Comparative analysis of genotype imputation strategies for SNPs calling from RNA-seq by Kaixuan Guo, Zhanming Zhong, Haonan Zeng, Changliang Zhang, Teddy Tinashe Chitotombe, Jinyan Teng, Yahui Gao, Zhe Zhang

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Metabolomics analysis of extracellular vesicles derived from bovine colostrum and mature milk by Sitong Zhang, Xipeng Sun, Yameng Zhang, Rong Huang, Wenyou Situ, Huaxi Yi, Lingjun Tong

“…However, most research on mEVs has focused on their proteomics, lipidomics, and transcriptome, while metabolome analysis are still lacking. …”
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WGCNA analysis and identification of key genes in tobacco in response to different nitrogen levels by Xinwang Zhang, Shouhui Pan, Dong Chen, Yuqi Pan, Deepak Bhanot, Tianju Xu, Sachin Gupta, Jinling Zhang, Yin Huang

“…To decipher molecular responses to N gradients, we integrated transcriptomics and weighted gene co-expression network analysis (WGCNA) on leaves from four N treatments: 0 (inherent soil fertility), 60 (low), 105 (standard), and 150 kg/hm2 (high). …”
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Identification and Expression Pattern Analysis of Odorant Receptor Family Genes of Tuta absoluta by Zhonglin ZHOU, Gang LIAO, Tingting XIANG, Zhongxiang SUN

“…The coding sequences (CDS) of these genes had an average length of 1 029 bp, with an average of seven exons per gene. Phylogenetic analysis revealed that four genes (TabsOR01, TabsOR28, TabsOR34, and TabsOR38) clustered in a well-defined branch, while the remaining genes were distributed across other branches. …”
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Proteomic analysis reveals chromatin remodeling as a potential therapeutical target in neuroblastoma by Zan Liu, Zitong Zhao, Longlong Xie, Zhenghui Xiao, Ming Li, Yong Li, Ting Luo

“…Results Our proteomic analysis reveals that pathways associated with the cell cycle and DNA replication are significantly upregulated in NB, while oxidative phosphorylation, pyruvate metabolism, and the TCA cycle are notably downregulated compared to GNB and GN. …”
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Genetic predisposition to immune dysregulation and extracellular matrix remodeling in cardiac arrhythmia reveals potential mediation by SPP1+ macrophages by Jie-Yuan Jin, Jie-Yuan Jin, Shuai Guo, Yao Deng, Ya-Qin Chen, Chen Liang, Yu-Jie Jiang, Wang Zhao, Rong Xiang

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Interpretable machine learning-guided single-cell mapping deciphers multi-lineage pancreatic dysregulation in type 2 diabetes by Xueqin Xie, Changchun Wu, Yuhe Yang, Wei Su, Fuying Dao, Jian Huang, Zheng Shi, Hao Lyu, Hao Lin

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Cloning and Bioinformatics Analysis of Vitellogenin Genes and Its Receptor Genes in Thalassodes immissaria by Guolin ZHU, Qiong YAO, Wenjing LI, Shu XU, Kai LIU, Shuanggang DUAN

“…【Objective】Vitellogenin (Vg) and its receptor (VgR) play key roles in insect reproduction by mediating nutrient transport during oocyte vitellogenesis.This study aimed to clone Vg and VgR from the Thalassodes immissaria, a notorious defoliator in lichee, and analyzed their bioinformatics characteristics and expression patterns across developmental stages to infer their roles in reproductive regulation.【Method】Using transcriptome data of T.immissaria, the full-length cDNA sequences of TiVg and TiVgR were cloned via PCR.Bioinformatics tools, such as ORF Finder, SignalP 5.0, ProtParam, SMART, TMHMM 2.0, and MEGA v5.05, were used for sequence analysis.Expression profiles of TiVg and TiVgR across different developmental stages and different tissues were quantified using transcriptomic TPM values and qRT-PCR.…”
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Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes. by Sophie Garnier, Vinh Truong, Jessy Brocheton, Tanja Zeller, Maxime Rovital, Philipp S Wild, Andreas Ziegler, Cardiogenics Consortium, Thomas Munzel, Laurence Tiret, Stefan Blankenberg, Panos Deloukas, Jeannette Erdmann, Christian Hengstenberg, Nilesh J Samani, Heribert Schunkert, Willem H Ouwehand, Alison H Goodall, François Cambien, David-Alexandre Trégouët

“…At the Bonferroni correction level of 1.2 × 10(-4) (~0.05/412), 193 haplotypic signals replicated. 1000 G imputation was then conducted, and 105 haplotypic signals still remained more informative than imputed SNPs. In-depth analysis of these 105 cis eQTL revealed that at 76 loci genetic associations were compatible with additive effects of several SNPs, while for the 29 remaining regions data could be compatible with a more complex haplotypic pattern. …”
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Identification of RNA binding protein genes associated with colorectal cancer by bioinformatics analysis by Rong-Chao He, Haibo Wang, Jun He, Hou-Dong Wang, Zhong Shen

“…Integrating risk score, stage, and age, a nomogram was established to further enhance clinical applicability. Enrichment analysis linked high-risk groups to extracellular matrix remodeling, PI3K-Akt signaling, and immune evasion, while low-risk groups exhibited metabolic and immune activation pathways. …”
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Microbiome-driven gene dysregulation in oesophageal cancer: a multi-omics analysis by Chaitali Nath

