Jonathan Gootenberg (@jgooten) / X

Jonathan Gootenberg

801 posts

Jonathan Gootenberg

@jgooten

Pull apart the double helix like a wishbone || Ars longa, tweeta brevis

Cambridge, MA

Joined December 2012

Pinned
Jonathan Gootenberg
@jgooten
Nov 22, 2024
How can foundational models + directed evolution make proteins >100x-fold better? We (@omarabudayyeh, @idmjky, @mat10_d, @zyan216) report in @ScienceMagazine on EVOLVEpro, a general active learning approach to improve protein and enzyme function science.org/doi/10.1126/sc…
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Jonathan Gootenberg
@jgooten
Nov 24, 2022
CRISPR-based genome editing has been transformative, but insertion of large sequences requires DNA damage machinery How can we efficiency place DNA cargos anywhere in the genome? Today we report on PASTE, out in @NatureBiotech w/ @omarabudayyeh @MIT nature.com/articles/s4158… 1/🦃
Jonathan Gootenberg
@jgooten
Jun 14, 2023
CRISPR nucleases have been transformative. What if there were similar RNA-programmed nucleases in eukaryotic genomes? Turns out, they are abundant (>3500) and functional! Today we share findings on novel RNA-guided DNA nucleases in eukaryotes. biorxiv.org/content/10.110… 1/14
biorxiv.org
Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses
TnpB proteins are RNA-guided nucleases that are broadly associated with IS200/605 family transposons in prokaryotes. TnpB homologs, named Fanzors, have been detected in genomes of some eukaryotes and...
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Jonathan Gootenberg
@jgooten
Aug 18, 2022
You know CRISPR complexes can cut DNA/RNA….what if some of them cleaved proteins too? Today in @biorxivpreprint, we (+ @omarabudayyeh @hnisimasu) continue our study of Cas7-11 and type III-E systems, revealing a new triggered protease function biorxiv.org/content/10.110… 1/6
biorxiv.org
RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-pr...
The type III-E Cas7-11 effector nuclease forms a complex with a CRISPR RNA (crRNA) and the putative caspase-like protease Csx29, catalyzes crRNA-guided target RNA cleavage, and has been used for RNA...
Jonathan Gootenberg
@jgooten
Sep 6, 2023
Me when my gel fails
46K
Jonathan Gootenberg
@jgooten
Jan 28, 2022
Genome editing owes a huge debt to genome sequencing With efforts like @humancellatlas, we’re sequencing cells like mad. What is the "Cas9" of single cell? With @omarabudayyeh @insitubiology: RADARS, for programmable cell-specific sensing/expression biorxiv.org/content/10.110… 🧵👇
biorxiv.org
Programmable eukaryotic protein expression with RNA sensors
The diversity of cell types and states can be scalably measured and defined by expressed RNA transcripts. However, approaches to programmably sense and respond to the presence of specific RNAs within...
Jonathan Gootenberg
@jgooten
Apr 9, 2025
Precise DNA integration is key for many therapies, but inserting large, scarless sequences remains challenging. What if we could reprogram nature's mobile elements for programmable genome writing? Today we (+ @omarabudayyeh) debut Stitchr in @Nature
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Jonathan Gootenberg
@jgooten
Jul 19, 2024
Directed evolution won a Nobel prize by unlocking new protein functions How can we augment evolution to engineer proteins 10-100 times better? By using large language models! Here we present EVOLVEpro, an LLM for accelerated protein evolution biorxiv.org/content/10.110… 1/
biorxiv.org
Rapid protein evolution by few-shot learning with a protein language model
Directed evolution of proteins is critical for applications in basic biological research, therapeutics, diagnostics, and sustainability. However, directed evolution methods are labor intensive,...
42K
Jonathan Gootenberg
@jgooten
Feb 2, 2024
Genome editing has revolutionized the treatment of rare disease. What if we could put any change into RNA safely and reversibly? Today we (+ @omarabudayyeh ) debut PRECISE, allowing for RNA edits, deletions, and insertions from 1 to >1,000nt biorxiv.org/content/10.110… 🧵 1/x
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Jonathan Gootenberg
@jgooten
Nov 2, 2021
New preprint! How do you insert large genes efficiently + programmatically? CRISPR-based methods are programmable, integrases are efficient. Why not combine them? PASTE places short (~45bp) integrase landing sites that serve as beacons for insertion (up to 36kb)! @omarabudayyeh
Jonathan Gootenberg
@jgooten
Jul 3, 2024
The AbuGoot lab is moving to HMS! Excited to be a faculty member at @BIDMChealth and @harvardmed. Interested in programmable biology, including nucleic acid editing, aging , and ML-driven protein/cell engineering? We're hiring - join us in pioneering biotech frontiers
37K
Jonathan Gootenberg
@jgooten
Sep 7, 2021
Our story on the newest CRISPR effector for RNA targeting, Cas7-11, is out now in @nature! So what’s the deal with the newest member of the CRISPR club? (surprisingly not an ad for @7eleven) @omarabudayyeh. Read the paper here rdcu.be/cxf6C. 1/n
GIF
Jonathan Gootenberg
@jgooten
Feb 12, 2025
How can better RNA form the basis of the next wave of biotechnology companies? Today we (+@omarabudayyeh, @pdhsu) are launching Terrain, a new platform for developing RNA medicines. Thankful to the @terrainbiosci team and our backers (incl @john_evans3 @JMaraganore)
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Jonathan Gootenberg
@jgooten
Sep 28, 2023
Can Eukaryotic RNA programmable DNA nucleases be used for efficient mammalian genome editing? Turns out they can! An update on our work on Fanzors (f.k.a Hermes) nucleases, now out! science.org/doi/10.1126/sc… 1/6
science.org
Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses
Fanzor is an RNA-guided DNA endonuclease widespread in eukaryotes and their viruses.
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