Identifying inflammatory bowel disease subtypes: a comprehensive exploration of transcriptomic data and machine learning-based approaches by Niyati Saini, Animesh Acharjee

“…Despite advances in transcriptomic analysis and machine learning (ML), consistent molecular subtyping across datasets remains a challenge. …”
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Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics by Xiaojuan Yang, Yutao Duan, Lei Qiu, Xia Huang, Fei Li

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Regulatory roles of long non-coding RNAs in minipigs revealed by cross-breed and cross-tissue transcriptomic analyses by Suyeon Wy, Heesun Kim, Minji Gu, Junyoung Kim, Hyeonji Kim, Jiyeong Ahn, Daehong Kwon, Woncheoul Park, Jaebum Kim

“…Notably, tcDELs were linked to pathways related to organ size and gene regulation across tissues, while tsDELs were associated with physiological functions specific to each tissue. …”
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Gonadal transcriptome analysis reveals MAG participates in ovarian suppression of intersex red claw crayfish (Cherax quadricarinatus) by Honglin Chen, Miaofeng Ouyang, Huan Zhou, Fangfang Liu, Huiyi Cai, Bao Lou

“…Furthermore, the analyses of gene regulation relationship revealed that IAG positively regulates MAG expression, while MAG negatively regulates vitellogenin gene (VTG) expression. …”
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Differential photosynthetic responses to drought stress in peanut varieties: insights from transcriptome profiling and JIP-Test analysis by Jingyao Ren, Pei Guo, Xinhua Zhao, Xinlei Ma, Xin Ai, Jing Wang, Hongtao Zou, Haiqiu Yu

“…Both cultivars exhibited substantial increases in Vj and Vi parameters at 24 h, while FH18 demonstrated a pronounced elevation in Vk during the O-J phase transition, suggesting severe impairment of the oxygen-evolving complex. …”
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A rare IDH-Mutant glioma case: insights from single-cell transcriptomic analysis of tumor recurrences by Wen Li, Yuanshuai Zhou, Shaheryar Shafi, Jun Dong, Minxuan Sun

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Comparative transcriptome analysis reveals key long noncoding RNAs for cadmium tolerance in Tibetan hull-less barley by Md Rafat Al Foysal, Md Rafat Al Foysal, Cheng-Wei Qiu, Feibo Wu

“…Among these, 1884 target genes were regulated by cis-acting lncRNAs, while 3428 were regulated by trans-acting lncRNAs. …”
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Aberrant c-AMP signalling in richter syndrome revealed by single-cell transcriptome and 3D chromatin analysis by Heng Li, Cheng Xing, Ji Li, Yihao Zhan, Ming Luo, Peilong Wang, Yue Sheng, Hongling Peng

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Deciphering spatially confined immune evasion niches in osteosarcoma with 3-D spatial transcriptomics: a literature review by Guangqiang Qiu, Yongcheng Tang, Junhui Zuo, Heng Wu, Yongxian Wan

“…Pre-clinical atlases link PD-L1 high SOX9 stem-like cells, LGALS3 macrophages and VEGFA-driven endothelial tips to chemoresistance and immune-checkpoint failure, while ligand–receptor inference highlights VEGFA–VEGFR2, CXCL12–CXCR4 and complement–CSF1R axes as actionable bottlenecks. …”
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Transcriptome profiling of L. infantum-infected human macrophages reveals sex-specific type I interferon induction. by Annika Bea, Helena Fehling, Fabian Hausmann, Fahten Margot Habib, Melanie Lütkemeyer, Lara Buer, Carola Schäfer, Charlotte Sophie Hansen, Barbara Honecker, Stefan Bonn, Bianca Elisabeth Schneider, Joachim Clos, Hanna Lotter

“…Genes associated with type I interferon responses (e.g., IFIT2, IFIT3, IFIT5, OASL, JAK1), specific cytokine response (IL-15, IL-1R1), and the matrix metalloproteinase MMP9 were up-regulated in female macrophages, while genes encoding proinflammatory chemokines involved in immune cell recruitment (CXCL1, CXCL3, CCL20, CCL7) were up-regulated in male macrophages. …”
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Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility. by Keita Ito, Tsubasa Hirakawa, Shuji Shigenobu, Hironobu Fujiyoshi, Takayoshi Yamashita

