Pavel Pevzner is starting a MOOC on Bioinformatics in Coursera (https://www.coursera.org/course/bioinformatics) and 23 & me is starting a MOOC on genomics in udacity
(https://www.udacity.com/course/bio110).
The opposite of clique completion: #Network deconvolution.. to distinguish direct dependencies http://go.nature.com/dVzNwC via @taziovanni
Network deconvolution as a general method to distinguish direct dependencies in networks
Soheil Feizi, Daniel Marbach, Muriel Médard & Manolis Kellis
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2635.html
My thoughts:
Indirect relationships in a network can confound the inference of true direct relationships in a network. T, so this paper sought to develop a quantitative framework, termed network deconvolution (ND), to infer direct relationships and remove false positives in a network by quantifying and then removing indirect transitive relationship effects. The mathematical framework assumes that (1) an indirect relationship (edge) can be approximated as the product of its component direct edges and that (2) the observed edge weights are the sum of the direct and indirect edge weights – a linear dependency. The main application seems to be in mutual information (MI) and
correlation-based (COR) networks. They applied ND to various scenarios such as local network connectivity prediction (FFL
prediction), gene regulatory network prediction (in E. coli), prediction of interacting amino acids in protein structures (MI network) and coauthorship relationship network and found that (1) it can be used with various networks beyond just MI and COR (2) it can be used alone or more powerfully in combination with existing
methods/algorithms to improve predictions. In a sense it is the opposite of clique and module completion approaches (such as k-core).
From Mars.. adventures in women’s #publishing: Why many writing cheaply beats a few pricey articles. nyr.kr/1b2n9sW MT @peterjblack
VIZ:
Interesting discussion of the economics of web publishing: why it’s better to get lots of people to cheaply write articles than rely on a few well written but expensive pieces
From Mars: A young man’s adventures in women’s publishing.
http://www.newyorker.com/reporting/2013/09/23/130923fa_fact_widdicombe
QT:”
By the time it was sold to Turner, Bleacher Report was making tens of millions of dollars a year. Brian Morrissey, the editor of Digiday, recently explained how publishers like Bleacher Report have managed to succeed by “gaming the Internet ad system.” Advertising on the Web is cheap: Bleacher Report charges roughly fifty dollars for every thousand people who see their most expensive type of ad, a “homepage takeover.” Meanwhile, Sports Illustrated, whose circulation is three million, charges almost four hundred thousand dollars for a full-page color ad. But, Morrissey said, “You make up for low ad rates by producing as many page views as possible at low costs.” A
well-researched exposé, such as the one Sports Illustrated recently ran about N.C.A.A. violations by the Oklahoma State football team, may take many months of work from a highly paid reporter and editor. But, in the end, Morrissey said, “it yields the same revenue as a ‘25 Sexiest Female Athletes Who Can Kick Your Ass’ post, which costs, like, two hundred dollars.”
“