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We also find that GPN-Promoter (152M params) performs comparably to Evo 2 40B when evaluating only on promoters, suggesting that if you only care about one region, you need vastly fewer parameters. 4/n

this could be very problematic for consortium science. ICs form their special emphasis panels to recruit highly specialized reviewers for RFAs. Unless CSR listens to IC POs on reviewer selections, review for RFAs can become very dysfunctional

Thanks Cell Genomics for highlighting our paper from 2022

the fact that the methylation clock works and is quite robust is one of the biggest scientific surprises (in a very nice way) to me in the past decade

our projects (ones running on mature experimental methods) have been 30% wet+70% dry for years. Bioinformatics takes way too long and is too stochastic.

the bottleneck of genomics is bioinformatics. now a data-heavy manuscript can take 1-2 years of bioinformatics involving 2-3 full-time computational people. this is way too long and should be 3-6 months at most.

Introducing CellBouncer, a unified demultiplexing toolkit built by Nathan Schaefer to check IDs and keep the riff raff out of single cell genomics datasets, including by using genetic variation as an external ground-truth for ambient RNA removal: biorxiv.org/content/10.110…

New preprint: The first whole-body map of both DNA methylation and 3D genome organization at single-cell resolution across 16 human tissues, with in-depth analyses of cell type diversity of these epigenome modalities at unprecedented resolutions. (1/5)

1/10 Excited to share our latest - the first whole-body map of both DNA methylation and 3D genome at single-cell resolution.

nice to see NIH Funding coming back to life

Comparing reagent budgets between now and 3 yrs ago, the only cost that went down is sequencing. everything else went up 30%. Illumina and its competitors are the only reason we can complete projects budgeted in 2021

Great work Rachel, Wei Tian Wei Tian Ecker lab and our long term collaborators Marga Behrens’s and Bing Ren’s groups

Our paper is just out nature.com/articles/s4147… from the Jacobsen, Doudna, and Banfield labs on viral delivery of a tiny CRISPR system for transgene free germline editing in plants, tinyurl.com/3k223r3x.  Looking for postdocs to join the team for the next phase of this work!

In March last year, at the age of 35, I was diagnosed with advanced stage III rectal cancer with a metastasis in my liver. This was a shock: I had no family history, and none of the doctors suspected it. In fact, I'd had a negative occult blood test when I went to ER with severe

A new paper "CMImpute: cross-species and tissue imputation of species-level DNA methylation samples across mammalian species" led by Emily Maciejewski building on our lab's mammalian methylation array collaboration with Prof Steve Horvath is now published genomebiology.biomedcentral.com/articles/10.11…

Our latest study in AJHG shows how chemoproteomics can help prioritize disease-linked missense variants 🧬 1/2

ChatGPT is just as confused as everybody about mammalian gene body methylation. Its answer is very "planty" reminding me of the two Arabidopsis MeDIP array papers Zhang 2006 Cell & Zilberman 2007 NG

Preprint alert: single-cell methylation signature of autism in collaboration with Geschwind Lab @ UCLA. Autism-mC signal is enriched in promoters and cell-type enhancers but uncorrelated with gene expression. Led by Geschwind Lab @ UCLA Postdoc Katie Eyring and grad student Cuining Liu.

I’m honored to join Fred Hutch as Professor and Program Head of Biostatistics, and as the Donald and Janet K. Guthrie Endowed Chair in Statistics. Excited to be part of a deeply collaborative and scientifically vibrant community with a rich legacy of impact.

Our paper on deep single-cell DNA methylation analysis is out in Nature Communications rdcu.be/evfJm. Super elegant work by Nathan Spix describing replication dynamics, X-inactivation, and cell lineage identification.