First publication on rAAV vector quality control by next-generation sequencing. Currently being used for several human gene therapy clinical trials. The method then got refined and published in 3 subsequent papers and reviews.
Although the paper was published in a journal without impact factor, this is my greatest impact research project. pycoQC has gained a lot of popularity in the Nanopore community and was downloaded more than 60,000 times, highlighting that the impact on the research community is much more than a mere impact factor. The Journal of Open Source Software is very developer friendly and I enjoyed the open peer-review process via Github.
Short communication in response Kaeppel et al highlighting a major flaw in a next generation sequencing method used to map rAAV vector integration sites in clinical trial human samples. The story goes that we were trying to develop a method very similar and realised thanks to robust controls that the library preparation protocol was generating random artifactual integration sites with a profile extremely similar to the one they published. We were about to abandon the project but decided that the data should be published to avoid the flawed protocol being used further in the gene therapy field.
In this work recently released on BioRxiv, we described the first method for accurate detection of several RNA modifications at high spatial and single molecule resolution. This was an exciting bioinformatics co-development experience with Tommaso Leonardi resulting in NanoCompore, a significant piece of software which is gaining traction in the field.
My main PhD paper describing my vain search for DNA methylation on the rAAV vector genome. I was an early adopter of pyrosequencing (not the high throughput 454 version) to detect CpG methylation after bisulfite conversion. We managed to painstakingly demonstrate that rAAV genomes stay free of DNA methylation throughout the transduction of the host cell.Full list available at ORCID and Google Scholar