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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology by Alexandra Chera, Mircea Stancu-Cretu, Nicolae Radu Zabet, Octavian Bucur

“…Interestingly, nanopore sequencing can also extract epigenetic status of the nucleotides (including both 5-Methylcytosine and 5-hydroxyMethylcytosine), and a large variety of bioinformatic tools have been developed for improving its detection properties. …”
Get full text

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. …”
Get full text

Comprehensive analyses reveal the promising value of gasdermins as prognostic biomarkers and immunotherapeutic targets in head and neck squamous cell carcinoma by Huageng Huang, Jingjing Ge, Shunzhen Lu, Xinyi Deng, Ying Tian, He Huang, Zhao Wang, Yuyi Yao, Huangming Hong, Tongyu Lin

“…Methods: We performed comprehensive analyses of the expression profile, prognostic value, regulatory network, and immune infiltration modulation of GSDMs in HNSC on the basis of a computational approach and bioinformatic analysis of publicly available datasets. …”
Get full text

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.…”
Get full text

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. …”
Get full text

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. …”
Get full text