bacteriology

Inofficial R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber). https://api.bacdive.dsmz.de/client_examples seems to be the official alternatives.

BioMight - Human Biological Animation Engine

BacDoc: Web-based bacterial identification & cultivation media predictor for resource-limited labs. Flask app with 800+ organism database, fuzzy matching, hybrid media generation from phenotypic parameters. Addresses AMR diagnostic gaps (free alternative to MALDI-TOF or VITEK system).

Code developed and used in my master thesies investigating natural transformation in Chromobacteriaceae

A reproducible nf-core/ampliseq pipeline characterizing antibiotic-mediated gut dysbiosis via paired-end 16S rRNA (V4) sequencing. Implements DADA2 exact sequence variant inference, SILVA-based taxonomic classification, and multivariate ecological ordination to quantify compositional perturbations in human fecal microbiomes.

A WGCNA pipeline systematically interrogating the Campylobacter resistome through topological network scaling to uncover co-expressed stress-response loci and significant module-trait biological correlations.

Diffusion model of a system where sender strains produce AHL and has induced motility in the presence of arabinose. AHL diffuses and motility in receiver strains.

A reproducible pangenomic analysis of seven Chlamydia trachomatis strains using anvi'o v9, exploring core and accessory gene clusters across different serovars and clinical isolates.

Bacteriology presentation of pyani summary/roadmap