@darachm@therealworld

same handle at other places sometimes
re: yeast genetics, dumb cloning tricks, life in the shell, pipelines, methodz and liberation, 👍CFUs👎 colonizing

[@darachm@therealworld @darachm]

@bwhite5290 @kenbwork "Trained on massive amounts of high-quality data"

[@darachm@therealworld @darachm]

Questions or comments? Please try the discussion options on the preprint so everyone can see it, and/or email me
Email on preep, also ppiseq AT-THE-DOMAIN-OF rhesis SEPARATED-BY-DOT com

[@darachm@therealworld @darachm]

Here's methods for pooled gen of PPI-screening split-tag yeast assay libraries
tldr; is gateway&gibson, then longread+Nextflow(w/ itermae), then select and shortread seq, fitness with FitSeq (fork) - a lotta PPI quants
Also: ~4x your yeast transforms with this one simple trick

[bioRxiv SysBio @biorxiv_sysbio]

Pooled PPIseq: screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform https://t.co/HEGq7whzi2 #biorxiv_sysbio

[@darachm@therealworld @darachm]

What do we find? Expressed in yeast, Nsp4 seems to stick to KDELR* - that could be part of mechanism for replication foci formation via retrograde, ORF7B seems to stick to taste-receptors 🤔, and many more.

Not complete screen, but methods ready for non-specialist applications!

[@darachm@therealworld @darachm]

"As our Arab and Muslim neighbors are beaten and silenced, we fear the atmosphere in Germany has become more dangerous—for Jews and Muslims alike—than at any time in the nation’s recent history. We condemn these acts committed in our names."

[@darachm@therealworld @darachm]

@mbeisen Overlay journal in your future?

ngl I am planning to submit something to PLoS One soon!

[@darachm@therealworld @darachm]

@gitlab @nextflow @SingularityApp And yall up and cancelled @mbeisen ? Wow. There's never a non-monetizable moment here on
The Platform....

[@darachm@therealworld @darachm]

Check it if you want a pipeline on @gitlab for doing de novo plasmid assembly of long-read data separated out by barcode. Yeah random-fragmentation works and you don't need to know the barcodes ahead of time (but that probably helps)

@nextflow + @SingularityApp

[bioRxiv Synthetic Biology @bioRxiv_synbio]

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries

https://t.co/VjJd0LPSHE
#biorxiv_synbio

[bioRxiv Synthetic Biology @bioRxiv_synbio]

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries

https://t.co/VjJd0LPSHE
#biorxiv_synbio

[@darachm@therealworld @darachm]

@iskander @myphysicsvoyage @bluesky take meee

[@darachm@therealworld @darachm]

@mossomest @markowenmartin Thanks for mention. I'd be down to help folks (students etc) work on standardizing a design, just for kicks. It's really cheap, basically a ministat (TM) with the IR LED & sensor setup

Probably start with a batch reactor, do the perturbations manually to show nutrient shifts

[@darachm@therealworld @darachm]

@skryazhi @_miloj @s_venkataram Also, I hope the community around the @varianteffects can engage with it. I think there's obviously a lot of methods/skills transfer, and they may have more niche applications to develop on top of and around the work

[@darachm@therealworld @darachm]

@skryazhi @_miloj @s_venkataram It looks really good. I haven't had a chance to go through it in detail, but y'all hit on pretty much everything, and I am looking forward to getting into it with a journal club next week. This is going to help a lotta people - good work!

[Sergey Kryazhimskiy 🇺🇦 @skryazhi]

Nice to see this out!

https://t.co/nGoFGiJ1uP

This was such an enjoyable collaboration with @_miloj and @s_venkataram. I learned so much in the process. Thank you guys!

Also thanks to @darachm for giving us valuable feedback on the preprint!

[@darachm@therealworld @darachm]

@kevinfolta @MIT @kesvelt And it's polio virus not polio

[@darachm@therealworld @darachm]

@kevinfolta @MIT @kesvelt 589 cases are vax derived. Esvelt point stands that virus genomes mutates a lot (to simplify), but this is not a sign of someone who is experienced or deeply familiar in what they are talking about.

[@darachm@therealworld @darachm]

@kevinfolta @MIT @kesvelt "perhaps the first biotechnology that will really spread on its own"

has he heard of myxoma virus

[@darachm@therealworld @darachm]

@kevinfolta @MIT @kesvelt Anyone who refers to recovering infectious virus as "the booting up process" is worth a bit of skepticism

[@darachm@therealworld @darachm]

@kevinfolta @MIT @kesvelt But hey good to interview some voices from outside of biotech

[@darachm@therealworld @darachm]

@kevinfolta @MIT @kesvelt So identifying and studying viruses is valuable because zoonotic spillover is the source of new viral threats, and yes a ranked order list is important for prioritizing limited research bucks, and yes you can get useful research done without it circulating in a pandemic