Golnaz Vahedi

New preprint in collaboration with the Faryabi lab: Optical Looping Interactive Viewing Engine (OLIVE), a web-based tool designed for high-throughput chromatin tracing data that functions similarly to genome browsers. If you work with these data, give a try: www.biorxiv.org/content/10.1...

If you are interested in T and B cells, you can look your favorite gene and its connectivity here: sorayoon.shinyapps.io/HiCociety/

Hi-Cociety does magic: it takes Hi-C data and determines cell-type specific highly connected regions without taking any additional input.

🚨 New #preprint alert!
We're excited to share the latest work from the brilliant Sora Yoon: "Inference of multi-enhancer interactions in T lymphocytes using Hi-Cociety"🔗 www.biorxiv.org/content/10.1...

🚨 New #preprint alert!
We're excited to share our latest work:
"Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T Cells"🔗 tinyurl.com/4ve26tbd

Deep gratitude to the Vahedi and Faryabi Labs and all our supporters and funders who made this possible! #Tcells #chromatin #generegulation #microscopy #epigenetics #immunology #developmentalbiology #ORCA #teamwork

✨ This is the first chromatin tracing study in immune cells, and we're incredibly proud of the team for reaching this milestone.

🧬 Key findings:
The dominant chromatin conformation pulls Ets1 close to its super-enhancer, spatially separating it from Fli1.
Deleting the super-enhancer rewires the locus, increasing Ets1–Fli1 promoter-promoter interactions.
This suggests that enhancer "pulling" override domain boundaries.

💡 Huge thanks to Alistair Boettiger, Guy Nir, Ting Wu, and their lab members for their generous help in troubleshooting the approach.

To investigate, we needed to resolve chromatin architecture at single-allele resolution in individual cells. Atishay and Yeqiao implemented ORCA (Optical Reconstruction of Chromatin Architecture)—a sub-diffraction microscopy method—that lets us walk along the chromosome.

🔍 Our question: Why are certain paralogous transcription factors—like Ets1 and Fli1—maintained in close genomic proximity across hundreds of millions of years?

This study was a huge team effort, led by the brilliant @atishayjay.bsky.social in close collaboration with Yeqiao Zhao in the @faryabi.bsky.social Lab, with key contributions from @arjunraj.bsky.social, whose Nimbus image analysis tool was essential.

🚨 New #preprint alert!
We're excited to share our latest work:
"Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T Cells"🔗 tinyurl.com/4ve26tbd

Wonderful news. Very well deserved

Wonderful news. Congrats!

Baby Is Healed With World’s First Personalized Gene-Editing Treatment

Sometimes you only need to focus on good news: www.nytimes.com/2025/05/15/h...

Thanks for the opportunity!

GLOBAL IMMUNOTALKS: Virtual immunology seminar series YouTube video by GLOBAL IMMUNOTALKS

The recorded video of Dr. Golnaz Vahedi seminar entitled Chromatin topology at paralogous transcription factors is now available at “Global Immunotalks” YouTube Channel youtube.com/live/7aw_Qx5...
Please ask questions in the Youtube comment section for Golnaz.
Hope you enjoy it!

Looking forward to our next #globalimmuno talk this Wednesday, May 7th, at 9am PST, noon EST, 4pm GMT by Dr. Golnaz Vahedi.

Title: “Chromatin topology at paralogous transcription factors”
ZOOM LINK: ucsd.zoom.us/j/91053505061
LIVE ON YOUTUBE: www.youtube.com/@GLOBALIMMUNOTALKS

It takes a special talent to observe the phenotype of an ETS1 super-enhancer deletion and see into the evolution of paralogous transcription factors.

Holy 🤯, @vahedilab.bsky.social!

Thanks Scott!

Congratulations to Katalin Karikó (@PennNSG), Virginia Lee (@pennpathlabmed.bsky.social), @ejohnwherry.bsky.social (@PennSysPharmATT) & Mark Devlin (@physatpenn) on their election to @nasonline.org! tinyurl.com/5eehdtms

Congrats! So well deserved.

Congrats Maria!

Congrats!

We were also incredibly lucky to have the talented Dr. Stacie Bumgarner create the cover art. The illustration draws a metaphor between T cell differentiation and the Pachinko game—capturing the dynamic and unpredictable nature of cell fate decisions.

Fantastic news. We love Nimbus so much. Saved us from pain and misery. Thanks Arjun and lab

NimbusImage

Super excited to be launching NimbusImage.com! Cloud-based image analysis to democratize machine learning!

Documentation here!
docs.nimbusimage.com

The epigenetic landscape of fate decisions in T cells - Nature Immunology Vahedi and colleagues review the mechanisms shaping the epigenetic landscape of CD4+ and CD8+ T cells during development and differentiation.

Congrats to Atishay and Carlos for their review article on the epigenetics regulation of T cells: www.nature.com/articles/s41...

Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data - Nature Biotechnology Accuracy of gene regulatory network inference is increased by combining multiome single-cell and atlas-scale bulk data.

Accuracy of gene regulatory network inference is increased by combining multiome single-cell and atlas-scale bulk data go.nature.com/43YySqO
rdcu.be/ebBio