iiinova — where your digital self keeps evolving

Mir Lab @mirlab.bsky.social · 07/06/2026

1/🧵 Can transcription factor condensate formation be explained without phase separation? Our new preprint introduces SPARK, a simulation tool that reproduces condensate behavior (clustering, fusion, FRAP) from diffusion & binding kinetics alone. Movie: 60 sec FRAP sim www.biorxiv.org/content/10.6...

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Mir Lab @mirlab.bsky.social · 16/04/2026

Very proud of Samantha "S" Fallacaro the first student from our lab to defend their thesis! Check out her latest work (tinyurl.com/42hdfssz) where she shows that "hubs" formed by the transcription factor Dorsal are emergent features of binding kinetics, not higher-order regulatory assemblies.

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CAMB Graduate Group @cambupenn.bsky.social · 13/04/2026

Samantha Fallacaro in the @mirlab.bsky.social defends her thesis tomorrow!

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Mir Lab @mirlab.bsky.social · 20/03/2026

@mukherja.bsky.social work on RNAPII clusters is in print today: www.nature.com/articles/s41... Congrats! TLDR: RNAPII clusters represent transcriptonally engaged molecules at single genes, not super-stochiometric assemblies. Please check it out and see the the thread below for a summary.

nature.com

A single cluster of RNA Polymerase II molecules is stably associated with active genes - Nature Communications

Live molecular-scale imaging in fly embryos shows that a single RNA Polymerase II cluster stays bound to active genes during transcription. Cluster formation requires initiation, and intensity represe...

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Mir Lab @mirlab.bsky.social · 05/01/2026

We are happy to have contributed single-molecule tracking and super-resolution imaging to this great work from Nik Sgourakis' lab. HLA-Shuttle restores antigen presentation in immunologically cold tumors enabling the identification of new targets for immunotherapy. www.science.org/doi/10.1126/...

science.org

HLA-Shuttle: A system for enhancing antigen presentation in immunologically cold tumors

HLA-Shuttle enhances production of HLA class I molecules in neuroblastoma, leading to the discovery of tumor-associated antigens.

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Apratim (Appy) Mukherjee @mukherja.bsky.social · 18/09/2025

Huge props to our grad student @manyakapoor.bsky.social for developing the simulations and the new MS2 analysis amongst other things! We also thank the transcription community for their invaluable feedback and always welcome further discussion😊

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Andrew Modzelewski @themodzlab.bsky.social · 13/05/2025

WE ARE HIRING! The lab got the Packard AND an R35! Please spread this PostDoc Ad around! Philly and Upenn are a great place to live and work!

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Mir Lab @mirlab.bsky.social · 11/04/2025

1/n We have an exciting new initiative at UPenn to provide custom advanced microscopy solutions: Advanced Core for Microscope Engineering (ACME): www.med.upenn.edu/cdbacme/ We are looking for a specialist to help run this new facility, job description is attached please help share widely!

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Mir Lab @mirlab.bsky.social · 09/04/2025

1/n: Excited to share our new preprint. We find that Dorsal transcription factor hubs exhibit gene-specific biophysical properties that tune transcriptional output. Read here: www.biorxiv.org/content/10.1.... Project was led by amazing graduate student Samantha Fallacaro (not on bsky)

biorxiv.org

Transcription factor hubs exhibit gene-specific properties that tune expression

The spatial and temporal control of gene expression relies on transcription factors binding to and occupying their target sites. Transcription factor hubs - localized, high-concentration microenvironm...

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Patrick S. Mitchell @psmitchej.bsky.social · 21/02/2025

In light of policies to defund biomedical research, and with judicial hearings happening today, we hope to highlight the many ways biomedical research improves people's lives, and to convey how damaging the proposed cuts would be... not just for us researchers, but for everyone.

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Mir Lab @mirlab.bsky.social · 12/02/2025

1/n Excited to share our new preprint! Using live imaging in Drosophila embryos, we show that RNA Pol II clusters switch from sites of initiation to elongation during zygotic genome activation and that they are stably associated with an active gene: www.biorxiv.org/content/10.1...

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Mir Lab @mirlab.bsky.social · 17/01/2025

Big congratulations to our MD/PHD student @driaadigun.bsky.social on receiving a F31 award from NIGMS to "Illuminate the Molecular Mechanisms of Replication and Transcription Coordination" during zygotic genome activation and support her training.

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Mir Lab @mirlab.bsky.social · 10/02/2024

#BPS2024 check out our lab's presentations & pls reach out if you want to chat! Posters:B128 (@littlescholar_ ) txn activator hubs, B195(@GHaywardLara ) repressive bodies. Talks: @mukherja PolII kinetics(13th,5:30 p 201AB), myself, on how hubs find their targets (14th,9:30a BRA)

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Mir Lab @mirlab.bsky.social · 22/12/2023

Happy holidays from our lab to yours!

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Mir Lab @mirlab.bsky.social · 31/10/2023

Happy Halloween from the lab, all whom decided to dress like their very scary PI this year 🎃

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