Discovering biomarkers associated with infiltration of CD8+ T cells and tumor-associated fibrosis in colon adenocarcinoma using single-cell RNA sequencing and gene co-expression ne... by Jinning Zhang, Jinning Zhang, Ziquan Sun, Ziquan Sun, Guodong Li, Guodong Li, Lixian Ding, Zitong Wang, Ming Liu, Ming Liu

“…Therefore, it is imperative to identify biomarkers with prognostic value and elucidate the precise role of CD8+ T cells and tumor-associated fibrosis.MethodsWe performed a single-cell transcriptome analysis of COAD samples from the GEO database. …”
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ELABELA promotes the migration and homing of bone marrow mesenchymal stem cells to myocardial injury sites through the ERK1/2/miR-299a-5p/Exo70 pathway by Jing-Yu Hou, Hao Wu, Shuang-Mei Li, Xiao-Jing Li, Shu-Jun Yang, Xu-Xiang Chen, Chang-Qing Zhou, Hui-Bao Long, Hai-Dong Wu, Jia-Ying Fu, Ya-Jie Guo, Tong Wang

“…Cardiac repair was evaluated through fluorescence imaging, echocardiography, and histological analysis. Transcriptome sequencing and bioinformatics analysis were employed to identify and validate the mechanisms by which ELA promoted the migration of BMSCs. …”
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RNA-seq analysis reveals key genes associated with downregulation of APE1 in esophageal squamous cell carcinoma by Alan Chu, Xiao Liu, Shijia Liu, Mengxi Li, Rui Song, Lanlan Gan, Yongtai Wang, Zongwen Liu, Chen Sun

“…ObjectiveThis study aims to explore the impact of APE1 gene knockout on the transcriptome of esophageal cancer cells and conduct a preliminary screening of APE1-regulated target genes to provide a basis for understanding APE1 target genes and finding new anti-esophageal cancer therapeutic targets.MethodsWe collected 100 patients with esophageal squamous cell carcinoma (ESCC), analyzed the expression of APE1 in ESCC by immunohistochemical, and analyzed the overall survival. …”
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Integrative genomics sheds light on the immunogenetics of tuberculosis in cattle by John F. O’Grady, Gillian P. McHugo, James A. Ward, Thomas J. Hall, Sarah L. Faherty O’Donnell, Carolina N. Correia, John A. Browne, Michael McDonald, Eamonn Gormley, Valentina Riggio, James G. D. Prendergast, Emily L. Clark, Hubert Pausch, Kieran G. Meade, Isobel C. Gormley, Stephen V. Gordon, David E. MacHugh

“…Integrating our cis-eQTL data with bTB susceptibility GWAS summary statistics, we perform a transcriptome-wide association study and identify 115 functionally relevant genes (including RGS10, GBP4, TREML2, and RELT) and provide important new omics data for understanding the host response to mycobacterial infections that cause tuberculosis in mammals.…”
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A quantitative prediction method utilizing whole omics data for biosensing by Takahiko Koizumi, Kenta Suzuki, Inoue Mizuki, Kie Kumaishi, Yasunori Ichihashi

“…Abstract Omics data provide a plethora of quantifiable information that can potentially be used to identify biomarkers targeting the physiological processes and ecological phenomena of organisms. …”
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Effect of RNF113A deficiency on oxidative stress-induced NRF2 pathway by Namjoon Cho, Yong-Eun Kim, Yunkyeong Lee, Dong Wook Choi, Chungoo Park, Jung-Hwan Kim, Keun Il Kim, Kee K. Kim

“…In this study, we performed transcriptome profiling of RNF113A knockout (KO) HeLa cells using RNA sequencing and revealed the upregulation of NRF2 pathway-associated genes. …”
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Aspergillus Niger 129B promotes plant growth by inducing the interaction between SAUR32 and PP2C72 by Juan He, Li Yuan Gao, Yong Ping Luo, Min Chai, Hua Feng Wang, Lu Hong Yang, Kang Zhao, Yushanjiang Maimaiti, Yuan Jun Nie, Wei Chen

“…Subsequently, molecular and genetic experiments were conducted to reveal the mechanism promoting root, stem, and leaf development.ResultsIt demonstrated that 129B significantly promoted the growth of tomato plants. Plant transcriptome and metabolome analysis revealed that this effect was associated with the plant hormone signaling pathway, particularly the expression of SAUR32 and PP2C72 genes. …”
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CNOT6L regulates energy metabolism in the ovarian granulosa cells associated with polycystic ovary syndrome by Shan Han, Shan Han, Yanqiu Xie, Jiale Lv, Xuedong Sun, Yuhua Shi, Yuhua Shi, Yuhua Shi

“…The endocrine functions exerted by ovarian granulosa cells (GCs) are crucial factors in maintaining follicle development, as oocyte development relies on providing energy substrates and cytokines by ovarian granulosa cells. …”
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Detoxification of coumarins by rumen anaerobic fungi: insights into microbial degradation pathways and agricultural applications by Yuqi Li, Jian Gao, Yaxiong Cao, Xinming Cheng, Zhanying Sun, Jiyu Zhang, Weiyun Zhu, Martin Gierus, Yanfen Cheng

“…Results In this study, we investigated in vitro fermentation by microbial enrichment, transcriptome sequencing, and high-resolution mass spectrometry to evaluate the ability of rumen anaerobic fungi to degrade coumarins. …”
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Deciphering the role of cuproptosis in the development of intimal hyperplasia in rat carotid arteries using single cell analysis and machine learning techniques by Miao He, Hui Chen, Zhengli Liu, Boxiang Zhao, Xu He, Qiujin Mao, Jianping Gu, Jie Kong

