Charles Tapley Hoyt My name is Charles Tapley Hoyt. I’m a bio/cheminformatician using biological knowledge graphs to generate biological hypotheses that assist in drug discovery and precision medicine.

Here’s some more details about me and my research. My résumé can be found here and everything else on ORCID at ORCID


  • How to Fix Your Monolithic Pull Request

    We’ve all been there. You started a new branch from master. You had a very specific goal in mind, The Original Goal. You made a pull request (PR) to go with it, too, The Original Pull Request. But then, you had an idea! And also, someone on your team asked you to solve another problem! Now the original code you wrote to address The Original Goal relies on that code … and now you’ve got dozens of files changed, hundreds of lines of diff, and nobody (including you) can understand what you’ve done. Like I said, we’ve all been there. Here’s what you can do to fix it:

  • Host a Graduate Seminar Before Writing Your Thesis

    The other day I saw a tweet lamenting the drag that is literature review during preparation for writing your thesis.

  • Encoding Biology in Knowledge Graphs

    How many molecular biology papers have you read today? This week? This month? If you’re like me, its not so many, and we’re falling behind very quickly. Here’s a chart made by the new PubMed that summarizes how many papers were published mentioning RAS in the last 50 years.

  • Biosemantics vs. Biopragmatics

    In language, semantics describe the names and meanings of words. The bioinformatics community has aptly adopted biosemantics as a concept that encompasses the issues with the names and meanings of biological entities, usually in natural language processing and data integration. However, semantics does not capture the context of words, and biosemantics fails to describe the biological context and complex relationships between biological entities.

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