This is the fourth in a series of high-level posts reviewing foundational concepts and technologies in genomics. The first three were: “How Many Genes Does a Person Have,” “How do Genomes Vary, Person to Person,” and “Sanger Sequencing.” This one is about high throughput DNA…
More than 20 years ago, fresh out of school in the 90s, I built artificial intelligence (AI) systems for a military contractor. I trained neural nets, used natural language processing to populate decision support systems, experimented with genetic algorithms, and refined support vector machines. In…
This is the third post in a series reviewing basic concepts in genomics. The first one was titled “How Many Genes Does a Person Have?” and the second was “How do Genomes Vary, Person to Person?” This is a breezy summary of the Sanger method…
This is the second post in a series where I review and explore some basic concepts and confounders in genomics. The first one was titled “How Many Genes Does a Person Have?” Until quite recently, genetic variation was described in terms of difference from a…
Somebody recently asked me, innocently enough, “how many genes are there in the human genome?” As one does in these situations, I answered a slightly different question: We are made up of about 20,000 unique proteins. This sufficed to move the conversation along, but I…
Once a year, bioinformatics.org gives the “Benjamin Franklin” award to a person whose practice has “advanced open access in data and methods for life sciences.” There’s no cash prize, and the recipient doesn’t even get to give a talk. It usually gets presented in the…
Earlier this year, I purchased Dante Labs “whole genome Z” service, which includes 30x sequencing of every base pair of my DNA, plus an additional 100x on the protein coding regions. I mostly did this for the raw data. I work in this space and…
We are living through an uncomfortable period in the practice of medicine. The dialogue between patient and physician is critically underserved, both in terms of tools for patients and physicians, and also in terms of the data context where that conversation takes place. This is…
Biology is weird. The data are weird, not least because models evolve rapidly. Today’s textbook headline is tomorrow’s “in some cases,” and next year’s “we used to think.” It can be hard for non-biologists, particularly tech/math/algorithm/data science/machine learning/AI folks, to really internalize the level of…
In my previous blog post, I talked about the fact that medical records are a dumpster fire from a scientific data perspective. Apparently this resonated for people. This post begins to sketch some ideas for how we might start to correct the problem at its…