Tcf4 regulates secretory cell fate decisions in the small intestine and colon tumors: insights from transcriptomic, histological, and microbiome analyses by Lucie Janeckova, Monika Stastna, Dusan Hrckulak, Linda Berkova, Jan Kubovciak, Jakub Onhajzer, Vitezslav Kriz, Stela Dostalikova, Tereza Mullerova, Katerina Vecerkova, Marketa Tenglerova, Stepan Coufal, Klara Kostovcikova, Richard S. Blumberg, Dominik Filipp, Konrad Basler, Tomas Valenta, Michal Kolar, Vladimir Korinek

“…In colon adenomas, Paneth-like tumor cells drive antimicrobial gene expression and provide Wnt3 ligands, which may have implications for cancer therapy. …”
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Single-cell transcriptome profiling of m6A regulator-mediated methylation modification patterns in elderly acute myeloid leukemia patients by Zhe Wang, Xin Du, Peidong Zhang, Meiling Zhao, Tianbo Zhang, Jiang Liu, Xiaolan Wang, Doudou Chang, Xiaxia Liu, Sicheng Bian, Xialin Zhang, Ruijuan Zhang

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The effects of different doses of compound enzyme preparations on the production performance, meat quality and rumen microorganisms of yak were studied by metagenomics and transcri... by Chenyang Zhang, Chenyang Zhang, YongFu La, YongFu La, Xiaoming Ma, Xiaoming Ma, Pingcuo Zhandui, Xiaoyun Wu, Xiaoyun Wu, Xian Guo, Xian Guo, Ping Yan, Ping Yan, Luosan Dunzhu, Chunnian Liang, Chunnian Liang

“…The results of this study provide a scientific basis for adding ruminant enzymes to yaks.…”
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Integrated Physiological, Transcriptomic, and Metabolomic Analysis Reveals Mechanism Underlying the <i>Serendipita indica</i>-Enhanced Drought Tolerance in Tea Plants by Gaojian Shen, Hongli Cao, Qin Zeng, Xiaoyu Guo, Huixin Shao, Huiyi Wang, Liyong Luo, Chuan Yue, Liang Zeng

“…Particularly, the flavonoid biosynthesis pathway was identified from the metabolomic and transcriptomic analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. …”
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Single-cell transcriptomic profiling reveals the heterogeneity of epithelial cells in lung adenocarcinoma lymph node metastasis and develops a prognostic signature by Qiuqiao Mu, Qiuqiao Mu, Qiuqiao Mu, Han Zhang, Ying Shi, Mengli Xue, Jingxian Wang, Yun Ding, Lin Tan, Hui Yuan, Xin Li, Xin Li, Daqiang Sun, Daqiang Sun, Daqiang Sun

“…BackgroundLymph node metastasis markedly worsens prognosis in lung adenocarcinoma (LUAD); however, the evolutionary dynamics and regulatory mechanisms underlying the heterogeneity of malignant epithelial cells during this process remain poorly understood and warrant comprehensive investigation.MethodsWe performed a comprehensive single-cell transcriptomic analysis of epithelial cells from 18 samples comprising normal lung tissue and lymph node metastases. …”
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Genetic parameters and identification of genomic regions and candidate genes associated with vaginal discharge score in Holstein cattle based on genomic and transcriptomic analyses by Junxing Zhang, Liyun Han, Hui Sheng, Hailiang Zhang, Luiz F. Brito, Shanshan Li, Guoshang Ji, Xingang Dan, Bei Cai, Yamei Hu, Yachun Wang, Yun Ma

“…The VSTM1, IL10RA, FXYD5, C2CD5, CETN4, ALS2CL, and PBX1 genes were considered to be the most promising candidate genes influencing postpartum uterine health in Holstein cows. This study provides novel insights on the genetic background of postpartum uterine health in Holstein cows. …”
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Single-cell transcriptomics and machine learning unveil ferroptosis features in tumor-associated macrophages: Prognostic model and therapeutic strategies for lung adenocarcinoma by Ting Ji, Ting Ji, Juanli Jiang, Juanli Jiang, Xin Wang, Xin Wang, Kai Yang, Kai Yang, Shaojin Wang, Shaojin Wang, Bin Pan, Bin Pan

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Transcriptome Analysis Reveals the Molecular Mechanisms for Mycorrhiza-Enhanced Drought Tolerance in Maize by Regulating the Ca²⁺ Signaling Pathway by Qiaoming Zhang, Wenjing Yang, Miaomiao Wang, Junwei Chen, Zhaoran Zhang, Yanan Wei, Qingshan Chang, Minggui Gong

“…However, comprehensive transcriptome analysis to reveal the molecular mechanism of drought tolerance in the symbiotic process between AMF and maize is still limited. …”
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Single-cell transcriptome analysis reveals the malignant characteristics of tumour cells and the immunosuppressive landscape in HER2-positive inflammatory breast cancer by Juan Huang, Yongwei Zhu, Wenjing Zeng, Yulong Zhang, Weizhi Xia, Fan Xia, Liyu Liu, Kuansong Wang, Yidi Guan, Taohong Shen, Bingjian Jiang, Lunquan Sun, Ayong Cao, Shouman Wang, Zhi Li

