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Old-Shatterhand/README.md

Welcome to my GitHub Repo

My name is Roman Joeres. I'm PhD student in the kalininalab of the Helmholtz Center for Pharmazeutical Research Saarland (HIPS) and Saarland University. My thesis covers explainable and generalizable methods for drug target interaction prediction.

Scientific Interests

  • Graph Neural Network
  • Drug Target Interaction Prediction
  • all other types of Deep Learning

Personal Interests

  • Climbing/Bouldering
  • Chess
  • Programming
  • Cycling
  • Running
  • Swimming
  • Dan Brown and Karl May (obviously 😉)

Some links to my recent work

Work Projects

  • DataSAIL: A Python framework to compute biochemically informed splits of datasets for ML
  • GlyLES: Grammar based parsing of Glycans in IUPAC notation into SMILES

Bachelor Thesis

  • MSADRL: The code of my bachelors thesis

Master Thesis

  • GraphPLI: A fully GNN-based framework to predict interactions between proteins and ligands. The branch thesis_roman covers the code of my Masters Thesis.

Hobby Projects

  • pytest_assertcount: A plugin for pytest to count the actual number of asserts performed during a pytest run.
  • PyWLK: A Python package implementing Weisfeiler-Lehman graph kernels and a template for professional python packages
  • ProtViewer: View the activities in a protein in a browser interface in 3D.
  • SortSolver: Solve sorting games of mobile phones in the browser

Pinned

  1. kalininalab/GlyLES kalininalab/GlyLES Public

    A tool to convert IUPAC representations of glycans into SMILES strings.

    Python 9 5

  2. kalininalab/DataSAIL kalininalab/DataSAIL Public

    DataSAIL is a tool to split datasets while reducing information leakage.

    Python 13 1

  3. pytest_assertcount pytest_assertcount Public

    Pytest Plugin to count actual number of asserts in a pytest run

    Python

  4. kalininalab/GraphPLI kalininalab/GraphPLI Public

    Structure-informed Prediction of Interactions of Lectins and Glycans

    Python

  5. MSADRL MSADRL Public

    (Deep) Reinforcement Learning Framework to align multiple sequences.

    Python 2