An effective multistage mouse model of esophageal carcinogenesis for preclinical and computational pathology applications by Yuxia Fu, Guoqing Zhang, Yue Liu, Lei Xu, Yuanyuan Hu, Liyan Xue, Huiqin Guo, Yan Fu, Yigang Cen, Xiao Li, Wei Jiang, Xiying Yu

“…Taken together, this mouse CIMCM of ESCC provides a versatile platform for ESCC early diagnosis, basic and preclinical research and therapeutic strategy.…”
Get full text

High expression of THY1 is a prognostic marker for gastric Cancer: Deciphering its transcriptional regulation as a component of the Epithelial–mesenchymal transition by Paulo Rohan, Everton Cruz dos Santos, Pedro Leite Azevedo, Jessica Oliveira da Conceição, Eliana Abdelhay, Renata Binato

“…By integrating multicohort transcriptomic data (n = 945), we inferred consensus transcriptional regulatory networks (TRNs) and identified six putative transcription factors (PRRX1, TWIST1, SNAI2, MEIS3, VENTX, and EGR2) as robust regulators of THY1. …”
Get full text

Ecophysiological transition mediated by hybridization in a hybrid pine species complex by Zhi-Chao Li, Chao-Qun Xu, Wei Zhao, Shuai Nie, Yu-Tao Bao, Hui Liu, Zhen Xing, Jian-Feng Mao, Xiao-Ru Wang

“…By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. …”
Get full text

IPEC-J2 Autophagy Induced by TLR4 and NSP6 Interactions Facilitate Porcine Epidemic Diarrhea Virus Replication by Haiyuan Zhao, Dianzhong Zheng, Qinyuan Chang, Hailin Zhang, Yilan Shao, Jiaxuan Li, Wen Cui, Yanping Jiang, Lijie Tang, Yijing Li, Xiaona Wang

“…However, some viruses have evolved mechanisms to hijack this defensive process to provide favorable conditions for virus replication in host cells. …”
Get full text

Histone Signatures Predict Therapeutic Efficacy in Breast Cancer by Shamim A. Mollah, Shankar Subramaniam

“…” The method integrates proteomic/phosphoproteomic, transcriptomic and regulatory genomic data to provide a causal mechanistic network and histone signatures of drug response. …”
Get full text

Small extracellular vesicles from human bone marrow mesenchymal stromal cells enhance migration and regulate reparative gene expression in dermal fibroblasts by Rui Lei, Tamiris Borges da Silva, Zhanfeng Cui, Hua Ye

“…In this study, we harvested the conditioned medium (CM) from human bone marrow mesenchymal stromal cells (hBM-MSCs) and normal human dermal fibroblasts (NHDFs), fractionated into the sEV fraction and non-small extracellular vesicle (NsEV) fraction, and compared their functions on NHDF migration and proliferation—key processes in wound healing, coupled with transcriptomic analysis through mRNA sequencing to assess gene expression changes in the recipient NHDFs. …”
Get full text

Dissecting the Cellular Heterogeneity Underlying Liver Diseases Through the Integration of GWASs and Single-Cell RNA Sequencing by Miao Zhou, Meng Liu, Chao Xue

“…In this study, we integrated genome-wide association study (GWAS) data from six liver diseases and two metabolic traits with transcriptomic profiles of approximately 168,000 human liver cells at single-cell resolution, using the single-cell disease relevance score (scDRS) approach. …”
Get full text

Plant–Microbe Interactions for Improving Postharvest Shelf Life and Quality of Fresh Produce Through Protective Mechanisms by Wajid Zaman, Adnan Amin, Atif Ali Khan Khalil, Muhammad Saeed Akhtar, Sajid Ali

“…Advancements in omics technologies, such as metabolomics, transcriptomics, and microbiomics, have provided deeper insights into plant–microbe interactions, facilitating more targeted and effective microbial treatments. …”
Get full text

A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association study. by Cherif Ben Hamda, Raphael Sangeda, Liberata Mwita, Ayton Meintjes, Siana Nkya, Sumir Panji, Nicola Mulder, Lamia Guizani-Tabbane, Alia Benkahla, Julie Makani, Kais Ghedira, H3ABioNet Consortium

“…This novel database of candidate genes, transcription factors, and rSNPs associated with SCD provides new markers that may help to identify new therapeutic targets.…”
Get full text

Ventricular, atrial, and outflow tract heart progenitors arise from spatially and molecularly distinct regions of the primitive streak. by Kenzo Ivanovitch, Pablo Soro-Barrio, Probir Chakravarty, Rebecca A Jones, Donald M Bell, S Neda Mousavy Gharavy, Despina Stamataki, Julien Delile, James C Smith, James Briscoe

