Epigenetics Update - Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription go.nature.com/49iRJkK Albert W. Cheng and Yijun Ruan (Jackson Laboratory) reporting in NSMB #Epigenetics #Chromatin --- Discover the breakthrough at epigenometech.com

20 years ago today we first reported the TCF7L2 association with type 2 diabetes @natgenet.nature.com. Much to still figure out for this locus.... www.nature.com/articles/ng1...

Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes - Nature Genetics

Nature Genetics - Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes

nature.com

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-...

Inside AJHG: A Chat with Max Dudek

Editors of The American Journal of Human Genetics sat down with Max Dudek, BS, to discuss his recently published paper, “Characterization of non-coding variants associated with transcription-factor bi...

ashg.org

🚨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.

The Coming Out of a Transgender Scientist

"I know that I am making the right decision because whenever I think about changing my gender role, I am flooded with feelings of relief."

thereader.mitpress.mit.edu

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...

Mapping chromatin interactions at melanoma susceptibility loci and cell-type specific dataset integration uncovers distant gene targets of cis-regulation

Genome-wide association studies (GWAS) of melanoma risk have identified 68 independent signals at 54 loci. For most loci, specific functional variants and their respective target genes remain to be es...

medrxiv.org

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: <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

Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits - Nature Genetics

This study introduces AdipoExpress, an eQTL meta-analysis of 2,344 subcutaneous adipose tissue samples, which triples the size of previous studies and expands the discovery of eQTLs colocalized with G...

nature.com

Sarah Brotman@sarahbrotman.bsky.social · 3y ago

I am excited to share our preprint describing a collaborative effort to identify conditionally distinct signals in the largest adipose eQTL dataset to date (AdipoExpress). @kerrinsmall.bsky.social @klmohlke.bsky.social Laura Scott, and others 🧪🧬 🖥️ #GeneSky 1/8 www.biorxiv.org/content/10.1...

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...

Central control of dynamic gene circuits governs T cell rest and activation - Nature

Resting and activated T cell states are established by context-specific regulators and dynamic gene circuits.

nature.com

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