Category: Academia

  • FAQ for Rule-based modeling of cell-level networks in immune-oncology

    FAQ for Rule-based modeling of cell-level networks in immune-oncology

    COVID-19 has limited discourse related to scientific projects. Here we address a number of FAQs related to a proposed rule-based modeling approach for inferring alterations in cell-to-cell communication associated with oncogenesis.

  • It’s not you, it’s me

    It’s not you, it’s me

    In looking for love, most people have experienced the “It’s not you, it’s me” breakup strategy. Here I talk in Bayesian terms about this strategy in the context of academic peer review.

  • Trying to not be a hypocrite

    Trying to not be a hypocrite

    At Entelos, a common refrain was that biologist don’t take the right data when it comes to building mechanistic mathematical models of disease. Yet, the company was reluctant to publish primary research articles showing how existing data are used and what kind of data are needed. Over time, this blanket critique of biologists, to me,…

  • [Old Man Yells at Cloud]

    [Old Man Yells at Cloud]

    Creating a mathematical model of disease based on the available literature requires reading a lot of papers. In the 5 years that I was at Entelos, I had read close to 3000 papers.

  • Butterflies and rainbows

    I recently followed my wife to a conference in Denver and I attended a hospitality event. In making casual conversation with someone at the event, the conversation followed the typically script: Casual conversant (CC): “What do you do?”  Me: “I’m a professor” CC: “Oh what in?” Me: “Chemical and Biomedical Engineering” CC scrunches up their…

  • Paper Tales – Klinke DJ PLoS One 2008

    At Entelos, I saw first hand that developing mathematical models of disease requires significant investment before you have a simulation platform that you can market to pharma. These PhysioLab models were complicated and required multiple PhD-level engineers and life scientists working elbow to elbow for 6 months to a year or more before we had…