Andrew C. Adey
@acadey.bsky.social
Professor of Molecular & Medical Genetics at OHSU.
Runner.
Runner.
Pinned
Andrew C. Adey
@acadey.bsky.social
· Oct 14
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 ...
www.nature.com
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...
www.nature.com/articles/s42...
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...
www.nature.com/articles/s42...
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 ...
www.nature.com
October 14, 2025 at 9:47 PM
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...
www.nature.com/articles/s42...
Reposted by Andrew C. Adey
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...
www.biorxiv.org/content/10.1...
October 14, 2025 at 6:45 PM
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...
www.biorxiv.org/content/10.1...
Awesome!
Leading epigenetics researcher and longtime Broad member
@jbuenrostro.bsky.social has been named core institute member of the Broad. His lab will study how cells change in response to life experiences, and how those alterations affect health and disease.
@jbuenrostro.bsky.social has been named core institute member of the Broad. His lab will study how cells change in response to life experiences, and how those alterations affect health and disease.
Jason Buenrostro named core institute member at Broad
An expert in epigenetics and longtime member of the Broad community, Buenrostro will focus on how life experiences can alter the epigenome and increase risk of disease.
broad.io
October 1, 2025 at 6:53 PM
Awesome!
Reposted by Andrew C. Adey
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
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 ...
www.biorxiv.org
September 11, 2025 at 7:55 PM
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
Reposted by Andrew C. Adey
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
September 11, 2025 at 7:55 PM
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
I am excited to work with 10x to take single-cell technologies to the next level - lots of new directions!
This acquisition will bring together two pioneering companies with a shared vision: to make single cell analysis more powerful, affordable and accessible to researchers worldwide.
Learn more: bit.ly/4mAWAS8
Learn more: bit.ly/4mAWAS8
August 7, 2025 at 8:44 PM
I am excited to work with 10x to take single-cell technologies to the next level - lots of new directions!
Reposted by Andrew C. Adey
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/vierstralab/...
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
github.com
July 8, 2025 at 3:07 AM
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/vierstralab/...
Reposted by Andrew C. Adey
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)
Online now -- a new Review:
"Molecular circuits for genomic recording of cellular events"
by Wei Chen & Junhong Choi (@choijunhong.bsky.social)
FREE to read till June 25th using this link:
authors.elsevier.com/a/1l2gMcQbJF...
"Molecular circuits for genomic recording of cellular events"
by Wei Chen & Junhong Choi (@choijunhong.bsky.social)
FREE to read till June 25th using this link:
authors.elsevier.com/a/1l2gMcQbJF...
May 6, 2025 at 2:39 PM
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)
Reposted by Andrew C. Adey
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
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.
buff.ly
April 29, 2025 at 8:02 PM
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
Reposted by Andrew C. Adey
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!
Check out our latest preprint, led by Dr. Siyu Chen, that brings together an amazing team of scientists from several labs ( @vram142.bsky.social, Tavazoie, and Navickas) to tackle a fundamental problem in biology: how do cells regulate expression of their tRNAs? www.biorxiv.org/content/10.1...
Discovery of a tRNA-regulatory transcription factor that suppresses breast cancer metastasis
Transfer RNAs (tRNAs), once viewed as static adaptors in translation, are now recognized as dynamic regulators of gene expression. While recent studies have illuminated roles for tRNA stability, the u...
www.biorxiv.org
May 1, 2025 at 3:22 AM
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!
Reposted by Andrew C. Adey
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
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
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...
www.findaphd.com
April 23, 2025 at 9:49 AM
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
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
Reposted by Andrew C. Adey
Whenever my kid sees a Cybertruck she says "that's a stupid truck" and I feel like I'm succeeding at parenting
April 20, 2025 at 11:36 PM
Whenever my kid sees a Cybertruck she says "that's a stupid truck" and I feel like I'm succeeding at parenting
Reposted by Andrew C. Adey
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...
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 ...
www.biorxiv.org
April 4, 2025 at 9:04 AM
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...
Reposted by Andrew C. Adey
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...
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...
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...
www.biorxiv.org
April 4, 2025 at 9:04 AM
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...
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...
Reposted by Andrew C. Adey
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
March 8, 2025 at 1:03 AM
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
Reposted by Andrew C. Adey
Interesting work from the Tomkova group relating DNA hypermethylation of polycomb-repressed regions with gene upregulation. #Epigenetics #DNA_Methylation
De-novo DNA Methylation of Bivalent Promoters Induces Gene Activation through PRC2 Displacement https://www.biorxiv.org/content/10.1101/2025.02.07.636872v1
February 14, 2025 at 1:41 PM
Interesting work from the Tomkova group relating DNA hypermethylation of polycomb-repressed regions with gene upregulation. #Epigenetics #DNA_Methylation
Reposted by Andrew C. Adey
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.
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.
February 8, 2025 at 3:04 AM
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.
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.
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...
(Plus lots more)
www.cell.com/cell-genomic...
December 24, 2024 at 5:36 PM
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...
(Plus lots more)
www.cell.com/cell-genomic...
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.
December 16, 2024 at 5:46 PM
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.