@abbythurm.bsky.social
stanford md/phd student in the bintu lab, thinking about all things RNA in gene expression
Reposted
1/ Happy to share our preprint from the Greenleaf Lab: beCasKAS, our method to directly detect CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 29, 2025 at 6:28 PM
1/ Happy to share our preprint from the Greenleaf Lab: beCasKAS, our method to directly detect CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
🚀 Our new paper is out @natmethods.nature.com!
Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells.
🔗 www.nature.com/articles/s41...
🧬 www.addgene.org/John_Ngo/
Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells.
🔗 www.nature.com/articles/s41...
🧬 www.addgene.org/John_Ngo/
September 22, 2025 at 6:27 PM
🚀 Our new paper is out @natmethods.nature.com!
Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells.
🔗 www.nature.com/articles/s41...
🧬 www.addgene.org/John_Ngo/
Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells.
🔗 www.nature.com/articles/s41...
🧬 www.addgene.org/John_Ngo/
Reposted
Our new pre-print from the Greenberg and Churchman labs shows that activity-dependent modulation of RNA stability is a major, and underappreciated, mechanism of gene regulation in neurons. Tutorial below! www.biorxiv.org/content/10.1... (1/11)
HuD controls widespread RNA stability to drive neuronal activity-dependent responses
Neuronal activity shapes brain development and refines synaptic connectivity in part through dynamic changes in gene expression. While activity-regulated transcriptional programs have been extensively...
www.biorxiv.org
September 9, 2025 at 2:41 PM
Our new pre-print from the Greenberg and Churchman labs shows that activity-dependent modulation of RNA stability is a major, and underappreciated, mechanism of gene regulation in neurons. Tutorial below! www.biorxiv.org/content/10.1... (1/11)
Interested in synthetic approaches to both understand and manipulate gene expression? We (the Bintu lab) wrote a review that discusses just that - how modern low- and high-throughput approaches can dissect gene regulation at the DNA, RNA, and protein level. www.annualreviews.org/content/jour...
April 28, 2025 at 5:24 PM
Interested in synthetic approaches to both understand and manipulate gene expression? We (the Bintu lab) wrote a review that discusses just that - how modern low- and high-throughput approaches can dissect gene regulation at the DNA, RNA, and protein level. www.annualreviews.org/content/jour...
Reposted
The latest live-cell imaging work from the Boettiger lab measures chromosomal kinetics across genomic scales — it’s moving faster than you think! —, and puts a number on the ‘in vivo’ speed of cohesin loop extrusion itself.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
April 3, 2025 at 2:03 AM
The latest live-cell imaging work from the Boettiger lab measures chromosomal kinetics across genomic scales — it’s moving faster than you think! —, and puts a number on the ‘in vivo’ speed of cohesin loop extrusion itself.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Proteases might serve as versatile control knobs for gene and cell therapies, but there looms the risk of immunogenicity as we and others have been using viral proteases. We now report a control system based on a an engineered human protease and its clinically approved inhibitor. rdcu.be/d6kVt
Orthogonalized human protease control of secreted signals
Nature Chemical Biology - Engineering of a human-derived protease controlled exogenously by its FDA-approved inhibitor enables control over cytokine activity in cell-based therapies with reduced...
rdcu.be
January 15, 2025 at 7:25 PM
Proteases might serve as versatile control knobs for gene and cell therapies, but there looms the risk of immunogenicity as we and others have been using viral proteases. We now report a control system based on a an engineered human protease and its clinically approved inhibitor. rdcu.be/d6kVt
Reposted
Amtrak set an all-time ridership record in FY 2024, carrying 32.8 million riders.
Of that, 43% was on Northeast Corridor routes; 44% was on state-supported routes; and 13% was on long-distance routes.
Most-used routes:
—NEC Regional
—Acela
—Pacific Surfliner
—Empire S
—Keystone
—Capitol Corridor
Of that, 43% was on Northeast Corridor routes; 44% was on state-supported routes; and 13% was on long-distance routes.
Most-used routes:
—NEC Regional
—Acela
—Pacific Surfliner
—Empire S
—Keystone
—Capitol Corridor
Amtrak Sets All-Time Ridership Record in Fiscal Year 2024 - Amtrak Media
Invests more than $4.5 billion in major infrastructure projects to support future growth WASHINGTON – Amtrak achieved an all-time ridership record in
media.amtrak.com
December 4, 2024 at 7:53 PM
Amtrak set an all-time ridership record in FY 2024, carrying 32.8 million riders.
Of that, 43% was on Northeast Corridor routes; 44% was on state-supported routes; and 13% was on long-distance routes.
Most-used routes:
—NEC Regional
—Acela
—Pacific Surfliner
—Empire S
—Keystone
—Capitol Corridor
Of that, 43% was on Northeast Corridor routes; 44% was on state-supported routes; and 13% was on long-distance routes.
Most-used routes:
—NEC Regional
—Acela
—Pacific Surfliner
—Empire S
—Keystone
—Capitol Corridor
Reposted
In theory, my project will be:
1. Do a screen.
2. Follow up on the interesting biology.
In practice, my project will be:
1. Start a screen.
2. Finish the screen.
1. Do a screen.
2. Follow up on the interesting biology.
In practice, my project will be:
1. Start a screen.
2. Finish the screen.
November 25, 2024 at 7:03 PM
In theory, my project will be:
1. Do a screen.
2. Follow up on the interesting biology.
In practice, my project will be:
1. Start a screen.
2. Finish the screen.
1. Do a screen.
2. Follow up on the interesting biology.
In practice, my project will be:
1. Start a screen.
2. Finish the screen.
Reposted
🧬 Excited to share our new preprint! DMS chemical mapping, a key technique for studying RNA structure. Everyone assumes low DMS reactivity = Watson-Crick , high = non-WC. However, analyzing 7,500 RNA structures containing known 3D structures reveals it's not that simple. doi.org/10.1101/2024...
A quantitative framework for structural interpretation of DMS reactivity
Dimethyl sulfate (DMS) chemical mapping is widely used for probing RNA structure, with low reactivity interpreted as Watson-Crick (WC) base pairs and high reactivity as unpaired nucleotides. Despite i...
www.biorxiv.org
November 25, 2024 at 3:42 PM
🧬 Excited to share our new preprint! DMS chemical mapping, a key technique for studying RNA structure. Everyone assumes low DMS reactivity = Watson-Crick , high = non-WC. However, analyzing 7,500 RNA structures containing known 3D structures reveals it's not that simple. doi.org/10.1101/2024...