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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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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Impact of <i>Ectropis grisescens</i> Warren (Lepidoptera: Geometridae) Infestation on the Tea Plant Rhizosphere Microbiome and Its Potential for Enhanced Biocontrol and Plant Healt... by He Liu, Wei Chen, Xiaohong Fang, Dongliang Li, Yulin Xiong, Wei Xie, Qiulian Chen, Yingying You, Chenchen Lin, Zhong Wang, Jizhou Wang, Danni Chen, Yanyan Li, Pumo Cai, Chuanpeng Nie, Yongcong Hong

“…By conducting 16S rRNA sequencing on the collected soil samples, we found significant shifts in bacterial communities by the seventh day, suggesting a lag in community adaptation. Transcriptomic analysis revealed that <i>E. grisescens</i> attack induced reprogramming of the tea root transcriptome, upregulating genes related to defensive pathways such as phenylpropanoid and flavonoid biosynthesis. …”
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Combined Effects of Marine Heatwaves and Light Intensity on the Physiological, Transcriptomic, and Metabolomic Profiles of <i>Undaria pinnatifida</i> by Hanmo Song, Yan Liu, Qingli Gong, Xu Gao

“…In this study, the effects of MHW intensities (moderate: +3 °C; severe: +6 °C) and light intensities (normal: 90 μmol photons m⁻² s⁻¹; high: 270 μmol photons m⁻² s⁻¹) on cultivated <i>Undaria pinnatifida</i> were investigated through an integrated analysis of physiological, transcriptomic, and metabolomic responses. …”
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Transcriptomic signatures in response to antioxidants supplementation in Korean cattle beef, Hanwoo: a 7-month feeding study by Kangwook Lee, La Yoon Choi, Jun Sang Ahn, Jae Yong Song, Joong Kook Park, Suk Jun Yun, Jeong Heon Lee, Eui-Cheol Shin, Soo-Jin Yeom, Jiangchao Zhao, Tae Jin Cho, Nam Su Oh, Jeong-Oh Shin, Dahye Kim, Tae Gyun Kim, Hyung Taek Cho, Hyo Ri Shin, Young Jun Kim, Jae Kyeom Kim, Jae Kyeom Kim

“…Growth performance and carcass traits were evaluated, and liver transcriptomic changes were assessed using RNA sequencing.Results and discussionWhile no significant differences were observed in phenotypic traits such as weight gain and feed conversion ratio, transcriptomic analysis identified 641 differentially expressed genes between the CON and FEED groups. …”
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Single-cell transcriptome and multi-omics integration reveal ferroptosis-driven immune microenvironment remodeling in knee osteoarthritis by Yushun Wu, Jing Liu, Wenying Yu, Xiaoding Wang, Jian Li, Weiquan Zeng

“…BackgroundKnee osteoarthritis (KOA) is a chronic inflammatory joint disorder marked by cartilage degradation and immune microenvironment dysregulation. While transcriptomic studies have identified key pathways in KOA, the interplay between ferroptosis (an iron-dependent cell death mechanism) and immune dysfunction at single-cell resolution remains unexplored. …”
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Unraveling ScAPD1-mediated resistance mechanism to Verticillium dahliae through integrated host-pathogen transcriptomics by Qilin Yang, Ruirui Yang, Huan Zhang, Fangliu Yin, Leyi Wang, Daoyuan Zhang, Xiaoshuang Li

“…Transcriptomic analysis revealed a striking divergence in host response: while V. dahliae infection severely suppressed photosynthesis-related pathways in wild-type (WT) plants, SC lines maintained their photosynthetic capacity; this preservation of primary metabolism indicates a key component of ScAPD1-mediated resistance. …”
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Unveiling the molecular mechanisms of γ-polyglutamic acid-mediated drought tolerance in cotton through transcriptomic and physiological analyses by Ziyu Wang, Xin Zhang, Yunhao Liusui, Wanwan Fu, Aixia Han, Dongmei Zhao, Jisheng Yue, Yongfeng Tu, Jingbo Zhang, Yanjun Guo

“…Subsequently, transcriptome sequencing was performed on the leaves of cotton plants under drought stress in both the γ-PGA-treated and control groups. …”
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Selection and validation of reference genes for qRT-PCR normalization in dayflower (Commelina communis) based on the transcriptome profiling by Yuejiao Yang, Gaohui Cao, Lulu Tang

