Check out our new preprint with Jie Liu's lab on a general AI model that can predict diverse genomic outputs such as transcription and genome structure, which is now on BioRxiv.

Congratulations to Clarice and Varshini on their new preprint - in collaboration with co-first author Fan Feng and Jie Liu - describing Cleopatra, a new ML model that can predict 3D genome structure at very high resolution. You can read the full preprint on BioRxiv.

Congratulations to Viraat - now Dr. Goel - on successfully defending his PhD Friday April 11th, 2025. Well done Viraat!

Congratulations to Masahiro on the publication of his new Preview in Cell Genomics, where he highlights and discusses a very nice new paper from Tjalsma...de Laat and co-workers entitled Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations.

We are sad to say goodbye to Daria Sels, who visited the lab for 9 months as a Master's student from Belgium, but we wish you all the best for your upcoming travel and your future PhD!

Congratulations to Viraat on his collaborative paper with Nick Aboreden and Gerd Blobel, where he used RCMC to show that LDB1 is a true looping factor. You can read the full paper in Molecular Cell.

The lab turned 5 years old on Feb 1st, 2025. To celebrate, we went candlepin bowling in Southie!

Congratulations to James on his new preprint in collaboration with Simon, Michele, Pia, and Ilya among our lab and the Zechner, Giorgetti, and Mirny labs. You can find the preprint on BioRxiv.
3D Genomics methods such as Hi-C and Micro-C can identify many thousands of loops across the genome, but all the quantifications are relative. By integrating super-resolution live-cell imaging with Micro-C and new computational methods, James now reports absolute quantification of chromatin loops for the first time (as in, e.g. this loop is present 3% of the time). Across the genome, James finds loops to be generally rare with implications for gene regulation and the mechanisms of enhancer-promoter interactions. Congratulations to James!