Multi-omics analysis constructs a novel neuroendocrine prostate cancer classifier and classification system by Junxiao Shen, Luyuan Lu, Zujie Chen, Wei Guo, Shuwen Wang, Ziqiao Liu, Xuke Gong, Yiming Qi, Ruyi Jin, Cheng Zhang

“…This study aims to identify a robust NEPC classifier and provide new perspectives for resolving intra- tumoral heterogeneity. Multi-omics analysis included 19 bulk transcriptomics, 14 single-cell transcriptomics, 1 spatial transcriptomics, 16 published NE signatures and 10 cellular experiments combined with multiple machine learning algorithms to construct a novel NEPC classifier and classification. …”
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Comparative analysis of dorsal and tail skin reveals region-dependent heterogeneity in axolotl skin regeneration by Lieke Yang, Qian Chen, Jinman Li, Yan Hu, Yaoxin Liu, Binbin Lu, Shuaibin Pei, Tingyi Huang, Yanmei Liu, Ji-Feng Fei

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Polycystic ovary syndrome and epithelial-mesenchymal transition: Mendelian randomization and single-cell analysis insights by Dong Liu, Dan Liu, Kunyan Zhou

“…Objective This study aimed to explore key genes associated with EMT in PCOS and their potential molecular regulatory mechanisms, exclusively from the perspective of transcriptomics and single-cell RNA sequencing (scRNA-seq), combined with Mendelian Randomization (MR) analysis. …”
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Molecular characterization and functional analysis of CYP315 A1 in ovarian development in Macrobrachium nipponense by Sufei Jiang, Wenyi Zhang, Jufeng Jiang, Mengying Zhang, Jisheng Wang, Yiwei Xiong, Hui Qiao, Hongtuo Fu

“…Expression in mature ovaries increased sharply (P < 0.01), while it was relatively low in other stages (P < 0.05). …”
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Whole-Genome Resequencing Analysis of Copy Number Variations Associated with Athletic Performance in Grassland-Thoroughbred by Wenqi Ding, Wendian Gong, Tugeqin Bou, Lin Shi, Yanan Lin, Xiaoyuan Shi, Zheng Li, Huize Wu, Manglai Dugarjaviin, Dongyi Bai

“…In addition, a total of 195 genes overlapping with CNVRs were identified. Transcriptomic analysis revealed 120 differentially expressed genes, with <i>MTPN</i> expressed in both CNVR-overlapping genes and mRNA. …”
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Epithelial and macrophage cell interaction in cervical cancer through single-cell RNA-sequencing and spatial analysis by Zhichao Wang, Long Cheng, Guanghui Li, Huiyan Cheng

“…This study explored the cellular composition and immunological landscape of CC using various genomic data sources.MethodsData from the Cancer Genome Atlas and Gene Expression Omnibus were analyzed, including single-cell RNA sequencing, spatial transcriptome analysis, and survival data. Gene set variation analysis (GSVA) identified pathways in CD8+ cells, macrophages, and epithelial cells. …”
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Genome-wide cataloging and orthology analysis of long noncoding RNA expression in three species of Anopheles mosquito by Waseem Akram Malla, Kuldeep Singh, Niha Ayman, Chandini Boro, Naorem Chaoba Devi, Priyanka Mech, Nida Siddiqui, Anupkumar R. Anvikar, Praveen Kumar Bharti

“…Various bioinformatics tools were subsequently used for lncRNA identification, conservation analysis, and differential expression analysis across sexes and tissues. …”
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The Diagnostic Utility of Host RNA Biosignatures in Adult Patients With Sepsis: A Systematic Review and Meta-Analysis by Mervin V. Loi, MBBS, MSc, FRCPCH, Rehena Sultana, MSc, MBA, Tuong Minh Nguyen, MSc, Shi Ting Tia, Jan Hau Lee, MBBS, MCI, MRCPCH, Daniel O’Connor, DPhil

“…A total of 117 studies (n = 17,469), comprising 132 separate patient datasets, were included in our final analysis. Performance of transcriptomics for the diagnosis of sepsis against pooled controls showed area under the receiver operating characteristic curve (AUC, 0.86; 95% CI, 0.84–0.88). …”
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Analysis of CYP701A1 genes in gossypium species and functional characterization through gene silencing by Zhao Liang, Di Jiachun, Guo Qi, Xu Zhenzhen, Zhao Jun, Xu Peng, Xu Jianwen, Liu Jianguang, Shen Xinlian, Chen Xusheng

“…Transcriptome analysis of the gene silencing plants identified 15,962 differentially expressed genes, including 8376 upregulated and 7586 downregulated genes. …”
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Unraveling the molecular landscape of congenital pseudoarthrosis of the tibia: insights from a comprehensive analysis of 159 probands by Rui Wang, Yu Zheng, Ge Yang, Zhenchao Xu, Yaoxi Liu, Weihua Zhao, Hua Wang, Haibo Mei, Guanghui Zhu

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Identification of osteoarthritis-associated chondrocyte subpopulations and key gene-regulating drugs based on multi-omics analysis by Ting Hao, Zhiwei Pei, Sile Hu, Zhenqun Zhao, Wanxiong He, Jing Wang, Liuchang Jiang, jirigala Ariben, Lina Wu, Xiaolong Yang, Leipeng Wang, Yonggang Wu, Xiaofeng Chen, Qiang Li, Haobo Yang, Siqin Li, Xing Wang, Mingqi Sun, Baoxin Zhang

