MD/PhD Student @StanfordMed | thinking about all things RNA in gene expression @BintuLab | B.S. @uclachem | she/her
Joined April 2020
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Do human RNA-binding proteins have modular regulatory domains that downregulate RNA lifetimes? Our preprint @BintuLab studying this question is now out on bioRxiv, where we indeed identify small domains in RBPs that potently induce RNA degradation! biorxiv.org/content/10.1101/… (1/9)
Abby Thurm retweeted
Have you ever looked at a gene in IGV or a genome browser and wondered “What are all those (ATAC-seq/H3K27ac/CTCF ChIP-seq/…) peaks doing?” 🤔 I’m thrilled to share that we developed a new technology called Swap-seq to answer that exact question.
biorxiv.org/content/10.64898…
Abby Thurm retweeted
Three years ago, my lab at @MSKCancerCenter set out to see if we could harness AI for new therapeutic proteins.
Today in @natBME, our first step in developing these AI-designed molecules as anti-tumor therapies is online.
Read more here: 1/n mskcc.org/news/using-ai-to-d…
Abby Thurm retweeted
Excited to share my PhD work, now on @bioRxiv! 🎓🦠Viruses are packed with small ORFs with unknown function. At @JswLab w/ collaborators, we built a pan-viral microprotein atlas that uncovered the oncogenic activity of BNLF2b, an EBV gene linked to cancer.
biorxiv.org/content/10.64898…
Abby Thurm retweeted
RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) biorxiv.org/content/10.64898…
Abby Thurm retweeted
Does every enhancer work with every promoter?
With @jengreitz and @WJGreenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field.
A tour 🧵👇
biorxiv.org/content/10.64898…
Great experience compiling years of collective screening experience to produce what we hope is a comprehensive protocol for others to accessibly scale up experiments! And some fun new data hidden in there :) thanks @JoshTycko for being better and faster at Twitter than me 🎉
We hope this protocol is useful for people doing large scale protein function work! nature.com/articles/s41596-0…
Led by @abbythurm from @BintuLab
Abby Thurm retweeted
We hope this protocol is useful for people doing large scale protein function work! nature.com/articles/s41596-0…
Led by @abbythurm from @BintuLab
Abby Thurm retweeted
1/ Over the past 50 years, we have learned much about how transcription factors and other DNA-binding proteins search for their targets, but we know much less about how sequence-specific RNA-binding proteins (RBPs) search for their targets.
🧵⤵️
Abby Thurm retweeted
Excited to share our first story. Preprint: RNA 3D Motif Dynamics Guide Assembly of the Replication Initiation Complex in Flaviviruses. biorxiv.org/content/10.64898… Led by superstar student @LorenaStreit01 supported by @TakaOni61 and also @miroastore @EmilyCioppa et al. Check it out!
Abby Thurm retweeted
A holy grail for our lab has been tracking myeloid cells in human tumors in the same way that we track T and B cells with TCR/BCR.
@vincentzliu and @CalebLareau solved it!
We developed Mitotrek using scATAC-seq + mitochondrial DNA to do exactly this. Using Mitotrek, we find that new myeloid cells clones constantly infiltrate the tumor via circulating monocytes — and that their macrophage or dendritic cell fate is epigenetically programmed before tumor entry.
@10xGenomics @parkerici @CancerResearch @TheMarkFdn
cell.com/cancer-cell/fulltex…
Abby Thurm retweeted
🚨What if we could reliably program macrophage polarization state?🚨
biorxiv.org/content/10.64898…
Macrophages are highly plastic immune cells that perform critical functions by polarizing into distinct cellular states. The polarization state of macrophages can substantially influences the progression of cancers, infections, and autoimmunity. (1/11)
Abby Thurm retweeted
Now out in @NatureBiotech ! Do lncRNAs commonly bind 1000s of genomic sites? Maybe they do, but the dozens of studies that report genomic binding maps of lncRNAs are deeply flawed, with probes binding suprious DNA sites rather than RNA-bound ones. nature.com/articles/s41587-0…
A preprint‼️that's bound to ruffle some 🪶 "Widespread DNA off-targeting confounds studies of RNA chromatin occupancy" led by our @MicahGoldrich and Louis Delhaye from @pieter_mestdagh. TL;DR we show that many of lncRNA chromatin occupancy maps are flawed🧵biorxiv.org/content/10.1101/…
Abby Thurm retweeted
1/ Preprint alert 🚨🚨🚨 How do cells decide where an mRNA should end?
And how is that decision coordinated with splicing and transcription while the RNA is still being made?
Here's what first author @HopeMerens found 👇
Abby Thurm retweeted
We’re unwrapping a new method today @MSKCancerCenter!
Led by @SydneyBlattman, @NabihMaslah, @AustinAVarela, Ronan Chaligne and @dana_peer, plus colleagues at @10xGenomics, we’re delighted to share Genotyping In Fixed Transcriptomes (GIFT):
biorxiv.org/content/10.64898…
1/n
Abby Thurm retweeted
Have you ever wanted to do single-molecule biophysics in high-throughput? @DejongMatt (amazing joint grad student with @Dunn_Lab) invented a way & measured >100,000 single molecules across 241 different sequences. (1/3)
biorxiv.org/content/10.64898…
First preprint of the @fordycelab and @Dunn_Lab collaboration! We used high-throughput microfluidics for sequence-strength mapping at the single-molecule level. Our new tech allowed us to discover a fundamental nonequilibrium property of multivalent systems. 1/13
How can we move toward a quantitative, predictive framework for how RBPs bind and regulate their RNA partners? In a new preprint @Cheers2LO @BintuLab, we show that structural profiling via DMS-MaPseq can be used to measure fractional occupancies of RBPs at single-base resolution.
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.
Read the whole story in our preprint! biorxiv.org/content/10.64898…
This was an amazing collaboration to drive between the Hagler and Bintu labs, and seeing the data was a dream come true. Congrats to @Cheers2LO on her lab's first of many important papers!
Abby Thurm retweeted
Read the full story in our preprint! 👇
biorxiv.org/content/10.64898…
Excited to share this work with my co-first author Kevin Sabath - a fantastic collaboration between the @AlexanderStark8 and @plaschka_lab labs! 🤝🧪