Andrew C. Adey

GitHub - lrylaarsdam/amethyst: A comprehensive toolkit for single-cell methylation sequencing data analysis A comprehensive toolkit for single-cell methylation sequencing data analysis - lrylaarsdam/amethyst

The goal is to provide a lot of flexibility in a familiar framework, while delivering robust analysis methods coupled with extensive visualization options.

Check it out!

github.com/lrylaarsdam/...

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 ...

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...

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...

Awesome!

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 ...

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

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!

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

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/...

Thanks for this! What is your take when sample quality means only modest ATAC-seq quality is possible. (too low is not usable, so let's say borderline) In many cases, eg primary tumors etc... high quality can never be achieved. What is the threshold for different analyses that can be performed?

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)

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.

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

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!

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...

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

Whenever my kid sees a Cybertruck she says "that's a stupid truck" and I feel like I'm succeeding at parenting

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 ...

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...

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...

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...

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

Interesting work from the Tomkova group relating DNA hypermethylation of polycomb-repressed regions with gene upregulation. #Epigenetics #DNA_Methylation

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.

"Single" cell... no editing typos on bluesky I guess.

Finally, we leverage stepwise, indexed tagmentation to produce ATAC and DNA methylation profiles from the same cells. We believe this will be particularly useful for bridging to ATAC atlases to better facilitate Cell type annotation.

To enable more sequencing options, we also developed primers for direct preparation for sequencing on Ultima Genomics instruments. We sequenced >140k cells from human cortex.

We also show you can use enzymatic conversion methods instead of bisulfite.

sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden - Genome Biology DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. Robust, high-throughput single-cell DNA methylation assays are no...

The core of the improvement is an additional layer of indexing. This is done while maintaining the same molecular structure as sciMETv2 which enables compatibility with our sciMET-CAP capture workflow. (genomebiology.biomedcentral.com/articles/10....)

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...

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.