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The computational biology research group develops new computational methods, efficient algorithms, and powerful software tools to help answer fundamental biological questions. We are especially interested in problems related to understanding the evolution of genes, genomes, and species. Some of our specific projects include:

  • Inferring gene family and genome evolution through gene duplication, horizontal transfer, and loss.
  • Understanding evolution at the sub-gene/domain level.
  • Reconstructing highly accurate gene trees in both eukaryotes and prokaryotes for evolutionary and functional genomic studies.
  • Building whole-genome and multi-locus species phylogenies.

Open Positions

PhD positions: Positions are available in the computational biology group for bright and motivated PhD students. Please click here for further details.

Research opportunities for undergraduate students: Positions are also available for motivated undergraduate students who wish to gain research experience by working on exciting research problems. Please click here for further details.


April 2018: Paper describing RANGER-DTL 2.0 accepted to Bioinformatics.

December 2017: Soumya's paper on the uncertainty of gene tree rooting and its impact accepted to BMC Bioinformatics.

October 2017: Lei's paper on integrated analysis of domain, gene, and species level evolution accepted to APBC 2018 and to IEEE/ACM TCBB.

August 2017: Software for simultaneous analysis of domain, gene, and species level evolution, SEADOG 1.0, is now available.

July 2017: Two new PhD students Lina Kloub and Farzaneh Rastegari join our research group.