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Especially in the 21st century, science is about finding new pathways and discoveries that also will advance our national interest, the United States' broader contribution to global progress, and personal well-being for each of us.
One of my favorite teachers liked to say that "half of education is reflection". This means that a huge part of learning is thinking about what you've encountered making sense of it, connecting with it, finding new pathways for exploration.
By comparing our methodology to the original enrichment method using both simulation data and real-world data, we demonstrate the efficacy of our method in finding new pathways from biological perspective.
First, finding new pathways in microbes or pinpointing proteins to create new antibiotics is difficult, in part because of what could be considered an embarrassment of possibilities with too many unknowns.
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Therefore, since pathways correspond to parts of PPI networks that are of relatively large diameters, the simple direct neighborhood approach is not appropriate for finding new pathway members, since it can only produce subgraphs of small diameters.
In contrast, our GDV-based method generates EDNRB network of diameter 9. Also, since GDVs are based on all up to 5-node graphlets hence covering parts of the PPI network of diameter < 9 around an SPR of interest, the GDV-based approach is more appropriate for finding new pathway members than the direct neighborhoods.
An alternative approach to finding new pathway members would be to consider simply an SPR and its direct neighbors as cluster members, since it has been shown that proteins that are closer in the network (i.e., direct neighbors) are more likely to be functionally similar (i.e., involved in a same biological process) than proteins that are further apart in the network [ 20].
Unlike other human trials carried out at Stanford, the Experimental Medicine Unit would focus not on testing a drug's dosing and effectiveness in Phase 1, 2 and 3 clinical trials, but on better understanding human biology – ideally finding new biological pathways, identifying molecules that could be targeted by drugs and providing initial study of new therapeutics and diagnostics in humans.
It may not only help to deliver the pharmaceuticals but also to assist in finding new signaling pathways that may help in diagnosis, assimilation of drugs, and its active functions in infectious tissues.
Regarding approaches to non-model organism transcriptomes, the algorithms applied and dataset selection are of the same importance as de novo assembling for finding new evolutionary events or pathways.
Therefore, completion of the human pathway requires either finding new genes or demonstrating that the pathway is fully functional without them.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com