“…Furthermore, differential gene expression analysis and GO/KEGG pathway enrichment analysis were performed on the identified subgroups. …”
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Genome-wide identification and gene expression analysis of the malate dehydrogenase (MDH) gene family in Eucalyptus grandis by Yifan Xing, Yifan Xing, Huiming Xu, Deming Yang, Lichuan Deng, Guolong Li, Guolong Li, Zhixin Zhao, Zhixin Zhao, Zhaohua Lu, Liuyin Ma, Guangyou Li

“…Phylogenetics revealed three MDH clades: green algal-derived Groups I/II and red algal-derived Group III. Phylogenetics analysis with model plants revealed that Eucalyptus lacked Group III MDHs, while Poplar lacked Group II members, indicating lineage-specific gene loss in woody angiosperms. …”
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Potential Targets Related to Skin Aging: Based on eQTL and GWAS Datasets by Shi H, Cao X

“…Finally, the CIBERSORT evaluation was used to assess the infiltration of immune cells related to SG.Results: Seven AS-IGs were selected through intersection from 612 DEGs and 399 eQTL genes. Then, enrichment analysis results showed there were 60 GO terms may involved in the process of SG, like fatty-acyl-CoA metabolic process, while KEGG enrichment pathways identified mainly involved in mechanisms related to fatty acid metabolism, energy generation, and inflammation regulation. …”
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RNA-seq analysis reveals key genes associated with downregulation of APE1 in esophageal squamous cell carcinoma by Alan Chu, Xiao Liu, Shijia Liu, Mengxi Li, Rui Song, Lanlan Gan, Yongtai Wang, Zongwen Liu, Chen Sun

“…TE-1 cells with APE1 knockout were used for transcriptome sequencing (RNA sequencing, RNA-Seq) detection, and GO and KEGG enrichment analysis of differentially expressed genes was conducted. …”
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QTL-based dissection of three key quality attributes in maize using double haploid populations by Zitian He, Jianping Wang, Jianping Wang, Jialei Li, Jianwei Li, Lei Chen, Xiaolei Zhang, Xiaolei Zhang

“…Genotyping employed a 3K SNP panel, and genetic maps were constructed using QTL IciMapping. QTL analysis integrated single linkage mapping (SLM) and NAM approaches, with candidate genes identified via maizeGDB annotation and transcriptome data.ResultsThe broad-sense heritability of the populations with a range of 63.98-80.72% indicated the majority of starch content, oil content and lysine content variations were largely controlled by genetic factors. …”
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Multi-omics analysis of SFTS virus infection in Rhipicephalus microplus cells reveals antiviral tick factors by Marine J. Petit, Charlotte Flory, Quan Gu, Mazigh Fares, Douglas Lamont, Alan Score, Kelsey Davies, Lesley Bell-Sakyi, Pietro Scaturro, Benjamin Brennan, Alain Kohl

“…Collectively, our results provide insights into the antiviral responses of R. microplus vector cells and highlight critical SFTSV restriction factors, while enriching transcriptomic and proteomic resources for future research.…”
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Integrative Analysis of Shared Pathogenic Genes and Potential Mechanisms in Gardnerella vaginalis and Persistent HPV16 Infection by Ye Li, Yue Wang, Xianhua Liu, Huifeng Xue, Liying Wang, Maotong Zhang, Pengming Sun

“…Mendelian randomization (MR) and colocalization analyses linked RSAD2 downregulation to an increased risk of cervical carcinoma in situ (rs2595163, PPH4 = 0.62), while ROC analysis demonstrated strong diagnostic potential for the combined hub gene expression. …”
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Genome-Wide Analysis of GmMYB S20 Transcription Factors Reveals Their Critical Role in Soybean Nodulation by Junchen Leng, Ruobing Xu, Yanshuang Liu, Tianshu Jiang, Haiying Hu, Zhaojun Ding, Shaojun Dai

“…Functional analyses revealed that loss of <i>GmMYB62s</i> function significantly reduced nodule density, while overexpression promoted nodulation. Transcriptomic analysis (RNA-seq) further demonstrated that <i>GmMYB62s</i> regulate key pathways, including hormone signaling, immune responses, and cell wall metabolism, thereby coordinating symbiotic interactions. …”
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Combined transcriptional and metabolomic analysis of flavonoids in the regulation of female flower bud differentiation in Juglans sigillata Dode by Jinyan Chen, Wenwen Li, Wen’ e Zhang, Chunxiang Li, Ruipu Wang, Xuejun Pan, Jian Peng

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Longitudinal analysis of genetic and epigenetic changes in human pluripotent stem cells in the landscape of culture-induced abnormality by Yun-Jeong Kim, Byunghee Kang, Solbi Kweon, Sejin Oh, Dayeon Kim, Dayeon Gil, Hyeonji Lee, Jung-Hyun Kim, Ji Hyeon Ju, Tae-Young Roh, Chang Pyo Hong, Hyuk-Jin Cha

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