“…Using a single-cell transcriptomic assay combined with genetic lineage tracing and live imaging, we find the FHF and SHF are subdivided into distinct pools of progenitors in gastrulating mouse embryos at earlier stages than previously thought. …”
Get full text

Reactive oxygen species mediate bioeffects of static magnetic field via impairment of long-chain fatty acid degradation in Escherichia coli by Haodong Li, Yanwen Fang, Jirong Huang

“…Taken together, our findings provide novel insights into the molecular mechanism by which oxygen serves as a magnetic target, triggering ROS signaling, and enabling bacteria to adapt to SMF exposure.…”
Get full text

Improving synergistic drug combination prediction with signature-based gene expression features in oncology by Mozhgan Mozaffarilegha, Sajjad Gharaghani

“…Despite these advancements, most algorithms primarily rely on drug-specific features, such as chemical structures, with limited incorporation of functional drug information and cellular content features.Methods:We propose a novel approach that integrates Drug Resistance Signatures (DRS) as a biologically informed representation of drug information. This approach provides a more comprehensive framework for identifying effective combination therapies. …”
Get full text

Unraveling the immune evasion mechanisms in the tumor microenvironment of head and neck squamous cell carcinoma by Xuri Zhao, Yaping Zhu, Youya He, Weiyan Gu, Qi Zhou, Bei Jin, Shenguo Chen, Haisheng Lin

“…Leveraging cutting-edge single-cell sequencing and spatial transcriptomics, we elucidate the spatiotemporal heterogeneity of the HNSCC immune landscape and propose a new paradigm of “lineage plasticity-driven immune adaptation.” …”
Get full text

The nonhost mycorrhizal status of weeds and its relevance to weed management in agroecology by Irene Pagliarani, Arianna Grassi, Monica Agnolucci, Alessandra Turrini, Luciano Avio, Manuela Giovannetti

“…These effects have been attributed to the activation of plant root defenses diverting resources from plant growth. This review provides qualitative and quantitative data on the interactions between AMF and nonhost weeds and on the mechanisms underlying weed fitness reduction. …”
Get full text

An R package for survival-based gene set enrichment analysis by Xiaoxu Deng, Jeffrey Thompson

“…However, researchers sometimes want to understand the relationship between transcriptomic variation and health outcomes like survival. …”
Get full text

Role of Liquid Biopsy for Early Detection, Prognosis, and Therapeutic Monitoring of Hepatocellular Carcinoma by Faris Alrumaihi

“…This review provides an overview of current liquid biopsy strategies in HCC and their use for early detection, prognosis, and monitoring the effectiveness of HCC therapy.…”
Get full text

High-throughput sequencing of small RNAs from pollen and silk and characterization of miRNAs as candidate factors involved in pollen-silk interactions in maize. by Xiao Ming Li, Ya Lin Sang, Xiang Yu Zhao, Xian Sheng Zhang

“…The results of our study provide novel information for understanding miRNA regulatory roles in pollen-pistil interactions.…”
Get full text

Ensemble machine learning-based pre-trained annotation approach for scRNA-seq data using gradient boosting with genetic optimizer by Osama Elnahas, Waleed M. Ead, Yushan Qiu, Jian Lu

“…Abstract Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression by allowing researchers to analyze the transcriptomes of individual cells. This technology provides unprecedented insights into cellular heterogeneity, cellular states, and biological processes at a single-cell resolution. …”
Get full text

LEVERAGING ORGANOID TECHNOLOGIES TO CHARACTERIZE DYNAMIC TUMOR CELL STATES DRIVING TREATMENT RESISTANCE IN PANCREATIC CANCER

“…Using integrated phenotypic and transcriptomic profiling, we map this diversity to specific biological functions in vivo, demonstrating that each organoid phenotype corresponds to a tumor-cell state with unique metastatic potential, and therapeutic vulnerabilities. …”
Get full text

Characterization of exosomal RNAs derived from human gastric cancer cells by deep sequencing by Jia Ren, Quan Zhou, Hao Li, Jianfang Li, Li Pang, Liping Su, Qinlong Gu, Zhenggang Zhu, Bingya Liu

“…We also predicted novel microRNA candidates but they need to be validated. This research provided an atlas of small non-coding RNA in exosomes and may make a little contribution to the understanding of exosomal RNA composition and finding parts of differential expression of RNAs in exosomes.…”
Get full text