Hello Bluesky friends! I am a #newPI starting at UC Irvine in April, interested in gene regulation and functional genomics in stem cell models of development (esp neural crest). We are hiring at all levels – please reach out/spread the word! sskimlab.org
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
Relative to the preprint, we added enhancer reporter assays testing the effect of homotypic binding on SOX9 dosage response, as well as analyses of inferred nucleosome positioning as a function of TWIST1 dosage
I'm delighted to release the first half of my new textbook in human genetics:
web.stanford.edu/group/pritch...
"An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"
We are looking for two exceptional Research Assistants!
1) Experimental, to drive forward quantitative studies of transcription factor function in development
2) computational, to develop and apply cutting-edge deep learning models of gene regulation.
Links below
Job Details: Position Summary: Research Assistant in Quantitative Gene Regulation/Stem Cell BiologyThe Naqvi lab at B
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...
Excited to share the peer-reviewed version of our paper on predicting the chromatin response to TF dosage using transfer learning
www.cell.com/cell-genomic...
We are building upon this approach in my lab @bostonchildrens.bsky.social @harvardmed.bsky.social and are recruiting at all levels: if interested see naqvilab.org and reach out!
Exciting update: we have a lab website! naqvilab.org
Stay tuned for formal ads for research assistant and postdoc positions, but please reach out in the mean time if interested in joining!
Thanks to the Greene lab for the excellent lab website template
Aiming to release our long awaited ChromBPNet preprint by early next week as well. I'm recovering from back to back infections for the past 6 weeks. But we're almost there. We have some solid variant prediction benchmarks in there against large supervised models and lots more. Stay tuned.
Anshul Kundaje
The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics
