Galaxy, one of my favorite bioinformatics websites now offers the conversion of existing history into a work flow. Obviously source data (by UCSC or Ensembl) may be produced in the same format but everything else can then be delegated to a workflow – just a set of instructions how to modify your data.
The authors put a question mark at the end of the above statement while I would not hesitate to put an exclamation mark there. Writing this as a comment to a new study in the IJE they summarize the evidence that the ‘epidemic’ of asthma in Western countries has begun to decline – as hygiene standards are not declining this might indicate the end of the hygiene hypothesis. (Show me more…)
Having a free copy of the Lancet at the moment, I found a nice book review about “Dissent over Descent” by Steven Rose.
[He] takes a pleasure, which in part I share, in puncturing the often hyperbolic claims of natural scientists to be unimpeachable purveyors of absolute truth (Show me more…)
The experts in the field will immediately notice what I am suggesting here – an improved GWA plot that does not take into account p values alone but also effect sizes. I was experimenting some time with smile plots but finally ended with this bubble plot. Bubble size for 0.5<OR>2 is set to a minimum while all other ORs get increasing bubbles (BTW use for OR<1 a 1/OR transformation beforehand). Chromosomal colors are from a self defined palette using the colorRampPalette function in R which makes it look like pointillism art. The real question: Did the previous GWA p value screening miss some important effects? For example the important dot at x=4 and y=4?
Three large studies on schizophrenia now all agree that rare structural variants (CNVs) have a causal role in disease causation – probably by affecting large regions at 1q21 and 15q11 that contain all some “neuro”-genes (Harvard, Decode, Seattle). There are two major points that let me wonder if these papers even mark a turning point in our understanding of genetic causes of human diseases that is largely influenced by the Chakravarti hypothesis of common disease and common variants (CDVC). The Seattle paper had the most clever comment on that
We propose an alternative model: that some mutations predisposing to schizophrenia are highly penetrant, individually rare, and of recent origin, even specific to single cases or families.
Originally coined by Linda Stone 2007 as a Harvard Business Review “Breakthrough Idea” this gets a rapidly expanding disease among scientists and journal editors. A New Atlantis essay has some more details on the Myth of multitasking (Show me more…)