Publications

    PUBLICATION

    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 on 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 Read more

    PUBLICATION

    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 on 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 Read more

    PUBLICATION

    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 on 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 Read more

    PUBLICATION

    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 on 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 Read more

    PUBLICATION

    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 on 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 Read more

    PUBLICATION

    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 on 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 Read more

    PUBLICATION

    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 on 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 Read more

    PUBLICATION

    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 on 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 Read more

    PUBLICATION

    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 on 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 Read more

    PUBLICATION

    HSF2 drives breast cancer progression by acting as a stage-specific switch between proliferation and invasion 

    Jenny C Pessa et al.

    Sci Adv. 2025 Sep 5;11(36):eady1289. doi: 10.1126/sciadv.ady1289. Epub 2025 Sep 3.

    Published on September 3, 2025

    Breast cancer is hallmarked by phenotypic transitions enabling abnormal cell proliferation and invasion. The stress-protective transcription factor heat shock factor 2 (HSF2) is associated with Read more

    PUBLICATION

    Breast Milk Proteome: Changes in the Different Stages of Lactation and Impacts of Gestational Diabetes Mellitus and Body Mass Index 

    Timo Seitz et al.

    Mol Nutr Food Res. 2025 Sep 1:e70225. doi: 10.1002/mnfr.70225. Online ahead of print.

    Published on September 2, 2025

    Breast milk proteome comprises hundreds of bioactive proteins supporting infant development. The extent to which maternal metabolic conditions modify the proteome is poorly known. This Read more

    PUBLICATION

    Metabolome informs about the chemical exposome and links to brain health 

    Matej Orešič et al.

    Environ Int. 2025 Aug 22;203:109741. doi: 10.1016/j.envint.2025.109741. Online ahead of print.

    Published on September 1, 2025

    The metabolome is an intermediate phenotype, summarizing the profile of all small molecules (