Genomics

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Category archives for Genomics

A couple of years ago, there was talk in the bioblogosphere about getting the general public interested in bioinformatics and molecular evolution: Amateur bioinformatics? Lowering the Ivory Tower with Molecular Evolution Molecular Evolution for the Masses The idea was inspired by the findings of armchair astronomers — people who have no professional training, but make…

Do people still use microarrays?

Larry Moran points to a couple of posts critical of microarrays (The Problem with Microarrays): Why microarray study conclusions are so often wrong Three reasons to distrust microarray results Microarrays are small chips that are covered with short stretches of single stranded DNA. People hybridize DNA from some source to the microarray, which lights up…

Genome Sequenced, Published via Press Release

Back in the day, you could sequence a genome and get a Nature paper out of it. Pretty soon, the sexiness of genome sequencing wore off, and it took a bit more to get into a vanity journal. You had to sequence something cute and cuddly, something extinct, or a lot of genomes at once.…

Adaptationist Junk

The human genome (like all mammalian genomes) is loaded with sequences that don’t perform any known function. And many of these sequences are junk. And it’s not just mammals — many animal genomes are loaded with junk, as are those of other eukaryotes. That’s not to say that some of the sequences of unknown function…

Synteny — A Semantic Debate

There’s a post up at Pharyngula describing the concept of synteny in comparative genomics (Basics: Synteny). The definition given by PZ Myers will sound pretty familiar to those of you who have read some of the genomics literature. The problem: it’s not quite correct. It’s actually the definition that I think most comparative genomics folks…

Good-bye Frank!

Francis Collins, head of the National Human Genome Research Institute (NHGRI), will be stepping down from that position in August. Collins has overseen the sequencing of the human genome, the HapMap project, the ENCODE project, and many other large advances in genomics. The NHGRI has had a major impact in the field of genetics while…

Watson’s Genome

Last year, Craig Venter became the first single person to have his genome sequence published (doi:10.1371/journal.pbio.0050254). That genome was sequenced using the old-school Sanger technique. It marked the second time the complete human genome had been published (which led to some discussion as to whether the publication deserved to be published in a high profile…

Evidence that Men Think With Their Junk

Us dudes are always accused of thinking with our dicks. Perhaps it’s because the genes expressed in our brains are similar to those expressed in our ‘nads: Among the 17 tissues, the highest similarity in gene expression patterns was between human brain and testis, based on DDD and clustering analysis. Genes contributing to the similarity…

As I have mentioned before, de novo sequencing of whole eukaryotic genomes may be a thing of the past (or, at least, these whole genome projects won’t be getting very much more common). Instead, I proposed that people would use the new high-throughput technologies to sequence parts of the genome they found interesting. What did…

The Next Generation Sequencing blog has a post on low coverage of A/T regions with Solexa sequencing. The post is in reference to a paper in Nature Methods on genome resequencing in C. elegans (doi:10.1038/nmeth.1179). Here’s how the NextGen Sequencing blog summarizes it: However, it points to a general lack of coverage in A/T rich…