Work
I do cancer genomics. The through-line is measurement: taking properties of tumours that are agreed to matter — how unstable a genome is, which route it took to its present state — and turning them into something a sample can actually be scored on.
That means methods as often as findings, and software as often as papers.
Cancer Genomics
What tumour genomes record about the processes that shaped them, read off sequencing rather than inferred from models alone.
Chromosomal Instability
CIN exists at levels that matter clinically, but the rate itself is hard to measure. Most of my work has been on quantifying it.
Complex Tumor Evolution
Genome doubling and multipolar division push tumours into copy-number states that no simple sequence of events explains.
Phenotype Plasticity
How much of what a tumour does is written in its genome, and how much is a state it can move into and back out of.
Methods & Software
Tools that make the above measurable: inference of mis-segregation rates, and figures built to argue rather than to browse.
Writing
Publications
| Date | Venue | Title |
|---|---|---|
| Aug 2024 | Cancer Discovery | The History of Chromosomal Instability in Genome-Doubled Tumors |
| Apr 2024 | PNAS | A survey of chromosomal instability measures across mechanistic models |
| Feb 2024 | Chromosome Res | The reckoning of chromosomal instability: past, present, future |
| Oct 2023 | PLOS Biology | Diverse microtubule-targeted anticancer agents kill cells by inducing chromosome missegregation on multipolar spindles |
| Apr 2022 | eLife | Quantifying chromosomal instability from intratumoral karyotype diversity using agent-based modeling and Bayesian inference |
| May 2015 | JUCR | Short Proline-Substituted Muc1 Mucin Peptides Can Bind To Mouse Muc1 Monoclonal Antibody as Revealed by STD NMR |
Software
| Project | What it does | Source |
|---|---|---|
| CINFER | scDNAseq-based estimates of chromosome mis-segregation rates. | Repository ↗ |
| ggsuperviolin | Violin SuperPlots for ggplot2 | Repository ↗ |
| iBover | Models the karyotypic consequences of multipolar mitotic divisions. | |
| SeqPlotR | Flexible, grid-based genomic track plots. | Repository ↗ |