Month: February 2011
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Friday Fluff – February 18th, 2011
1) First, a post from the past: A History of Iran: Empire of the Mind. 2) Weird search query of the week: “pictures of a famous woman drinking alcohol.” 3) Comment of the week, in response to D.I.Y. population structure inference, part 1…
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Eurasia + Mozabites + Papuans
I’m in a hurry right now, and won’t be posting much this week. But, I thought I’d dump some of the ADMIXTURE runs I have. This is one with 80,000 markers, and Eurasian populations, Papuans and Mozabites. I removed the New World and Af…
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Real three dimensional PCA!
Sort of. Check out what Doug McDonald’s done with javascript. The HGDP populations in three dimensions.
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Culture differences matter (even within Islam)
I’ve been keeping track of events in the Arab world only from a distance. There’s been a lot of excitement on twitter and Facebook. Since I’m not an unalloyed enthusiast for democracy I’ve not joined in in the exultation. But I&…
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Evolutionary Genetics
Short comment: Enough mathematical formalism to be technically illuminating, but not so much as to be opaque to the non-specialist.
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Evolutionary Genetics
Short comment: Enough mathematical formalism to be technically illuminating, but not so much as to be opaque to the non-specialist.
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Who are those Houston Gujus?
The figure to the left is a three dimensional representation of principal components 1, 2, and 3, generated from a sample of Gujaratis from Houston, and Chinese from Denver. When these two populations are pooled together the Chinese form a very homogen…
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D.I.Y. population structure inference, part 1 of many
If you’ve been reading this weblog for a while you’ve seen many images like the one above. It comes from the 2008 paper Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. The data set is from the Human Genome D…
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A problem of aggregation of information
In a post below I regenerated the HGDP PCA plot you’ve probably seen around, except that I added my parents (and a few HapMap populations) into the plot. The PCA below was basically a visualization of the two largest independent dimensions of ge…
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Friday Fluff – February 11th, 2011
1) First, a post from the past: Adaptation might not be a spherical cow. 2) Weird search query of the week: “shemale escort bald.” I’m not making this up. The user who searched for this is a Wiener. 3) Comment of the week, in respo…
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“Inadvertent” incest detection?
Ruchira and Randall Parker point me to a new story about routine genomics screens detecting first degree incest: Beaudet wrote in the letter that “clinicians uncovering a likely incestuous relationship may be legally required to report it to chil…
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“Inadvertent” incest detection?
Ruchira and Randall Parker point me to a new story about routine genomics screens detecting first degree incest: Beaudet wrote in the letter that “clinicians uncovering a likely incestuous relationship may be legally required to report it to chil…
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D.I.Y. PCA
Long time readers know that I have a fixation on people not taking PCA too literally as something concrete. Tonight I finally merged the HGDP data set with some of the HapMap ones I’ve been playing with, and tacked my parents onto the sample. I…
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Swedes not so homogeneous?
Credit: David Shankbone The more and more I see fine-scale genomic analyses of population structure across the world the more and more I believe that the “stylized” models which were in vogue in the early 2000s which explained how the worl…
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Personal genomics around the web
Just some pointers. Dr. Daniel MacArthur has put up a guest post where I outline my own experience with personal genomics. Cool times that we live in. Also, Zack Ajmal has started posting higher K’s of HAP participants. He’s now in the second batch. My parents will be in the third. Lots of Tamils and…
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My genetic odyssey
I have a guest post at Genomes Unzipped, summarizing what I’ve found via ancestry analysis over the past 6 months with the results from 23andMe. It is in many ways a brief overview of the detailed posts which you’ve see in this space.
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Counting beans the proper way
Apropos of several of my recent posts, The New York Times has an interesting article up, Counting by Race Can Throw Off Some Numbers. Basically it outlines the difficulty of enumerating different racial and ethnic groups for different purposes in a mor…
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Inferring and visualizing patterns in genomic data
I’ve been playing around with ADMIXTURE and EIGENSOFT with the the HapMap data set along with a few friends & family merged into it. It is interesting to see how the intuitive inferences you make from ADMIXTURE bar plots differ somewhat from …