Impact of developmental state, p53 status, and interferon signaling on glioblastoma cell response to radiation and temozolomide treatment. by Artem Berezovsky, Oluwademilade Nuga, Indrani Datta, Kimberly Bergman, Thais Sabedot, Katherine Gurdziel, Susan Irtenkauf, Laura Hasselbach, Yuling Meng, Claudius Mueller, Emanuel F Petricoin, Stephen Brown, Neeraja Purandare, Sidhesh Aras, Tom Mikkelsen, Laila Poisson, Houtan Noushmehr, Douglas Ruden, Ana C deCarvalho

“…Differentiated CSC progenies retained the expression of key stemness genes and survival pathways, while activating the BMP-Smad signaling pathway and upregulating extracellular matrix components. …”
Get full text

Mitochondrial SLC25A10 promotes prostate cancer progression by inhibiting ferritinophagy by Guopeng Yu, Kailei Chen, Bin Xu, Qi Cao

“…In this study, we systematically analyzed transcriptomic data from The Cancer Genome Atlas (TCGA) and performed Venn analysis to identify genes associated with PCa progression. …”
Get full text

Refining the annotation of Rhodnius prolixus aspartic proteases A1 family genes through proteogenomics by Radouane Ouali, Sabrina Bousbata

“…Notably, 11 of these genes were confirmed at the protein level, while two were supported by transcriptomic data. …”
Get full text

RegAB Homolog of Burkholderia pseudomallei is the Master Regulator of Redox Control and involved in Virulence. by Julia Phenn, Jan Pané-Farré, Nikolai Meukow, Annelie Klein, Anne Troitzsch, Patrick Tan, Stephan Fuchs, Gabriel E Wagner, Sabine Lichtenegger, Ivo Steinmetz, Christian Kohler

“…Further investigations of the RegAB regulon, using a global transcriptomic approach, identified 20 additional regulators under transcriptional control of RegAB, indicating a superordinate role of RegAB in the B. pseudomallei anaerobiosis regulatory network. …”
Get full text

Harnessing Artificial Intelligence and Machine Learning for Identifying Quantitative Trait Loci (QTL) Associated with Seed Quality Traits in Crops by My Abdelmajid Kassem

“…I also explored AI-driven integration of multi-omics data—genomics, transcriptomics, metabolomics, and phenomics—to improve resolution in QTL mapping. …”
Get full text

Cbf11 and Mga2 function together to activate transcription of lipid metabolism genes and promote mitotic fidelity in fission yeast. by Anna Marešová, Michaela Grulyová, Miluše Hradilová, Viacheslav Zemlianski, Jarmila Princová, Martin Převorovský

“…Interestingly, Mga2 binding appears to be dependent on the presence of Cbf11 and Cbf11 likely acts as a tether to DNA, while Mga2 is needed to activate the target genes. …”
Get full text

Differential retinal ganglion cell resilience to optic nerve injury across vertebrate species by Julie D. De Schutter, Anyi Zhang, Pieter-Jan Serneels, Lieve Moons, Luca Masin, Steven Bergmans

“…In this study, we compare RGC densities and survival rates following optic nerve crush (ONC) in three vertebrate models—mice, zebrafish, and killifish—under standardized experimental conditions. Transcriptomic analysis confirmed that, similar to RBPMS in mice, Rbpms2 serves as a pan-RGC marker in zebrafish and killifish. …”
Get full text

Integrating Agronomic and Molecular Advancements to Enhance Nitrogen Use Efficiency (NUE) and Promote Sustainable Rice Production by Uttam Bahadur Kunwar, Nazer Manzoor, Jiancheng Wen, Naba Raj Pandit

“…Additionally, this paper offers deep insights into recent advancements in molecular genetics, such as multi-omics approaches (transcriptomics, metabolomics, and metagenomics), the Genome-Wide Association Study (GWAS), Quantitative Traits Loci mapping (QTLs), Single Nucleotide Polymorphisms (SNPs) analysis, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-Cas9)-mediated genome editing, which serve as valuable tools for developing rice cultivars with enhanced NUE and grain yield.…”
Get full text

