Comprehensive pan-cancer analysis of NLRs family as prognostic and immunity markers based on multi-omics data by Xianhui Wen, Miaomiao Cui, Junhua Zhang, Hai Huang

“…Methods A multi-omics analysis was performed on data from over 10,000 individuals, integrating genomics, epigenomics, transcriptomics, proteomics, and immunogenomics. …”
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Cross-Species Multi-Omics Analysis Reveals Myeloid-Driven Endothelial Oxidative Stress in Ischemic Stroke by Ziqi Cheng, Hua Zhu, Shi Feng, Yonggang Zhang, Xiaoxing Xiong

“…Methods: In this study, we integrated bulk RNA-sequencing (RNA-seq), single-cell RNA-seq (scRNA-seq), spatial transcriptomics, and flow cytometry data from human and mouse models of ischemic stroke. …”
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Multiple-omics analysis of aggrephagy-related cellular patterns and development of an aggrephagy-related signature for hepatocellular carcinoma by Jiafen Xie, Xiaoming Wang

“…The high-risk group exhibited significantly worse survival outcomes, heightened drug resistance, and enrichment in cell cycle, mTORC1 signaling, and reactive oxygen species pathways. Single-cell transcriptomic analysis revealed 11 distinct cell types within the HCC tumor microenvironment (TME), including hepatocytes, T cells, NK cells, macrophages, monocytes, dendritic cells, plasma B cells, mature B cells, mast cells, endothelial cells, and fibroblasts. …”
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Enhanced hierarchical attention networks for predictive interactome analysis of LncRNA and CircRNA in oral herpes virus by Pradeep Kumar Yadalam, Carlos M. Ardila

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Identification and Expression Analysis of miR166 Gene Family in Response to Salt Stress in <i>Chrysanthemum</i> by Di Wang, Shuheng Wang, Dongyang Zhang, Yuan Meng, Ying Qian, Siyu Feng, Yun Bai, Yunwei Zhou

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Identification of a novel chemotherapy benefit index for patients with advanced ovarian cancer based on Bayesian network analysis. by Shuxiao Ma, Lu Zhou, Yi Liu, Hui Jie, Min Yi, Chenglin Guo, Jiandong Mei, Chuan Li, Lei Zhu, Senyi Deng

“…The AUC of internal validation and two external validation cohorts were 0.87, 0.71 and 0.70, respectively. Molecular function analysis indicated that the CBI-low subgroup is characterized by the activation of cancer-related signaling pathways, immune-related biological processes, higher TP53 mutation rate, particularly with a better response to immune checkpoint blockade (ICB) treatment, while the CBI-high subgroup is characterized by inhibition of cell cycle, less response to ICB treatment, and potential therapeutic targets.…”
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Identification and Analysis of Stress-Associated Protein (SAP) Transcription Factor Family Members in <i>Pinus massoniana</i> by Yulu Zhao, Xingyue Ren, Jingjing Zhang, Wenya Yu, Qiong Yu, Kongshu Ji

“…Using transcriptome data and qRT-PCR, we analyzed their expression patterns and employed yeast systems to validate their transcriptional activities. …”
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Comprehensive Analysis of Multi-Omics Data on RNA Polymerase as an Adverse Factor in Head and Neck Squamous Cell Carcinoma by Gu YJ, Zhang J, Liu YJ, Zhang Q, Geng QF

“…Focusing on head and neck squamous cell carcinoma (HNSC), we integrated bulk RNA sequencing, single-cell, and spatial transcriptome data to identify POLR2C expression patterns and its potential regulation by Yin Yang 1 (YY1). …”
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Identification and expression analysis of ACBPs family members of Hippophae rhamnoides subsp. sinensis Rousi in response to lead stress by CHEN Ke, LI Xinjuan, ZHANG Tian, REN Qiandan, SUN Jing, ZHOU Wu

“…Protein 3D structure predictions revealed that Group 3 proteins were the most complex with high model similarity; Group 1 proteins were simpler but also similar; Group 4 proteins showed low similarity and large differences. Transcriptome analysis and qRT-PCR validation indicated that, except for HrLACBPs1, the other genes had lower expression levels at 2000 mg·kg-1 lead compared to controls, while their expression increased at 5000 mg·kg-1 lead. …”
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Detecting Predicted Cancer-Testis Antigens in Proteomics Datasets of Healthy and Tumoral Samples by Karla Cristina Tabosa Machado, Tayna da Silva Fiuza, Sandro Jose de Souza, Gustavo Antonio de Souza

