Adam Smiley

BMBB PhD candidate at UMN in @WRgordonlab | @AndyArsham lab alumnus

[Alex Rives @alexrives]

We have trained ESM3 and we're excited to introduce EvolutionaryScale.

ESM3 is a generative language model for programming biology. In experiments, we found ESM3 can simulate 500M years of evolution to generate new fluorescent proteins.

Read more: https://t.co/iAC3lkj0iV

[Sergey Ovchinnikov @sokrypton]

Now everyone customize/share protein language models for their custom task/dataset via
@GoogleColab 🤓

Paper: https://t.co/In0PNg9avy

Colab: https://t.co/qqdlYRw1cS

Credit: @LTEnjoy, Zhikai Li, @ChenchenHa42849, @BonnieSwt, Junjie Shan, @XibinBayesZhou, Dacheng Ma, @duguyuan

[bioRxiv Synthetic Biology @bioRxiv_synbio]

A Genetically Encoded System to Quantify and Evolve RuBisCO-Catalyzed Carbon Fixation

https://t.co/0A8tDRoGjF
#biorxiv_synbio

[Artem Nemudryi, PhD @artemnemudryi]

Cellular repair of DNA breaks enables editing of the human genome.

Do human cells repair RNA breaks, and can we use it to edit transcriptomes?

Our work with @ANemudraia and @WiedenheftLab is now online in @ScienceMagazine!

#ScienceResearch

https://t.co/L5qKw1tYrl

[Jeff Ruffolo @jeffruffolo]

One of the first projects we took on at @ProfluentBio was designing novel gene editing proteins with language models. This grew into an initiative called OpenCRISPR, and today I’m excited to share that work (including the sequences we designed)!

https://t.co/4afhk4vT6B

[Tominaga K. (tomiken) @pacyc1841]

Phage defence system CBASS is regulated by a prokaryotic E2 enzyme that imitates the ubiquitin pathway | Nature Microbiology https://t.co/jw1qVvQrOq

[Building Better Bugs @Smanski_Lab]

AmberBio is hiring: https://t.co/iDpCSnEpVf. I highly recommend looking into it if you want to work at a fast-moving startup with a creative and impactful technology. @themicrobeguy

[Joseph E. Peters @JoePetersLab]

It was a pleasure working with @PopoMicro on this review of CRISPR-Cas associated transposons (CAST). Hopefully it gives a sense for the diversity of Tn7-like transposons and CRISPR systems that independently combined.https://t.co/Aq8lz2HG3O

[Adam Smiley @AdamSmiley17]

@TLan_OChemLover Congrats, Tian! Very well deserved.

[Anthony Gitter @anthonygitter]

Our manuscript "Biophysics-based protein language models for protein engineering" with @romerolab1 is now on bioRxiv. We present Mutational Effect Transfer Learning (METL), a protein language model trained on biophysical simulations, and showcase it for protein engineering. 1/

[bioRxiv @biorxivpreprint]

HUHgle: An Interactive Substrate Design Tool for Covalent Protein-ssDNA Labeling Using HUH-tags https://t.co/fPbhoO8PpU #bioRxiv

[Manuel Ares Arroyo @M_AresArroyo]

New preprint alert! 🚨

Our latest work on plasmid mobility with @epcrocha & @NucciAmandine is now available.

Identification of novel origins of transfer across bacterial plasmids.

Read the full paper here:
https://t.co/Ww8KuXyNZf

Thread🧵below!

[Seth Shipman @seth_shipman]

New Preprint, New Retrons! More than a hundred of them. We synthesized a ton of bioinformatically predicted retrons and put them through a battery of tests, from RT-DNA production to editing in human cells, E. coli, and phage https://t.co/6j08tzIkoD @GladstoneInst @UCSF @UCSF_BTS

[Rongzhen Tian @RZTian_Alvin]

Excited to share - EcORep! Now you can simply electroporate a PCR product into E. coli and let the linear DNA replicate orthogonally in the cell. EcORep can be used to evolve proteins rapidly and continuously! https://t.co/jzIRnci3Jf

[Matt Durrant @mgdurrant]

What if you could recombine any two DNA sequences in a programmable manner? We discovered an RNA-guided recombinase that can do just that! So happy to have co-led this project with @ntperry13

[Garton Lab @GartonLab]

Check out our new generative AI tool for gene therapy published in Nature Machine Intelligence!
Work conducted by the fantastic Suyue Lyu and @shahin_s_h

https://t.co/z8hhVb6PL6

[Phil Holliger @PhilHolliger]

New paper out from my group https://t.co/Nd2wf2mQPn. CryoEM structure of the triplet polymerase ribozyme apoenzyme, with improved resolution from https://t.co/KsivdCigd5. Great collaboration with @mcrae_ewan and @esandersen

[Jeff Martell @JeffChem]

Enzymes are promising catalysts for eco-friendly plastic recycling, but how can we make them faster? We developed a method to screen millions of enzyme mutants for enhanced plastic degradation! @J_A_C_S
1/n
https://t.co/QQOSTfSLPR

[Adam Smiley @AdamSmiley17]

@mikejmander @WRgordonlab The one on the top left is excellent.

[Delip Rao @ COLM26 @deliprao]

NEWS: Apple just entered the AI open source arena by quietly releasing their new DL framework called MLX! It runs code natively on Apple Silicon with a single pip install and no other dependencies. https://t.co/UGyoLSg0oj

Sharing what I discovered from this initial release: