Brain high-throughput multi-omics data reveal molecular heterogeneity in Alzheimer's disease. by Abdallah M Eteleeb, Brenna C Novotny, Carolina Soriano Tarraga, Christopher Sohn, Eliza Dhungel, Logan Brase, Aasritha Nallapu, Jared Buss, Fabiana Farias, Kristy Bergmann, Joseph Bradley, Joanne Norton, Jen Gentsch, Fengxian Wang, Albert A Davis, John C Morris, Celeste M Karch, Richard J Perrin, Bruno A Benitez, Oscar Harari

“…Our cross-omics analyses provide novel critical molecular insights into AD.…”
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Metabolic reprogramming in hepatocellular carcinoma: an integrated omics study of lipid pathways and their diagnostic potential by Peng Dai, Jing Feng, Yanyan Dong, Shujing Zhang, Jianghong Cao, Xiaopeng Cui, Xueliang Qin, Shiming Yang, Daguang Fan

“…In this study, we employed an integrated multi-omics approach, combining transcriptomic, proteomic, and metabolomic analyses, to explore the lipid metabolism pathways in HCC and evaluate their diagnostic potential. …”
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Ability of SPP1 to Alleviate Post‐Intracerebral Hemorrhage Ferroptosis via Nrf2/HO1 Pathway by Pengpeng Li, Zhenxin Tao, Yangyang Gao, Zhengqian Mu, Jiajia Tian, YaTing Zhang, Wenhui Yang, Yilu Li, Xudong Zhao

“…Conclusion This study provides novel evidence for SPP1/OPN as a key modulator of ferroptosis in ICH, highlighting its potential as a therapeutic target. …”
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RNA velocity—current challenges and future perspectives by Volker Bergen, Ruslan A Soldatov, Peter V Kharchenko, Fabian J Theis

“…Abstract RNA velocity has enabled the recovery of directed dynamic information from single‐cell transcriptomics by connecting measurements to the underlying kinetics of gene expression. …”
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Comparative analysis of WC1.1+ and WC1.2+ γδ T cell subset responses from cattle naturally infected with Mycobacterium bovis to repeat stimulation with mycobacterial antigens. by Alia Parveen, Sajad A Bhat, Mahmoud Elnaggar, Kieran G Meade

“…Previous studies have identified a preferential transcriptomic response in WC1.1+ cells during natural bTB infection, suggesting a subset-specific response to mycobacterial antigens. …”
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Comprehensive profiling of extrachromosomal circular DNAs in colorectal cancer progression by Lu Lu, Mingjie Chen, Guicheng Zhang, Yujing Liu, Xiangyuan Xu, Zenghua Jiang, Yangxian Xu, Tao Liu, Fan Yang, Guang Ji, Hanchen Xu

“…Using Circle-Sequencing and whole transcriptomic sequencing, we comprehensively profile circular DNAs and transcriptomes in healthy individuals, colorectal adenoma, and CRC patients. …”
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Molecular profiling of frontal and occipital subcortical white matter hyperintensities in Alzheimer’s disease by Sulochan Malla, Sulochan Malla, Annie G. Bryant, Annie G. Bryant, Rojashree Jayakumar, Benjamin Woost, Nina Wolf, Andrew Li, Sudeshna Das, Sudeshna Das, Susanne J. van Veluw, Susanne J. van Veluw, Rachel E. Bennett, Rachel E. Bennett

“…Taken together, our study characterizes the diverse molecular profiles of white matter changes in AD and provides mechanistic insights into the processes underlying AD-related WMHs.…”
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Mechanisms of epigenomic and functional convergence between glucocorticoid- and IL4-driven macrophage programming by Dinesh K. Deochand, Marija Dacic, Michael J. Bale, Andrew W. Daman, Vidyanath Chaudhary, Steven Z. Josefowicz, David Oliver, Yurii Chinenov, Inez Rogatsky

“…These findings provide a mechanistic framework for homeostatic macrophage programming by distinct signals, to better inform anti-inflammatory drug design.…”
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Exploring the Molecular Mechanisms of Fisetin in Treating Periodontitis Through Multiomics and Network Pharmacology by Lingzhi Ma, Hongrong Zhang, Yali Liu, Yan Liu, Jing Zhou, Hefeng Yang, Biao Xu

“…Additionally, we utilised single-cell and spatial transcriptomics technologies to identify key cell populations in PD and their spatial distribution. …”
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Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413. by Ali Malek Shahkouhi, Ehsan Motamedian

“…Study on metabolic interactions of the two differentiated cells provides a better understanding of its metabolism especially for improving hydrogen production. …”
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Immune characteristics and SALL1 methylation as prognostic biomarkers in primary and metastasis colorectal cancer by Yiwen Zhang, Tianqi Han, Hui Zhang, Jiali Li, Jun Chu, Jiaqi Liu

