Evolutionary Biologist. Ancient epidemics. Genomic adaptation.
David Enard
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Some deep work by my former student Matthew Aguirre on what the properties of cis- and trans eQTLs can teach us about the structure of gene regulatory networks!
Deeply interesting comment on a paper on compensatory evolution following "host" adaptation to a selfish genetic element. Reminescent of our finding of compensatory protein stability evolution after ancient viral epidemics. #evolution www.nature.com/articles/s41...
It is unfortunate that this has to be reminded so much to reviewers at all steps: doing this things right or at least as well as possible IS in itself a strong innovation.
You know you have great collaborators when they bring your own enthusiasm back at times when it has been vacillating. You know who you are :).
A bad case of using a non official gene/protein name that makes it even worse by introducing ambiguity with another gene name. This makes curation efforts far more difficult:
pmc.ncbi.nlm.nih.gov/articles/PMC...
2/2) lastz requires to pre-softmask the genomes extensively which is itself very computationally costly, and since it is often a handful of problematic jobs, it seems more efficient to have lastz mask problematic repeats itself? @hillermich.bsky.social have you though about improving lastz?
1/2) #bioinformatics people interested in #genome alignment, has anyone tried to do "adaptive seeding throttling" where after a long run time a lastz job would go into an adaptive mode where it detects that a specific repeat is initiating too many seeds, which would trigger lastz to mask it?
