AdamArkin_Lab

Tweets from Adam Arkin's Lab @UCBerkeley @LBNLBioSci. represent personal views only.

[Vivek Mutalik @vivek_mutalik]

🔔 New Preprint 🎉 from https://t.co/22jmPoaXR8
🥳 Super excited to share our work on generating systematic 95 phage-99 MDR P. aeruginosa strain interaction dataset & use of ML to predict phage susceptibility & phage cocktails from target genome sequences alone, w validations.

[Vivek Mutalik @vivek_mutalik]

🥳 Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by
@LucasMoriniere We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something crazy!

[AdamArkin_Lab @AdamArkinLab]

This is the first of a powerful set of work from this amazing team! I am extremely grateful to work with these amazing young scientists-@AveryNoonan and @LucasMoriniere, my long time colleague and friend @vivek_mutalik and the EDGE and Phage Foundry teams. This group is on fire.

[Vivek Mutalik @vivek_mutalik]

Posting here after a year to share:
📣 New preprint from https://t.co/tVwZIrsnTc team 📣🎊🎉

We developed a solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone.

https://t.co/k1mRum70FP

[AdamArkin_Lab @AdamArkinLab]

@victornizet @f_askarian @ARPA_H Also, big props to @kelseyehern and @j_hilzinger who have been critical in building this on the Berkeley side! Kelsey is now at Northwestern and will continue with the project. Also, it going to be fun to work with the brilliant Karsten Zengler at UCSD on this!

[AdamArkin_Lab @AdamArkinLab]

@victornizet @f_askarian @ARPA_H I am really looking forward to working with you all! What an opportunity! The Berkeley announcement is here: https://t.co/w1rqQt5Z6t

[Aaron Berliner @aaronjberliner]

New article explores the intersection of biology and space exploration, highlighting fields like Astrobiology, Bioastronautics, and Space Bioprocess Engineering.
https://t.co/416ccq7u82

@AdamArkinLab @CharlesCockell

[PLOS Biology @PLOSBiology]

#Phages are key drivers of #MicrobialEvolution, but many #phage genes are poorly understood. @denish_piya @AdamArkinLab @vivek_mutalik &co use arrayed genome-wide #CRISPRi to map gene the essentiality landscape in the iconic coliphages λ & P1. #PLOSBiology https://t.co/JmAI9a8cmK

[Vivek Mutalik @vivek_mutalik]

If you are excited about gut microbiome, phages, & tools/tech to study their interactions, join/follow the awesome @_YHuang lab 🎊

[Chang Liu @chang_c_liu]

In this work, we bring OrthoRep’s mutation rate up to 10^-4 substitutions per base, allowing us to durably hypermutate and evolve chosen genes in vivo at 1-million times the genomic mutation rate of the host yeast cell. What does this afford? https://t.co/5Cgn39jpax

[José P. Faria @jplfaria]

Today we released ModelSEED v2 in KBase (https://t.co/278dNvr3YE). If you try the new tools any feedback is appreciated.

ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction https://t.co/hMKCfuLtKU

[AdamArkin_Lab @AdamArkinLab]

Thanks to Rob Ferl and Krysyn van Vliet for leading us! The NAS staff, the folk who briefed us and helped with the analysis of the large scale proposed studies, and the panel members were all an honor to work with-- and more importantly--fun!

[AdamArkin_Lab @AdamArkinLab]

It was great to work with the NAS team helping to thing of the next decade of biology of in space. Just released!

Thriving in Space: Decadal Survey for the Biological and Physical Sciences in Space

Explore the digital interactive summary: https://t.co/qBlRUomSS5

[AdamArkin_Lab @AdamArkinLab]

The full report is:
https://t.co/VYlEMuAwPR

For those of us interested in the bioengineering side check out "Bioregenerative Life Support Systems" (BLiSS) and "Manufacturing Materials and Processes for Sustainability in Space" (MATRICES)!

[Vivek Mutalik @vivek_mutalik]

First round of positions open💥. If interested, please apply.
Project Scientist (Phage Foundry) - https://t.co/kQBpfRS4vq
Postdoctoral Fellow (Phage Foundry) - https://t.co/2v3LfUQ22O
Research Associate (Phage Foundry) - https://t.co/Uq48M1YLJI

[AdamArkin_Lab @AdamArkinLab]

Come join the next generation of open and collaborative biological data science with me and a great team! https://t.co/b5ekqJQiYo

[AdamArkin_Lab @AdamArkinLab]

Seriously happy to have an excuse both to continue my long association with @vivek_mutalik, @DeutschbauerLab and @HansCarlson3 and these others that I have admired and can’t wait to learn from!

[Vivek Mutalik @vivek_mutalik]

A dream team really. 🎉 @simroux_virus @AdamArkinLab @DeutschbauerLab @bkoskella @HansCarlson3 @bradyfcress @mark_mimee @AAthalassophile @cmageeney & Drs Elisabeth, Snijders & Mukundan at @LBNLBioSci

[AdamArkin_Lab @AdamArkinLab]

@vivek_mutalik will explain I am sure.

[AdamArkin_Lab @AdamArkinLab]

Congrats @vivek_mutalik and the amazing BRaVe on our new phage foundry! Realization of a long held dream. https://t.co/L7rnDd3X3o

[Brady Cress @bradyfcress]

With an incredible cast of invited speakers @AdamArkinLab @LabSonnenburg @omalleylab @jennbrophy7 @Geneticdesigner @trentn @mark_mimee @ericmyces Venessa Ridaura (@gatesfoundation), Kara Nelson (@UCBerkeley), Seth Rakoff-Nahoum (@harvardmed), Zack Abbott (@ZBioticsCompany)!

[Vivek Mutalik @vivek_mutalik]

A fast comparative genome browser for diverse bacteria and archaea

https://t.co/f3bI7hk1SE

Super cool work from Morgan Price ⁦@LBNLBioSci⁩ ⁦⁦⁦@AdamArkinLab⁩ https://t.co/39JAW6QTJg