“…Abstract This study aims to explore the regulatory role of cuproptosis in carotid intimal hyperplasia (IH), providing new insights into its pathophysiological mechanisms and potential diagnostic and therapeutic strategies. …”
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Traditional Chinese medicine phenomics research on glycolipid metabolism disorder: a review by Xinyi Fang, Linxuan Miao, Yanjiao Zhang, Yuxin Zhang, Runyu Miao, Huifang Guan, Jiaxing Tian

“…As an emerging interdisciplinary field, phenomics integrates multi-dimensional data including genome, transcriptome, proteome, metabolome, and microbiome. …”
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Integrative Proteomics and Genomics Identify Novel Biomarkers and Therapeutic Targets in Vitiligo via Mendelian Randomization by Chenjue Yan, Ling Jiang, Yibo Hu, Ting You, Jing Chen, Songjiang Wu

“…Abstract Introduction Given that the proteome is a major source of therapeutic targets, we conducted a proteome-wide Mendelian randomization (MR) combined with transcriptome sequencing analysis to identify candidate protein markers and therapeutic targets for vitiligo. …”
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Novel marker genes and small molecule drugs for radiotherapy resistance in cervical cancer identified based on single-cell multi-omics analysis by Yang Liu, Xin Pan, Xu Zhang, Bo Tan, Rui Ran, Li Liu, Lin Yang, Zhiliang Wang

“…We downloaded and processed transcriptome sequencing, methylation and single-cell sequencing data from the TCGA and GEO databases. …”
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Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation and metal homeostasis. by Odette Verdejo-Torres, David C Klein, Lorena Novoa-Aponte, Jaime Carrazco-Carrillo, Denzel Bonilla-Pinto, Antonio Rivera, Arpie Bakhshian, Fa'alataitaua M Fitisemanu, Martha L Jiménez-González, Lyra Flinn, Aidan T Pezacki, Antonio Lanzirotti, Luis Antonio Ortiz Frade, Christopher J Chang, Juan G Navea, Crysten E Blaby-Haas, Sarah J Hainer, Teresita Padilla-Benavides

“…This research highlights the importance of mCrip2 in muscle development and metal homeostasis, providing new insights into the Cu-network in cells.…”
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Single-Cell Sequence and Machine Learning Identify a CD79A+B Cells-Related Transcriptional Signature for Predicting Clinical Outcomes and Immune Microenvironment in Breast Cancer by Haihong Hu, Wendi Zhan, Hongxia Zhu, Bo Hao, Ting Yan, Jingdi Zhang, Siyu Wang, Taolan Zhang

“…Conclusion: This study comprehensively explored the heterogeneity of CD79A + B cells through transcriptome analysis and chromatin analysis, which contributes to an in-depth understanding of the function of CD79A + B cells in biological processes as well as the molecular mechanism of breast carcinogenesis, providing a theoretical basis for treatment and prevention.…”
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Microevolution of longan flowering behaviors from primitive characteristic to KClO3 induction is driven by artificial selection for agricultural benefit by Suparat K. Lithanatudom, Panurat Pipatchananan, Natnapa Jaitan, Pimonrat Tiansawat, Pathrapol Lithanatudom

“…Here, we report an extensive dataset of 606.72 Gb of the whole-genome resequencing data obtained from 31 Dimocarpus longan and 1 Dimocarpus obtusus samples performed on Illumina HiSeq PE150, providing the coverage over 30-fold of the reference genome (averaging 15 Gb per sample) with an addition of 12 longan accessions from China. …”
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Light-regulated microRNAs shape dynamic gene expression in the zebrafish circadian clock. by Zuo Wang, Shuang Wang, Yi Bi, Alessandra Boiti, Shengxiang Zhang, Daniela Vallone, Xianyong Lan, Nicholas S Foulkes, Haiyu Zhao

“…Circadian clocks in zebrafish peripheral tissues and even zebrafish-derived cell lines are entrainable by direct light exposure thus providing unique insight into the function and evolution of light regulatory pathways. …”
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Integrative bioinformatics frameworks for abdominal aortic aneurysm using GWAS meta-analysis, biological network construction, and structural modeling by Pakorn Sagulkoo, Hathaichanok Chuntakaruk, Apichat Suratanee, Kitiporn Plaimas, Nuttinee Teerakulkittipong

“…In conclusion, our integrative bioinformatics frameworks links genomics and transcriptomics with network biology and structural modeling, providing valuable insights into the molecular mechanisms of AAA and potential therapeutic strategies.…”
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Establishment of rat model for aspiration pneumonia and potential mechanisms by Hanbing Hu, Junfeng Chen, Yiru Shao, Yuedong Tang, Yu Dun, Obulkasim Memet, Xuanrong Bao, Jie Shen

“…Conclusions This optimized model closely mimics clinical aspiration pneumonia, providing a valuable tool for studying pathophysiology and therapeutic strategies.…”
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Molecular cloning and functional characterization of the shikimate kinase gene from Baphicacanthus cusia by Yuxiang Huang, Yuxiang Huang, Yuxiang Huang, Hexin Tan, Qing Li, Xunxun Wu, Zhiying Guo, Zhiying Guo, Junfeng Chen, Lei Zhang, Yong Diao

“…In this study, the BcSK gene was isolated and cloned from the transcriptome data of B. cusia. The full-length cDNA of BcSK is 1,657 bp, comprising a 265 bp 5’ UTR, a 507 bp 3’ UTR, and an 885 bp ORF encoding 295 amino acids. …”
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