Postdoc in Doudna Lab (UC Berkeley). Previously PhD in Bartel lab (MIT/Whitehead). Biochemical + biophysical principles of protein/RNA mechanisms.

Berkeley, CA
Joined June 2014
Excited to share the published version of our work @Nature! We revealed the mechanism + structural basis of microRNA degradation, and showed how ZSWIM8 defines a novel class of Cullin–RING E3 ligases + targets an asymmetric substrate as a dimer + uses RNAs in recognition. [1/2]
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Peter Wang retweeted
Viruses have parasites too. Our new preprint shows how phages use VIPR to silence parasitic satellites, and how the satellites fight back with its own decoy VIPR RNAs that redirect VIPR to DNA REP elements in the host genome!! biorxiv.org/content/10.64898…
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Peter Wang retweeted
VIPR is now out in @ScienceMagazine! What started with a mysterious RNA led us to an unexpected way of recognizing DNA, as well as some clues to CRISPR’s origins. So happy to share these two papers with an incredible team. Links below; original discovery thread here ↓
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Finally a more intuitive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_… (Character idea from @HannesStaerk & Alex Waldherr)
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Peter Wang retweeted
Today we're announcing ESMFold2, an open scientific engine to power prediction, design, and discovery across protein biology. The new model delivers state of the art performance on protein interactions, especially antibodies, a critical modality for therapeutics. We have designed and validated miniprotein binders and single chain antibodies across five therapeutic targets that are important in cancer and immunology. We are seeing very high success rates, and affinities at levels consistent with therapeutic activity. We’re also releasing an atlas of 6.8 billion proteins, and 1.1 billion predicted structures. ESMFold2 is built on a state of the art language model that has been trained on billions of protein sequences. A world model of protein biology emerges through language modeling. We’ve used the techniques of mechanistic interpretability developed to understand large language models to understand the concepts ESM uses to represent proteins. The model’s representation space has a compositional organization of features across scales, levels of complexity, and abstraction, that reflects and mirrors the understanding of protein biology developed through a century of empirical science. This understanding emerges without prior knowledge, just from language modeling of protein sequences. Language models are becoming a powerful substrate to understand and program biology. The design of protein interactions is one of the most fundamental problems in biophysics, and has critical implications for the discovery of new medicines. A simple gradient based search with the model was able to discover high-affinity protein binders. I'm excited by the potential this has to accelerate basic science and the understanding of proteins. And especially for the new avenues it opens up for therapeutic design and medicine.
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Peter Wang retweeted
Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer.
Bridge recombinase enables versatile rewriting of bacterial genomes biorxiv.org/content/10.64898… #biorxiv_synbio
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Peter Wang retweeted
Saying it because @kenjmloi didn't: This is really close to a RNA system that targets protein sequences because of wobble bases in codons. Truly amazing discovery!
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Check out this awesome discovery of the RNA-guided VIPR RNP by the Doudna lab. Everything about the system, from its functional context to its targeting code and structural geometry, is truly remarkable. Congrats to the team!
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Peter Wang retweeted
A beautiful story on the origins of CRISPR -- congrats to @PeterHYoon @kenjmloi and team! Cool to see the Evo 2 likelihoods being useful for identifying a tricky repeat region. biorxiv.org/content/10.64898…
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Excited to share our work with @DMSabatini & @JswLab. How do lysosomes change with age? We present a metabolic atlas of lysosomal aging, and reveal a lysosomal “aging clock” of metabolites linked to lysosomal storage disorders. Grateful to all co-authors! biorxiv.org/cgi/content/shor…
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Target RNA recognition drives PIWI∗ complex assembly for transposon silencing dlvr.it/TMvgMj
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A conserved PIWI silencing complex detects piRNA-target engagement dlvr.it/TMwC69
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I am so incredibly excited to share our latest work, on the exploration of #RNA secondary structure ensembles and discovery of RNA regulatory structural switches in bacteria and human cells, out today in @NatureBiotech: nature.com/articles/s41587-0…. A short tread! (1/n)
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New preprint countdown! Mitochondria are cells within our cells. They need the same core activities - replication, transcription, translation. How do cells enable these diverse activities in both compartments? We uncover an unexpected strategy with ancient origins. Stay tuned!
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