Patricia Agudelo‐Romero

Editorial: Allergic diseases through precision medicine

Patricia Agudelo‐Romero, Enza D'Auria, Anthony Bosco

au, fr, de, it, us (code pays fourni par la source)

What goes up must come down: dynamics of type 1 interferon signaling across the lifespan

Lucy Hartnell, Patricia Agudelo‐Romero, Samuel Montgomery, Rym Ben-Othman et autres

Type 1 interferons (T1IFNs) are typically expressed in low concentrations under homeostatic conditions, but upon pathogenic insult or perturbation of the pathway, these critical immune signaling molecules can become either protectors from or drivers of pathology. While essential for initiating antiviral defense …

au, de, ca (code pays fourni par la source)

Programming of the respiratory epithelium in utero - insights from the amniotic epithelial methylome

Patricia Agudelo‐Romero, Thomas Iosifidis, James I. Lim, Nina Kresoje et autres

Abstract Background Dysregulation of the airway epithelium contributes to recurrent wheezing and asthma and may have developmental origins. Direct interrogation of fetal airway epithelium is not feasible in humans limiting investigation of prenatal epithelial programming. Methods We performed high-throughput target-capture DNA methylation …

au, de, us (code pays fourni par la source)

Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers–focused program at The Kids Research Institute Australia

Patricia Agudelo‐Romero, Talya Conradie, Jose Antonio Caparros-Martin, David Martino et autres

The increasing adoption of high-throughput "omics" technologies has heightened the demand for standardized, scalable, and reproducible bioinformatics workflows. Nextflow and nf-core provide a robust framework for researchers, particularly early- and mid-career researchers (EMCRs), to navigate complex data analysis. At The Kids Research …

au, de (code pays fourni par la source)

Insights into the relationship between nasal bacterial composition and susceptibility to early-life respiratory disease: a pilot observational study

Jose Antonio Caparros-Martin, Elizabeth Kicic‐Starcevich, Patricia Agudelo‐Romero, David G. Hancock et autres

Abstract Background Early-life susceptibility to viral respiratory infections is associated with long-term respiratory morbidity in children. Currently, no reliable tools exist to predict susceptibility to these infections. Because the endogenous microbiota can influence pathogen virulence and airway inflammation, it represents a potential …

au, de, us (code pays fourni par la source)

Conservation of gene expression patterns between the amniotic and nasal epithelium at birth

David G. Hancock, Patricia Agudelo‐Romero, Elizabeth Kicic‐Starcevich, James I. Lim et autres

Background Amniotic epithelial cells are fetal-derived stem cells, capable of differentiating into all three germ layers, including mature epithelial cell populations. Here, we hypothesised that the amniotic epithelium might serve as a surrogate tissue source for investigating transcriptional profiles in the respiratory …

au, de (code pays fourni par la source)

target-methylseq-qc: a lightweight pipeline for collecting metrics from targeted sequence mapping files.

Abhinav Sharma, Talya Conradie, David Martino, Stephen Michael Stick et autres

Sharma et al., (2025). target-methylseq-qc: a lightweight pipeline for collecting metrics from targeted sequence mapping files.. Journal of Open Source Software, 10(109), 7608, https://doi.org/10.21105/joss.07608

Afrique du Sud, au, ru (code pays fourni par la source)

Metagenome Processing in Clinical Setting for Respiratory Pathogens v1

Abhinav Sharma, J. Caparrós, Patricia Agudelo‐Romero

Metagenomic bioinformatics pipelines are essential for extracting meaningful biological insights from the vast amounts of sequencing data generated in microbial studies. However, current approaches face several challenges that limit their utility and accessibility. A major hurdle is the efficient and accurate removal …

Afrique du Sud, in (code pays fourni par la source)

Metagenome Processing in Clinical Setting for Respiratory Pathogens v2

Abhinav Sharma, Jose A Caparros-Martin, Patricia Agudelo‐Romero

Metagenomic bioinformatics pipelines are essential for extracting meaningful biological insights from the vast amounts of sequencing data generated in microbial studies. However, current approaches face several challenges that limit their utility and accessibility. A major hurdle is the efficient and accurate removal …

Virome assembly reveals draft genomes of native Pseudomonas phages isolated from a paediatric bronchoalveolar lavage sample

Patricia Agudelo‐Romero, Jose Antonio Caparros-Martin, Abhinav Sharma, Montserrat Saladié et autres

ABSTRACT We present lung virome data recovered through shotgun metagenomics in bronchoalveolar lavage fluid from an infant with cystic fibrosis, who tested positive for Stenotrophomonas maltophilia infection. Using a bioinformatic pipeline for virus characterization in shotgun metagenomic data, we identified five viral …

au, de, us, Afrique du Sud, ie (code pays fourni par la source)

Database for EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion).

Patricia Agudelo‐Romero, Abhinav Sharma, Talya Conradie, Anthony Kicic et autres

Database for EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Funding Statement: This work was supported by the National Health and Medical Research Council of Australia, Synergy grant (APP1183640).

au (code pays fourni par la source)

Bile acids in the lower airways is associated with airway microbiota changes in chronic obstructive pulmonary disease: an observational study

Jose Antonio Caparros-Martin, Montserrat Saladié, Patricia Agudelo‐Romero, Kristy Nichol et autres

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a complex disorder with a high degree of interindividual variability. Gastrointestinal dysfunction is common in patients with COPD and has been proposed to influence the clinical progression of the disease. Using the presence of bile …

au, ie (code pays fourni par la source)