Yingjie Wang^1,#, Wanlin Dong^1,#, Can Wang², Zirui Li¹, Yongqiang Wang¹, Qi Li¹, Cheng-Ya Dong^1,*

Oncology Research, Vol.33, No.12, pp. 4093-4111, 2025, DOI:10.32604/or.2025.068313 - 27 November 2025

Abstract Objectives: Glioblastoma is a prevalent malignant brain tumor, and the actions of the long non-coding RNA HOXA10-AS in its invasion and migration remain unclear. Here, the function of HOXA10-AS in glioblastoma cell invasion and migration and associated mechanisms were investigated. Methods: HOXA10-AS was knocked down in glioblastoma cells, and Transwell and wound healing assays were conducted to elucidate its impacts on cell invasion and migration. Western blotting and quantitative reverse transcription polymerase chain reaction (qRT-PCR) assessed HOXA10-AS’s impact on the epithelial-mesenchymal transition (EMT). Microarray analysis identified differentially expressed genes, complemented by bioinformatics approaches to explore… More >

Mingxin Zhong^1,#, Yuanyuan Zhang^1,#, Xinlei Guo¹, Bainian Zhang², Chengjia Tan¹, Zhuo Xu¹, Xin Hu¹, Daren Feng³, Zhenpeng Xi⁴, Qian Wang^1,*, Hui Tian^1,*

Phyton-International Journal of Experimental Botany, Vol.94, No.10, pp. 3061-3084, 2025, DOI:10.32604/phyton.2025.070560 - 29 October 2025

Abstract Magnolia officinalis is a perennial deciduous tree that has medicinal properties. The AP2/ERF gene family has a number of roles in long-term growth and metabolism. The expression of this function varies with the growth period. In this work, based on the transcriptome data of Magnolia officinalis, the complete coding gene of Magnolia officinalis was obtained, and the corresponding protein sequence was retrieved from NCBI and compared with the model plant Arabidopsis thaliana. After screening, 75 protein sequences from the AP2/ERF gene family were identified and called MoAP2/ERF1–MoAP2/ERF75, followed by bioinformatics analysis. 75 AP2/ERF gene families were found and classified into four… More >

Shuyan Kong^1,#, Danting Li^1,#, Haonan Meng^1,#, Haoxiang Zhang¹, Xiaochun Jiang¹, Peilin Zheng², Shoujun Huang^1,*

BIOCELL, Vol.49, No.8, pp. 1481-1504, 2025, DOI:10.32604/biocell.2025.066205 - 29 August 2025

Abstract Background: Small ubiquitin-like modifier (SUMO)-specific proteases (SENPs) cleave the isopeptidic bond between SUMO1/2/3 and protein substrates, thus regulating the structure, activity, and lifetime of a variety of proteins. Recently, accumulating evidence has suggested that SENPs play a role in the initiation and progression of human cancers. Nevertheless, the potential role of the SENP family of proteins in liver cancer has yet to be fully elucidated. Methods: This study conducted a comprehensive bioinformatics analysis of the SENP family in liver cancer, including differential expression profiling, survival analysis, mutation and copy number variations (CNVs) assessment, immune infiltration… More >

Dumitru Baleanu^1,2, Carla M. A. Pinto³, Sunil Kumar^4,*

CMES-Computer Modeling in Engineering & Sciences, Vol.143, No.2, pp. 1297-1299, 2025, DOI:10.32604/cmes.2025.067010 - 30 May 2025

Abstract This article has no abstract. More >

Jiawei Shi^1,2,3,#, Zhen Wang^1,2,3,#, Ying Bai^1,2,3, Shiying Li^1,2,3, Xin Zhang^1,2,3, Tianshu Liu^1,2,3, Liu Hong^1,2,3, Li Cui^1,2,3, Yi Zhang^1,2,3, Jing Ma^1,2,3, Juanjuan Liu^1,2,3, Jing Zhang^1,2,3, Haiyan Cao^1,2,3,*, Jing Wang^1,2,3,*

Congenital Heart Disease, Vol.20, No.2, pp. 213-229, 2025, DOI:10.32604/chd.2025.064950 - 30 April 2025

Abstract Background: Tetralogy of Fallot (TOF), the predominant cyanotic congenital heart defect, arises from multifactorial gene-environment interactions disrupting cardiac developmental networks. This study investigated TOF-specific transcriptional alterations and identified high-confidence candidate genes. Methods: Based on GSE36761 transcriptome data, a weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network were conducted to identify TOF-related sub-network and Hub genes. The potential biological functions among these genes were revealed by enrichment analysis. Genetic, epigenetic and transcriptional alteration in the Hub genes were analyzed with leveraged public resources: a methylation dataset (GSE62629) and two single-cell datasets (EGAS00001003996 and GSE126128). Results:… More >

