The Chedin Lab @ UC Davis. All about R-loops! Director of the MCB T32 training program. Passionate about grad education, mentoring, and rigorous science.
UC Davis
Joined July 2015
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Fred Chedin retweeted
What if a single RNA transfection could program human stem cell fate or enable functional biosensing for more than a month?
Our new @CellRepMethods paper explores how self-amplifying RNA makes this possible, without genomic integration. 1/n :🧵
Self-amplifying RNA enables rapid, durable, integration-free programming of hiPSCs dlvr.it/TVWHCk
Fred Chedin retweeted
Today I am sharing a new preprint and accompanying blog post. Hundreds of published papers include impossible western blots showing protein expression in cell lines that have deleted or mutated genes. These clumsy mistakes are widespread and repeated by LLMs.
Fred Chedin retweeted
1/ Excited to share our new preprint from a joint collaboration between @JswLab + @Bruce_Ksander!
Aging is marked by a progressive loss of resilience to stress. Can we systematically search the human ORFome for genes that make vulnerable cells more resilient?
Performing such a genome-scale ORF screen led us to NKX2-5—a heart transcription factor we engineered to restore vision, and improve health in aged mice.
A breakdown🧵
🔗 doi.org/10.64898/2026.09.29.…
Fred Chedin retweeted
Our new paper in PNAS reports the presence of Na+ and Li+ #aptamer RNAs in mammals. The latter hints at natural roles for #lithium in humans and provides direct links to #BipolarDisorder. Now seeking funding to study Li+ biology and create new therapeutics.
Fred Chedin retweeted
A few months ago I was browsing google images looking at p53 western blots in the SK-OV-3 cell line for an unrelated project. I noticed an unusual western blot hosted on Thermo Fisher's website which I posted on social media. Usually I just post weird blots to PubPeer. 👇
Fred Chedin 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…
Fred Chedin retweeted
Very excited to announce ENCODE GRAMMAR (Genomic Regulatory Atlas of sequence Models, Motifs, Annotations & Rules): 3,865 experiment-specific deep learning model sets and sequence annotations for decoding human regulatory DNA. 1/
Fred Chedin retweeted
Excited to share my piece in @NatureCareers on why scientists are already trained for AI, plus ten places to start. 🔬🧪🤖
nature.com/articles/d41586-0…
Hope it helps! 🙏
Incredibly grateful to editors Jack Leeming and Jeff Perkel for the opportunity and collaboration.
Fred Chedin retweeted
Why is the X chromosome rich in L1 mobile elements? @ScienceMagazine X-chromosome inactivation draws L1 mutagenesis to the human X chromosome | Science science.org/doi/10.1126/scie…
Fred Chedin 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…
Fred Chedin retweeted
A spliceosome-independent eukaryote generated by complete intron removal: Cell cell.com/cell/fulltext/S0092…
Fred Chedin retweeted
Introns have a hidden regulatory role! 🧬🎉
Delighted to share our latest paper showing that inefficiently spliced introns and spliceosomal proteins direct RNA methylation, engaging RNAi to silence retrotransposons and regulate gene expression
nature.com/articles/s41467-0…
🤖 Made with AI
Fred Chedin retweeted
Beyond housekeeping: snRNA diversity, regulation, and human disease dlvr.it/TTCWvT
Fred Chedin retweeted
🎉In this fun collaboration with @yeo_lab, we screened over 800 RNA-binding proteins for their activities in regulating poly(A) selection and found some expected hits! Co-led by @pratibhajagann_ from Gene's lab and @YoseopYoon in my lab.
Molecular Cell cell.com/molecular-cell/full…
Fred Chedin retweeted
🧬 ⛓️💥 Our paper is now out in @NatureSMB! We examined the fate of replication forks that collapse at single-strand DNA breaks (SSBs) in vertebrates 🐸, comparing the consequences of collapse at single vs convergent forks. nature.com/articles/s41594-0…
Fred Chedin retweeted
Online Now: Apical localization of RNA polymerases modulates transcription dynamics and supercoiling domains revealed by cryo-ET dlvr.it/TSVTdL
Instructure, the company running Canvas apparently hit by ransomware attack affecting 1000s of school worldwide. This was my screen an hour ago as I was about to post a quiz. Great….
Fred Chedin 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 👇
Fred Chedin retweeted
Detecting plectonemes using RCMC nature.com/articles/s41588-0…
For contact probability, we used Region Capture Micro-C (RCMC) a methods developed by @Anders_S_Hansen's lab which supports targeted pulldown of a region of interest (figure from Goel, V et al. Nature Genetics. 2023) . Since we are just looking at one locus (CLYBL), we want to spend our sequencing dollars getting high resolution at this locus! And boy did we! ( 23/n)
Fred Chedin retweeted
Water is 70–80% of a cell, with our mspSA + SGAG affinity grid, we capture a near atomic (<2 Å) view showing water actively driving gene transcription inside RNA Pol II. Not just background,water is part of the machinery. Now published in Molecular Cell.doi.org/10.1016/j.molcel.202…