Integrating transcriptomics and proteomics to analyze new regulatory genes related to rice grain development by Zhixuan Du, Qitao Su, Haihui Fu, Dahu Zhou, Linjuan Ouyang, Junru Fu, Haohua He

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Combined metabolome and transcriptome to analyze the regulatory network of key enzymes in the synthesis of senkirkine in Emilia sonchifolia by Jinli Yao, Yanqing Qin, Dongping Tu, Yumei Huang, Liuguan Liang, Wenhui Cai, Mingli Huang, Xiaoqi Zhu, Xinling Lao

“…This study applied metabolomics to analyze alkaloid compositions in the plant’s roots, stems, leaves, and flowers. …”
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Integrating metabolomics and transcriptomics to analyze differences in muscle mass and flavor formation in Gayal and yellow cattle by Lin Han, Lin Han, Runqi Fu, Runqi Fu, Binlong Fu, Binlong Fu, Qian Li, Qian Li, Ye Yu, Ye Yu, Huan Gao, Huan Gao, Jiawei Zhang, Min Qi, Min Qi, Chunjia Jin, Chunjia Jin, Shengyong Mao, Jing Leng, Jing Leng

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Response of astrocytes and their interaction with surrounding brain cells after acute ischemia-reperfusion analyzed by single-cell transcriptome sequencing by YongHong Wu, Lei Xie, Jing Sun, Qing Wang, WangXiao Xia, Qiang Cai, XiaoYun Lu, XingChun Gou

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A Comparative Transcriptomics Approach to Analyzing the Differences in Cold Resistance in Pomacea canaliculata between Guangdong and Hunan by Jing Liu, Zhiying Sun, Zhi Wang, Yuande Peng

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Exploring and analyzing two aging related genes FPR1 and UCHL1 and their potential molecular mechanisms in aggravating lumbar disc herniation by Di Zhao, Bang-xin Sha, Ling-feng Zeng, Gui-hong Liang, He-tao Huang, Jian-ke Pan, Jun Liu, Shuai Zhao

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New insights into the transcription factor regulatory networks driving peel coloration under hormone induction analyzed by transcriptomics and metabolomics in tangor ‘Murcot’ by Yang Chen, Yang Chen, Lei Yang, Lei Yang, Shuang Li, Min Wang, Jianjun Yu, Wenqin Bai, Wenqin Bai, Wenqin Bai, Lin Hong, Lin Hong

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Analyzing the Transcriptomes of Two Quorum-Sensing Controlled Transcription Factors, RcsA and LrhA, Important for Pantoea stewartii Virulence. by Alison Kernell Burke, Duy An Duong, Roderick V Jensen, Ann M Stevens

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Combining whole genome and transcriptome sequencing to analyze the pathogenic mechanism of Diplodia sapinea blight in Pinus sylvestris var. mongolica Litv. by Ruiqi Wang, Yuting Wang, Sina Fu, Shixian Liao, Tingbo Jiang, Boru Zhou

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An integrated approach for analyzing spatially resolved multi-omics datasets from the same tissue section by Thao Tran, Felicia Wee, Craig Ryan Joseph, Wanqiu Zhang, Jeffrey Chun Tatt Lim, Zhen Wei Neo, Li Yen Chong, Francis Hong Xin Yap, Nathan Heath Patterson, Marc Claesen, Alice Ly, Joe Yeong, Joe Yeong, Joe Yeong

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De novo transcriptome assembly of Aureobasidium melanogenum CGMCC18996 to analyze the β-poly(L-malic acid) biosynthesis pathway under the CaCO3 addition by Genan Wang, Haisong Yin, Tingbin Zhao, Donglin Yang, Shiru Jia, Changsheng Qiao

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In Vitro Pollen Viability, Fluorescence Microscopy, and Transcriptomic Comparison of Self-Pollinated and Cross-Pollinated Inflorescence of <i>Artemisia annua</i> L. to Analyze Candidate Self-Incompatibility-Associated Genes by Yimei Zang, Shengrong Cui, Shugen Wei, Limei Pan, Lingyun Wan, Xiaojun Ma, Zuliang Luo, Jine Fu, Chongnan Wang

