Genomics

Mike the Mad Biologist

Category archives for Genomics

By way of Matthew Yglesias, we read that,over at National Review Online, Kevin Williamson claims progressives only care about science as a way to wage culture war (yes, coming from movement conservatives, that’s rich): There are lots of good reasons not to wonder what Rick Perry thinks about scientific questions, foremost amongst them that there…

Will the Cloud Save Genomics?

I’ve blogged before about some of the technical issues surrounding how we can handle the massive increase in the size of genomics datasets. There’s also a need to grapple with the

Update/clarification: I want to clarify something critical. This is not about picking on a researcher or a country. It very well could have happened in the U.S. or anywhere else. I, nor you the reader, have any idea about the internal constraints these groups experience, or what was communicated to government officials. To the extent…

I recently was in a conversation with a collaborator who isn’t in the genomics biz, and said collaborator remarked that there was a lot of online criticism of the quality of the genomic data that has been generated for the E. coli O104:H4 outbreak isolates. I’ve been following it very closely (not surprised by that,…

Regarding the German outbreak strain of E. coli, the data are fairly clear: it is an enteroaggregative E. coli (‘EAEC’) which has acquired antibiotic resistance genes and a Shiga-like toxin from an Shiga-toxinogenic E. coli (‘STEC’). EAEC are interesting–according to the European Food Safety Authority: EAEC have been implicated as a cause of persistent diarrhea…

After Friday’s post, I’ve held off on writing much about the German E. coli outbreak, often referred to by its serotype, O104:H4, or as HUSEC041 (HUS stands for hemolytic uremic syndrome). Having had the weekend to digest some of the ongoing analysis and news reports, here are some additional thoughts: 1) The multilocus sequence type…

…in Europe. I’ll get to that in a moment. You’ve probably heard of the E. coli outbreak sweeping through Germany and now other European countries that has caused over one thousand cases of hemolytic uremic syndrome (‘HUS’). What’s odd is that the initial reports are calling this a novel hybrid or some new strain of…

The Wall Street Journal reports an estimate of the economic impact of the Human Genome Project (italics mine): Of the $3.8 billion federal funding for the human-genome project, $2.8 billion originated at the U.S. National Institutes of Health, and the rest at the Department of Energy. That $3.8 billion, along with subsequent capital provided by…

Doug Natelson raises a good question about when data should be made publicly available: How much public funding triggers the need to make something publicly available? For example, suppose I used NSF funding to buy a coaxial cable for $5 as part of project A. Then, later on, I use that coax in project B,…

Nick Loman listed the fifty most sequenced bacterial genomes according to NCBI. A reader at Nick’s blog came up with an improved list–one that reflects the genomes for which we actually have data (depending on who is doing the sequencing, a project will be registered with NCBI, often months before any sequencing is done). Here’s…