“…Among these, the methylation level at the cg13755795 site emerged as an independent prognostic biomarker, offering predictive value for patient outcomes.Our findings provide a comprehensive view of the transcriptomic and epigenetic differences between CRC and mCRC, identify novel prognostic biomarkers and therapeutic targets, and propose potential strategies for personalized prognosis prediction and targeted therapy. …”
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GAG Protein of <i>Arabidopsis thaliana</i> LTR Retrotransposon Forms Retrosome-like Cytoplasmic Granules and Activates Stress Response Genes by Alexander Polkhovskiy, Roman Komakhin, Ilya Kirov

“…Here, we present a comprehensive analysis of the structural features, intracellular localization, and transcriptomic effects of the EVD GAG (evdGAG) protein. …”
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GPATCH3, a splicing regulator that facilitates tumor immune evasion via the modulation of ATPase activity of DHX15 by Tingrong Ren, Gaigai Wei, Gaigai Wei, Jingjing Yi, Jingjing Yi, Yuqi Zhang, Haiping Zhao, Nana Wu, Huiling Zhang, Zhihan Guo, Yihan Wang, Jiating Kuang, Zhaoying Sheng, Duanwu Zhang

“…Immune infiltration patterns were analyzed using TIMER2.0 based on TCGA transcriptomic data.ResultsGPATCH3 interacts with the RNA helicase DHX15 and enhances its ATPase activity, promoting proper spliceosome disassembly. …”
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ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. by Agatha Treveil, Balazs Bohar, Padhmanand Sudhakar, Lejla Gul, Luca Csabai, Marton Olbei, Martina Poletti, Matthew Madgwick, Tahila Andrighetti, Isabelle Hautefort, Dezso Modos, Tamas Korcsmaros

“…In this way, the workflow provides a mechanistic insight from previously identified knowledge of virally infected cells. …”
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Characterization of a Drosophila model to study functions of guarana seeds. by Maria Fernanda Manica-Cattani, Ivana Beatrice Mânica da Cruz, Yukiko Sato-Miyata, Lucas Siqueira Trindade, Felipe Rogalski, Euler Esteves Ribeiro, Manabu Tsuda, Toshiro Aigaki

“…Transcriptomic analysis identified 58 upregulated and eight downregulated genes in guarana-fed flies. …”
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Investigating the role of tumor cell heterogeneity and angiogenesis genes in the prognosis of multiple myeloma by Xue Qiao, Zhengrong Song, Li Geng, Lina Xing, Ying Wang

“…By constructing a prognostic model, it provides new theoretical insights for the precise diagnosis and personalized treatment of MM.…”
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Differential behavior responses and genetic alteration underpinning exercise effectiveness in stress-susceptible mice by Dong-Joo Hwang, Ji-Eun Kim, Joon-Yong Cho, Jung-Hoon Koo, Yongchul Jang, Tae-Kyung Kim

“…Examining individual adaptation to exercise provides insights into the biology of such variations. …”
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Identification and Expression Analysis of Na⁺/K⁺-ATPase and NKA-Interacting Protein in Ark Shells by Man Song, Xiao Liu, Jie Zhang, Wuping Li, Jingfen Pan, Yanglei Jia

“…These findings provide a molecular foundation for understanding the osmotic adaptation mechanisms in ark shells and offer novel insights into their ability to thrive in mudflat habitats. …”
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Behavioral, physiological and genetic responses of the Yesso scallop Mizuhopecten yessoensis to the predation of sea star by Xuetao Li, Xuetao Li, Xuetao Li, Xian Li, Xian Li, Danyang Li, Danyang Li, Dandan Zhang, Xingyue Zhai, Xubo Wang, Xubo Wang, Junxia Mao, Junxia Mao, Ying Tian, Ying Tian, Ming Liu, Yaqing Chang, Yaqing Chang, Zhenlin Hao, Zhenlin Hao

“…These findings demonstrate coordinated behavioral and molecular adaptations to predator stress in M. yessoensis and provide a foundation for improving predator management and selective breeding strategies in scallop aquaculture.…”
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The carRS-ompV-virK operon of Vibrio cholerae senses antimicrobial peptides and activates the expression of multiple resistance systems by Annabelle Mathieu-Denoncourt, Gregory B Whitfield, Antony T Vincent, Cécile Berne, Julien Pauzé-Foixet, Feriel C Mahieddine, Yves V Brun, Marylise Duperthuy

“…In this study, a transcriptomic analysis in Vibrio cholerae showed that expression of the uncharacterized gene ompV is stimulated in response to PmB. …”
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