Sahin Naqvi

Naqvi Lab Quantitative principles of gene regulation in development and disease. Quantitative principles of gene regulation in development and disease

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!

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

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage Naqvi et al. reveal how DNA sequence determines the chromatin response to transcription factor (TF) dosage changes. By combining deep learning and chemical genetics, they uncover specific sequence fea...

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...

Congrats Ryan!

Thanks Benoit! Likewise, I have been following your work on cardiac TFs for a while and look forward to the next iteration! Hope to run into you at a conference or elsewhere in the future

We’re also happy to hear any other questions and feedback from you and your lab - email may be easier. sahin dot naqvi at childrens dot harvard dot edu

Hi Benoit, thanks for pointing this out. In almost all of the cases (I think) you’re referring to, N (which we do provide) is so high that every comp. is p<2.2e-16, so we focused on the distribution of values instead. But we should have still indicated p-values. Will do in the accepted version.

Kim Lab at UC Irvine Visit the post for more.

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/

The single-molecule accessibility landscape of newly replicated mammalian chromatin By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...

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

Naqvi Lab Quantitative principles of gene regulation in development and disease. Quantitative principles of gene regulation in development and disease.

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

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"

Looking forward to being neighbors, Ryan!

Excited to share that I will be starting my lab as faculty at Boston Children’s Hospital and Harvard Medical School
in July 2024! We will seek a quantitative understanding of gene expression control in development and resulting “tipping points” in disease. Please reach out if interested!

Congratulations Vijay!

We're looking for a postdoc! Cool ERC-funded project digging into gene dosage variation with CRISPR+sc+computational methods. Dynamic environment at KTH / SciLifeLab Stockholm campus, plus interactions with our New York team. Apply or email for more info:
kth.varbi.com/se/what:job/...

Excited to present our recent work on TF dosage sensitivity (www.nature.com/articles/s41...) and a sneak peak at what’s in the pipeline at the Fragile Nucleosome series, tomorrow (Wed) 9 AM PST! Register here: generegulation.org/fragile-nucl...