XenoSite Regions

Published online in Bioinformatics in February 2015 Extending P450 Site-of-Metabolism Models with Region-Resolution Data Jed Zaretzki, Michael Browning, Tyler B. Hughes, S. Joshua Swamidass  Motivation: Cytochrome P450s are a family of enzymes responsible for the metabolism of approximately 90% of FDA approved drugs. Medicinal chemists often want to know which atoms of a molecule— its … Continue reading XenoSite Regions

Identifying Cancer Mutations With Parsimony

This study uses  an algorithm first developed in our group for modeling metabolism from ambiguous data. Often we know the region of a molecule that is metabolized, but not the specific atom. A clever trick using the EM algorithm lets us train a neural network, even without knowing the right targets. An analogous problem arises in cancer genomics. We … Continue reading Identifying Cancer Mutations With Parsimony

More Than Just Apes

This article is directed at scientists and religious leaders that want to non-combatively, creatively and productively engage with mainstream science. Curious and honest questions are welcome.1 Those that want to debate the science will be handled elsewhere. Scientifically speaking, humans appear to be genetically-modified apes, with genomes that are more than 98% similar to chimpanzees in … Continue reading More Than Just Apes

Evidence and Evolution

This article is directed at religious leaders that hope to engage with mainstream science in a non-combative, creative and productive way. The controversy over science in this article is considered elsewhere, but my real interest is in how I might respond theologically to what I see so clearly in science. Please consider responding to my theological question here.  Recently, several curious … Continue reading Evidence and Evolution

Evidence and Evolution (The Debate)

Recently, several curious religious leaders privately asked me to explain the genetic evidence supporting evolution. They found out about me through my prior work on faith and evolution (WSJ, Nature, Ken Fong,  Creation Pacifism and Multnomah) and my work with the Science for Seminaries Program. After several emails and conversations with these open-minded leaders, I decided to summarize my … Continue reading Evidence and Evolution (The Debate)