I am a computational biologist, specialised in the development and implementation of mathematical models for evolutionary processes. I have worked extensively with Bayesian phylogenetic inference, and contributed to both BEAST2 and RevBayes.

I am interested in birth-death processes, and developed a new model for the inference of lineage-specific birth and death rates from a phylogeny. I have also explored the behaviour of the fossilized birth-death (FBD) process in several simulation studies.

Additionally, I care about improving the reliability and usability of scientific software. I explore ways to improve both the developer and the user experience, as well as import best practices from other areas of software development.

Interests: Bayesian phylogenetic inference, birth-death processes, scientific software

Programming languages: Java, C++, R, Python (beginner)

Selected publications

J. Barido-Sottani, T. G. Vaughan, T. Stadler. “A multi-types birth-death model for Bayesian inference of lineage-specific birth and death rates” Systematic Biology, 2020. DOI: 10.1093/sysbio/syaa016

J. Barido-Sottani, G. Aguirre-Fernández, M. J. Hopkins, T. Stadler, R. C. M. Warnock. “Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process” Proceedings of the Royal Society B, 2019. DOI: 10.1098/rspb.2019.0685

J. Barido-Sottani, W. Pett, J. E. O’Reilly, R. C. M. Warnock. “FossilSim: an R package for simulating fossil occurrence data under mechanistic models of preservation and sampling” Methods in Ecology and Evolution, 2019. DOI: 10.1111/2041-210X.13170

J. Barido-Sottani, T. G. Vaughan, T. Stadler. “Accurate detection of HIV transmission clusters from phylogenetic trees through a multi-states birth-death model” Journal of the Royal Society Interface, 2018. DOI: 10.1098/rsif.2018.0512

A complete list of my publications can be found in my CV.

Software

CV

CV_Barido-Sottani.pdf