Literature-search thoughts: can we not, as a community, come up with a better term than "evolutionary design principles" for bio systems? Natural selection lacks forward planning, so they're more like "frequently, accidentally reinvented wheels". Any ideas for an alternative?

I'm happy to have contributed to this one: Phosphorylation-Dependent Assembly of a 14-3-3 Mediated Signaling Complex During Red Blood Cell Invasion by Plasmodium falciparum Merozoites

"Few examples exist regarding the dispensability of signaling networks... Here, we show that signaling network function carries a fitness cost in yeast evolving in a constant environment." (2013)

Your daily dose of "intracellular protein signaling in Plasmodium parasites is weird": a usual cell cycle-related phosphatase is re-employed for post-replicative parasite egress

To clarify, I'm looking for a hierarchical data serialization format that is widely supported by prog. languages, is good for numeric data, but need not be optimized for size.

I just learned the hard way that NaN is not a valid value in JSON. What's the best, widely supported alternative hierarchical exchange format for small (~20kb) data? HDF5? msgpack? I guess my website is blocked by some web filters for "weapons". Like all my not-so-killer apps or maybe all those sick records I used to spin?
RT @ben11kehoe
@dataandme @joncfoo @brandoninvergo I can't decide whether to make a joke about how powerful a tool it must be, or one about footguns

Do you have transcriptomics data & want to understand a regulatory signalling network?
We present CARNIVAL, a method to integrate biological knowledge & transcriptomics to infer sample-specific causal networks -, & et. al

What's the best way to name a new bioinformatics method these days? Asking for a friend.

New preprint from our lab. PAMOGK: A Pathway Graph Kernel based Multi-Omics Clustering Approach for Discovering Cancer Patient Subgroups:

So, apparently protein phosphorylation on "non-canonical" (i.e. not S/T/Y) amino acids is far more common in vertebrates than usually appreciated. This opens things up...

🚨JOB ALERT🚨We're recruiting up to two Research Fellows! Join our interdisciplinary research team, we use quantitative techniques to address important biological, biomedical and clinical research questions. Deadline for applications 18 Nov

Scientific knowledge is drowning in a flood of research - a great comic-metaphor about how has changed along the years, from few meticulously thought projects to a frency of data collection and obession on quantity over quality... vía

Our article about phenotypic effects of variants in TRIM21 is now online: For 22 1000G variants, we tested their effect on protein stability, ligand binding, viral neutralization, innate immune signaling and protein expression.

I have two questions for experimental biologists working on protein kinases:

1) How likely is it that a 'kinase-dead' mutant will still have residual catalytic activity?

2) Why is it that the K72 mutant (PKA numbering) has been used more often historically than D166? Thanks

Whoever programmed the elevators at work made an off-by-one error for the floor announcements.

I'm beginning to think that I don't want to be on a topic-specific Mastodon instance. No complaints about this server; I just don't want to think about which posts are on-topic and which are off-topic.

Any suggestions?

After years of temptation, my other keyboard broke and I finally gave in...

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