Publications

    All Publications (240)

    Coralysis enables sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration 
    António G G Sousa et al. Nucleic Acids Res. 2025 Nov 13;53(21):gkaf1128. doi: 10.1093/nar/gkaf1128. Published November 16, 2025
    Complex single-cell analyses now routinely integrate multiple datasets, followed by cell-type annotation and differential expression analysis. Current state-of-the-art integration methods often struggle with imbalanced cell...
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    Single-cell to pre-clinical evaluation of Trem2, Folr2, and Slc7a7 as macrophage-associated biomarkers for atherosclerosis 
    Tiit Örd et al. Cardiovasc Res. 2025 Nov 7:cvaf210. doi: 10.1093/cvr/cvaf210. Online ahead of print. Published November 9, 2025
    CONCLUSIONS: Our findings provide novel insights into macrophage-specific gene programs during atherosclerosis progression and identify a set of promising biomarkers that can serve as a...
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    Drug target proteome profiling identifies HES1-driven mitotic catastrophe in ovarian serous carcinoma 
    Jie Bao et al. Biomed Pharmacother. 2025 Nov 6;193:118716. doi: 10.1016/j.biopha.2025.118716. Online ahead of print. Published November 7, 2025
    Ovarian high-grade serous cancer (HGSC) is the most aggressive ovarian cancer subtype with limited treatment options. We identify the PDPK1 inhibitor BX-912 as a promising...
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    Nextpie: a web-based reporting tool and database for reproducible nextflow pipelines 
    Bishwa Ghimire et al. Bioinform Adv. 2025 Oct 10;5(1):vbaf252. doi: 10.1093/bioadv/vbaf252. eCollection 2025. Published November 3, 2025
    MOTIVATION: High-throughput genomic data analysis consists of the inexorably intertwined inputs and outputs of a vast array of bioinformatic analysis tools. To guarantee streamlined and...
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    Reinstating Niche Failure in Diabetic Cranial Defects via Chronotaxic Signal-Amplifying Fluidic Biomimetic Hydrogel 
    Yingji Mao et al. Adv Sci (Weinh). 2025 Oct 15:e16398. doi: 10.1002/advs.202516398. Online ahead of print. Published October 15, 2025
    Cranial stem cell niches (SCNs) are intrinsically scarce and hypoactive, and, exacerbated by chronic inflammation in diabetes, lead to niche failure and regenerative deficit after...
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    Characterization of Visceral Adipose Tissue Proteome Reveals Metabolic Changes and Inflammatory Signatures in Severe Obesity 
    Prince Dadson et al. Obesity (Silver Spring). 2025 Oct 12. doi: 10.1002/oby.70041. Online ahead of print. Published October 12, 2025
    CONCLUSIONS: These findings demonstrate significant molecular alterations in the VAT proteome associated with severe obesity, providing insights into the underlying mechanisms of metabolic disease. The...
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    Prenatal exposure to perfluoroalkyl substances predicts multimodal brain structural and functional outcomes in children aged 5 years: a birth cohort study 
    Aaron Barron et al. Lancet Planet Health. 2025 Oct 9:101309. doi: 10.1016/j.lanplh.2025.101309. Online ahead of print. Published October 12, 2025
    BACKGROUND: Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are ubiquitous persistent organic pollutants associated with adverse health outcomes in humans. Although they are associated with autism spectrum...
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    LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis 
    Ali Mostafa Anwara et al. Bioinformatics. 2025 Oct 11:btaf570. doi: 10.1093/bioinformatics/btaf570. Online ahead of print. Published October 11, 2025
    MOTIVATION: Differential expression analysis plays a vital role in omics research enabling precise identification of features that associate with different phenotypes. This process is critical...
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    MicroRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution 
    Ana Hernández de Sande et al. Genome Med. 2025 Oct 6;17(1):112. doi: 10.1186/s13073-025-01530-9. Published October 7, 2025
    CONCLUSIONS: We demonstrate that miRNA gene transcriptional activity is widely impacted in immune cells by aging and during disease development and further identify the corresponding...
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    Functional characterization and directed evolution of Cicer arietinum glutathione transferases for enhanced hydroperoxidase activity and ligandin function 
    Anni Kontouri et al. Phytochemistry. 2025 Sep 27;242:114692. doi: 10.1016/j.phytochem.2025.114692. Online ahead of print. Published September 29, 2025
    Tau class glutathione transferases (GSTUs) play essential roles in plant defense by facilitating the nucleophilic attack of glutathione (GSH) to a wide range of electrophilic...
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    Early life gut microbial and metabolic shifts reflected in stool consistency- a gut transit time proxy 
    Anna-Katariina Aatsinki et al. bioRxiv [Preprint]. 2025 Sep 16:2024.06.05.597641. doi: 10.1101/2024.06.05.597641. Published September 26, 2025
    Transit time, fluid intake, diet, and overall gut health all influence stool consistency. However, the relationships between the gut microbiota, metabolome (microbial metabolites), and stool...
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    Anisomelic acid promotes proteasomal degradation of HPV16 E6 via E3 ligase recruitment: A mass spectrometry-based interactome study 
    Michael Santos Silva et al. J Proteomics. 2025 Sep 16;322:105536. doi: 10.1016/j.jprot.2025.105536. Online ahead of print. Published September 18, 2025
    Human papillomavirus (HPV) is a major driver of cervical and other epithelial cancers, with the viral oncoprotein E6 playing a central role in tumorigenesis by...
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