linkstream2 microblog

http://www.40tech.com/2015/03/17/3-notetaking-apps-used-together/

http://mobile.nytimes.com/2015/05/16/opinion/joe-nocera-the-greatest-generation-of-scientists.html?_r=1

http://www.the-scientist.com/?articles.view/articleNo/42950/title/Microbiome-Fingerprints/

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As microbiome signatures mature, law enforcement or intelligence agents could theoretically track people by looking for traces of them left in the microbes they shed. Mark Gerstein, who studies biomedical informatics at Yale University and was not involved in the new study, suggested, for instance, that one could imagine tracking a terrorist’s movements through caves using their microbiome signature.

Huttenhower and his colleagues were identifying individuals out of pools of just hundreds of project participants, however. It is currently unclear how well the algorithm will perform when applied to the general population, though the researchers estimate that their code could likely pick someone out from a group of 500 to 1,000. “I would expect that number to get bigger in the future as we get more data and better data and better coding strategies,” Huttenhower said.

But the work raises privacy concerns similar to those faced by scientists gather human genomic data. Microbiome researchers are already wary of the human genomic DNA that gets caught up in microbiome sequences, but it increasingly appears that the microbiome sequences themselves are quite personal.

In the genomics field, researchers have increasingly limited access to databases containing human genomic sequencing data. Researchers must apply to use these data. “People might increasingly want to put the microbiome data under the same type of protection that they put normal genomic variants under,” said Gerstein. “Your microbiome is associated with various disease risks and proclivities for X and Y. I don’t think it’s a completely neutral identification. It potentially says things about you.”

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Identifying personal microbiomes using metagenomic codes
http://www.pnas.org/content/early/2015/05/08/1423854112.abstract Pot. tracking & #privacy implications
http://www.the-scientist.com/?articles.view/articleNo/42950/title/Microbiome-Fingerprints

http://www.pnas.org/content/early/2015/05/08/1423854112.abstract

doi: 10.1073/pnas.1423854112

Identifying personal microbiomes using metagenomic codes

Eric A. Franzosa
Katherine Huang
James F. Meadow
Dirk Gevers
Katherine P. Lemond
Brendan J. M. Bohannanc
Curtis Huttenhower

http://yalecollege.yale.edu/academics/calendars/2015-2016-academic-calendar

Comparative #genomics reveals insights into avian…#evolution http://www.sciencemag.org/content/346/6215/1311 Less repeats & dups in birds; woodpecker, an exception

Science 12 December 2014:
Vol. 346 no. 6215 pp. 1311-1320
DOI: 10.1126/science.1251385

Comparative genomics reveals insights into avian genome evolution and adaptation

Guojie Zhang1,2,*,†,
Cai Li1,3,*,
….
Avian Genome Consortium§,
Erich D. Jarvis20,†,
M. Thomas P. Gilbert3,56,†,
Jun Wang1,55,57,58,59,†

Spalding Gray’s Catastrophe http://www.newyorker.com/magazine/2015/04/27/the-catastrophe-oliver-sacks What role did a head injury play in a brilliant writer’s decline & suicide

What role did the car crash and the damage to his frontal lobes play in his decline?

Characterization of #SVs w. single molecule & hybrid sequencing http://bioinformatics.oxfordjournals.org/content/30/24/3458.abstract Probabilistic read mapping, re-evaluating adjacencies

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We present MultiBreak-SV, an algorithm to detect structural variants
(SVs) from single molecule sequencing data, paired read sequencing
data, or a combination of sequencing data from different platforms.
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Scents of #Smell Rooted in Math
http://www.wsj.com/articles/scents-of-smell-rooted-in-math-1431079201 electrical spiking in #neurons simply (linearly) related to amount of odorant

http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg3931.html