COph100: A comprehensive fundus image registration dataset from infants constituting the “RIDIRP” database by Yan Hu, Mingdao Gong, Zhongxi Qiu, Jiabao Liu, Hongli Shen, Mingzhen Yuan, Xiaoqing Zhang, Heng Li, Hai Lu, Jiang Liu

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Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures by Mxolisi Nene, Mxolisi Nene, Nokuthula Winfred Kunene, Rian Pierneef, Rian Pierneef, Rian Pierneef, Khanyisile Hadebe

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miR-432-5p Inhibits the Ferroptosis in Cardiomyocytes Induced by Hypoxia/Reoxygenation via Activating Nrf2/SLC7A11 Axis by Degrading Keap1 by Wei Geng, Shaohua Yan, Xinyue Li, Qiumei Liu, Xuefei Zhang, Xinshun Gu, Xiang Tian, Yunfa Jiang

“…Upregulation of miR-432-5p inhibited ferroptosis of cardiomyocytes induced by RAS-selective lethal 3 (RSL3), an inhibitor of GPX4 and ferroptosis inducer through decreasing the binding protein of Nrf2, Keap1, which was confirmed by bioinformatics and mutation assay. Knockdown Nrf2 attenuates the protection effect of miR-432-5p on H/R cardiomyocytes. …”
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Insulin Resistance Mediates the Association Between Vitamin D and Non-Alcoholic Fatty Liver Disease by Caiyan Zou, Xuekui Liu, Maosheng He, Yan Sun, Yiquan Sang, Gangshan Peng, Yamei Ma, Houfa Geng, Jun Liang

“…Mediation analysis revealed that IR mediated the association between VD and both CAP and LSM, and the estimated mediation effects were 29.0% and 39.8%, respectively. Bioinformatics analysis showed that seven differentially expressed genes (DEGs) (solute carrier family 2 member 2 [SLC2A2], protein phosphatase 1 regulatory subunit 3E [PPP1R3E], CAMP responsive element binding protein 3-like 3 [CREB3L3], Interleukin-6 [IL-6], peroxisome proliferator-activated receptor gamma coactivator 1-alpha [PPARGC1A], nuclear factor kappa B inhibitor alpha [NFKBIA], and phosphoenolpyruvate carboxykinase 2 [PCK2]) were enriched in the IR pathway in comparison groups (VD group vs. lipid group), suggesting that VD improved NAFLD via changed IR. …”
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Mir-615-5p inhibits cervical cancer progression by targeting TMIGD2 by Yan Zhao, Haitao Chen, Wenhui Zhang, Wei Shang, Jinwei Cao, Huijuan Zhao, Zhixiang Zou

“…The potential mechanism of miR-615-5p was elucidated by bioinformatics analyses and Dual-luciferase reporter assay. …”
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Mechanistic insights into pachymic acid’s action on triple-negative breast Cancer through TOP2A targeting by Ming Liu, Li Zheng, Yang Zhang, Jinhui Tian

“…The related targets of PA were predicted and screened using the following 6 databases: Swiss Target Prediction, HERB (Herbal Medicine Database), ETCM (Encyclopedia of Traditional Chinese Medicine), BATMAN (Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine), HIT (Herb Ingredients’ Targets Database), and PharmMapper. …”
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Metagenomic characterization of oral microbiome signatures to predict upper gastrointestinal and pancreaticobiliary cancers: a case–control study by Sujin Oh, Jaihwan Kim, Cheol Min Shin, Hyo-Jung Lee, Hye Seung Lee, Kyoung Un Park

“…Methods Saliva samples from cancer patients and age- and sex-matched healthy controls were analyzed using 16S rRNA-targeted sequencing, followed by comprehensive bioinformatics analysis. Results Significant dissimilarities in microbial composition were observed between cancer patients and controls across esophageal cancer (EC), gastric cancer (GC), biliary tract cancer (BC), and pancreatic cancer (PC) groups (R2 = 0.067, = 0.075, = 0.068, and = 0.044; p = 0.001, = 0.001, = 0.002, and = 0.004, respectively). …”
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Analysis of a Family with Brugada Syndrome and Sudden Cardiac Death Caused by a Novel Mutation of SCN5A by Yao-Bin Zhu, Jian-Hui Zhang, Yuan-Yuan Ji, Ya-Nan Hu, Han-Lu Wang, Dan-Dan Ruan, Xiao-Rong Meng, Xin-Fu Lin, Jie-Wei Luo, Wei Chen

“…Among the surviving family members, only those with a Brugada wave on their electrocardiogram carried the c.4313dup(p.Trp1439ValfsTer32) variant. Bioinformatics prediction revealed that the frameshift of the c.4313dup (p.Trp1439ValfsTer32) mutant led to a coding change of 32 amino acids, followed by a stop codon, resulting in a truncated protein product. …”
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In vivo interspecies dissemination of IncM2-type blaNDM-1 carrying plasmid by Mor N. Lurie-Weinberger, Darya Bychenko-Banyas, Meirav Mor, Sivan Laviad-Shitrit, Ella Kaplan, Nadya Rakovitsky, Alona Keren-Paz, Chaim Ben-Zvi, Yehuda Carmeli