“…Mass spectrometry-based proteomics allows the characterization of many cellular types and the production of large amounts of data while computational tools allow the comparison of multiple datasets, and together those may corroborate insights obtained at the transcriptomic level. …”
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DRomics, a workflow to exploit dose-response omics data in ecotoxicology by Delignette-Muller, Marie Laure, Siberchicot, Aurélie, Larras, Floriane, Billoir, Elise

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Beyond the nuclear border: single-cell analysis of in situ sequenced human brain tissue using cellular features by Janssen M. Kotah, Thomas Rust, Hilmar R. J. van Weering, Janneke Bosma, Amber L. Woudstra, Susanne M. Kooistra, Bart J. L. Eggen

“…A key challenge in ISS data analysis is optimizing transcript allocation while minimizing misallocation, particularly in the morphologically complex central nervous system (CNS). …”
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Comprehensive bioinformatics analysis of the common mechanism of atherosclerosis and atrial fibrillation: emphasizing mitochondrial metabolic disorder and immune inflammation by Rui Dai, Xiaotong Lei, Xiaojun Liu, Chen Bian

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Cross-species single-nucleus analysis reveals the potential role of whole-genome duplication in the evolution of maize flower development by Huawei Feng, Wenjuan Fan, Min Liu, Jiaqian Huang, Bosheng Li, Qing Sang, Baoxing Song

“…Combining the cell cluster resolved transcriptome comparison with genome alignment, our analysis suggested that maize ear and tassel inflorescence diversity is associated with the maize-specific whole genome duplication. …”
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Shared genetic architecture between stroke and blood lipids: a large-scale genome-wide cross-trait analysis by Wenya Bai, Guilin Zhou, Huan Jiang, Xuelian Li, Jianlin Shao

“…Two-sample MR analysis indicated that higher HDL-C levels were associated with reduced risks of stroke and IS, while elevated TG levels increased IS risk. …”
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Multi-omics analysis reveals Lactobacillus and Indolelactic acid involved in small intestinal adaptation of piglet with short bowel syndrome by Weipeng Wang, Ying Lu, Bo Wu, Shicheng Peng, Wei Cai, Yongtao Xiao

“…Transcriptomic analysis on ileal mucosa was performed. …”
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Single cell analysis identifies distinct CD4 + T cells associated with the pathobiology of pediatric obesity related asthma by David A. Thompson, Yvonne B. Wabara, Sarai Duran, Anna Reichenbach, Laura Chen, Kayla Collado, Changsuek Yon, John M. Greally DMed, Deepa Rastogi

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Differential Analysis of Early-Onset and Late-Onset Colorectal Cancer Based on Multidimensional Evidence Integration: A Review by Xiaoying Mi MS, Peng Zheng MS, Xiangbai Wu MS

“…At the biomolecular level, PIK3CA mutation and TP53 deletion exhibits a higher mutation rate in EO-CRC compared to LO-CRC, while other common gene mutations such as APC, KRAS, and SMAD4 are relatively less frequent. …”
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Integrative analysis of ceRNA networks and immune cell infiltration in thyroid cancer for enhanced diagnostic and prognostic insights by Chang Lv, Huazhe Wu, Dejun Yin, Wei Fang, Liming Zhou

“…This study aims to identify molecular markers and construct a comprehensive ceRNA regulatory network to enhance thyroid cancer diagnosis and prognosis. Using transcriptomic data from TCGA, GTEx, and GEO datasets, we performed differential expression analysis and WGCNA to identify key lncRNAs, miRNAs, and mRNAs involved in thyroid cancer. …”
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A meta-analysis approach for annotation and identification of lncRNAs controlling perirenal fat deposition in suckling lambs by María Alonso-García, Beatriz Gutiérrez-Gil, Rocío Pelayo, Pablo A. S. Fonseca, Héctor Marina, Juan José Arranz, Aroa Suárez-Vega

“…Long non-coding RNAs (lncRNAs) are being studied in farm animals due to their association with traits of economic interest, such as fat deposition. Based on the analysis of perirenal fat transcriptomes, this research explored the relevance of these regulatory elements to fat deposition in suckling lambs. …”
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