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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Therapeutic Effect of Gypenosides on Antioxidant Stress Injury in Orbital Fibroblasts of Graves’ Orbitopathy by Chao Ma, Haoyu Li, Wei Liu, Shuwen Lu, Xian Li, Jinyuan Chen, Kaijun Li, Wenzhan Wang

“…The relationship between Gyps and GO oxidative stress was understood by bioinformatics analysis. Orbital connective tissues of GO and non-GO patients were obtained for primary OF culture. …”
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A strategy to increase identification of patients with Familial Hypercholesterolemia: Application of the Simon Broome lipid criteria in a large-scale retrospective analysis by James K. Fleming, Renee M. Sullivan, David Alfego, Natalia T. Leach, Tamara J. Richman, Jill Rafalko

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Unravelling the TCRβ repertoire: a key to unlocking the immunopathogenesis and precision medicine in SLE by Qiao Zhou, Li Zeng, Zhixin Zhang, Jian Liu, Yichen Zhang, Yang An, Lijing Yang, Tianzuo Lan, Pengming He, Xueping Wen, Shaoping Deng

“…Our study aimed to delineate the variances in the TCRβ repertoire between patients with SLE and healthy individuals, correlating these differences with the severity and subtypes of SLE.Methods We conducted an analysis of blood samples from 50 treatment-naive patients with SLE and 50 healthy donors, employing RNA extraction, high-throughput sequencing and subsequent bioinformatics analysis.Results Our findings revealed significant alterations in TRBV and TRBJ gene usage frequencies, indicative of a skewed TCR repertoire in patients with SLE. …”
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Hypericin mediated photodynamic therapy induces ferroptosis via inhibiting the AKT/mTORC1/GPX4 axis in cholangiocarcinoma by Wei An, Kai Zhang, Guangbing Li, Shunzhen Zheng, Yukun Cao, Jun Liu

“…Then, we conducted transcriptome sequencing and bioinformatics analysis and observed that HY-PDT was most likely involved in ferroptosis, apoptosis, the EMT process and AKT/mTORC1 signaling pathways in cholangiocarcinoma cells. …”
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Vaginal Microbiota Diversity of Patients with Embryonic Miscarriage by Using 16S rDNA High-Throughput Sequencing by Linfen Xu, Lingna Huang, Chengying Lian, Huili Xue, Yanfang Lu, Xiujuan Chen, Yong Xia

“…To further dissect the microbiota of the vagina in the two groups, 16S rDNA sequencing was performed. Bioinformatics analysis showed that 1096 and 998 overlapped operational taxonomic units were identified from the embryonic miscarriage and control groups, respectively. …”
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Engineering of Dihydroxy Biphenyl Dioxygenase Enzyme to Improve Its Performance In Removing PCBs: A Molecular Docking Study by Susan Yazdankhah, Alireza Zakeri, Saeed Khalili, Abolfazl Jahangiri, ZahraalSadat Hashemi, Alireza Heidari

“…This research has been carried out in bioinformatics to strengthen the enzyme and weaken the inhibitory effect through mutation in the amino acids of the active site. …”
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A universal DNA microarray for rapid fish species authentication by Patrizia Bade, Sebastian Stix, Kristina Kappel, Jan Fritsche, Ilka Haase, Andrew Torda, Nils Wax, Markus Fischer, Dirk Brandis, Ute Schröder

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Resetting the Hsc70-mediated lysosomal degradation of PD-L1 via a supramolecular meso peptide for the restoration of acquired anti-tumor T cell immunity by Yujia Zhao, Dan Liu, Wenguang Yang, Wangxiao He, Jin Yan, Leiqing Yao

“…Furthermore, based on bioinformatics analysis of mRNA expression data from 30 types of tumors obtained from TCGA database, malignant melanoma was identified as the most suitable indication for CTAC-PDL1 due to its specific characteristics of tumor immune. …”
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Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing by Doori Park, Dongin Kim, Green Jang, Jongsung Lim, Yun-Ji Shin, Jina Kim, Mi-Seong Seo, Su-Hyun Park, Ju-Kon Kim, Tae-Ho Kwon, Ik-Young Choi

“…Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.…”
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Crotonylation-Related Prognostic Model of Esophageal Squamous Cell Carcinoma Based on Transcriptome Analysis and Single-Cell Sequencing Analysis by Lin RY, Chen RP, Lin FQ

“…This study aimed to investigate the role of crotonylation-related genes (CRGs) in ESCC using bioinformatics approaches.Methods: We included three ESCC datasets and 24 CRGs. …”
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Differential Regulation of NK Cell Receptors in Acute Lymphoblastic Leukemia by Le Jie Lee, Norfarazieda Hassan, Siti Zuleha Idris, Suresh Kumar Subbiah, Heng Fong Seow, Norhafizah Mohtaruddin, Kian Meng Chang, Raudhawati Osman, Hishamshah Mohd Ibrahim, Sheila Nathan, Maha Abdullah

“…Quantitative PCR (q-PCR) further investigated copy number variation (CNV), methylation index (MI), and mRNA expression of significant genes in T-ALL (14 males), NC (12 males and 12 females), and B-ALL samples (N=12 males and 12 females). Bioinformatics revealed unique variants particularly rs2253849 (T>C) in KLRC1 and rs1141715 (A>G) in KLRC2 only among T-ALL (allele frequency 0.8-1.0). …”
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LncRNA GAS5 reduces blood glucose levels and alleviates renal fibrosis in diabetic nephropathy by regulating the miR-542-3p/ERBB4 axis by Qinghua Yin, Na Guo, Ruoxi Liao

“…ELISA was executed to examine the levels of IL-1β, IL-6, and TNF-α; and the superoxide dismutase (SOD), catalase (CAT), and malondialdehyde (MDA) activities were evaluated. Bioinformatics analysis, dual-luciferase and RIP assays were performed to verify the relationship between lncRNA GAS5 and miR-542-3p, and miR-542-3p and ERBB4. …”
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Identification of the Key Genes and Pathways in Esophageal Carcinoma by Peng Su, Shiwang Wen, Yuefeng Zhang, Yong Li, Yanzhao Xu, Yonggang Zhu, Huilai Lv, Fan Zhang, Mingbo Wang, Ziqiang Tian

“…Differentially expressed genes (DEGs) were screened by bioinformatics analysis. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network construction were performed to obtain the biological roles of DEGs in EC. …”
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Establishing a GRU-GCN coordination-based prediction model for miRNA-disease associations by Kai-Cheng Chuang, Ping-Sung Cheng, Yu-Hung Tsai, Meng-Hsiun Tsai

“…Although traditional wet-lab experiments provide direct evidence for miRNA-disease associations, they are often time-consuming and complicated to analyze by current bioinformatics tools. In recent years, machine learning (ML) and deep learning (DL) techniques are powerful tools to analyze large-scale biological data. …”
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Identification of a New Prognostic Risk Signature of Clear Cell Renal Cell Carcinoma Based on N6-Methyladenosine RNA Methylation Regulators by Yan Zhang, Yao Yao, Xiaochen Qi, Jianyi Li, Meihong Liu, Xiangyu Che, Yingkun Xu, Guangzhen Wu

“…In this study, we researched the RNA-seq transcriptome data of ccRCC in the TCGA dataset and used bioinformatics analyses to detect the relationship between m6A RNA methylation regulators and ccRCC. …”
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