“…Seven New Delhi metallo-beta-lactamase(NDM) positive and one NDM-negative bacteria were sent for WGS followed by bioinformatics analysis. Here, we describe three separate cases of patients simultaneously colonized by two NDM producing-species (Escherichia coli and Klebsiella pneumoniae), in which we documented interspecies dissemination of the blaNDM-1 by an 87,450 bp IncM2 type multi-drug resistance plasmid (here named pNCICAN_NDM-01_21-il). …”
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Thermodynamics and solar radiative analysis in Jeffery-Hamel flow through non-parallel channel by novel improved residual power series method by Mohamed Bouzidi, Mohsin Ul Haq, Ikram Ullah, Saira Shukat, Hijaz Ahmad, Mohammad Mahtab Alam, Hamid Khan, Marouan Kouki

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Tumour heterogeneity and personalized treatment screening based on single-cell transcriptomics by Xinying Zhang, Jiajie Xie, Zixin Yang, Carisa Kwok Wai Yu, Yaohua Hu, Jing Qin

“…By integrating multiple bioinformatics analyses, we explored the biological differences underlying tumour cell heterogeneity at the single-cell level and identified tumour cell subcluster-specific biomarkers and potential therapeutic drugs for each subcluster. …”
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Genetic variation in zona pellucida-3 (ZP3) gene and its association with litter size variation in Kari sheep by Izaz Ali, Muhammad Ibrahim, Sohail Ahmad, Sher Hayat Khan, Ihtesham Ul Haq, Ibrahim A. Alhidary, Rifat Ullah Khan, Naseer Khan Momand, Marco Ragni

“…The entire ZP3 gene was amplified using PCR and sequenced at 30× with Next Generation Sequencing. Bioinformatics analysis identified 70 variants across the three breeds, located in upstream regions, introns, and exons. …”
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Macrophage Infiltration and ITGB2 Expression in ESCC: A Novel Correlation by Tao Huang, Longqian Wei, Huafu Zhou, Jun Liu

“…Methods In this study, we integrated high‐throughput sequencing data, gene chip data, single‐cell sequencing data, and various bioinformatics analysis methods along with experimental approaches to identify key genes involved in immune infiltration in ESCC and investigate their relationship with immune cell development, as well as the potential of these key genes in immunotherapy. …”
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Public perceptions on the application of artificial intelligence in healthcare: a qualitative meta-synthesis by Jing Gao, Xinyu Chen, Xiaolian Jiang, Chenxi Wu, Huiqiong Xu, Dingxi Bai

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Comprehensive analysis of differential mRNA and circRNA profiles in primary and metastatic pancreatic neuroendocrine tumors by Gang Li, Jing Zhang, Bentuo Zhang, Dan Wang, Zequn Wang, Yan Pan, Lijie Ma

“…To address this, we utilized mRNA expression data from human pNET and metastatic pancreatic tumor tissues available in the GEO database and integrated this data with bioinformatics analyses. And then we collected clinical primary tumor and liver metastasis samples from patients with pNETs, we conducted a comprehensive analysis of circular RNAs (circRNAs) to identify key circRNAs associated with the onset and metastasis of pNETs. …”
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A Novel Prognostic Signature Revealed the Interaction of Immune Cells in Tumor Microenvironment Based on Single-Cell RNA Sequencing for Lung Adenocarcinoma by Xing Jin, Zhengyang Hu, Qihai Sui, Mengnan Zhao, Jiaqi Liang, Zhenyu Liao, Yuansheng Zheng, Hao Wang, Yu Shi

“…The code for cell-type mapping algorithms was downloaded from the CIBERSORTx portal. The bioinformatics data of LUAD patients could be approached from The Cancer Genome Atlas (TCGA) portal. …”
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Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study by Yoon Hyun Sung, Yong Kuk Ju, Hak Jun Lee, Seung Min Park, Jin Woong Suh, Jeong Yeon Kim, Jang Wook Sohn, Young Kyung Yoon

“…However, these values may be overestimated due to challenges in distinguishing significant pathogens from background noise. Meanwhile, the bioinformatics module in EPI2ME reduced the turn-around time to 10 min. …”
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VibrioBase: A Model for Next-Generation Genome and Annotation Database Development by Siew Woh Choo, Hamed Heydari, Tze King Tan, Cheuk Chuen Siow, Ching Yew Beh, Wei Yee Wee, Naresh V. R. Mutha, Guat Jah Wong, Mia Yang Ang, Amir Hessam Yazdi

“…Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. …”
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Exploration of the diagnostic and prognostic roles of decreased autoantibodies in lung cancer by Ying Ye, Ying Ye, Yi Huang, Yi Huang, Jianbo Pan, Jianbo Pan

“…Diagnosing malignant small lung nodules (≤3cm) in CT scans remains a challenge in clinical practice.MethodsIn this study, we applied the HuProt array and the bioinformatics analysis to assess the diagnostic values of the decreased autoantibodies in lung cancers.ResultsIn total, 15 types of decreased autoantibodies were identified, and 6 of them were constructed into a predictive model for early lung cancer, reaching a sensitivity of 76.19% and a specificity of 55.74%. …”
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Genetic analysis of scab disease resistance in common bean (Phaseolus vulgaris) varieties using GWAS and functional genomics approaches by Shadrack Odikara Oriama, Benard W. Kulohoma, Evans Nyaboga, Y. O. Masheti, Reuben Otsyula

“…Modern computational biology and bioinformatics tools were utilized to identify scab disease resistance genes in the common bean by identification of genomic regions and genes associated with resistance to scab disease during natural infection in the field. …”
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