Integrated multi-sample transcriptomic analysis of COVID-19 patients against controls using a bioinformatics pipeline by Li Ying Khoo, Sarinder Kaur Dhillon

“…Abstract Prior coronavirus disease 2019 (COVID-19) transcriptomic studies using diverse methods for differential gene expression (DGE) profiling of specific samples yielded inconsistent results. …”
Get full text

Transcriptomics Analysis of the Mechanism Underlying the Synthesis of Phenolic Compounds in Fresh-Cut Red Cabbage under Ultrasound Stress by HONG Chen, GUO Lina, ZHANG Xinyan, OUYANG Ningning, WU Ping, MA Haile

“…Meanwhile, ultrasound washing enabled fresh-cut red cabbage to maintain high levels of energy charge during storage, thus providing energy for this series of reactions. In conclusion, this study provides a theoretical basis for further research on the molecular mechanism of phenolic biosynthesis in fresh-cut fruits and vegetables under ultrasound stress.…”
Get full text

Transcriptomic analysis reveals potential crosstalk genes and immune relationship between triple-negative breast cancer and depression by Zhili Zhuo, Wenping Lu, Ling Zhang, Dongni Zhang, Yongjia Cui, Xiaoqing Wu, Heting Mei, Lei Chang, Qingya Song

Get full text

Exploring hypoxia driven subtypes of pulmonary arterial hypertension through transcriptomics single cell sequencing and machine learning by Jianghao Xiong, Jiali Chen, Jianjun Zhou, Chao Li, Jifeng Wu

Get full text

SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution by Linbu Liao, Esha Madan, António M. Palma, Hyobin Kim, Amit Kumar, Praveen Bhoopathi, Robert Winn, Jose Trevino, Paul Fisher, Cord Herbert Brakebusch, Gahyun Kim, Junil Kim, Rajan Gogna, Kyoung Jae Won

“…Results We present SC2Spa, a deep learning-based approach that learns intricate spatial relationships from spatial transcriptomics (ST) data. Benchmarking tests show that SC2Spa outperformed other predictors and accurately detected tissue architecture from transcriptome. …”
Get full text

Single-cell transcriptome atlas reveals mitophagy dynamics in acute chemical injury model and the role of MSCs transplantation by Sang Luo, Fang Wu, Xiaojun Yang

“…MSCs are capable of alleviating disease progression by modulating the distinct mitophagy states of cells, providing an important resource for investigating mitophagy regulation in hepatic homeostasis and disease development.…”
Get full text

Transcriptomic and Functional Validation Reveals PAQR3/P6-55 as Potential Therapeutic Targets in Colon Cancer by Xue You, Yikuo Gai, Ziyun Wang, Yanqi Wang, Jingran Ye, Yujia Cao, Hengshuo Zhang, Ziyi Zhang, Ying Feng

Get full text

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

Get full text

Integration of epigenomic and transcriptomic profiling uncovers EZH2 target genes linked to cysteine metabolism in hepatocellular carcinoma by Jaehyun Lee, Chaelin You, Geunho Kwon, Junho Noh, Kyubin Lee, Kyunghwan Kim, Keunsoo Kang, Kyuho Kang

“…By reanalyzing transcriptomic data of HCC patients, we demonstrate that EZH2 overexpression correlates with poor patient survival. …”
Get full text

Genetic and metabolic mechanisms underlying webbed feet pigmentation in geese: Insights from histological, transcriptomic, and metabolomic analyses by Yi Liu, Kaiqi Weng, Guangquan Li, Huiying Wang, Yu Tan, Daqian He

“…Correlation analysis between transcriptomic and metabolomic data further validated the central role of tyrosine metabolism and melanin biosynthesis pathways in pigmentation. …”
Get full text

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.…”
Get full text

The Swimming Performance and Transcriptomic Insights Into Diverse Gene Regulation in Grass Carp Brain Under Water Velocity Stress by Mian Adnan Kakakhel, Nishita Narwal, Alam Khan, Majid Rasta, Liming Liu, Ihsan Ali, Yujiao Wu, Shi Xiaotao

