Welcome to Ziheng Yang Lab
Our group is based at Department of Genetics, Evolution and Environment (GEE), University College London (UCL). We are connected to the UCL Centre for Computational Biology and the Centre for Life’s Origins and Evolution (CLOE) in UCL. We have ongoing collaborations with scientists around the world, including UCL statistics (Professor Petros Dellaportas), California, Duke, Seattle, China, Japan, Zurich, and Heidelberg.
We are a small group of friendly and highly motivated researchers with varied backgrounds, including evolutionary genetics, genomics, computer science and statistics. We develop statistical models and computer software for population genetic and phylogenetic analysis of DNA or protein sequence data, both from different species and from the same species. We make heavy use of maximum likelihood and Bayesian methods, and develop sophisticated Markov chain Monte Carlo algorithms that can meet the challenges of huge datasets resulting from genome projects. Analysis of genome-scale datasets is also a major undertaking in the group, which helps to test the new methods we develop and motivate the methodological work.
Current projects in the group include (i) development and implementation of the multispecies coalescent model to incorporate cross-species gene flow, using both maximum likelihood and Bayesian MCMC, (ii) Bayesian estimation of species divergences integrating information from both the fossil record and molecular sequence data, (iii) mixing efficiency of MCMC, especially trans-model MCMC, and (iv) analysis of genome-scale datasets from viruses, mammals, and plants.
We welcome bright students with background in probability theory (e.g., Markov chains and stochastic processes), mathematical statistics (in particular computation-intensive methods such as MCMC), computer science (such as high-performance computing, C programming), as well as population genomics and phylogenomics to join us as MSc/PhD students. If you are good at one of those areas (probability and statistics, computer science, and evolution and genomics) and hope to improve your skills in the other areas, then there is a high chance that we have the right projects for you.
News
23. January 2023The 'Evolutionary Analysis Using PAML' Workshop with Sandra and Ziheng has come to an end! Check some pictures of our visit during the workshop at University of Sydney!.
17. January 2023Sandra and Ziheng are flying to Sydney to teach the 'Evolutionary Analysis Using PAML' Workshop as part of the USyd-UCL PCA Sandra received together with Prof Simon Ho.
16. December 2022'Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks' is published in Systematic Biology and Evolution.
1. December 2022After many years, we have had the first joint lab dinner with Mario's lab before the winter holidays! You can see our group picture here.
11. November 2022
Tom Roberts will be joining the lab as an MSc student and will work with Tomas to test different features of BPP. Welcome to the lab, Tom!
1. November 2022'Inference of gene flow between species under misspecified models' is published in Molecular Biology and Evolution.
21. October 2022New PhD position available on establishing evolutionary timescales at Bristol University. More information about how to apply here.
13. October 2022Sandra has been awarded the USyd-UCL Partnership Collaboration Award (PCA) together with Prof Simon Ho (USyd) for the project 'Reconstructing the evolutionary timescale of the Tree of Life'. Congratulations!
18. August 2022Sandra will be giving a talk at the ESEB 2022 conference! Join her on August 19 at 12.15h at South Hall 1B to learn more about the Bayesian sequential-subtree approach for timetree inference!
