Category Archives: Genomics

Bacterial Whole Genome Sequencing And The Clinic: The Future Is Almost Here

I heard this talk almost a year ago*, so I’m glad this paper is finally out (I’ll translate into English below; boldface mine): The increasing prevalence of multidrug-resistant (MDR) bacteria is a serious global challenge. Here, we studied prospectively whether … Continue reading

Posted in Antibiotics, E. coli, Genomics, KPC, MRSA, NDM-1, Public Health | 1 Comment

Barriers To Data Sharing

I’ve made this point about the role of funders before, but Fiona Nelson is absolutely right (boldface mine): Genomics is a data science. The human genome is vast – 3 billion base pairs. To make any significant findings from the … Continue reading

Posted in Data Stuff, Funding, Genomics | Comments Off on Barriers To Data Sharing

Just As We’re Getting Good At Genomic Surveillance…

…we run into a problem. From Morbidity and Mortality Weekly Report (what you don’t read it? Loser. Boldface mine): To evaluate progress toward prevention of enteric and foodborne illnesses in the United States, the Foodborne Diseases Active Surveillance Network (FoodNet) … Continue reading

Posted in Genomics, Public Health | Comments Off on Just As We’re Getting Good At Genomic Surveillance…

Saturday Sermon: How To Avoid P-Hacking

Outsourced to Daniel MacArthur: A couple of years ago, it was discovered that two very prominent economists, who based on erroneous data (which was also not very robust), were telling governments that when debt reaches ninety percent of GDP (or … Continue reading

Posted in Economics, Genomics, Statistics | 4 Comments

Zika, Data Release, and the Tragedy of the Commons

This does not bode well for public health-related sharing (boldface mine): When researchers in Brazil posted four Zika virus genome sequences in the online repository GenBank on 26 January, they were complying with a call for scientists to openly release … Continue reading

Posted in Ethics, Genomics, Public Health | 1 Comment

A Potential Ethics Problem With Massive Genomic Screening

It’s the metadata. Thankfully, I’m not a bioethicist (just a Mad Biologist), so I won’t have my concerns ruled out immediately. But when I read about proposals like this one to sequence everyone’s genome on the planet, I have concerns–which … Continue reading

Posted in Ethics, Genomics | 5 Comments

An Alternative Hypothesis For Academic Obscurantism

Which is: they’re not writing for you. Noah Smith argues that difficult, if not impossible to penetrate, jargon-laden social science papers exist as a way to enforce artificial entry barriers (boldface mine): To many readers not steeped in critical theory, … Continue reading

Posted in Bullshit As a Load Bearing Structure, Education, Genomics | 8 Comments

Not Everyone Who Wants To Look At Genomic Data Is a Researcher

Well, this is disturbing (boldface mine): When companies like Ancestry.com and 23andMe first invited people to send in their DNA for genealogy tracing and medical diagnostic tests, privacy advocates warned about the creation of giant genetic databases that might one … Continue reading

Posted in Civil Liberties, Genomics | Comments Off on Not Everyone Who Wants To Look At Genomic Data Is a Researcher

NCBI To Rename Incorrect Genomes…

…microbiologists everywhere rejoice. I spent part of last week at the ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens, which for obvious reasons is also referred to as ASMNGS. Lots of good … Continue reading

Posted in Genomics, NIH, Speciation | 3 Comments

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

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)