Tag Archives: disease

Graphical display of outbreaks: Transmission trees

Let’s start with some examples from the literature, find out necessary elements, compare different versions and develop a R template for general use.

“Exploding Stars”

CDC Field Epidemiology Handbook, 2019, ISBN 9780190933692 p115


https://doi.org/10.1016/S0140-6736(20)30154-9 (2020)

“Clean Undeterministic”
“Clean Tree”


“Tree Addons”




“Simple ”



“star bus”






Leaflet.js – layer order, layer address and links

Leaflet is great for mapping in epidemiology with quick results of just cut & pasting a few lines. Problems do start, however, whenever running a more advanced project. It’s a pain, as plugins overwrite functions and basic css layouts. Or layers do not allow clickable links (as propation is being prohibited). Or geojson data that are rejected for whatever reason.
A showcase project, that had been planned for 2 days, took more than 1 week as the documentation is frequently unclear, incomplete and often hard to understand without any (jsfiddle) example. Numerous Google searches helped, as well as peaking into the sourcecode, while also other stack overflow posters have been very helpful. Continue reading Leaflet.js – layer order, layer address and links

The human disease network (no need to call it diseasome)

There was the 2077 Goh PNAS paper using that title. And it is a sound approach probably better than any division of chapters in Harrison’s Internal Medicine!

A network of disorders and disease genes linked by known disorder–gene associations offers a platform to explore in a single graph-theoretic framework all known phenotype and disease gene associations, indicating the common genetic origin of many diseases. Genes associated with similar disorders show both higher likelihood of physical interactions between their products and higher expression profiling similarity for their transcripts, supporting the existence of distinct disease-specific functional modules. We find that essential human genes are likely to encode hub proteins and are expressed widely in most tissues.

I found this on a slide at the recent vitamin D congress in London and was just interested to see, how often this paper has been cited. So far as I remember only the Barabasi update. And the result is impressing Continue reading The human disease network (no need to call it diseasome)

We are the model organisms

Genomeweb today reports Sidney Brenner (Nobel Prize winner 2002 and pioneer in the use of Caenorhabditis elegans as a model organism) speaking on a conference. These days he’s pushing a new model organism: humans.

“We don’t have to look for a model organism anymore,” Brenner said. “Because we are the model organisms.”