Fay Lin

The work was led by @adambroerman.bsky.social at @uwproteindesign.bsky.social!

AI-Designed Protein Switches Control Drugs with Speed David Baker’s Nobel Prize-winning lab has designed protein on/off switches as a tool for tunable cancer immunotherapies and biosensors.

David Baker's Nobel Prize-winning lab has now designed a molecular on/off switch to control the speed of protein binding, supporting safer medicines that quell harmful side effects and activate drugs on cue, and sensitive biosensors for SARS-CoV-2 testing!

www.genengnews.com/topics/artif...

AI Designs Viable Bacteriophage Genomes, Combats Antibiotic Resistance AI-guided design of 16 functional bacteriophage genomes offers a path for phage-based therapies against antibiotic-resistant infections.

Genome foundation models, Evo 1 and Evo 2, have now generated viable bacteriophage genomes, demonstrating experimental validation of whole genomes designed by AI!

@arcinstitute.org @brianhie.bsky.social @samuelhking.bsky.social

Read more at GEN:
www.genengnews.com/topics/artif...

@martinpacesa.bsky.social @sokrypton.org @pranam.bsky.social

BindCraft AI Model Achieves One-Shot Functional Protein Design The open-source pipeline designs proteins with improved success rates for therapeutic targets, including gene editing proteins and allergens.

BindCraft is now published in @nature.com!

The open-source pipeline for de novo protein binder design achieves significantly improved success rates with nanomolar affinity and therapeutic potential from gene editing to allergens.

Read more at GEN:
www.genengnews.com/topics/artif...

Given the high uptake for a “Cas9 look-alike,” the team is inspired to expand toward new territories, including base editors, prime editors, large insertion techniques, and more to demonstrate the generalizability of its protein design platform. 4/4

Since OpenCRISPR-1's open source release in April 2024, tens of thousands of academic and industry researchers have accessed the sequence across a variety of verticals, from developing drought-resistant crops to drug discovery. 3/

Despite being hundreds of mutations away from any known natural protein. Profluent's LLM generated CRISPR proteins show improved activity, specificity, and immunogenicity relative to naturally occurring gene editors. 2/

Profluent’s AI-Designed Gene Editor Provides Glimpse Into Generalizable Platform OpenCRISPR-1, an AI-generated custom gene editor capable of precision editing of the human genome. is just the beginning of Profluent’s AI applications.

OpenCRISPR-1, Profluent's AI-designed gene editor, is now published in Nature!

@thisismadani.bsky.social emphasizes the need to move away from random discovery and into bespoke design using AI. 1/

Read more at GEN:
www.genengnews.com/topics/artif...

Jura Bio’s AI Data Loop Enables Large-Scale De Novo Antibody Design VISTA, an AI-controlled data loop system, guides large-scale antibody design from scratch for applications in cancer therapy.

Great coverage of VISTA by the wonderful @faylinphd.bsky.social over at GEN: www.genengnews.com/topics/artif...

Read about VISTA: www.jurabio.com/blog/vista

Undruggable No More: AI Hits Disordered Proteins, Unlocks Therapy Targets David Baker’s lab has successfully designed binders to disordered proteins, expanding therapeutic access to over 50% of the human proteome.

David Baker's Nobel Prize-winning lab has now designed binders to "undruggable" disordered proteins, unlocking therapeutic access to over 50% of the human proteome!

‪@uwproteindesign.bsky.social‬

Read more at GEN:
tinyurl.com/4fw6wvkm

Democratizing Artificial Intelligence in Pre-Clinical Drug Discovery While AI-driven approaches tout increased speed and lower costs, commercial interests compromise scientific collaboration.

Excited to see our new AI Small Molecule Drug Discovery Center #MountSinai featured in GEN!
🧬🧠 Read more: genengnews.com/topics/artif... Thank you @faylinphd.bsky.social
#AI #DrugDiscovery #Genetics

As a baseline, competitors will initially go head-to-head with Arc’s first virtual cell model, STATE, which is designed to predict how various stem cells, cancer cells, and immune cells respond to drugs, cytokines, or genetic perturbations. 3/3

The initiative is a step toward virtual cell benchmarking and acceleration, and follows in the footsteps of the CASP competition, the biannual experiment that assesses the latest state-of-the-art models in protein structure prediction, which enabled Nobel Prize-winning, AlphaFold. 2/

Arc Institute Launches Virtual Cell Challenge to Accelerate AI Model Development The open benchmark competition will evaluate the ability of AI-powered virtual cell models to generalize to new cell contexts for therapeutic applications.

@arcinstitute.org‬ has announced the inaugural “Virtual Cell Challenge,” sponsored by NVIDIA, @10xgenomics.bsky.social and Ultima Genomics,
which will evaluate the ability of AI models to generalize to new cell contexts for therapeutic applications. 1/

www.genengnews.com/topics/artif...

Xaira Therapeutics Releases Largest Perturb-Seq Dataset to Power the Virtual Cell The AI unicorn's Perturb-seq atlas is publicly available and detects dose-dependent genetic effects to enhance predictive power for drug discovery.

Xaira Therapeutics has released the largest publicly available Perturb-seq dataset to train the AI-powered virtual cell for drug discovery!

The work is described in Xaira's first preprint, capping a year after the company's $1 billion launch.

www.genengnews.com/topics/artif...