Pathological and Molecular Characterization of Grass Carp Co-Infected with Two <i>Aeromonas</i> Species by Wenyao Lv, Zhijie Zhou, Lingli Xie, Xinyue Wang, Yifei Zhou, Lang Gui, Xiaoyan Xu, Yubang Shen, Jiale Li, Junqiang Qiu

“…Histopathological evaluation revealed severe hepatic lesions characterized by cellular necrosis, cytoplasmic vacuolization, and hemorrhagic manifestations. Comparative transcriptomic analysis of hepatic tissues between co-infected and control specimens identified 868 and 411 differentially expressed genes (DEGs) at 1 and 5 dpi, respectively. …”
Get full text

Nanoliposome-sericin hydrogel microneedle patches effectively alleviate inflammation and scavenge ROS for the treatment of CKD-aP by Lichang Liu, Longbao Feng, Yuanyuan Zhang, Junjie Xu, Le Liu, Lichun Wang, Weihong Hong, Yuyan Jin, Jiahao Zeng, Peihua He, Xusheng Liu

“…The Cap@Lip/Dife-MNs system demonstrates excellent drug delivery capabilities, promoting skin cell proliferation, reducing oxidative stress, and alleviating pruritus by modulating neural signaling pathways. In vivo transcriptomic analysis revealed significant modulation of immune-related genes and reduction of oxidative stress markers, confirming its immune-regulatory and anti-inflammatory effects. …”
Get full text

Synergistic effects of ectoine and biostimulants combinations on tomato seedling growth and heat stress resilience by Yanyan Chen, Weimin Xu, Chuankun Han, Miao Zhang, Ying Chen, Yujia Ma, Xinjun Zhang, Huhu Liu, Wenna Zhang

“…Transcriptomic analysis revealed significant differences in differentially expressed genes (DEGs) among treatments. …”
Get full text

Integrated omics reveals the regulatory role of PKCα in Sertoli cell proliferation and apoptosis through the MAPK/ERK signaling pathway in goose testis by Yupu Song, Qiuyuan Liu, Jingyun Ma, Ichraf Mabrouk, Yuxuan Zhou, Xinyue Li, Guizhen Xue, Xiaoming Ma, Jing Xu, Jingbo Wang, Hongxiao Pan, Guoqing Hua, Heng Cao, Jingtao Hu, Yongfeng Sun

“…This study employed integrative transcriptomic and proteomic analysis methods to identify critical regulators of testicular development in geese across three reproductive periods. …”
Get full text

The Development and Assessment of a Unique Disulfidptosis-Associated lncRNA Profile for Immune Microenvironment Prediction and Personalized Therapy in Gastric Adenocarcinoma by Jiyue Zhu, Xiang Zhu, Tingting Su, Huiqing Zhou, Shouhua Wang, Weibin Shi

“…A three-drlncRNA risk model was built using three common regression analysis methods. Then we used receiver operating characteristic (ROC) curves, independent prognostic analysis, and additional statistical approaches to assess the precision of the model. …”
Get full text

Identification and Validation of Ferritinophagy-Related Biomarkers in Periodontitis by Yi-Ming Li, Chen‑Xi Li, Reyila Jureti, Gulinuer Awuti

“…ABSTRACT: Objective: While ferritinophagy is believed to play a significant role in the development of periodontitis, the exact mechanisms remain unclear. …”
Get full text

A myeloid IFN gamma response gene signature correlates with cancer prognosis by Yuchao Zhang, Asma Khanniche, Yizhe Li, Zhenchuan Wu, Hailong Wang, Hongyu Zhang, Xiaoxue Li, Landian Hu, Xiangyin Kong

