Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data by Joshua Chuah, Carmalena V. Cordi, Juergen Hahn, Jennifer M. Hurley

“…Abstract Background The circadian clock is a central driver of many biological and behavioral processes, regulating the levels of many genes and proteins, termed clock controlled genes and proteins (CCGs/CCPs), to impart biological timing at the molecular level. While transcriptomic and proteomic data has been analyzed to find potential CCGs and CCPs, multi-omic modeling of circadian data, which has the potential to enhance the understanding of circadian control of biological timing, remains relatively rare due to several methodological hurdles. …”
Get full text

High-throughput sequencing unravels placental vascular dysfunction and oxidative stress as mechanistic drivers of advanced maternal age-associated pregnancy by Xin Sun, Yao Chen, Feifei Hu, Yumeng Qiao, He Wu, Yao Su, Yue Hu, Jie Wu, Jie Wu, Mingli Huang

“…IntroductionWomen with advanced maternal age (AMA) face a higher risk of pregnancy complications including preeclampsia, fetal growth restriction, and preterm birth. While placental dysfunction is implicated, the underlying mechanisms remain unclear. …”
Get full text

Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions by Konstantina Athanasopoulou, Vasiliki-Ioanna Michalopoulou, Andreas Scorilas, Panagiotis G. Adamopoulos

“…In cancer research, AI enables precise tumor subtyping, biomarker discovery, and personalized therapy prediction, while in drug discovery, it accelerates target identification and repurposing. …”
Get full text

Distinct characteristics of brain metastasis in lung adenocarcinoma: development of high-confidence cell lines by Jintao He, Zen-ichi Tanei, Dao-Sian Wu, Lei Wang, Yoshitaka Oda, Masumi Tsuda, Shinya Tanaka

“…Through RNA sequencing and bioinformatics analyses, we identified transcriptomic differences among these cell lines, revealing that H1975-BM1 cells primarily exhibit stem cell function and migration characteristics, while H1975-BM3 cells display enhanced chemotaxis, cell adhesion, and cytokine secretion associated with interactions. …”
Get full text

Seasonal anti-androgen activity in the brackish Baltic waters in relation to the gene expression profiles of the blue mussel Mytilus trossulus by Paulina Goździk, Katarzyna Smolarz, Magda Caban, Anna Hallmann

“…Simultaneously, the gonadal transcriptome profiles of Mytilus trossulus were analyzed to investigate potential responses at the molecular level. …”
Get full text

Mitochondrial-derived gene expression in hibernation: tissue-specific responses in the thirteen-lined ground squirrel by Sarah Viola Emser, Eva Millesi

Get full text

Knowledge of the genetics of human pain gained over the last decade from next-generation sequencing by Dario Kringel, Jörn Lötsch

“…NGS has uncovered critical alternative splicing events and facilitated single-cell transcriptomics, revealing cellular heterogeneity within tissues. …”
Get full text

Extraction of a stromal metastatic gene signature in breast cancer via spatial profiling by Giorgio Bertolazzi, Valeria Cancila, Davide Vacca, Beatrice Belmonte, Daniele Lecis, Parsa Sirati Moghaddam, Arianna Di Napoli, Mario Paolo Colombo, Giancarlo Pruneri, Giannino Del Sal, Giorgio Scita, Matteo Fassan, Andrea Vecchione, Silvio Bicciato, Claudio Tripodo

“…We identified a stromal metastatic (Met) signature, which was subsequently validated across transcriptomic reference human breast cancer (BC) datasets and in spatial transcriptomics of a murine model. …”
Get full text

Altered aminoacid and lipid metabolism in a rat orofacial inflammation model determined by omics approach: potential role in trigeminal sensitisation by Krisztina Takács-Lovász, Timea Aczél, Violetta Mohos, Máté Harmath, Jennet Pirkuliyeva, Gellért Karvaly, Róbert Farkas, Michal Ciborowski, Joanna Godzien, Kata Bölcskei, József Kun, Zsuzsanna Helyes

“…Next-generation sequencing of the trigeminal ganglia (TG) was performed, furthermore, transcriptomic and plasma metabolomic data were analysed together. …”
Get full text

Production, characterization, and potential utility of a newly synthesized allohexaploid wheat Triticum kiharae by Tariq Aslam, Tianying Zhang, Taotao Lian, Jiawen Zhai, Jinning Jia, Han Wang, Ruili Lyu, Bao Liu

Get full text

Transcriptional landscape of pleural mesothelioma patients in relation to NF2 gene mutational status by Carlos Orozco-Castaño, Alejandro Mejía-Garcia, Hsuan Megan Tsao, Diego A. Bonilla, Carlos Carvajal-Fierro, Ricardo Bruges-Maya, Alba Combita, Rafael Parra-Medina

“…Logistic regression was used to evaluate associations with clinical variables, while transcriptomic differences were examined through differential expression and functional enrichment analyses. …”
Get full text

