Skip to content
View SizheQiu's full-sized avatar
🏠
Working from home
🏠
Working from home
12 followers · 9 following

Block or report SizheQiu

Block user

Prevent this user from interacting with your repositories and sending you notifications. Learn more about blocking users.

You must be logged in to block users.

Please don't include any personal information such as legal names or email addresses. Maximum 100 characters, markdown supported. This note will be visible to only you.
Report abuse

Contact GitHub support about this user’s behavior. Learn more about reporting abuse.

Report abuse
SizheQiu/README.md

你好 👋

Keywords: Computational biology🖥️/Systems biology🔢/Microbiology🦠/Machine learning⚙️

Projects🌟:

  • DLTKcat⚗️
    • Deep learning-based prediction of temperature dependent enzyme kcat.
  • Seq2Topt⚗️
    • Seq2Topt: A Sequence-Based Deep Learning Predictor of Enzyme Optimal Temperature.
    • Seq2pHopt-v1.0: protein sequence -> enzyme optimal pH
    • Seq2Tm: protein sequence -> enzyme melting temperature
  • LbPtEPS🦠🧪
    • Multi-omics analysis of L. plantarum at different pH values.
    • RPCFBA: regulatory proteome constrained flux balance analysis
  • IM-ML🦠
    • Regulon inference of E. coli based on gene sequences.
  • LPiModulons🧬
    • Independent component analysis of L. plantarum transcriptomes.
    • In-silico reconstruction of transcriptional regulatory network.
  • MetaStLbCom🧫
    • Metagenomic analysis of yogurt starter culture.
    • Dynamic metabolic modeling of major species in yogurt starter.

Publications📑

Education

  • PhD Engineering Science University of Oxford
  • BSMS Bioengineering University of California, San Diego

Learning in progress🌱:

  • Generative AI
  • Database

Contact📫:

If you would like to discuss collaborations👯 on genome-scale metabolic modeling/metagenomic analysis/application of ML on biological problems, feel free to contact me: sizhe.qiu@eng.ox.ac.uk

Pinned Loading

  1. DLTKcat DLTKcat Public

    Deep learning based prediction of temperature dependent enzyme turnover rates

    Jupyter Notebook 11 8

  2. Seq2Topt Seq2Topt Public

    A predictor of enzyme optimal temperature

    Jupyter Notebook 7 1

  3. MetaStLbCom MetaStLbCom Public

    Dynamic community-level metabolic modeling for fermentation kinetics and metabolic interactions of the yogurt starter culture based on metagenomic analysis

    Jupyter Notebook 4

  4. LPiModulons LPiModulons Public

    Independent component analysis (ICA) of Lactobacillus plantarum transcriptomes

    HTML 1

  5. SBRG/IM-ML SBRG/IM-ML Public

    Jupyter Notebook 1 1

  6. LbPtEPS LbPtEPS Public

    Jupyter Notebook