Abby Thurm

Grammarly turned me into an AI editor against my will and I hate it The company tells Platformer it will let experts opt out of the controversial feature — but how different is it than what every other AI company is doing?

This is f-ing outrageous www.platformer.news/grammarly-ex...

Read the whole story in the preprint! This was an amazing collaboration to drive between the Hagler and Bintu labs, and seeing the data was a dream come true. Congrats to Professor Lauren Hagler on her lab's first of many important papers!

We use the MCP-MS2 model system to show that RNA folding is imperative for binding, that single-nucleotide mutations are enough to change affinity, and that precise fraction bound measurements predict RNA degradation.

Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells RNA structures that form inside living cells influence processes ranging from translation to RNA decay, many of which are controlled by RNA-binding proteins (RBPs). Because RBP specificity depends on ...

How can we move toward a quantitative, predictive framework for how RBPs bind and regulate their RNA partners? In a new preprint, we show that structural profiling via DMS-MaPseq can be used to measure fractional occupancies of RBPs at single-base resolution. #rnasky
www.biorxiv.org/content/10.6...

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...

🚀 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/

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...

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)

Thanks to Geo and Lacra for help writing, and @annualreviews.bsky.social for the invitation. Let us know what you think, and apologies in advance for any novel works we didn't have the space to cite!

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...

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...

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...

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

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

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

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.

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...

🧬 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...