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)
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.
- RevBayes: revbayes.github.io, source at github.com/revbayes/revbayes
- MSBD package for BEAST2: accessible via BEAUti or at bitbucket.org/bjoelle/msbd
- FossilSim package on CRAN: CRAN.R-project.org/package=FossilSim
- ML.MSBD package on CRAN: CRAN.R-project.org/package=ML.MSBD