Algorithms & microbial life

Biography

I am a computational microbiologist developing algorithms and open-source software for large-scale genomics, metagenomics, and microbiome analysis. I work at the intersection of probabilistic data structures, high-performance computing, and microbial ecology.

My research turns large biological datasets into tractable scientific questions. I develop methods for genome search, phylogenetic community comparisons, and biological network embedding, including DartUniFrac, GSearch, and Annembed. I also study microbial populations through long-read metagenomics and genome-resolved ecology.

I received my Ph.D. in Bioinformatics from Georgia Tech in 2024, following an M.S. at Tsinghua University. My postdoctoral research at UC San Diego (2024–2026) focused on scalable methods for microbiome and genomic analysis. Much of my software is written in Rust.

Research Interests

  • Probabilistic data structures & algorithms
  • Genomics & long-read metagenomics
  • Microbiome analysis & microbial ecology
  • Biological network embedding
  • High-performance scientific computing

Education

  1. Ph.D. in BioinformaticsGeorgia Institute of Technology
  2. M.S. in Environmental Science
    and Engineering
    Tsinghua University
  3. B.S. in Environmental ScienceNanjing Agricultural University

Publications

BibTeX

* First or co-first author.

Research Software

GitHub
04

BinDash-rs

MinHash-based methods for fast genome search and comparison.

Sequence comparison
bioRxiv
More software & libraries

Contributions

Presentations & Posters

  1. Promiscuous and unbiased recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean

    Poster · ASM Microbe · Atlanta, USA

  2. High-performance parallel and concurrent programming for bioinformatics and computational biology

    Poster · International Summer School on High Performance Computing · Atlanta, USA

  3. Time-series metagenomics enables quantification of the rare biosphere to natural disturbances

    Poster · ASM Microbe · Washington, DC, USA

Contact

jiz322@ucsd.edu

San Diego, California, USA

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