Department of Genetics · Harvard Medical School
A cell makes thousands of mRNAs every minute and controls every one of them — where it is made, how it is processed, how long it survives, and whether it is ever translated. We build quantitative methods that make those steps measurable, in both the nuclear and the mitochondrial genome.
Leidy Churchman, Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA (2024)
Recent work
By measuring RNA production, processing, ribosome association and degradation across both genomes, we found that nearly every step runs at a starkly different rate. The mitoribosome acts as a key point of coordination between the two systems.
McShane et al., Molecular Cell 2024
How this fits together →
Long-read chromatin fiber sequencing lets us see RNA polymerases in their native chromatin context along 30 kb fibers, revealing direct coordination and anti-coordination between neighboring genes, enhancers and insulators.
Tullius et al., Molecular Cell 2024
Read the paper →
AIR-seq marks new RNA with N4-hydroxycytidine, which base-pairs ambiguously and so shows up as mismatches in standard libraries — no chemical conversion, no enrichment. RNA synthesis and decay rates now come out of ordinary bulk and single-cell experiments.
Hansen & Couvillion et al., bioRxiv 2026
How this fits together →The lab
The lab has always been a mix. Stirling trained as a physicist and the people here now came in through biochemistry, neuroscience, chemistry, and computation.
Use our work
Identifies which functions of a gene actually matter in your biological context, by learning vector representations of genes and GO terms on a condition-specific network. pip install genewalk.
Published, benchtop-ready protocols for NET-seq, nano-COP, subcellular RNA-seq and mitoribosome profiling — with the corrections we have issued since publication.
71 papers, every one linked out to the journal or PubMed record, searchable by title, author, method or year.
All publications →We take people from biology, chemistry, physics, computer science, mathematics and engineering. If you want to answer a question about gene regulation with our novel set of methods--or develop your own--we should talk!