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Achievement: Pull SharkAchievement: Starstruck

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deweihu96/README.md

Hi, I'm Dewei 👋

PhD Fellow in Bioinformatics & Network Biology at the Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen.

  • 🧬 My PhD is on representation learning for biological networks and multi-omics integration, supervised by Simon Rasmussen and Lars Juhl Jensen.
  • 🕸️ I build cross-species protein embeddings on top of the STRING database.
  • 📊 I integrate metabolomics, proteomics, and protein interaction networks at population scale to study complex disease.
  • 🔬 Currently thinking about single-cell perturbation prediction and metabolic disease target discovery.
  • 🇩🇰 Based in Copenhagen.

Selected repositories

  • SPACE: cross-species protein embeddings, now part of STRING v12.0
  • net2rank: molecular maps of disease from omics data and network embeddings
  • SLIM: a small linear model with STRING embeddings for virtual cell perturbation

Where to find me

Website · Google Scholar · LinkedIn · Email

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  1. SPACE SPACE Public

    SPACE: STRING proteins as complementary embeddings

    Python 44 1

  2. larsjuhljensen/net2rank larsjuhljensen/net2rank Public

    Jupyter Notebook 4

  3. virtual-cell-wiki virtual-cell-wiki Public

    Knowledge database for virtual cell models that can be easily read by AI models.

    7

  4. RasmussenLab/SLIM RasmussenLab/SLIM Public

    SLIM is a small bilinear model that uses gene embeddings (e.g. STRING) to predict single-cell genetic perturbation responses.

    Python 11

  5. RasmussenLab/AugMent RasmussenLab/AugMent Public

    Contrastive alignment transfers proteomic disease predictive signals to metabolomics

    Python 2