“…Deep learning techniques are increasingly utilized to analyze large-scale single-cell RNA sequencing (scRNA-seq) data, offering valuable insights from complex transcriptome datasets. Geneformer, a pre-trained model using a Transformer Encoder architecture and human scRNA-seq datasets, has demonstrated remarkable success in human transcriptome analysis. …”
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Programmed cell death signatures-driven microglial transformation in Alzheimer’s disease: single-cell transcriptomics and functional validation by Mi-Mi Li, Ying-Xia Yang, Ya-Li Huang, Shu-Juan Wu, Wan-Li Huang, Li-Chao Ye, Ying-Ying Xu

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Responses of rice plant to multiple abiotic stresses revealed by transcriptome meta-analysis and identification of novel genetic factors by Asadollah Ahmdikhah, Mehdi Safaeizadeh, Alireza S. Tehranian

“…Several tolerant rice varieties were subjected to drought, salt and cold stresses and their transcriptomic responses were evaluated using affymetrix probe set. …”
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Exploring potentially synthetic genes related to diarrhetic shellfish toxins production in Prorocentrum sp. via comparative transcriptomics by Danlin Zheng, Jingyi Cen, Peiliang Chen, Ligong Zou, Jian Zou, Qun Li, Songhui Lu

“…We conducted a comprehensive comparative transcriptomic analysis to identify potential toxin-related genes, focusing on polyketide synthases (PKSs) and fatty acid synthases (FASs). …”
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The short-term effect of nitrogen and phosphorus fertilizers on cold resistance in Urtica cannabina based on transcriptomics and metabolomics analysis by Siqi Liu, Xiaoxue Zhang, Guorui Zhang, Jinmei Zhao, Xiaoqing Zhang, Xiaoqing Zhang

“…IntroductionFreezing injury in winter is a major abiotic stress that significantly limits plant growth and survival. While nitrogen and phosphorus fertilizers have been demonstrated to alleviate the impact of freezing injury in various plant species, their role of fertilizers in the cold tolerance of Urtica spp. is still unknown.MethodsThis study investigated the effects of fertilizers on the cold resistance of U. cannabina by comprehensively analyzing the physiological and biochemical indices, transcriptome, and metabolome of the U. cannabina under applications of 150 kg nitrogen ha-1 (N) and 90 kg phosphorus ha-1 (P), using “no fertilizer” (CK) as the control.ResultsThe results showed that applying nitrogen and phosphorus fertilizers reduced the malondialdehyde concentration and had much higher superoxide dismutase activity and soluble sugar and proline concentrations. …”
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Transcriptome and Metabolome Reveal Ferulic Acid as a Critical Phenylpropanoid for Drought Resistance in <i>Dendrobium sinense</i> by Huiyan You, Ao Yi, Qiongjian Ou, Jia Wang, Jun Niu

“…Using polyethylene glycol (PEG)-induced drought stress, chlorophyll content decreased significantly with increasing PEG concentration, while MDA and proline content, SOD, POD CAT, and APX activity showed a significant increase. …”
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Integrated transcriptome profiling and in vitro analysis reveals MLN4924’s role in inducing ferroptosis in acute myeloid leukemia by Jinli Jian, Yuancheng Guo, Xiao Tang, Long Zhao, Bei Liu

“…Objectives: While ferroptosis induction emerges as a therapeutic strategy for solid tumors, its role in acute myeloid leukemia (AML) remains unexplored. …”
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Integrated physiological, transcriptomic and metabolomic analysis of the response of Brassica napus L. to pruning residues from tea plant by Min Cai, Xu Zhang, Zheng Feng, Xinzhuan Yao, Litang Lu, Yujie Jiao, Weidong Wang

“…The CT extracts solution promoted seed germination and seedling growth, while the UT extracts solution had the opposite effect. …”
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Identification of crucial drought-tolerant genes of barley through comparative transcriptomic analysis and yeast-based stress assay by Xiaoyan He, Congjun Su, Xinyi Zhang, Zhaoxia Shi, Yanjie Wang, Huandi Peng, Shuying Fang, Xinyu Chen, Huayan Yin, Jianbin Zeng, Ping Mu

“…This study revealed the drought tolerance mechanism of Hindmarsh by comparing transcriptomes while also providing a set of candidate genes for genetic efforts to improve drought tolerance in this and other crop species.…”
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Saliva-derived transcriptomic signature for gastric cancer detection using machine learning and leveraging publicly available datasets by Catarina Lopes, Andreia Brandão, Manuel R. Teixeira, Mário Dinis-Ribeiro, Carina Pereira

“…This study aims to assess the potential of saliva as a proxy for malignant gastric transformation and its diagnostic value through transcriptomic profiling. Leveraging transcriptomic data from the Gene Expression Omnibus (GEO), we constructed and validated predictive models through machine learning algorithms within the tidymodels framework. …”
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