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a-r-j/README.md

Hi there 👋

  • 🔭 I’m a PhD student at the University of Cambridge. I work on deep learning applied to structural biology and drug discovery.

  • I'm currently doing things with proteins at Genentech / Roche / Prescient Design

  • Previously, I was a visiting researcher at EPFL and MILA, AI Resident at X - The Moonshot Factory (formerly Google X) and an ML Consultant at Relation Therapeutics.

  • 🌱 I’m currently developing Graphein, a data processing library for geometric deep learning in biology.

    • Graphein supports construction and featurisation of:
      • Protein structure graphs
      • Protein meshes
      • Small molecule graphs
      • RNA structure graphs
      • Protein-protein interaction graphs
      • Gene regulatory interaction graphs
  • 📫 How to reach me:

Pinned

  1. graphein Public

    Protein Graph Library

    Jupyter Notebook 526 65

  2. VSCode Extension for interactively visualising protein structure data in the editor

    TypeScript 52 7

  3. Working with molecular structures in pandas DataFrames

    Python 516 102

  4. R package for translating between drug identifiers using the Chemical Translation Service (CTS)

    R 3 2

  5. Repository containing a benchmark dataset for machine learning property prediction of photoswitch molecules: https://arxiv.org/abs/2008.03226

    Python 53 7

  6. graphtype Public

    Type hinting for networkx Graphs

    Jupyter Notebook 4

897 contributions in the last year

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Mon Wed Fri
Activity overview
Contributed to a-r-j/graphein, rasbt/biopandas, molstar/VSCoding-Sequence and 20 other repositories

Contribution activity

September 2022

Created 4 commits in 1 repository

Created a pull request in a-r-j/graphein that received 3 comments

fix disulphide bond node filtering #205

Reference Issues/PRs #205 What does this implement/fix? Explain your changes Disulfide bond edges were adding nodes to the graph (e.g. if we are on…

+8 −3 3 comments
Opened 4 other pull requests in 3 repositories
a-r-j/graphein 2 merged
kamurani/graphein 1 open
rasbt/biopandas 1 open
Reviewed 3 pull requests in 2 repositories
a-r-j/graphein 2 pull requests
rasbt/biopandas 1 pull request
Opened 1 issue in 1 repository
Started 1 discussion in 1 repository
a-r-j/graphein
  • 1.5.2
    This contribution was made on Sep 19
Answered 1 discussion in 1 repository
a-r-j/graphein

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