“…The prognostic and therapeutic relevance of the IFGRNS score was assessed across cancer types, considering tumor pathology, genomic alterations, tumor mutation burden, and microenvironment. Single‐cell transcriptomic analysis identified cellular contributors, and a murine pancreatic cancer (PAN02) model was used to validate findings with anti‐PD1 therapy. …”
Get full text

Diallyl disulfide attenuates hydrogen peroxide-induced oxidative damage of ovine rumen epithelial cells through the nuclear factor erythroid-2 related factor 2 signaling pathway by Rui Pang, Qingyue Zhang, Yuxin Wang, Xiaona Dong, Li Huang, Yingying Tang, Chunhuan Ren, Yanfeng Xue, Zijun Zhang, Wen Zhu

“…Transcriptomic analysis revealed that DADS might influence glutathione synthesis through cysteine and methionine metabolism, thereby affecting the transcription of genes involved in immunity and oxidative stress. …”
Get full text

Enhancement of direct interspecies electron transfer and methane production by co-culture of dual Methanosarcina species and Geobacter metallireducens by Lu Liu, Pengsong Li, He Dong, Chuanqi Liu, Haoyong Li, Zihao Ma, Ruoyu Li, Ruoyu Li, Yan Dang

“…This corresponds to a 3.8-fold increase over the SM-G co-culture system with M. barkeri and G. metallireducens, and a 3.0-fold increase over that with M. acetivorans and G. metallireducens. Transcriptomic analysis showed that in the DM-G co-culture system, M. barkeri up-regulated key genes related to methane metabolism and acetate utilization, while the core methanogenic pathway of M. acetivorans was down-regulated, but it could still effectively utilize the electron transfer pathway, indicating metabolic complementarity. …”
Get full text

Unveiling PANoptosis in Acute Kidney Injury: An Integrative Multi-Dimensional Approach to Identify Key Biomarkers by Wang N, Zhang L, Xu Z, Xu Q, Lu Y, Niu P, Yan L, Wang L, Cao H, Shao F

“…PANoptosis, a highly regulated and complex form of programmed inflammatory cell death, integrates the molecular mechanisms of apoptosis, pyroptosis, and necroptosis. While this process has been implicated in various inflammatory conditions, its specific role in AKI remains unclear.Methods: The role of PANoptosis in AKI was investigated using single-cell RNA sequencing (scRNA-seq) and bulk transcriptomic data. …”
Get full text

Sirt6 deficiency promotes senescence and age-associated intervertebral disc degeneration in mice by Pranay Ramteke, Bahiyah Watson, Mallory Toci, Victoria A. Tran, Shira Johnston, Maria Tsingas, Ruteja A. Barve, Ramkrishna Mitra, Richard F. Loeser, John A. Collins, Makarand V. Risbud

“…Histological studies showed a degenerative phenotype in knockout mice compared to Sirt6 fl/fl control mice at 12 months, which became pronounced at 24 months. RNA-Seq analysis of NP and AF tissues, in vitro quantitative histone analysis, and RNA-seq with ATAC-seq multiomic studies revealed that SIRT6-loss resulted in changes in acetylation and methylation status of specific Histone 3 lysine residues and affected DNA accessibility and transcriptomic landscape. …”
Get full text

Interferon activation in bone marrow long-lived plasma cells in systemic lupus erythematosus by Diana F. Alzamareh, Nida Meednu, Neha Nandedkar-Kulkarni, Daria Krenitsky, Jennifer Barnard, Ken Yasaka, Wesley Durrett, Juilee Thakar, Juilee Thakar, Javier Rangel-Moreno, Jennifer H. Anolik, Jennifer L. Barnas

“…Expression of Ki-67 associates with the PBL compartment where it is found on all PC subsets regardless of CD19 or CD138 expression. Transcriptomic analysis identifies an interferon (IFN) gene signature in transitional B cells in the SLE BM, but surprisingly also in the BM PC derived from SLE. …”
Get full text