CV | alienzj | Microbiome Informatics

Personal Summary

Microbiome Informatics researcher and bioinformatics engineer dedicated to developing robust tools for metagenomics data analysis. Focused on high-throughput pipeline development, workflow automation, and AI-powered scientific discovery.

Technical Stack

Metagenomics

ATLAS, MetaPhlAn, HUMAnN, MEGAHIT, CheckM, GTDB-Tk, QIIME2

Workflow & Ops

Snakemake, Nextflow, Docker, Singularity, Conda, GitHub Actions

Data Science

Python (pandas, numpy, scikit-learn), R (tidyverse, phyloseq)

AI & Agents

LLM orchestration, LangChain, Autonomous Agents for Science

Open Source Projects

metapi: A general metagenomics data mining system for robust microbiome research.
quantpi: Microbiome profiling pipeline with comprehensive QC and statistical analysis.
rnapi: RNA-seq analysis pipeline for transcriptomics studies.
qiimepi: Snakemake implementation of QIIME2 for amplicon analysis.
skillpi: Knowledge base and skill management for scientific workflows.
clawpi: AI-powered workflow orchestration and automated scientific discovery.
metagenome-atlas/atlas: Automated metagenome analysis pipeline — "Three commands to analyze your metagenome".
BioConda: Contributor to the bioinformatics conda channel, participating in packaging and maintenance.

Research Interests

Recovery and analysis of Metagenome-Assembled Genomes (MAGs).
Microbiome data mining and functional profiling.
Reproducible research through workflow automation.
Artificial Intelligence for scientific discovery (AI4Science).