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szhan/README.md

Hi there 👋

I am an NDPH Intermediate Fellow at the University of Oxford studying the evolutionary, ecological, and epidemiological forces driving the spread of pathogens. I have a multidisciplinary background in genomics, population genetics, phylogenetics, and community ecology. My research involves developing novel computational methodologies and applying them to large-scale genomic datasets that are publicly available or generated through collaborations.

Ancestral recombination graphs
Phylogenetic tools and methods
TODO
Chromosomal evolutionary dynamics
Community ecology of extremophiles

Pinned Loading

  1. tsimpute Public

    Genome-wide genotype imputation using tree sequences.

    Jupyter Notebook

  2. tskit Public

    Forked from tskit-dev/tskit

    Population-scale genomics

    Python

  3. lshmm Public

    Forked from astheeggeggs/lshmm

    code to run Li and Stephens

    Python

  4. sc2ts Public

    Forked from jeromekelleher/sc2ts

    Infer a succinct tree sequence from SARS-COV-2 variation data

    Python

1,786 contributions in the last year

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Contribution activity

February 2025

Created 10 commits in 1 repository

Created a pull request in jeromekelleher/sc2ts-paper that received 14 comments

Initial methods comparison table

Partially address #322

+154 −0 lines changed 14 comments
Opened 9 other pull requests in 1 repository

Created an issue in jeromekelleher/sc2ts-paper that received 20 comments

Big methods comparison table

Curate a table with the recombinant detection results for the Pango X lineages of sc2ts and other methods alongside the "ground-truth" information …

20 comments
Opened 25 other issues in 1 repository
257 contributions in private repositories Feb 3 – Feb 26
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