Our latest paper has just been published in Cell!

doi.org/10.1016/j.ce...

We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.

Great to see @maxdudek.bsky.social in the @upenngcb.bsky.social program interviewed by @ajhgnews.bsky.social

www.ashg.org/ajhg/inside-...

🚨New Paper Alert🚨

Now out in @bloodjournal.bsky.social

We scoured the ends of the earth for rare human PU.1 variants and subjected 134 of them to suite of functional assessments.

We're disappointed to see Ben Barres's powerful book "The Autobiography of a Transgender Scientist" among the ~400 titles removed from the Naval Academy Library. Needless to say, we're proud to have published his book and will keep it — and his memory — alive.

Our recent preprint about using a custom chromatin capture assay, to identify potential target genes for cancer risk variants. For several variants, the target gene for cis regulation was ~ +/- 1Mb away, and we experimentally confirmed this for multiple targets.
www.medrxiv.org/content/10.1...

This Friday! Job Dekker, PhD presents the Monthly Seminar on Physical Genomics: Mechanisms of Chromosome Folding

January 31, 2025 - Live on Zoom @ 12pm CT - Registration is free at tinyurl.com/5n6ep25m

#chromatin #genomics #northwestern #research #dna #umass #biophysics #epigenetics #biology

Excited to share James Jusuf's preprint:

By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)

We quantify mESC 36k loops: are generally rare (2.3%)

www.biorxiv.org/content/10.1...

I’m excited to share that this manuscript is now published in Nature Genetics! 🧪🧬 🖥️

www.nature.com/articles/s41...

The AdipoExpress data can be accessed here: zenodo.org/records/1384...

An interactive browser of the colocalization results can be accessed here: adipose.colocus.app

Clean image of galaxy cluster MACS J1423, where the Firefly Sparkle galaxy is located.
🔭 🧪

scRNA-seq data sets exploding in number and size - check out scanpy & anndata for >1b cells: new experimental update includes APIs for scaling with dask from anndata, integrated with lots of scanpy and rapids-singlecell functions.
gist.github.com/ilan-gold/98...

Beautiful work led by Maya Arce from Marson lab reveals a fascinating story about rewiring of a critical gene regulatory circuit in different T cell types: T effectors and Tregs
www.nature.com/articles/s41...

If you use SHAP, LIME or Data Shapley, you might be interested in our new #neurips2024 paper. We introduce stochastic amortization to speed up feature + data attribution by 10x-100x 🚀 #XML

Surprisingly we can "learn to attribute" cheaply from noisy explanations! arxiv.org/abs/2401.15866