linkstream2 microblog

VIRGO: computational prediction of gene function http://nar.oxfordjournals.org/content/34/suppl_2/W340.full Webserver propagates GO terms over PPI & gene-expression #networks

This work was said to be the first web server for gene function
annotation (not the first algorithm).
The idea is to predict gene functions from known molecular interaction
networks (such as PPI), which includes both annotated and unannotated
genes. The potential function of an unannotated gene is predicted
using a propagation diagram, which takes into account the neighbors’
functions. The weight of edge in the network is determined by user uploaded expression data. Weight = |Pearson correlation| of expression
profiles of the gene pair. Weight reflects the confidence of the edge.

[tag jobs,startedreading,jobs0mg,itunes0mg]

http://www.amazon.com/Steve-Jobs-Walter-Isaacson/dp/1442369051

Can #AIDS Be Cured? http://www.newyorker.com/magazine/2014/12/22/can-aids-cured Now a chronic disease, treatable w/ HAART cocktails? Parallels w/ cancer evolution & resistance

MEDICAL DISPATCH DECEMBER 22, 2014 ISSUE
CAN AIDS BE CURED?
Researchers get closer to outwitting a killer.
BY JEROME GROOPMAN

Weird wet worlds…Earth is lucky to have oceans http://www.newscientist.com/article/mg22429930.600 Surface ones absent in solar system, except for Titan’s hydrocarbons

Titan has 2 oceans, one under another

Major Discovery About #Prime Numbers
http://www.wired.com/2014/12/mathematicians-make-major-discovery-prime-numbers Extension of trick to find spans of composites, eg start w/ 101! add 2,3,4…101

QT:{{”
The two new proofs of Erdős’ conjecture are both based on a simple way to construct large prime gaps. A large prime gap is the same thing as a long list of non-prime, or “composite,” numbers between two prime numbers. Here’s one easy way to construct a list of, say, 100 composite numbers in a row: Start with the numbers 2, 3, 4, … , 101, and add to each of these the number 101 factorial (the product of the first 101 numbers, written 101!). The list then becomes 101! + 2, 101! + 3, 101! + 4, … , 101! + 101. Since 101! is divisible by all the numbers from 2 to 101, each of the numbers in the new list is composite: 101! + 2 is divisible by 2, 101! + 3 is divisible by 3, and so on. “All the proofs about large prime gaps use only slight variations on this high school construction,” said James Maynard of Oxford, who wrote the second of the two papers.
“}}

http://en.m.wikipedia.org/wiki/Mona_Simpson

https://www.quantamagazine.org/20141218-machine-intelligence-cracks-genetic-controls/

http://www.designntrend.com/articles/32141/20141223/ai-teams-up-genomics-find-disease-causing-mutations.htm

Sensitive detection of pathway perturbations in #cancers
http://www.biomedcentral.com/1471-2105/13/S3/S9/abstract Differential expression of #pathways (in toto or a sub-part)

** Sensitive detection of pathway perturbations in cancers. Rivera et al. BMC Bioinfo (2014)

In this paper, the authors introduce a new computational method that identifies subsets of pathways that exhibit differential gene expression between cancer and normal tissue. Some previous methods only considered differential expression in sets of genes without considering the structure of interactions between the genes or their protein products. Other previous methods looked at pathway
perturbations, but required all members of a pathway to exhibit differential gene expression in order for the pathway to appear significant. The authors demonstrate the general superiority of their method to these previous methods, as well as the robustness of their method to missing data. The authors also consider future enhancements, such as taking into account the direction of differential expression, using more information on the nature of each gene interaction involved, and using universal protein interaction networks to incorporate data beyond what is found in curated pathway databases.

http://mashable.com/2014/10/29/private-internet-tools/