Yuxin Zhao, Zhanxiang Tan, Yuying Li, Kaiyue Zhang, Lili Guo^*, Xiaogai Hou^*

Phyton-International Journal of Experimental Botany, Vol.94, No.4, pp. 1159-1176, 2025, DOI:10.32604/phyton.2025.063737 - 30 April 2025

Abstract Receptor-like cytoplasmic kinases (RLCKs) play a crucial role in the physiological processes of plant growth and development and stress response. To elucidate the characteristics and functions of the PBL gene family in tree peonies, the whole genome identification of PBL family members in tree peonies was conducted using a bioinformatics approach based on the published Arabidopsis thaliana PBL protein sequence. A total of 51 PoPBL members were identified, which were distributed unevenly on five chromosomes in the tree peony. PoPBL proteins were localized in the nucleus, cytoplasm, chloroplasts, and mitochondria, with most members of the same clade… More >

Hariharasakthisudhan Ponnarengan^1,*, Sivakumar Rajendran², Vikas Khalkar³, Gunapriya Devarajan⁴, Logesh Kamaraj⁵

CMES-Computer Modeling in Engineering & Sciences, Vol.142, No.1, pp. 1-48, 2025, DOI:10.32604/cmes.2024.056605 - 17 December 2024

Abstract The purpose of this review is to explore the intersection of computational engineering and biomedical science, highlighting the transformative potential this convergence holds for innovation in healthcare and medical research. The review covers key topics such as computational modelling, bioinformatics, machine learning in medical diagnostics, and the integration of wearable technology for real-time health monitoring. Major findings indicate that computational models have significantly enhanced the understanding of complex biological systems, while machine learning algorithms have improved the accuracy of disease prediction and diagnosis. The synergy between bioinformatics and computational techniques has led to breakthroughs in More >

Ying Wang¹, Weijun Zhang¹, Fei Cai¹, Yong Tao^2,*

Congenital Heart Disease, Vol.19, No.6, pp. 653-669, 2024, DOI:10.32604/chd.2025.060406 - 27 January 2025

Abstract Background: Previous studies combined integrated scRNA-seq with bulk RNA data to screen biomarkers for cardiomyopathy. This study extended this approach to identify biomarkers specific for hypertrophic cardiomyopathy (HCM). Methods: Datasets GSE36961, GSE130036, GSE249925 and GSE203274 were analyzed in this study. ScRNA-seq analysis was employed to identify distinct cell populations. Differentially expression analysis was conducted to screen vascular endothelial cells (VECs)-related feature genes. After calculating VECs score, WGCNA was used to correlate gene modules with the VECs score. Key HCM biomarkers were determined using random forest analysis, and LASSO regression analyses to construct a diagnostic model… More >

ATIEH POURBAGHERI-SIGAROODI¹, MAJID MOMENY², NIMA REZAEI^3,4,5, FATEMEH FALLAH^1,*, DAVOOD BASHASH^6,*

BIOCELL, Vol.48, No.12, pp. 1781-1804, 2024, DOI:10.32604/biocell.2024.055848 - 30 December 2024

Abstract Background: Despite progress in therapeutic strategies, treatment failure in hepatocellular carcinoma (HCC) remains a major challenge, resulting in low survival rates. The presence of bacteria and the host’s immune response to bacteria can influence the pathogenesis and progression of HCC. We developed a risk model based on bacterial response-related genes (BRGs) using gene sets from molecular signature databases to identify new markers for predicting HCC outcomes and categorizing patients into different risk groups. Methods: The data from the Cancer Genome Atlas (TCGA) portal was retrieved, and differentially expressed BRGs were identified. Uni- and multivariate Cox… More >

RONG LIU^1,#, SHENG LI^2,#, SITU XIONG², FUCUN ZHENG², XIANGPENG ZHAN², JIN ZENG², BIN FU², SONGHUI XU², SHAOXING ZHU^1,*, RU CHEN^1,*

Oncology Research, Vol.32, No.11, pp. 1733-1746, 2024, DOI:10.32604/or.2024.050851 - 16 October 2024

Abstract EVI2A has emerged as a significant biomarker in various diseases; however, its biological role and mechanism in kidney renal clear cell carcinoma (KIRC) remains unexplored. We used TCGA and GEO databases to analyze EVI2A gene expression comprehensively and performed pan-cancer assessments. Clinical relevance was evaluated through Kaplan-Meier analysis and ROC curves. The gene’s immune relevance was explored through analyses of the tumor microenvironment (TME), Tumor Immune Single-cell Hub (TISCH), immune checkpoints, and immunotherapy sensitivity. Our results indicate that EVI2A expression is upregulated in KIRC, showing correlations with tumor grade and T/N/M stage. EVI2A demonstrates high… More >