same handle at other places sometimes re: yeast genetics, dumb cloning tricks, life in the shell, pipelines, methodz and liberation, 👍CFUs👎 colonizing
south bay CA biotech
Joined April 2011
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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
Pooled PPIseq: screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform biorxiv.org/cgi/content/shor… #biorxiv_sysbio
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!
"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."
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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
Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries
ift.tt/sIBVFiK
#biorxiv_synbio
And yall up and cancelled @mbeisen ? Wow. There's never a non-monetizable moment here on
The Platform....
@darachm@therealworld retweeted
Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries
ift.tt/sIBVFiK
#biorxiv_synbio
@darachm@therealworld retweeted
Nice to see this out!
link.springer.com/article/10…
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!
Do you use DNA barcodes to track lineages? Ever wondered how to design random barcodes and process sequencing data?
@_miloj, @s_venkataram and I have a new pre-print for you!
Best practices in designing, sequencing and identifying random DNA barcodes
ecoevorxiv.org/t58xw/
@darachm@therealworld retweeted
“If the strikers get their way I won’t be able to pay them all” is the classic gripe of middle management, exploited by business owners to pit natural allies against each other.
Really glad Needhi is articulating how the research system is structured with tiers of research workers having conflicting interests
PI solidarity with researchers is essential to flex power against unis and agencies (srsly)
What are PIs doing that also deserve solidarity?
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@darachm@therealworld retweeted
In the end, this argument is a distraction. If you object to some people getting paid more, well, object to that. But don't hide behind arguments saying "this would be impossible since they are supported on a grant". Those arguments are bogus .. 5/n
@darachm@therealworld retweeted
I mean, why not just go all in with this logic and cut everyone's salary in half? Then you could do much more on the grant. Should we do that? Or how about we pay everyone minimum wage? #ucstrike 3/n
@darachm@therealworld retweeted
Also, this is even more powerful than Twitter for stepping outside your bubble.
I'm just so excited for people to actually learn about the fediverse, *who's been quietly building it* over the years, and why 🥲✊✌️🏴
Until then, theyll be pulling hot takes out of their butts 🤣🤣🤣
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Which is fine! I'm just happy it's gonna be fine (except for centralized capitalized algo'd clout yall gonna have to give that up at the door, sorry #personalBrand 😂)
I don't know if exports are working from Twitter anymore, but I used "debirdify" a few days ago to pull put handles. fedifinder.glitch.me/ looks similar. It would probably be helpful to pull contacts so you can reconnect. Anyone lemme know if you want help
hey it's gonna be okay, it's okay that you hate change and hate the people building tools to serve the purposes of marginalized communities instead of ads. Disruption of business network sucks. But we take care of us, we're gonna build something better
autostraddle.com/mastodon-10…
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I don't know if exports are working from Twitter anymore, but I used "debirdify" a few days ago to pull put handles. fedifinder.glitch.me/ looks similar. It would probably be helpful to pull contacts so you can reconnect. Anyone lemme know if you want help
@darachm@therealworld retweeted
I don’t really get the OP. Yeah it sucks to start over (if you even have to-we don’t know for sure yet) but mastodon was created by queer and disabled people specifically to be a welcoming and safe place. Every group OP mentioned is able to join or make their own communities