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…
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…
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…
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…
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…
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.…
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 –…
It’s summertime – season of thunderstorms. Most days are punctuated with ominous clouds and distant thunder. Actual rain, however, is rare. The forecast is consistent – temperatures may spike up to uncomfortably hot in the afternoon, and there are low odds of a thunderstorm. I…