Novel Insights into Pigment Composition and Molecular Mechanisms Governing Flower Coloration in Rose Cultivars Exhibiting Diverse Petal Hues by Yingxia Cheng, Yanling Tian, Pengyu Guo, Junjie Luo, Chan Xu, Yang Zhang, Guoping Chen, Qiaoli Xie, Zongli Hu

Get full text

Evaluation of <i>Sapindus mukorossi</i> Gaertn Flower Water Extract on In Vitro Anti-Acne Activity by Zibing Zhao, Aohuan Zhang, Liya Song, Congfen He, Huaming He

“…Currently, the investigations of <i>S. mukorossi</i> mainly focus on the pericarp and seed kernel parts, while other parts are yet to be studied and developed. …”
Get full text

Overexpression of Lol-miR11467 negatively affects osmotic resistance in Larix kaempferi 3 × L. gmelinii 9 by Sufang Zhang, Shanshan Yan, Li Zhang, Pingyu Yan, Hanguo Zhang, Lei Zhang

“…The results showed that the fresh weight, peroxidase (POD), soluble protein and soluble sugar content of the overexpressing Lol-miR11467 were lower than that of the wild-type, while malondialdehyde (MDA) content increased under PEG osmotic stress. …”
Get full text

Gene expression profiling in pure neural leprosy: insights into pathogenesis and diagnostic biomarkers by Mariana Martins de Athaide, Thyago Leal-Calvo, Tatiana Pereira Da Silva, Thabatta Leal Silveira Andrezo Rosa, Helen Ferreira, Bernardo Miguel de Oliveira Pascarelli, Ana Caroline Siquara de Sousa, Marcia Rodrigues Jardim, Marcia Rodrigues Jardim, Marcia Rodrigues Jardim, Marcia Rodrigues Jardim, Marcia Rodrigues Jardim, Roberta Olmo Pinheiro, Roberta Olmo Pinheiro, Roberta Olmo Pinheiro

“…Downregulated genes included GAS2L2, TRIM67, IL1RAPL1, MAP1LC3B2, and NTNG1, implicated in neuronal development and autophagy, while upregulated genes were linked to immune responses. …”
Get full text

Functional omics of ORP7 in primary endothelial cells by Juuso H. Taskinen, Minna Holopainen, Hanna Ruhanen, Miesje van der Stoel, Reijo Käkelä, Elina Ikonen, Salla Keskitalo, Markku Varjosalo, Vesa M. Olkkonen

“…Results Pharmacological inhibition of ORP7 leads to an increase in gene expression related to lipid metabolism and inflammation, while genes associated with cell cycle and cell division were downregulated. …”
Get full text

Shanling Jiangzhi Tea treats hyperuricemia by inhibition of COMT/MAOA signaling pathway and p53/SERPINE1/NLRP3 signaling pathway by Hao-nan Chen, Hao-nan Chen, He-zhen Wu, He-zhen Wu, He-zhen Wu, Yan-fang Yang, Yan-fang Yang, Yan-fang Yang

“…Kit-based assays indicate that SLJZ increases dopamine (DA) levels in the kidneys of mice while reducing the levels of interleukin-6 (IL-6), interleukin-1β (IL-1β), and tumor necrosis factor-α (TNF-α). …”
Get full text

The transcription factor PoMbp1 promotes the growth and development of Pleurotus ostreatus by regulating polysaccharide utilisation by Lijiao Zhang, Yingjie Zhang, Zeyin Wu, Mengran Zhao, Xiangli Wu, Chenyang Huang

“…Transcriptome sequencing showed that the DEGs between PoMbp1 transformants and wild-type mainly enriched in carbohydrate metabolism, cell growth and death, etc. …”
Get full text

Investigating the Mechanisms Underlying Citral-Induced Oxidative Stress and Its Contribution to Antifungal Efficacy on <i>Magnaporthe oryzae</i> Through a Multi-Omics Approach by Yonghui Huang, Ruoruo Wang, Yumei Tan, Yongxiang Liu, Xiyi Ren, Congtao Guo, Rongyu Li, Ming Li

“…Importantly, citral at EC₇₅ reduced the activities of mitochondrial respiratory chain complex I, complex III and ATP content, while increasing the activity of mitochondrial respiratory chain complex II. …”
Get full text

Fluridone promotes the germination of Polygonatum cyrtonema seeds by modulating hormone signal transduction, phenylpropanoid biosynthesis, and energy metabolism by Xiaogang Jiang, Darong Li, Hua Wang, Yuying Yang, Kaidi Yu, Jinwen You, Haihua Liu, Xiaoliang Guo, Yinsheng He, Wuxian Zhou, Qingfang Wang

“…Furthermore, fluridone treatments significantly promoted the germination by reducing abscisic acid (ABA) content, while increasing the levels of auxin (IAA) and cytokinin (CTK). …”
Get full text