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Beta-lactamase dependent and independent evolutionary paths to high-level ampicillin resistance | Nature Communications nature.com/articles/s4146…

Temporal gene regulation enables controlled expression of gas vesicles and preserves bacterial viability biorxiv.org/content/10.110… #biorxiv_synbio

Multi-Level Regulation in RNA-Protein Hybrid Incoherent Feedforward Loop Circuits for Tunable Pulse Dynamics in Escherichia coli biorxiv.org/content/10.110… #biorxiv_synbio

Static AF2 PDB snapshots are so 2024 😂 AlphaFold is no longer just a crystal‑structure oracle🪄, bAIes turns its distograms into atom‑level movies, useful for IDPs It matches Anton‑scale MD in GPU hours, not months at a fraction of the cost🔥

Check out our PhD student Hannah Sleath’s paper on vesicle-based synthetic cells that can crawl up surface concentration gradients using DNA receptors — great collaboration with DiMicheleLAB and Bortolo Mognetti pubs.acs.org/doi/full/10.10…

Excited to announce Arc Institute's first virtual cell model: State. Reliably predicting cellular responses to drug and genetic interventions is arguably the next frontier in AI & biology. arcinstitute.org/manuscripts/St… arcinstitute.org/news/virtual-c…

Rational Development of Recombinant ELP Bolaamphiphiles for the Controlled Construction of Multifunctionalized Globular Protein Vesicles biorxiv.org/content/10.110… #biorxiv_synbio

Ever wondered how to mine for and generate new antimicrobial peptides from scratch? We show how to do it with AI in our latest piece in Accounts of Chemical Research ACS Publications. Led by Paulina Szymczak, with Luis Pedro Coelho, Jun Wang, Ewa Szczurek! pubs.acs.org/doi/10.1021/ac…

Nice reference sheet to AI models for proteins: tamarind.bio/blog/a-compreh…

Our recent collaboration with Ben Schuster's lab to characterize "protein surfactants"!

Signed, Sealed, Delivered: A Generalizable Model for Probiotic Delivery and Metabolism in the Gut biorxiv.org/content/10.110… #biorxiv_sysbio

🧬 New tools for gene control! A recent publication highlights ligand-responsive condensates for controlled gene expression in mammalian cells. This modular system can target DNA, RNA, and proteins inside the nucleus.⬇️ nature.com/articles/s4158…

Mapping the space of protein binding sites with sequence-based protein language models １．This paper introduces EPoCS, an alignment-free method for representing and comparing protein binding sites using embeddings from protein language models combined with 3D structural

Uncovering encrypted antimicrobial peptides in health-associated Lactobacillaceae by large-scale genomics and machine learning | Microbiome | Full Text microbiomejournal.biomedcentral.com/articles/10.11…

Benchmarking gLMs across the central dogma of bio: Genomic Touchstone: 34 genomic LMs, 36 tasks, 88 datasets spanning DNA → RNA → protein I was kinda shocked to see models trained only on DNA can predict RNA mods & protein features better* than RNA/Protein LMs🤔

Homotypic RNA clustering accompanies a liquid-to-solid transition inside the core of multi-component biomolecular condensates: nature.com/articles/s4155…

Huge congratulations to Alina Emelianova, Pablo and Daniel on their paper on small-molecule partitioning into condensates now published in JACS Au and selected as ACS Editor’s Choice!! pubs.acs.org/doi/full/10.10…

Structurally Tunable Cell-Free System: to Expand the Synthetic Biology Toolkit for Studies on Extracellular Polysaccharide doi.org/10.1021/acs.ja…

Was extremely fun to work on this paper with Jerry Liu and finally fulfilling our 7 year plan from year one of undergrad to write a paper together! One of many I hope!

Excited to share our preprint on 3'UTR-chaperoned IDR functions!Check it out if you work on a protein with a long IDR and a highly conserved 3'UTR in the mRNA!