Andreas Solberg Sagen andreassag

Andreas Solberg Sagen

🧬 PhD Candidate in Molecular Microbiology & Bioinformatics

🔬 About Me

I am a PhD research fellow passionate about unraveling the molecular mechanisms of bacterial communication, gene regulation, and mutagenesis. My research bridges experimental molecular biology with computational genomics & bioinformatics to understand microbial adaptation and antimicrobial resistance (AMR) dissemination.

🎓 PhD Candidate in molecular microbiology and bioinformatics
🦠 Investigating the molecular mechanisms of competence regulation and natural genetic transformation in oral Streptococci
💻 Developing automated computational workflows and pipelines to accelerate in vitro discovery
🧪 Bridging wet-lab phenotypic assays with large-scale genomic data analysis

🧬 Research Focus

Focus	Description
🧫 Bacterial Signaling	Quorum sensing and peptide-mediated communication in microbial communities
🧬 Genetic Transformation	Molecular machinery of horizontal gene transfer and exogenous DNA uptake
🧪 Mutagenesis	Mutation pathways, spontaneous rates, and adaptation under selective pressure
💊 Antimicrobial Resistance	Quantifying the relative contributions of transformation vs. mutagenesis in AMR propagation
🦷 Oral Streptococci	Commensal and opportunistic pathobionts exhibiting high adaptability and clinical relevance

🔬 Deep Dive: Experimental & Wet-Lab Methodologies

Natural Transformation & Competence Induction: Quantitative transformation frequency assays, competence-stimulating peptide (CSP / XIP) response profiling, and targeted homologous recombination in Streptococcus constellatus.
Mutagenesis & Fluctuation Analysis: Luria–Delbrück fluctuation assays to determine spontaneous mutation rates and evaluate mutational spectra during antibiotic exposure.
In Vitro Toxicology & Co-culture Models: Evaluating innate immune responses (human alveolar cell co-cultures, neutrophil-like HL-60 models) exposed to micro/nanoplastics and microbial contaminants.
Antimicrobial Susceptibility Testing (AST): High-resolution growth curve kinetics, minimum inhibitory concentration (MIC) assays, and population survival dynamics.

💻 Deep Dive: Bioinformatics & Computational Genomics

Reproducible NGS Pipelines: Developing automated, containerized pipelines using Nextflow adhering to nf-core standards for whole-genome sequencing and variant calling.
Biosynthetic Gene Cluster (BGC) Mining: Mining and comparative exploration of secondary metabolite clusters using antiSMASH, GECCO, DeepBGC, and BiG-SCAPE (e.g., via Clystere).
AMR Determinant Mapping: Resistome annotation, mobile genetic element (MGE) tracking, and core- vs. accessory-genome alignment across clinical and commensal isolates.
Data Science & Tooling: Custom Python/R utilities for batch microplate normalization, statistical modeling, and image processing workflows.

📄 Selected Publications & Preprints

Recent peer-reviewed articles and preprints (chronological order):

Mapping Antibiotic Resistance Determinants in Oral Streptococci
K. S. M. Shawrob, A. S. Sagen, T. M. Lunde, B. Sribasgaran, S. Ghafoor, M. Al-Haroni, R. A. Gladstone, G. Salvadori, R. Junges (2026)
Journal of Dental Research
Genetic and functional characterization of the natural transformation system in Streptococcus constellatus
A. S. Sagen, K. S. M. Shawrob, G. Salvadori, R. Junges (2026)
Microbiology
Distinct pro-inflammatory responses to pristine and microbially contaminated PET nanoplastics in a human alveolar cell co-culture
Ø. P. Haugen, A. S. Sagen, F. Barbero, V. Alcolea-Rodriguez, R. Portela, I. Fenoglio, B. C. Brinchmann, H. Wallin, S. Zienolddiny-Narui, A. K. Afanou (2026)
Frontiers in Toxicology
Microplastics amplify the pro-inflammatory response to fungal mycelial fragments and spores in neutrophil-like cells
A. K. Afanou, A. S. Sagen, F. Barbero, I. Zanoni, A. Costa, Ø. P. Haugen, S. Zienolddiny-Narui (2026)
Frontiers in Toxicology