“…Abstract By linking gene regulation to swimming performance under different water flow conditions, the study could reveal how the fish adapt to their environments, providing insights into evolutionary biology and ecology. …”
Get full text

Transcriptome Analysis and CFEM Gene Overexpression in <i>Metschnikowia bicuspidata</i> Under Hemocyte and Iron Ion Stress by Bingnan Zuo, Xiaodong Li, Ji Zhang, Bingyu Li, Na Sun, Fang Liang

“…This study employs transcriptomic sequencing to analyze gene expression changes in <i>Metschnikowia bicuspidata</i> under hemocyte challenge, iron overload (1 mmol/mL), and combined stress, with functional validation through Common in Fungal Extracellular Membrane (CFEMgene) overexpression strains. …”
Get full text

Correlation Analysis of the Transcriptome and Gut Microbiota in <i>Salmo trutta</i> Resistance to <i>Aeromonas salmonicida</i> by Shuaijie Sun, Jun Lv, Kuankuan Lei, Zhuangzhuang Wang, Wanliang Wang, Zhichao Li, Ming Li, Jianshe Zhou

“…To mitigate the impact of <i>A. salmonicida</i> on <i>S. trutta</i>, we conducted a comprehensive study aimed at identifying genes associated with resistance to <i>A. salmonicida</i>. This involved transcriptome sequencing and 16S rRNA sequencing of intestinal flora, providing valuable insights for the study of disease resistance in <i>S. trutta</i>. …”
Get full text

Transcriptome analysis of Ochratoxin a (OTA) producing Aspergillus westerdijkiae fc-1 under varying osmotic pressure by Yanling Ma, Muyuan Zhuang, Tanvir Ahmad, Mingxuan Li, Guangyou Tan, Yingyao Deng, Yang Liu

“…This study analysed the transcriptome of the Aspergillus westerdijkiae fc-1 strain under NaCl concentrations of 0, 20, and 100 g/L using RNA-Seq technology to examine gene transcriptional changes linked to osmotic stress and OTA production. …”
Get full text

Transcriptomic and metabolomic analyses reveal molecular mechanisms of tobacco mosaic virus (TMV) resistance in Nicotiana tabacum L. by Caiyue Li, Qiang Zhang, Xuebo Wang, Zhengwen Liu, Xinyao Zhang, Caihong Jiang, Lirui Cheng, Aiguo Yang, Yangyang Li, Yan Ji, Dan Liu

“…To investigate TMV resistance mechanisms, we analyzed the transcriptomic and metabolomic profiles of susceptible (K326) and resistant (R_K326) tobacco lines. …”
Get full text

Single-cell transcriptomic analysis reveals characteristic feature of macrophage reprogramming in liver Mallory-Denk bodies pathogenesis by Zixuan Fang, Bei Zhong, Yi Shi, Wanmei Zhou, Maoping Huang, Samuel W. French, Xiaoping Tang, Hui Liu

Get full text

Transcriptomic and biometric parameters analysis in rainbow trout (Oncorhynchus mykiss) challenged with viral hemorrhagic septicemia virus (VHSV) by Mohammad Ghaderzadeh, Ghodrat Rahimi-Mianji, Ardeshir Nejati-Javaremi, Nastaran Shahbazian

Get full text

Unraveling tissue-specific molecular mechanisms orchestrating arsenic response processes in Pteris vittata through transcriptomic analysis by Shujun Wei, Ryota Moriuchi, Christine Dwi A.P. Wiyono, Chihiro Inoue, Mei-Fang Chien

“…Therefore, in this study, we investigated As - related processes by conducting transcriptomic analysis on hydroponically grown P. vittata exposed to 500 ppb arsenate (AsV). …”
Get full text

Molecular mechanism of bisphenols induction of breast cancer through PGR revealed by network toxicology and transcriptomics integration analysis by Baowen Yuan, Yu Li, Jinyuan Chang, Chang Guo, Wei Huang, Yan Wang

“…By integrating network toxicology, transcriptomics, and molecular docking technology, this study aims to methodically identify the possible targets and mechanisms of five bisphenols in causing breast cancer. …”
Get full text