“…Machine learning models were applied to determine the predictive power of microbial composition in distinguishing cancer vs non-cancer states, and results were compared with risk stratifications derived from the Nath Score.8 Results: Transcriptomic analysis revealed a significant upregulation of B cell-related immunoglobulin genes, including IGKV1D-13, IGKV2-29, IGLV3-27 and IGHV1-18, suggesting microbiome-driven immune activation in the tumour microenvironment.4,9 By contrast, genes essential for epithelial integrity (KRT1, PGA5 and KPRP) were markedly downregulated, indicative of microbial-induced epithelial dysfunction and tissue remodeling.2,5 Microbiome profiling identified F. nucleatum, Campylobacter spp., and P. gingivalis as predominant species in cancer-associated samples, exhibiting strong correlations with immune gene activation.4,5 Machine learning models achieved high predictive accuracy (>85%), reinforcing the potential of microbiome-based diagnostics. …”
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Lactylation Modification as a Promoter of Bladder Cancer: Insights from Multi-Omics Analysis by Yipeng He, Lingyan Xiang, Jingping Yuan, Honglin Yan

“…Spatial transcriptome analysis showed the spatial distribution characteristics of the model genes. …”
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Integrative genomic analysis identifies isoleucine and CodY as regulators of Listeria monocytogenes virulence. by Lior Lobel, Nadejda Sigal, Ilya Borovok, Eytan Ruppin, Anat A Herskovits

“…Here we used an integrative Metabolic Analysis Tool that combines transcriptome data with genome-scale metabolic models to define the metabolic requirements of Listeria monocytogenes during infection. …”
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Renal oncocytoma with liver metastasis: a case report with genetic analysis and literature review by Issa Al-kharouf, Carmen Miller, Ameer Hamza, Benyi Li, Da Zhang

“…This report describes a unique case involving transcriptome analysis to identify genes associated with the oncocytoma signature. …”
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Proteomic Analysis Reveals the Protective Effects of Selenomethionine Against Liver Oxidative Injury in Piglets by Kai Zhang, Shuhui Yan, Junhong Miao, Wen Li, Zhenxu Li

“…Additionally, it reduced the serum and liver levels of malondialdehyde and protein carbonyls in piglets exposed to DQ. Selenoprotein transcriptome analysis showed that the mRNA levels of five selenoprotein genes (<i>GPX1/3</i>, <i>DIO2</i>, and <i>SELENOF/M/W</i>) were significantly upregulated by dietary SeMet supplementation in the liver of DQ-challenged piglets. …”
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Multi-omics analysis of the mechanism of alfalfa and wheat-induced rumen flatulence in Xizang sheep by Jing Wu, Xiaoming Zhang, Khan Ayesha, Shahzad Khuram, Jianzhao Cui, Gaofu Wang, Zhaxi Yangzong, Mingyan Shi, Xunping Jiang, Long Li, Guiqiong Liu, Wangsheng Zhao, Tianzeng Song

“…Transcriptome analysis revealed many differentially expressed genes (DEGs). …”
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Evidence from a Comprehensive Bioinformatics Analysis Point to Possible Therapeutic Targets for Vitiligo by Wang Y, Yao T, Lin Y, Wu J

“…Validation across different cohorts confirmed the significance of GZMB and FCRL3. Colocalization analysis indicated that these targets share common variants with vitiligo, while PheW-MR analysis suggested that targeting these proteins would not result in significant side effects. …”
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Analysis of abscisic acid-insensitive gene (ABI) sequence and phylogenetic relationship in genus Fagopyrum by WANG Yan, LIANG Chenggang, CHEN Qingqing, SHI Taoxiong, CHEN Qijiao, MENG Ziye, DENG Jiao, HUANG Juan, CHEN Qingfu

“…Hierarchical cluster analysis indicated that the phylogenetic relationship of F. tataricum was close to F. megaspartanium, F. cymosum and F. urophyllum, then further grouped with F. pilus, while the F. esculentum was close to F. zuogongense based on the ABI gene sequence analysis. …”
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Functional analysis of NtPDX2 in Nicotiana tabacum L. associated with stem development by Li Xu, Yuxin Cui, Jiaxin Xing, Qili Mi, Zhixing Wang, Xujing Wang, Wanli Zeng, Haiying Xiang, Jiarui Jiang, Lele Deng, Kunmiao Wang, Jiangtao Yang, Qian Gao

“…Through bioinformatics analysis, we predicted the phylogenetic relationships and functions of these genes; the subcellular localization of NtPDX2 was found to be in the cytoplasmic structures. …”
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Comprehensive analysis of the multifaceted role of ITGAV in digestive system cancer progression and immune infiltration by Xinyue Shi, Jingyu Zang, Qi Gu, Mengmeng Zhang, Handi Sun, Lijun Yang, Jiahui Cheng, Ruonan Wang, Han Mao, Aitong Xu, Xin Wang, Yu Xiao, Jialing Cai, Fang Han, Depeng Yang, Yu Li, Huan Nie

“…However, no systematic digestive system cancer analysis has been conducted to explore its function in prognosis, diagnosis, and immunology.MethodsTranscriptome sequencing and clinical data of samples were obtained from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx), Human Protein Atlas (HPA), cBioPortal, TIMER and TISIDB databases. …”
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