@halper_1

SynBio PhD, Salis Lab Alumni

Joined October 2019
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  • Following73
  • Followers35
Very happy to announce the publication of Synthesis Success Calculator! Hearty congratulations to the fearless and amazing first author @halper_1! Paper: pubs.acs.org/doi/full/10.102…

Synthesis Success Calculator: Predicting the Rapid Synthesis of DNA Fragments with Machine Learning

Abstract. The synthesis and assembly of long DNA fragments has greatly accelerated synthetic biology and biotechnology research. However, long turnaround t

pubs.acs.org
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Sean Halper retweeted
Howard Salis@hsalis20 Mar 2020
Super Hat Tip to @bioalgorithmist who worked tirelessly on this massive design problem w/o much sleep. As always, thanks to @alexcampreis for help with conception, protocol dev, and schematics and to @SarthokR for cross-strain validation.
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Sean Halper retweeted
Howard Salis@hsalis20 Mar 2020
FOR IMMEDIATE RELEASE & USAGE: "A Massively Parallel COVID-19 Diagnostic Assay for Simultaneous Testing of 19200 Patient Samples" Protocol at docs.google.com/document/d/1…. Primers & Spike-in Controls at docs.google.com/spreadsheets…
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Sean Halper retweeted
EBRC@EngBioRC30 Jan 2020
Interested in designing your own Extra Long sgRNA arrays? Check out their ELSA calculator here: salislab.net/software/design… @hsalis Lab and @DeNovoDNA Have a great #ResearchThuRsday and please reach out if you'd like to get featured yourself!
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Sean Halper retweeted
Howard Salis@hsalis30 Jan 2020
Hat tip to @alexcampreis @halper_1 @grace_vezeau @DanielCetnar @bioalgorithmist @phillip_clauer for their great work!
EBRC@EngBioRC30 Jan 2020
The @hsalis Lab at @Penn_State showed that simultaneous and stable coexpression of up to 28 single-guide RNAs can regulate 20+ genes w #CRISPR interference! Potential for reprogramming cells in many #SynBio #EngBio applications. nature.com/articles/s41587-0… @NatureBiotech
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Replying to @NatureBiotech @PennStateChE @PennStateBME @BioinformPSU @hsalis @alexcampreis @halper_1 @grace_vezeau @DanielCetnar @bioalgorithmist
Science behind the scenes: Multiplexed CRISPR and sgRNA arrays with the @hsalis Lab #NBTintheNews via @NikoMcCarty @PLOSSynbio blogs.plos.org/synbio/2019/1…
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Replying to @NikoMcCarty
@NikoMcCarty just published a nice behind the scenes interview of my colleagues @alexcampreis, @halper_1 and my boss @hsalis on our recent ELSA paper. blogs.plos.org/synbio/2019/1…
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The November issue is live nature.com/nbt/volumes/37/is…
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Replying to @NatureBiotech @PennStateChE @PennStateBME @BioinformPSU @hsalis @alexcampreis @halper_1 @grace_vezeau @DanielCetnar @bioalgorithmist
Co-authors @alexcampreis, @halper_1 & @hsalis go #behindthepaper to show how adding many-site targeting to CRISPR will have profound biotech implications go.nature.com/2IvU3YI
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Open access link to the ❄️ELSA❄️ paper for anyone stuck behind the paywall: nature.com/articles/s41587-0…
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Sean Halper retweeted
Howard Salis@hsalis9 Oct 2019
Our work on Extra Long sgRNA Arrays (ELSAs) began during a free-wheeling graduate course. After designing several CRISPR-based circuits, we found many repetitive DNA sequences (a big #SynBio challenge). Learn more in this #NatureBiotech #BehindThePaper: bioengineeringcommunity.natu…
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My new startup leverages CRISPR-Cas gene editing technology and proprietary machine learning algorithms to develop super long pumpkins (spookier).
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Sean Halper retweeted
Setoh🍥@yxsetoh8 Oct 2019
This is a CRISPR-cas9 mediated deletion (IFNAR1). Done by my undergraduate student 🙌, in < 4 months 🙌, setting up everything from scratch 🙌, using resources from @zhangf @Addgene. Amazing sharing economy in research. Sorry, had to share this super proud supervisor moment.
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At a synthetic biology conference, a food truck handed out GMO papaya and yogurt samples to hundreds of attendees. “A lot of folks in our world aren’t using the term ‘GMO,’ and instead will say it’s something like ‘gene modification’ or ‘CRISPR’” cnbc.com/2019/10/03/synbiote…
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👀 youtu.be/WIIVh7H6nvI
Super useful for proteome and host engineering, its amazing how fast CRISPRi is moving #synbio
Howard Salis@hsalis7 Oct 2019
CRISPR is awesome, but if you stably co-express many sgRNAs, what could you do? You could: regulate many genes, edit many SNPs, redirect metabolism, & build cool circuits. Now introducing ELSAs to co-express 22 sgRNAs without introducing repetitive DNA. nature.com/articles/s41587-0…
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Sean Halper retweeted
Howard Salis@hsalis8 Oct 2019
In a nutshell: Pick your targeted genes (up to 20). A designed ELSA regulates them (repression shown). Fully non-repetitive sequences ==> easy to synthesize & assemble. Genetically stable & evolutionary robust, great for creating selective (growth-inhibiting) phenotypes.
Nature Biotechnology
@NatureBiotech8 Oct 2019
Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays go.nature.com/2IuqJSm
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Sean Halper retweeted
TonahNo@TonahN8 Oct 2019
Replying to @s_verkuijl
I read this. I think one of the most interesting things is that they show is that Cas9 quickly can become limiting in the formation of active RNPs when there are competing guides around. Something we have suspected but never proved.
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Congrats. Much anticipated. Relevant for those wanting to avoid repetitive DNA when multiplexing gRNAs in CRISPR gene drives.
Howard Salis@hsalis7 Oct 2019
CRISPR is awesome, but if you stably co-express many sgRNAs, what could you do? You could: regulate many genes, edit many SNPs, redirect metabolism, & build cool circuits. Now introducing ELSAs to co-express 22 sgRNAs without introducing repetitive DNA. nature.com/articles/s41587-0…
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If repetitive sequences are holding back your CRISPR d/Cas9, here is ELSA to the rescue. Very neat!! Congratulations @hsalis and team.
Howard Salis@hsalis7 Oct 2019
CRISPR is awesome, but if you stably co-express many sgRNAs, what could you do? You could: regulate many genes, edit many SNPs, redirect metabolism, & build cool circuits. Now introducing ELSAs to co-express 22 sgRNAs without introducing repetitive DNA. nature.com/articles/s41587-0…
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