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Andrew C. Adey

@acadey.bsky.social
59 followers 34 following 12 posts

Professor of Molecular & Medical Genetics at OHSU. Runner.

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Andrew C. Adey @acadey.bsky.social · 14/10/2025
Really excited to have our single-cell DNA Methylation analysis tool, Amethyst, published! Led by Lauren Rylaarsdam, who developed the tool as a way to tackle her own projects and developed it into a comprehensive scDNAm analysis package. www.nature.com/articles/s42...
nature.com
Single-cell DNA methylation analysis tool Amethyst resolves distinct non-CG methylation patterns in human astrocytes and oligodendrocytes - Communications Biology
A study uses Amethyst, a comprehensive single-cell methylation analysis tool, to resolve distinct non-CG methylation patterns in human astrocytes and oligodendrocytes. Findings challenge historically ...
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Jay Shendure @jshendure.bsky.social · 14/10/2025
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here: www.biorxiv.org/content/10.1...
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Andrew C. Adey @acadey.bsky.social · 01/10/2025
Awesome!
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
Huge thanks to all co-authors and the inimitable @jbuenrostro.bsky.social for supporting this new direction - I got to think about evolution, engineering, chromatin biophysics, and modeling during the course of this project. For more, check out the preprint: www.biorxiv.org/content/10.1... 8/9
biorxiv.org
Engineered histones reshape chromatin in human cells
Histone proteins and their variants have been found to play crucial and specialized roles in chromatin organization and the regulation of downstream gene expression; however, the relationship between ...
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9
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Andrew C. Adey @acadey.bsky.social · 07/08/2025
I am excited to work with 10x to take single-cell technologies to the next level - lots of new directions!
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Jeff Vierstra @jeffvierstra.bsky.social · 08/07/2025
We have created a new DNase I- & ATAC-seq peak caller that uses an adaptive background model that controls for copy number variation & aneuploidy. It performs a per-nucleotide test (+FDR correction) and is very fast. Please try it out and give us feedback! github.com/vierstralab/...
github.com
GitHub - vierstralab/hotspot3: A chromatin accessibility peak caller with an adaptive background model
A chromatin accessibility peak caller with an adaptive background model - vierstralab/hotspot3
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Junhong Choi @choijunhong.bsky.social · 06/05/2025
Happy to share our new review on molecular circuits for genomic recording with @chenomics.bsky.social! Here, we present our views on the remaining challenges in the field of genomic recording for reconstructing cell-fate decisions. (1/2)
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Genetics Society of America @genetics-gsa.bsky.social · 29/04/2025
Cuts to #NIH funding don't just hurt scientists, but everyone who depends on new treatments, cures, & medical breakthroughs. Research can't thrive without strong, sustained support. Read more in this @60minutes.bsky.social segment featuring former NIH director Francis Collins: buff.ly/REjVWPc
buff.ly
Scientists fear Trump administration cuts to NIH could impact the health of Americans for generations
Former National Institutes of Health Director Dr. Francis Collins, who abruptly left his NIH research lab in February, fears aggressive downsizing could impact Americans' health.
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Vijay Ramani @vram142.bsky.social · 01/05/2025
Delighted to see this out! Fun fact: I actually started my lab @ UCSF w/ goal of understanding tRNA txn regulation, which aligned perfectly w/ @genophoria.bsky.social & Sohail! 6+ years of amazing collaboration & stellar work by Siyu, Albertas, & co & we're making real progress w/ more to come!
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Duncan Sproul @sproullab.bsky.social · 23/04/2025
Want to work with us on DNA methylation and rare genetic disease? Fully funded PhD project with deadline 16th May: www.findaphd.com/phds/project... Excited to collaborate with @hannahlong.bsky.social and Daria Bunina (@uoe-igc.bsky.social/@mdc-berlin.bsky.social). Please share 🙏 #epigenetics
findaphd.com
Fully Funded PhD Studentship in Human Genetics, Genomics and Disease: Dissecting DNMT3B functions in Immunodeficiency-centromeric instability facial anomalies syndrome at University of Edinburgh on Fi...
PhD Project - Fully Funded PhD Studentship in Human Genetics, Genomics and Disease: Dissecting DNMT3B functions in Immunodeficiency-centromeric instability facial anomalies syndrome at University of E...
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Michael Hoffman @michaelhoffman.bsky.social · 21/04/2025
Whenever my kid sees a Cybertruck she says "that's a stupid truck" and I feel like I'm succeeding at parenting
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Stein Aerts @steinaerts.bsky.social · 04/04/2025
2) HyDrop-v2: with a new bead design it provides scalable and cost-effective generation of scATAC-seq atlases. With HyDrop atlases of the fly embryo and mouse cortex we show that CREsted models trained on HyDrop data are equivalent to models trained 10x atlases. www.biorxiv.org/content/10.1...
biorxiv.org
HyDrop v2: Scalable atlas construction for training sequence-to-function models
Deciphering cis-regulatory logic underlying cell type identity is a fundamental question in biology. Single-cell chromatin accessibility (scATAC-seq) data has enabled training of sequence-to-function ...
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Stein Aerts @steinaerts.bsky.social · 04/04/2025
Very proud of two new preprints from the lab: 1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...
biorxiv.org
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species
Sequence-based deep learning models have become the state of the art for the analysis of the genomic regulatory code. Particularly for transcriptional enhancers, deep learning models excel at decipher...
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Tanaya Shree @tanaya-shree.bsky.social · 08/03/2025
Proud to see so many fellow scientists and citizens standing up for science today! Every treatment option I'm able to offer my patients came to be because of careful persistent scientific inquiry. We cannot afford to be shortsighted when it comes to biomedical research. #StandUpForScience
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Daniel Lipka @dblipka.bsky.social · 14/02/2025
Interesting work from the Tomkova group relating DNA hypermethylation of polycomb-repressed regions with gene upregulation. #Epigenetics #DNA_Methylation
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Anshul Kundaje @anshulkundaje.bsky.social · 08/02/2025
What's happening is precisely outlined in Project 2025. Read it to understand what's coming next. None of this is a surprise. Also, I know this is extremely unnerving if u weren't expecting this. But let's not panic. Let's organize & give this the best fking fight of our lives.
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Andrew C. Adey @acadey.bsky.social · 24/12/2024
Excited to have our sciMETv3 paper out today in Cell Genomics! We can produce hundreds of thousands of sibgle-cell DNA methylome libraries in a single experiment! (Plus lots more) www.cell.com/cell-genomic...
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Andrew C. Adey @acadey.bsky.social · 16/12/2024
Just joined. Not sure how much I will post or follow. I have enjoyed the post-Twitter zen, but I do miss the collation of useful info and papers in the field.
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