Faculty

Biography

Chao has been dedicated in the development of phylogenetic algorithms and tools. He developed ASTRAL-IV (for large-scale phylogenetic inference), ASTRAL-Pro (for phylogenetic inference using multi-copy gene families), wASTRAL (for phylogenetic inference with uncertainty), CASTER (for whole-genome-alignment-based phylogenetic inference), WASTER (for cost-efficient phylogenomic reconstruction), D* statistic (for detecting ancient hybridization), and TAPER (for multiple sequence alignment error removal).
GitHub: https://github.com/chaoszhang
Gitee: https://gitee.com/chaos_zhang
Bioconda: https://bioconda.github.io/recipes/aster/README.html

Education

2017.9 - 2022.9 Ph.D in Bioinformatics and Systems Biology, University of California San Diego
2014.8 - 2017.6 B.S in Bioengineering: Bioinformatics, University of California San Diego
2014.8 - 2017.6 B.S in Mathematics - Computer Science, University of California San Diego

Professional Experience

2024.10-2025.8 Assistant Professor, University of Copenhagen
2022.11-2024.9 Visiting Scholar, University of California Berkeley
2022.10-2024.9 PostDoc, University of Copenhagen

Large-scale whole-genome-base phylogenetic inference, cost-efficient genome-base phylogenetic reconstruction, inter-species introgession detection, phylogenetic network reconstruction, large-scale phylogenomic analysis, large-scale whole genome alignment, large-scale alignment error detection, and theories in phylogenetics.

CASTER: Direct species tree inference from whole-genome alignments
C Zhang, R Nielsen, S Mirarab
Science 387 (6737), eadk9688

ASTER: A Package for Large-Scale Phylogenomic Reconstructions
C Zhang, R Nielsen, S Mirarab
Molecular Biology and Evolution 42 (8), msaf172