Category Archives: Genomics

How You ‘Pre-Treat’ Your Data Really Matters (It’s Not the P-Hacking)

Posted on August 21, 2015 by mikethemadbiologist

There’s an 538 article “Science Isn’t Broken” that’s winding its way through the tubes of the internet. It has a cool ‘p-hacking’ interactive feature, which is probably why most of the associated commentary has focused on the problem of p-hacking … Continue reading →

Posted in Education, Genomics, Statistics | Comments Off on How You ‘Pre-Treat’ Your Data Really Matters (It’s Not the P-Hacking)

A Question About Oxford Nanopore and the Cost Model

Posted on June 18, 2015 by mikethemadbiologist

This is the first mention of how much the much-vaunted Oxford Nanopore sequencing technology might cost (boldface mine): Oxford Nanopore said last month that it plans to make the MinIon sequencer commercially available through the MinIon Access Program. Customers need … Continue reading →

Posted in Genomics, Public Health | 4 Comments

Thoughts on the Promises of Big Genomics

Posted on May 27, 2015 by mikethemadbiologist

Last week, David Dobbs wrote a piece about Big Genomics, in which he took a critical look at the Human Genome Project (‘HGP’). Below are some thoughts about his piece and ‘Big Genomics’; this shouldn’t be construed as a ‘response’: … Continue reading →

Posted in Genomics | 5 Comments

A Visual Image of What “Understand the Limitations of Your Data” Means

Posted on May 6, 2015 by mikethemadbiologist

One of the things I’ve repeated on this blog a few times is people have to like this crap you have to understand the limitations of your data. In a good Nature piece about how the problems with using p-values … Continue reading →

Posted in Genomics, Statistics | 1 Comment

Misunderstanding the Progression of Big Science

Posted on April 27, 2015 by mikethemadbiologist

In an interesting article about large-scale science projects (aka ‘Big Science’), Tim Requarth wrote this, which seems to have received a lot of support in the intertoobz (or at least the Twitterz; boldface mine): But here may be the real … Continue reading →

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Ion Torrent Makes a Move: Bacterial Epidemiology

Posted on April 14, 2015 by mikethemadbiologist

I’ve argued repeatedly that the obvious, near-term commercialization of genomics isn’t human genomics, but microbial genomics: …microbial genomes are cheap, fast, and you can provide epidemiologically relevant information to clinical laboratories, hospital networks, and public health departments. I’m not arguing … Continue reading →

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I Have Your Genomics Killer App Right Here, Pal

Posted on April 10, 2015 by mikethemadbiologist

When I first saw this TechCrunch article “Genomics Needs A Killer App“, I thought it was April Fool’s Day come early (an aside: how about funding the applied genetics we already know to do? Just asking). But in fact, it … Continue reading →

Posted in Bidness, Genomics, Public Health | 1 Comment

High Quality Bacterial Genomes Are About to Get Cheaper

Posted on January 29, 2015 by mikethemadbiologist

I think. This seems like good news from PacBio (boldface mine): With regard to sequencing runs, as was the case in the previous three years, we expect to deliver another ~4-fold increase in throughput, reaching >4 Gb of data per … Continue reading →

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The Closing of Microbial Genomics Data?

Posted on January 23, 2015 by mikethemadbiologist

This post will have to be a little vague, but from my vantage point, I’m seeing two disturbing trends in terms of microbial genomics. For those who aren’t the cognoscenti, the weird thing about open access data arguments for anyone … Continue reading →

Posted in Genomics, Public Health, Publishing | 1 Comment

Finally, Someone Realizes There’s Money to Be Made in Microbial Genomics

Posted on November 20, 2014 by mikethemadbiologist

Even though most genomics-related business ventures seem to focus on human-related issues, I’ve argued that using genome sequencing to do clinical microbiology is not a ‘niche’ or a minor market: On the other hand, microbial genomes are cheap, fast, and … Continue reading →

Posted in Genomics | Comments Off on Finally, Someone Realizes There’s Money to Be Made in Microbial Genomics