[[* My comment cached: "I'm quite saddened to hear of Warren's passing. People in my lab were very active users of his PyMOL program. It was one of the best programs for visualizing molecules and was a great help to our research." *]]

[[* Changes in environmental variables are not entirely random. In many cases, variation in one variable can convey substantial information about variation in another and therefore offer a certain level of predictability. In the ecology of mammalian gut, transition from outside into the oral cavity exposes E. coli to an immediate increase in temperature, and then followed by an impending drop in oxygen levels as the bacterium gets into the gastro-intestinal tract. It will certainly be beneficial if E. coli is able to use the immediate increases in temperature as a predictive signal of oxygen drop and prepare for the correct physiological response. In this paper, Tagkopoulos et.al. demonstrate in this system (at least indirectly), microorganisms are capable of learning these correlations and exploit them in order to anticipate vital changes in the environment. ... *]]

[[* The article describes a method for finding sequence motifs that could potentially explain expression measurements. In a typical scenario, we have the expression levels of all genes under a certain condition on the one hand, and the promoter sequences of the genes on the other hand. With these, the algorithm looks for motifs whose presence/absence in the promoter sequences have high mutual information with the expression levels. The algorithm starts with all possible 7-mers, and then iteratively degenerates some characters (to allow multiple choices) if the resulting motif has a higher mutual information with the expression levels. The method was applied to yeast, the malaria parasite Plasmodium falciparum, human, mouse, and other species. A lot of previously known motifs were obtained, and many novel ones were found. ... *]]

[[* This paper makes a nice illustration of genotype-phenotype association. The attempt to look for genes that are specifically associated with certain phenotype is not new, yet this work is a first systematic exploration of this topic, and indeed it shows that gene phylogenetic profiles strongly correlate with bacterial phenotypic traits and behaviors. In addition, genes are clustered according to their phylogenetic profiles with the purpose of identifying metabolic modules, and it provides promising candidates for further experiments. More specifically, a gene’s phylogenetic profile describes the gene’s distribution among different species. In this paper, 202 bacteria are classified according to their phenotypes, such as motile vs. non-motile bacteria, gram-negative vs. gram-positive bacteria, etc. ... *]]

[[* might be interesting to combine with pubmed *]]

[[* contains MSB lecture *]]

[[* nice ppt on mean shift *]]

University expands high performance computing resources

[[* appears one has to re-initialize the TC *]]

[[* %20 is a space in a URL -- e.g.

http://www.tvo.org/cfmx/tvoorg/theagenda/index.cfm?page_id=7&bpn=104107&ts=2009-10-21%2020:00:00.0

==>

http://www.tvo.org/cfmx/tvoorg/theagenda/index.cfm?page_id=7&bpn=104107&ts=2009-10-21%2020:00:00.0

*]]

[[* homo sap. physically around 200K years ago but no real cult. trans. from hunter gather to settlements 'till about 10K years ago *]]

[[* contains a nice mashup simulator *]]

[[* Nobel Prize Predictions *]]

[[* h1n1 at 3.2 kbytes v mydoom at 22 kbytes *]]

[[* Why doesn't oral antibiotic have a stronger effect ? *]]

[[* 192.168.1.1 with default passwd as admin *]]

[[* mind affecting drug related to subj. of panel *]]

[[* claim that new worm species use "green bombs" to evade predators but have never seen these predators *]]

Brent Zanke, Chairman and Chief Medical Officer

Greg Hines, President and CEO

James Pelot, Chief Financial Officer

Alan Coley, V.P. Regulatory Affairs

[[* somethings to remember... Dantzig inventor of simplex; the "shop genome"; microsoft researcher on "HIV & spam"; Track movements at conf by RFID badge; marketing terms: "barnacles and buckets"; Politics: cats v dog as proxy for how one will vote, dem. v. rep.; FPs in different contexts: terrorists, marketing, casinos; health monitoring at Intel Res.; Fistula in cow stomach for monitoring; how to get out of the bathroom w. a skimpy towel: Over head; Wife and husband on chemistry.com *]]

[[* Researchers think finger length reflects exposure to the hormone testosterone in the womb. *]]

[[* Discusses non identifiablility issue of sample but I don't agree! Sampling strategy.....Population differences in haplotype frequencies are important for discovering genes that are related to health and disease. For example, an association study can have false-positive results if haplotypes in chromosomal regions other than those with the causal alleles differ in frequency between individuals with the disease and healthy controls; this problem often occurs when different proportions of cases and controls have been recruited from different populations. In addition, populations that have experienced recent bottlenecks might have longer haplotype lengths, potentially making initial identification of associated chromosomal regions more efficient15. On the other hand, shorter haplotypes (as is often seen in African populations, reflecting their longer history) might allow finer identification of the causative regions. *]]

