Josue Leonardo Castro Mejia
Microbiology and Fermentation
1958 Frederiksberg C
- Apply multivariate methods (e.g. dissimilarity-based, machine learning, covariance structures, permutation, dimensionality reduction) for analysis of experimental designs and integration of sequencing data (metagenomes, amplicons, gene-protein clusters) with multi-omics datasets (e.g. metabolome through GC-MS, NMR platforms), phenotype, clinical biomarkers and immunological data.
- Lead data integration of multidisciplinary projects in human studies, animal- and in-vitro models associated with metabolic/chronic diseases (e.g. diabetes, dyslipidemia and other chronic diseases), with emphasis on gut microbiome and phenotype manipulation for discovery of novel microbes and gain understanding of disease mechanisms.
- Design and implement state-of-the-art genomic computational pipelines/workflows for analysis of sequencing data (2nd and 3rd NGS) using UNIX-based (Linux/MAC) and Anaconda environments, e.g. reconstruction/assembly of (meta)-genomes, metabolic pathways, operons, gene-clusters, as well as amplicon-based profiling.
- Implement different approaches (MDA, PCR & PCR-free) for construction and sequencing of DNA/cDNA/RNA libraries on Illumina & Oxford-Nanopore platforms – extensive experience in process optimization, cost-effective steps and troubleshooting.
- Explore mutation and genetic content of DNA/RNA viromes –virus-host dynamics using bioinformatic approaches based on prediction-search of tRNAs/CRISPR-spacers, culture-dependent and epifluorescence microscopy.
- Manage cloud computing for computational genomic studies through batch systems.