Getting an accurate genome sequence requires that you collect the data at least twice argue Robasky, Lewis, and Church in their recent opinion piece in Nat. Rev. Genetics [1]. The DNA sequencing world kicked off 2014 with an audacious start. Andrew Pollack ran an article in the New York Times ...
It's a Solexa data directory. I've held off on blogging about Next Generation Sequencing here, but now that one of my colleagues has started blogging about it, it seems like a good time to write a little about FinchTalk, our company blog. We've decided that we can serve an educational ...
Last spring, I gave my first hands-on workshop in working with Next Generation Sequencing data at the Eighth Annual UT-ORNL-KBRIN Bioinformatics Summit at Fall Creek Falls State Park in Tennessee. The p roceedings from that conference are now on-line at BMC Bioinformatics and it's fun to look back and reflect ...
In our series on why $1000 genomes cost $2000, I raised the issue that the $1000 genome is a value based on simplistic calculations that do not account for the costs of confirming the results. Next, I discussed how errors are a natural occurrence of the many processing steps required ...
For the past few days I've been avidly following Daniel MacArthur's tweets from the Personal Genome Conference at Cold Spring Harbor( @dgmacarthur #cshlpg). The Personal Genomics tweets aren't just interesting because of the science, they're interesting because MacArthur and others have started to take on the conventional dogma in genetic ...
In simple Mendelian genetics, a single change in one gene can produce a large change in mortality. The National Human Genome Research Institute (NHGRI) will be funding genomics studies on Mendelian traits using a similar strategy. NHGRI will fund a small number of centers, dominant centers you might say, and ...
Cofactor Genomics is offering to sequence a genome for a few classes for free using Next Generation DNA Sequencing technology (either Illumina GA or via AB SOLiD). Quoting from their site: Cofactor will ask course organizers for a 1 page description of how their ~700Mb sequencing project could be used ...
These days, DNA sequencing happens in one of three ways. In the early days of DNA sequencing (like the 80's), labs prepared their own samples, sequenced those samples, and analyzed their results. Some labs still do this. Then, in the 90's, genome centers came along. Genome centers are like giant ...
You might think the coolest thing about the Next Generation DNA Sequencing technologies is that we can use them to sequence long-dead mammoths, entire populations of microbes, or bits of bone from Neanderthals. But you would be wrong. Sure, those are all cool things to do, but Next Generation DNA ...
I had the good fortune on Thursday to hear a fascinating talk on deep transcriptome analysis by Chris Mason, Assistant Professor, at the Institute for Computational Biomedicine at Cornell University. Several intriguing observations were presented during the talk. I'll present the key points first and then discuss the data. These ...
Watching the chIPs roll in, then I watch them roll away again, I'm just sitting on the DNA, wasting time (sung to the tune of "Sitting on the dock of the bay" by Otis Redding) Hesselberth et.al. recently published a paper about digital genomic footprinting that blew me away because ...
A couple of years ago, I answered a reader's question about the cost of genome sequencing. One of my readers had asked why the cost of sequencing a human genome was so high. At that time, I used some of the prices advertised by core labs on the web and ...
Scale, proportion, and quantity belong to one of the cross cutting concepts in the next generation science standards (NGSS). According to Volume 2 of the NGSS, "in engineering, no structure could be conceived much less constructed without the engineer's precise sense of scale." The authors go on to note that ...
One of my favorite web 2.0 technologies is the webinar. When you work at a company and not a University, with constant seminars, it gets a bit harder to hop on a bus and travel across town to learn about new things. Webinars are a good way to fill that ...
For the past few months, the shake-up that began with Next Generation DNA Sequencing has been forcing me to adjust to a whole new view of things going on inside of a cell. We've been learning things these past two years that are completely changing our understanding of the genome ...
