya, Claudia Leticia Mendoza-Macías, Felipe Padilla-Vaca, Bernardo Franco

“…However, no structural data are available for the aSMase6 enzyme. In this work, bioinformatic analyses showed that the protist aSMases are diverse enzymes, are evolutionarily related to hemolysins derived from bacteria, and showed a similar overall structure as parasitic, free-living protists and mammalian enzymes. …”
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Transcriptomic signatures of cold acclimated adipocytes reveal CXCL12 as a Brown autocrine and paracrine chemokine by Marina Agueda-Oyarzabal, Marie S. Isidor, Kaja Plucińska, Lars R. Ingerslev, Oksana Dmytriyeva, Patricia S.S. Petersen, Sara Laftih, Axel B. Pontoppidan, Jo B. Henningsen, Kaja Rupar, Erin L. Brown, Thue W. Schwartz, Romain Barrès, Zachary Gerhart-Hines, Camilla C. Schéele, Brice Emanuelli

“…For this, mRNA levels in mature adipocytes from mouse adipose depots were assessed using RNA sequencing upon chronic cold acclimation, and bioinformatic analysis was used to identify secreted factors. …”
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WWTR1-AS1 LncRNA as a Novel Potential Diagnostic and Prognostic Biomarker in Breast Cancer by Mohadese Safabakhsh, Sohrab Boozarpour, Kamran Ghaedi, Mina Lashkarboloki, Shaaban Ghalandarayeshi

“…In addition, these regulatory elements were related to three biological functions and 11 pathways. Finally, bioinformatic analysis identified lncRNA WWTR1-AS1 as having the highest node score involved in different mechanisms. …”
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