Genomics and Medicine

Should I take aspirin?

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 […]

N of one

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

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 […]

Fixing the Electronic Medical Mess

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 […]

The Electronic Medical Mess

I posted a quick tweet this morning about the state of data in health care. Over the years, I’ve worked with at least half a dozen projects where earnest, intelligent, diligent folks have tried to unlock the potential stored in mid to large scale batches […]

Letting the genome out of the bottle

About eleven years ago, in January of 2008, the New England Journal of Medicine published a perspective piece on direct to consumer genetic tests, “Letting the Genome out of the Bottle, Will We Get Our Wish.” The article begins by describing an “overweight” patient who […]

Data driven health decisions

I just had a personal experience with how timely, personal measurements can drive better health and lifestyle decisions. Unfortunately, it wasn’t related to any of the times that I’ve been genotyped, nor was it in the context of care by any physician. In fact, I […]

DeepVariant

Earlier this week, Google published DeepVariant, a machine learning (ML) based tool for genomics. The software is now available on the DNANexus platform. This is kind of a big deal, and also kind of not a big deal. Does it matter? It’s a big deal […]

Bioinformatics vs Computational Biology

In the past, I used the terms “bioinformatics” and “computational biology” somewhat interchangeably. I don’t do that anymore. Bioinformatics is about reusable tools and information resources for biology. Computational Biology is about biological insight. It’s not necessarily a distinction between two different types of person. […]

Genetics, Genomics, and the GI Doctor

Genome Fanboy I’m a personalized medicine and genomics nerd and fanboy. Have been for years. Back in 2008, I did 23andme. I immediately downloaded my raw data and began to tinker (as one does). I poked and prodded at the text files they provided – […]