Bioinformatics
What I do
I build reproducible bioinformatics workflows for microbial ecology and multi-omics—spanning metabarcoding, whole-genome sequencing, metagenomics, metatranscriptomics, and viromics—transforming raw sequencing data into interpretable ecological and functional insight.
Core Areas
Amplicon Sequencing and Analysis 16S / 18S / COI / ITS
- Study design and experimental planning (controls, contamination mitigation, metadata structure)
- Read QC, primer/adapter trimming, denoising (ASVs / OTUs)
- Taxonomic assignment and community profiling
- Diversity and ecological statistics (alpha, beta diversity, ordination, hypothesis testing)
- Publication-ready visualization and fully reproducible reporting
Genomics (Isolates / WGS) Short-read • Long-read • Hybrid
Short-read genomics
- QC → assembly → polishing → assessment
- Genome annotation and functional characterization
- Comparative genomics and phylogenomics
- Plasmid identification and analysis
Long-read genomics
- Nanopore read QC and assembly strategies
- Polishing, validation, and circularization checks
- High-contiguity genome reconstruction
- Structural variation and genome architecture assessment
Hybrid assembly (short + long reads)
- Hybrid assembly design and troubleshooting
- Optimization of assembly parameters
- Quality assessment and standardized reporting of assembly metrics
- Integration into downstream comparative analyses
Metagenomics Shotgun community sequencing
- Read QC, decontamination, and host-removal strategies
- Taxonomic profiling and functional profiling
- Genome-resolved metagenomics: assembly → binning → QC → dereplication
- Coverage-normalized abundance estimation across samples
- Metabolic modeling and pathway reconstruction
Metatranscriptomics RNA-based activity profiling
- RNA read QC and preprocessing strategies
- Mapping-based quantification and transcript abundance estimation
- DNA–RNA coupling analyses (activity vs potential)
- Differential expression workflows (when appropriate)
- Functional activity interpretation within ecological context
Viromics Viral community genomics
- Viral contig identification and QC (virome-aware pipelines)
- vOTU clustering and viral taxonomy assignment
- Auxiliary metabolic gene (AMG) identification
- Viral diversity and abundance profiling
- Viral–host comparative analysis
Functional Screening and Genome Mining AMR • Biosynthetic potential • Synthetic communities
- Antibiotic resistance gene profiling (genomes and metagenomes)
- Screening for biosynthetic gene clusters and production-associated genes
- Trait-based genome mining to support synthetic community development
- Functional complementarity analysis and candidate selection
Applied Statistics & Modeling Ecological modeling • Ordination • Resilience frameworks
- Community ecology statistics (Bray–Curtis, clustering, diversity metrics)
- Constrained ordination (RDA / db-RDA) and PERMANOVA
- Modeling relationships between environmental gradients and community structure
- Ecosystem resilience modeling (e.g., functional redundancy frameworks)