My research area revolves around computational models and methods for phylogenetics. In general, we use next generation sequencing (NGS) data as input. As output, we either infer orthology information or the species tree. To achieve this, we use probabilistic methods and approximation frameworks (like Markov Chain Monte Carlo (MCMC) and Expectation Maximization (EM)).

More specifically, I am interested in designing effecient algorithms for

  1. Inference of orthologous relationship among genes. (see DLRSOrthology)
  2. Reconstruction of species trees using gene sequence data. (see MixTreEM)
  1. Ullah, I., Sjöstrand, J., Andersson, P., Sennblad, B., and Lagergren, J. (2015). Integrating sequence evolution into probabilistic orthology analysis. Systematic Biology, 64(6):969--982. [ DOI | http ]
  2. Ullah, I., Parviainen, P., and Lagergren, J. (2015). Species tree inference using a mixture model. Molecular Biology and Evolution. [ DOI | http ]