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The dawn of spatiotemporal transcriptomics by Siying Wang, Shichao Lin, Chaoyong Yang

“…We also highlight the recent development of bioinformatics tools to analyze the spatiotemporal transcriptomics data, which contributes to the dynamical and predictive spatiotemporal modeling and deeper biological understanding. …”
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Transcriptomics resources of human tissues and organs by Mathias Uhlén, Björn M Hallström, Cecilia Lindskog, Adil Mardinoglu, Fredrik Pontén, Jens Nielsen

“…Recently, several large‐scale transcriptomics studies have analyzed the expression of protein‐coding genes across tissues. …”
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Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma by Wanchen Cao, Kai Gao, Yi Zhao

“…This study aims to identify robust transcriptomic biomarkers for PTC diagnosis through integrative bioinformatics approaches and elucidate the cellular mechanisms underlying PTC pathogenesis at single-cell resolution.MethodsBased on the Gene Expression Omnibus (GEO) database, we downloaded PTC-related RNA-seq datasets (GSE3467, GSE3678, GSE33630, GSE65144, and GSE82208) and an scRNA-seq dataset (GSE191288). …”
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Contamination Survey of Insect Genomic and Transcriptomic Data by Jiali Zhou, Xinrui Zhang, Yujie Wang, Haoxian Liang, Yuhao Yang, Xiaolei Huang, Jun Deng

“…In this study, COI barcodes were used to investigate contamination from insects and mammals in GenBank’s genomic and transcriptomic data across four insect orders. Among the 2796 WGS and 1382 TSA assemblies analyzed, contamination was detected in 32 (1.14%) WGS and 152 (11.0%) TSA assemblies. …”
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Systemic inflammatory responses to repeated and increasing endotoxin challenges in fetal sheep by Sanya Kathuria, Akash Gupta, Ayna R. Tracy, Rosa I. Luna Ramirez, Senthil Kumar Thulasingam, Nahla Zaghloul, Mohamed Ahmed, Sean W. Limesand

“…Fetal peripheral blood mononuclear cells (PBMCs) were analyzed for transcriptomic changes and tissue cytokine expression postmortem. …”
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Cadmium Exposure Disrupts Uterine Energy Metabolism and Coagulation Homeostasis During Labor in Institute of Cancer Research Mice: Insights from Transcriptomic Analysis by Yueyang Wang, Yichen Bai, Yi Wang, Yan Cai

“…The PPI results were visualized using Cytoscape software and further analyzed, with 18 hub genes (maximum clique centrality score > 10) identified through the MCC algorithm of the Cytohubba plugin. …”
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Analyzing the relationship of RNA and DNA methylation with gene expression by Shangqian Xie, Darren Hagen, Gabrielle M. Becker, Kimberly M. Davenport, Katie A. Shira, Morgan R. Stegemiller, Jacob W. Thorne, Sarem Khilji, Denise Konetchy, Patricia Villamediana, Brenda M. Murdoch, Stephanie D. McKay

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TRANSCRIPTOMIC DIFFERENCES IN MONOZYGOTIC TWINS WITH OVARIAN CANCER by Gözde Kuru Türkcan, Demet Akdeniz Ödemiş, Büşra Kurt Gültaşlar, Şeref Buğra Tunçer, Seda Kılıç Erciyas, Özge Şükrüoğlu Erdoğan, Hülya Yazıcı

“…Materials-Methods: In this context, the peripheral blood and ovarian tissues of monozygotic twins who are discordant in terms of ovarian cancer and the other healthy sibling who is a BRCA1 mutation carrier were compared in the study to analyze all RNA molecules transcribed at the genome level using next-generation sequencing technology.Through analyzing the molecules transcribed in the whole genome,the genetic variations underlying the development of ovarian cancer in a high-risk family bearing the BRCA1 mutation but only one of whom was found to have ovarian cancer were examined. …”
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