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Links 1 through 10 of 255 Steve Mount's Bookmarks

This looks like an incredibly useful resource. I have been teaching a "flipped" class in advanced genetics for three years now. I will of course want to review the videos before assigning them (it's amazing how many get important things wrong), but this list is a wonderful resource.

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"as the FDA frets about the accuracy of 23andMe’s tests, it is missing their true function, and consequently the agency has no clue about the real dangers they pose. The Personal Genome Service isn’t primarily intended to be a medical device. It is a mechanism meant to be a front end for a massive information-gathering operation against an unwitting public."

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"Scientists are discovering that — to a surprising degree — we contain genetic multitudes. Not long ago, researchers had thought it was rare for the cells in a single healthy person to differ genetically in a significant way. But scientists are finding that it’s quite common for an individual to have multiple genomes. Some people, for example, have groups of cells with mutations that are not found in the rest of the body. Some have genomes that came from other people." True chimerism (the fusion of what would have been identical twins) is probably still rare, but chimerism with a child's cells after pregnancy appears much more common than thought, and mosaicism due to somatic mutation (other than cancer, which is well-known) also appears common.

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Eduardo Eyras and coauthors taxonomy of methods for studying splicing from RNAseq data.

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Jim Hendler recommends these things when teaching programming: Share code, present code, critique, reuse and teach re-use, work in teams, set up a code library.

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There is a pattern of SNPs in aboriginal Australians that is not found in people from New Guinea or the Philippines. But it is found in some Indians—particularly in Dravidian speakers from the southern part of the subcontinent. That discovery both meshes with the Y-chromosome data and enriches it, because the pattern of the SNP data meant that she and her colleagues could calculate when the Indian genes (and thus the Indians who carried them) arrived in Australia.

The answer is 141 generations ago. Allowing 30 years a generation, that yields a date of 2217BC. Obviously, this is not a precise date. But it is probably good to within a century or two. And that is interesting for two reasons. One is that the 23rd century BC is slap-bang in the middle of the period when Indian civilisation was emerging. The other is that it coincides with a shift in both the culture of Australia and the composition of the continent’s wildlife.

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A summary of terminal shortcuts from someone just beginning bioinformatics. It is very useful to have this all in one place.
I am reminded of a student telling a TA at the CSH Programming for Biology course "you guys can type so fast!!" Here's how (it's not really typing).
Ctrl+a goes to the start of the command line
Ctrl+e move to the end of the command line
Ctrl+w delete the word before the cursor
...

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NPR has a nice, brief, summary of the year's research on Alzheimer's. Although a promising drug failed, the discovery of a protective variant, and evidence for very early changes that can be detected, are real breakthroughs.

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