Category Archives: Genomics

All Your Microbiome Are Belong to Platypus: The Perils of Plug-and-Chug Analysis

Posted on August 31, 2014 by mikethemadbiologist

By way of the Twitterz, we come across this fantastic poster (embiggened version here): To translate from Genomics, to examine the microbiome–the microorganisms that live on or in a certain habitat (e.g., your gut or skin, the surface of your … Continue reading →

Posted in Genomics, Microbiome | 5 Comments

Not to Flog the Genetic Testing Horse…

Posted on August 14, 2014 by mikethemadbiologist

Oh, who are we kidding? We love to flog metaphorical horses. Anyway, there’s an interesting article about non-invasive genetic testing that looked at the accuracy of determining if prenatal genetic testing could accurately identify if a child would have Trisomy … Continue reading →

Posted in Genetics, Genomics | Comments Off on Not to Flog the Genetic Testing Horse…

When Epidemiology Conflicts With Rapid Diagnosis: Whither/Wither Clinical Genomics?

Posted on April 29, 2014 by mikethemadbiologist

What Scary Disease Lady (aka ‘Maryn McKenna’) wrote a couple of weeks ago about the clinical shift from culturing microorganisms to rapid diagnosis that removes the need to grow the disease-causing critter is very important (boldface mine): To get diagnoses … Continue reading →

Posted in CDC, Genomics, Microbiology, Public Health | 1 Comment

The Phrase That Makes Bioinformaticians Grind Their Teeth: Another Short-Read Genome Assembler

Posted on April 21, 2014 by mikethemadbiologist

Michael Barton laments the state of bioinformatics software: Grants are harder and harder to obtain, yet we fund the current attrition of moving bioinformatics software forward one reinvention at a time. Where else is it acceptable to reinvent a tool … Continue reading →

Posted in Bioinformatics, Genomics | Comments Off on The Phrase That Makes Bioinformaticians Grind Their Teeth: Another Short-Read Genome Assembler

Forget Genomics, Just Do the Genetics That We Know How to Do: The Rape Kit Edition

Posted on March 19, 2014 by mikethemadbiologist

As genomics becomes cheaper and more accessible, the torrent of articles debating and discussing its effects on human health will only increase. My contribution to this genre is to argue that microbial genomics is also critical, and, in the short … Continue reading →

Posted in Funding, Genetics, Genomics, Rape | Comments Off on Forget Genomics, Just Do the Genetics That We Know How to Do: The Rape Kit Edition

There Is a Microbial Genomics Market and It Is Not a ‘Niche’

Posted on March 11, 2014 by mikethemadbiologist

Or it shoudn’t be. Last week, a good article summarizing the status of Pacific Biosciences (‘PacBio’) made the rounds in science/genomics bloggysphere–this is a pretty good summary of what PacBio can currently do (boldface mine): Turns out, PacBio didn’t die. … Continue reading →

Posted in Genomics | 1 Comment

Sequencing Has Always Been Undemocratic

Posted on January 30, 2014 by mikethemadbiologist

We just never realized it, thanks to hidden subsidies. Mick Watson asks: It seems such a long time ago (in reality: 5 years) that many people hailed next-generation sequencing as the “democratization” of sequencing. The heart of the idea was … Continue reading →

Posted in Genomics | 1 Comment

Some (Hopefully) Final Thoughts on 23andMe

Posted on December 2, 2013 by mikethemadbiologist

Because the third time is a charm, here are some additional thoughts on the 23andMe story (my first two takes are here and here; David Dobbs has a comprehensive roundup here): 1) If we all had read the relevant literature … Continue reading →

Posted in Bidness, Genomics | 2 Comments

Translating Basic Research Tools Into Diagnostics

Posted on November 28, 2013 by mikethemadbiologist

Because we like to snark around here, let’s snark first: Some of the same people who react with horror when parents, who know they’re being irresponsible, still demand an antibiotic to treat a childhood ear infection are the same people … Continue reading →

Posted in Genomics, Public Health | 1 Comment

23andMe Needs Better Fan Boys

Posted on November 27, 2013 by mikethemadbiologist

Because they’re just not getting it (boldface mine): We, the healthcare consumers of America, demand that we maintain access to genomics testing services like 23andMe’s, which serve as a 100% privately purchased complement to government-regulated healthcare. The FDA grossly overstates … Continue reading →

Posted in Fucking Morons, Genomics | Comments Off on 23andMe Needs Better Fan Boys