About this time last year, I posted about a new course I was going to teach, Phage Genomics. Briefly: Phage isolation, electron microscopy, DNA sequencing in the first semester, annotation and comparative genomics in the second. And I get to teach the bioinformatics bit: annotation and comparative genomics. Woo-hoo! The great thing about this course, [...]
Here is a study that looked for a type of genes that the authors felt was neglected by classic genomic annotation. The research shows how to employed concepts in molecular evolution to validate the existence of these genes. Some background: the first question we ask after assembling a genome is: “where are the genes”? Not [...]
NSF grant funded, woohoo! Now I am hiring a programmer. So if you want to be part of a dynamic, growing lab, do lots of interesting stuff and upgrade yourself from just a great bioinformatician to a super-bioinformatician, this job’s for you. You’ll be working primarily on microbial genome evolution, including setting up a kick-butt [...]
Man is the only animal that laughs and weeps, for he is the only animal that is struck with the difference between what things are and what they ought to be. – William Hazlitt We like to think that we are the only species capable of emotional self-awareness and therefore the only “animal that laughs [...]
Genomics is a new and exciting programming language based on Brainfsck. Here are the commands: g Move pointer to the right. e Move pointer to the left. n Increment the cell at the pointer. o Decrement the cell at the pointer. m Jump forward past the matching i if the cell at the current pointer [...]
Springville University’s Genome Center in collaboration with Prof. I. M. A. Bigschotte from IvyLeague University have announced that the genome of Mr. John Smith from Centertown, USA has been sequenced and is now available online. Dr. James Williams, director of the Center said: “We were running out of things to sequence, but I still had [...]
So here are EssOh and OhOne assembling a rather frustrating puzzle containing cows. The same 5-6 cow “characters” are repeated, which is a perfect way to illustrate low-complexity DNA sequences, and why they are hard to assemble, especially when the pieces are small, like those you get from some second generation sequencers.
The Genome Center at University of California Davis and researchers at UC Santa Cruz are organizing a genome assembly competition which they call The Assemblathon. They have released two simulated genomes for competing groups to assemble as best they can. Assemblies are due February 6th, 2011. So there is still time, if you would like [...]
Nature Genetics seems to have taken a page from the Food Network Magazine by timing two publications to the annual obsession with festive foods among many, NG readership included. I am talking about the genomes of the Strawberry and of the Cocoa plants. Both are important crops, both are components of luxurious eating. Both papers are comprehensive [...]
The personal genomics company 23&me is hosting a poetry contest. The winner receives a free pass to the Personalized World Medicine Conference. Poems should include a bunch of keywords having to do with 23&me, personalized genomics and all that jazz. I’m no poet (and don’t you know it), so here is my Haiku non-entry: My genome was seq- [...]
cag·ey /ˈkājē/ (adjective) Reluctant to give information owing to caution or suspicion CAGI /ˈkājē/ (acronym) Critical Assessment of Genomic Interpretations. For details keep reading. The ability to sequence one’s genome adds a new dimension to the ancient maxim “know thyself”. What could be more revealing of one’s self than one’s own blueprint, explaining existing [...]
It isn’t junk DNA: God just commented out a lot of crappy code as he rolled out releases. – An old bioinformaticians’ joke (Hey, I never said it was a funny joke…) Why are some genomes so big? I mean, seriously. Why would the marbled lungfish with a genome weighing 132.83 picograms (pg) need an [...]
The trouble with genomic sequencing, is that it is too cheap. Anyone that has a bit of extra cash laying around, you can scrape the bugs off your windshield, sequence them, and write a paper. Seriously? Yes, seriously now: as we sequence more and more genomes, our annotation tools cannot keep up with them. It’s [...]