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Transcriptomic Profiling Unravels the Disruption of Photosynthesis Apparatuses and Induction of Immune Responses by a Bipartite Begomovirus in Tomato Plants by Wen-Ze He, Ting Rong, Xun-Yue Liu, Qiong Rao

“…We then profiled the tomato transcriptomic changes in response to TYLCTHV infection. …”
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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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Effects of chlorogenic acid on growth performance, immunity, antioxidant capacity, intestinal microbiota, and liver transcriptome in Mauremys mutica by Hongyao Zhang, Jingu Shi, Zike Yan, Mingzuo Gao, Kaijie Lin, Yutian Zhan, Yuhan Li, Jingzhen Liang, Shuyu Han

“…Notably, the 200 mg/kg CGA treatment exhibited the most significant improvements in growth performance, digestive enzyme activity, intestinal morphology, villus length, immunity, and antioxidant capacity. Transcriptomic analysis demonstrated that CGA significantly modulated liver gene expression, with the 200 mg/kg CGA group exhibiting the highest number of differentially expressed genes (DEGs). …”
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Integration of Transcriptomics and Metabolomics Reveals Mechanisms of High-Temperature Stress Tolerance in the Hepatopancreas of <i>Penaeus monodon</i> by Li Liu, Peng Zhao, Lishi Yang, Yundong Li, Zhong Huang, Qibin Yang, Yukai Yang, Jianzhi Shi, Yibiao Chen, Jianhua Huang

“…The hepatopancreas of two groups was subjected to transcriptomic and metabolomic analysis. The results revealed that, compared to the S group, the T group exhibited a total of 3527 DEGs, including 2199 upregulated and 1328 downregulated genes. …”
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Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos by Malarmathi Muthusamy, Kannaki T. Ramasamy, Sunday Olusola Peters, Srinivasan Palani, Vasudevan Gowthaman, Murali Nagarajan, Sivakumar Karuppusamy, Vasanthakumar Thangavelu, Thiruvenkadan Aranganoor Kannan

“…Methods: This study employed transcriptome analysis to investigate host–pathogen interactions by analyzing gene expression changes in NDV-infected chicken embryos’ lungs. …”
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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

“…Cytokine profiling revealed elevated levels of TNF, IL-8, IL-10, and reduced levels of IL-18 and CCL2 in culture supernatants over the time of infection. Transcriptomic analysis showed the highest adaptation of gene expression at 6 hpi, which was more pronounced in female-derived macrophages (1428 down-regulated/2145 up-regulated genes) compared to male-derived macrophages (972 down-regulated/1637 up-regulated genes), and gradually decreased over time in both sexes. …”
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Transcriptome sequencing reveals novel Citrus bark cracking viroid (CBCVd) variants from citrus and their molecular characterization. by Yafei Wang, Sagheer Atta, Xuefeng Wang, Fangyun Yang, Changyong Zhou, Mengji Cao

“…The length of CBCVd from China ranged from 282 to 286 nucleotides, while that of the one from Pakistan ranged from 273 to 277 nucleotides. …”
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Gibberellin-induced germination enhancement in Chinese sour jujube seeds under cold stress by Qiang Chen, Guolong Li, Jinao Duan, Zhishu Tang, Zhongxing Song, Hongbo Liu, Xinbo Shi

“…Comprehensive metabolomics and transcriptomics analysis showed that phenylpropionic acid/zeatin biosynthesis gene (4CL, CCR) was up-regulated, while CKX and PAL were down-regulated, which were related to the increase of zeatin and the decrease of abscisic acid metabolites. …”
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A scRNA-seq reference contrasting living and early post-mortem human retina across diverse donor states by Luning Yang, Yiwen Tao, Qi Pan, Tengda Cai, Yunyan Ye, Jianhui Liu, Yang Zhou, Yongqing Shao, Quanyong Yi, Zen Huat Lu, Lie Chen, Gareth McKay, Richard Rankin, Weihua Meng

“…After standardized dissociation, single-cell transcriptomes were generated using 10x Genomics 3’ RNA-seq and applied scVI to generate batch-corrected integrated atlas. …”
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Comprehensive transcriptome, miRNA and kinome profiling identifies new treatment options for personalized lung cancer therapy by Shen Zhong, Yvonne Börgeling, Patrick Zardo, Danny Jonigk, Jürgen Borlak

“…Methods We performed molecular pathology, transcriptomics and miRNA profiling across 95 well‐characterized LC patients. …”
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