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, D. Żyła, T.A. Heath. “Estimating the age of fossil deposits using a total-evidence approach” Systematic Biology, 2022. DOI: 10.1093/sysbio/syac073
A.M. Wright, D.W. Bapst, J. Barido-Sottani, R.C.M. Warnock. “Integrating Fossil Observations Into Phylogenetics Using the Fossilized Birth-Death Model” Annual Review of Ecology, Evolution, and Systematics, 2022. DOI: 10.1146/annurev-ecolsys-102220-030855
J. Barido-Sottani, J.A. Justison, et al. “Lessons learned from organizing and teaching virtual phylogenetics workshops” Bulletin of the Society of Systematic Biologists, 2022. DOI:10.18061/bssb.v1i2.8425
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
A complete list of my publications can be found in my CV.
Software
- ClaDS package for BEAST2, accessible via BEAUti or at bitbucket.org/bjoelle/clads
- 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 and the corresponding web app FossilSimShiny, also on CRAN CRAN.R-project.org/package=FossilSimShiny
- ML.MSBD package on CRAN CRAN.R-project.org/package=ML.MSBD
Other contributions
- Organizing and teaching online workshops “Bayesian phylogenetic inference with BEAST2” with Transmitting Science, next one in November 2024 - register here
- Phyloseminar (part of a 3-part series on the Fossilized Birth-Death process), Youtube video
Internships
I am happy to supervise master students interested in evolution, paleontology and/or computational biology. A wide range of projects are possible, from model and software development to simulation studies to application to empirical datasets. I also have some smaller projects available for shorter internships.
Please don’t hesitate to contact me directly to discuss what you would like to do !