Million Species Listing: Basecamp Research Unearths Trove of Sequence Data From Novel Species BaseData aims to improve AI models in biology by offering a 10-fold expansion of protein diversity compared to all public databases combined.

More in GEN from @faylinphd.bsky.social: www.genengnews.com/topics/artif...

In collaboration with @recursionpharma.bsky.social, the work was led by Gabriele Corso @gcorso.bsky.social, Saro Passaro, and Jeremy Wohlwend from the lab of Regina Barzilay at @mit.edu!

Boltz-2 Released to Democratize AI Molecular Modeling for Drug Discovery The MIT model predicts molecular binding affinity at newfound speed and accuracy, offering a powerful tool for commercial drug discovery.

Boltz-2 now predicts molecular binding affinity at newfound speed and accuracy - and it's open source!

The permissive MIT license allows commercial drug developers to apply proprietary data and offers an advance over the structure prediction capabilities of AlphaFold 3.

tinyurl.com/37c96c6y

Scratch That? De Novo Antibody Design Enters the AI Drug Discovery Toolbox Debates over AI antibody design terminology have clouded the industry’s shared mission of bringing better therapeutics to the clinic faster.

AI hype or reality - can we design antibodies from scratch (de novo)?

In my latest for GEN, I unpack where de novo design is today and how arguments over terminology have clouded the industry’s shared mission of bringing better therapeutics to the clinic faster.

tinyurl.com/4uamc8c5

Excellent story from @faylinphd.bsky.social on the hot news from #ASGCT2025 — @kiranmusunuru.bsky.social and colleagues tailor the world’s first bespoke gene editor to treat KJ, an infant with an ultra-rare genetic disease, heralding a new era in precision med.
www.genengnews.com/topics/genom...

Imprint Labs Launches to Pioneer "Forensic Immunology" For Chronic Disease Imprint has raised $15 million to decode the body's immune memory for understanding chronic diseases, such as long-COVID and psychiatric disorders.

📣Major thanks to @faylinphd.bsky.social at GEN News for this lovely piece on IMPRINT! It was a pleasure for our founders — @beckbrachman.bsky.social, @victorgreiff.bsky.social, and Raymond Alvarez — to speak about our mission and research, and being NYC's first FRO.

@convergentresearch.bsky.social

ASGCT 2025: World’s First Patient Treated with Personalized CRISPR Therapy Treated with an individualized gene-editing therapy that corrects mutations directly on the genome, a patient shows improvement from a rare metabolic disease.

BREAKING NEWS: World’s first patient treated with personalized CRISPR therapy!

Born with a severe metabolic disease with a 50% mortality rate, an infant has improved after receiving an individualized gene editing therapy, a glimpse of a new era in genomic precision medicine.

tinyurl.com/m52udxht

A "ChatGPT prompter" for interrogating single-cell transcriptomics, TranscriptFormer probes cellular biology across organisms, with predictive capabilities for disease state classification and tissue context, and generative tasks, such as inferring cell type-specific transcription factors. 2/2

The Cross-Species Cell Atlas: Chan Zuckerberg Initiative Releases TranscriptFormer AI Model Trained on data covering 1.5 billion years of evolution, CZI’s new generative AI model probes cellular biology across species for therapeutic applications.

Introducing TranscriptFormer, the cross-species cell atlas!

This new generative #AI model from @chanzuckerberg.bsky.social is trained on data from over 110 million cells from 12 different species, covering 1.5 billion years of evolution.

tinyurl.com/2yet8k42

Machine Learning Engineers Bespoke Cas9 Enzymes for Gene Editing Researchers have developed a machine learning model that predicts Cas9 proteins that can be tailored with designer properties for therapeutic use.

Thanks to @faylinphd.bsky.social from @GEN for featuring our manuscript!

www.genengnews.com/topics/genom...

Arc Institute’s AI Model Evo 2 Designs the Genetic Code Across All Domains of Life Evo 2 now includes information from humans, plants, and other eukaryotic species to expand its capabilities in generative functional genomics.

New from @arcinstitute.org is "the largest publicly available #AI model for biology to date"!

Evo 2 now includes information from all domains in life to expand its capabilities in generative functional genomics. @pdhsu.bsky.social @brianhie.bsky.social

tinyurl.com/3t83vseh

AI-Guided Receptor Engineering to Improve Performance in Cell Therapies Using protein structure prediction tools, researchers have uncovered receptor structure-function relationships to improve cell therapies.

Leveraging protein structure prediction tools, researchers from Northwestern University present an #AI based framework to uncover potential structural design rules across receptor families for improved cell therapies.

Read more at GEN:
www.genengnews.com/topics/artif...

Recursion Announces Promising Clinical Data on Lead AI-Based Drug Candidate for Brain Disease Cerebral cavernous malformation (CCM) patients treated with oral drug, REC-994, showed reduction in total cerebral and brainstem lesion volume.

Congrats to @faylinphd.bsky.social on her first exclusive story for GEN - Recursion presents promising phase II data on its AI drug for CCM:
www.genengnews.com/topics/artif...

Recursion Announces Promising Clinical Data on Lead AI-Based Drug Candidate for Brain Disease Cerebral cavernous malformation (CCM) patients treated with oral drug, REC-994, showed reduction in total cerebral and brainstem lesion volume.

Read the full article on GEN:
tinyurl.com/yc6wspz5

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