[[* ...most common variants individually or in combination confer relatively small increments in risk (1.1–1.5-fold) and explain only a small proportion of heritability—the portion of phenotypic variance in a population attributable to additive genetic factors ... Population genetic theory suggests an explanation for the paucity of variants explaining a large proportion of disease predisposition, in that decreased reproductive fitness should typically act to reduce the frequencies of high-risk variants... Much of the speculation about missing heritability ... has focused ... low minor allele frequency (MAF), defined here as roughly 0.5% < MAF < 5%, or of rare variants (MAF < 0.5%)... For example, 20 variants with risk allele frequency of 1% and allelic odds ratio (or probability of an event occurring divided by the probability of it not occurring, compared in people with versus without the risk allele) of three would account for most familial aggregation of type 2 diabetes. *]]

[[* PINK1 & PARK2 involved in same biochem. pathway and implicated in Parkinson's disease. Will need 10K or more individuals to get sufficient power for rare variants. ORMDL3 & GSML assoc. with asthma *]]

[[* For example, the donor has a family history of cardiovascular disease prompting us to consider potentially associated alleles. The HuRef donor is heterozygous for variants in the KL gene... It has previously been observed that these heterozygous alleles present a lower risk for coronary artery disease [75]. However, the donor is also homozygous for the 5A/5A in rs3025058 in the promoter of the matrix metalloproteinase-3 (MMP3) [76]. This genotype is associated with higher intra-arterial levels of stromelysin and has a higher risk of acute myocardial infarction….We have also been able to detect inconsistencies between detected genotypes in the donor's DNA and the expected phenotype based on the literature given the known phenotype of the HuRef donor. For example, the donor's LCT genotype should confer adult lactose tolerance according to published literature [81], but this does not match with the self-reported phenotype of the donor's lactose intolerance. *]]

[[* He found that, on average, there had been a panic every 8.6 years. As he read more, he began to suspect that 8.6 was a highly significant number. In the early seventies, Armstrong became a trader and dealer in gold, and began compiling forecasts about commodities and currencies, which he sent out to clients. Over time, forecasting became his business. He constructed what he called an Economic Confidence Model, which he relied on to predict an upturn in the price of commodities in the early days of 1977. It worked. Later, he realized that 8.6 years was exactly three thousand one hundred and forty-one days: 3,141, the number pi times a thousand.... 1.618 = converging ratio of numb. i and i-1 in fibo. series (1,2,3,5,8,13...). For the market, 3 peaks on the way up and 5 on the way down.... *]]

[[*
although GWAS have been "strikingly successful" in identifying sites of common genetic variation associated with complex diseases, the variants they have found - both individually and altogether - explain a small fraction of the overall genetic contribution to common disease risk. ..

If common variants are responsible for most genetic components of type 2 diabetes, height, and similar traits, then genetics will provide relatively little guidance about the biology of these conditions, because most genes are "height genes" or "type 2 diabetes genes."

Goldstein's negative tone is balanced by a buoyant review from Joel Hirschhorn ...Hirschhorn argues... GWAS have in fact contributed substantially to our understanding of disease mechanisms. Here he has two striking examples to back him up: the revelations of the involvement of the complement pathway in age-related macular degeneration (AMD), and of the autophagy and IL23 pathways in Crohn's disease.
*]]

[[* Published Genome-Wide Associations through 6/2009: 439 published GWA at p < 5 x 10-8 *]]

[[* Some single-gene diseases: Familial hypercholesterolemia, Huntington disease, Sickle cell anemia, Cystic fibrosis, Tay-Sachs disease, Phenylketonuria, Glycogen storage diseases, Duchenne muscular dystrophy (xlinked), Hemophilia (xlinked)*]]

[[* The e4 version of the APOE gene increases an individual's risk for developing late-onset Alzheimer disease. People who inherit one copy of the APOE e4 allele have an increased chance of developing the disease; those who inherit two copies of the allele are at even greater risk. The APOE e4 allele may also be associated with an earlier onset of memory loss and other symptoms.

It is not known how the APOE e4 allele is related to the risk of Alzheimer disease. However, researchers have found that this allele is associated with an increased number of protein clumps, called amyloid plaques, in the brain tissue of affected people. A buildup of toxic amyloid beta peptide and amyloid plaques may lead to the death of neurons and the progressive signs and symptoms of this disorder. *]]