“…Previous studies have suggested that targeting the tumour microenvironment (TME) may provide new directions for IBC diagnosis and treatment. …”
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Integrated Single-Cell and Spatial Transcriptomic Analysis Identifies ISR-Related Genes Driving Immune Regulation in Parkinson&amp;rsquo;s Disease by Jiang H, Zhang X, Feng S, Feng W

“…In this study, we used advanced transcriptomic techniques, including single-cell RNA sequencing and spatial transcriptomics, to analyze gene expression patterns in PD. …”
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Multi-omics-Based Construction of ncRNA-Gene-Metabolite Networks Provides New Insights Into Metabolic Regulation Under Salt Stress in Rice by Haiyang Tong, Chao Wang, Xiaoqian Han, Qihao Sun, Enxi Luo, Chao Yang, Guo Xu, Xumin Ou, Shixuan Li, Jianing Zhang, Jun Yang

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Arginine-Enhanced <i>Termitomyces</i> Mycelia: Improvement in Growth and Lignocellulose Degradation Capabilities by Wenhui Yi, Jingfei Zhou, Qiwei Xiao, Wujie Zhong, Xuefeng Xu

“…The addition of arginine also upregulated the expression of the enzymes related to lignocellulose decomposition, leading to increased activities of cellulase, hemicellulase, and laccase, which accelerated the decomposition and utilization of corn straw. A transcriptome analysis revealed differential expression patterns of carbohydrate-active enzyme genes in arginine-supplemented <i>Termitomyces</i> mycelia, providing insights into the molecular mechanisms underlying these enhancements. …”
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Genetic regulation of mouse liver metabolite levels by Anatole Ghazalpour, Brian J Bennett, Diana Shih, Nam Che, Luz Orozco, Calvin Pan, Raffi Hagopian, Aiqing He, Paul Kayne, Wen‐pin Yang, Todd Kirchgessner, Aldons J Lusis

“…We also integrated the metabolomic data with transcriptomic and clinical phenotypic data to evaluate the extent of co‐variation across various biological scales.…”
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The abiotic stress gene (Asg) family member Asg2 as a modulator of plant responses to salt stress by Xiaona Tian, Ziru Chang, Ruigang Wang, Guojing Li, Yang Qi

“…In conclusion, this research emphasizes the important function of the Asg gene in influencing salt tolerance, providing a foundational framework and genetic resource for comprehending how plants respond to salt stress.…”
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Improvement in the prediction power of an astrocyte genome-scale metabolic model using multi-omic data by Andrea Angarita-Rodríguez, Andrea Angarita-Rodríguez, Andrea Angarita-Rodríguez, Nicolás Mendoza-Mejía, Nicolás Mendoza-Mejía, Janneth González, Jason Papin, Jason Papin, Jason Papin, Andrés Felipe Aristizábal, Andrés Pinzón

“…Existing methods often link transcriptome and proteome data independently to reaction boundaries, providing models with estimated maximum reaction rates based on individual datasets. …”
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Generation and characterization of induced pluripotent stem cells of small apes by Yusuke Hamazaki, Hiroto Akuta, Hikaru Suzuki, Hideyuki Tanabe, Kenji Ichiyanagi, Takuya Imamura, Masanori Imamura, Masanori Imamura, Masanori Imamura

“…These signatures highlighted processes linked to genomic stability and cell death, providing insights into small ape-specific adaptations. …”
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Transcriptomic and metabolomic analyses of root responses in Indigofera stachyodes seedlings under drought stress: a medicinal plant native to karst mountainous regions by Qingqing Ye, Na Zhang, Xin Tan, Li Yang, Ning Ding, Wei Zhou, Zhikun Wu

“…Root tissues from each treatment group were analyzed using transcriptomics (RNA-seq) and metabolomics (LC-MS/GC-MS) approaches to identify differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs). …”
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Context-specific eQTLs provide deeper insight into causal genes underlying shared genetic architecture of COVID-19 and idiopathic pulmonary fibrosis by Trisha Dalapati, Liuyang Wang, Angela G. Jones, Jonathan Cardwell, Iain R. Konigsberg, Yohan Bossé, Don D. Sin, Wim Timens, Ke Hao, Ivana Yang, Dennis C. Ko

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Genome wide identification of LcC2DPs gene family in Lotus corniculatus provides insights into regulatory network in response to abiotic stresses by Guangfen Yang, Yujie Liu, Zouxian Gong, Siya Chen, Juanying Wang, Li Song, Shihui Liu

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Integration of volatile and non-volatile metabolites and the transcriptome reveals the formation mechanisms of differential aroma compounds between Pyrus communis and Pyrus pyrifol... by Jiao Wang, Jiao Wang, Xianping Guo, Xianping Guo, Zhongying Wu, Zhongying Wu, Dongsheng Wang, Dongsheng Wang, Peng Guo, Yongping Han, Hui Jiang, Zhenzhen Lü

“…A comparative study on the formation of differential aroma compounds between the two species could provide a theoretical foundation for improving the aroma quality of P. pyrifolia cultivars. …”
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