y research group is focused on molecular evolution, phylogenetics and genomics. At the moment the research is entirely computational, involving model development, simulation, and analysis of real data. The approach is statistical, making use of maximum likelihood and Bayesian methods. The unifying theme of all this is the study of adaptation and diversification at the molecular genetic level.

Specific research areas:

Genetic co-option and gene family evolution: Genetic co-option is the tailoring of existing genetic systems to new uses. We are interested in the role of positive Darwinian selection following genetic co-option in protein coding genes. The current emphasis is to study this within the context of gene duplication. The research involves large scale surveys of gene families in public databases, with the goal of testing for different patterns of divergent selection pressure following gene duplication events. We also study individual cases in great detail, where we try to infer the mechanisms, pace and timing of adaptive evolution.

Modeling codon and amino acid evolution: This work involves extension and development of codon and protein models. One area of interest is developing realistic ways to model the effect of physiochemical properties on substitution probabilities among codons and amino acids. Empirical surveys are used to guide model development.

Comparative genomics of closely related prokaryotes: This area of research takes advantage of the increased power that the growing number of closely-related prokaryotic genomes can provide. Phylogenomic methods are used to (1) investigate the basis of adaptive diversification in a genomic context; (2) provide additional insights into the evolution of pathogenicity; and (3) to provide practical benefits such as aiding vaccine development.

Sabehi, G., M. Ramon, J.P. Bielawski, M. Rosenber, E. F. Delong, and O. Béjà. (2003) Novel Proteorhodopsin Variants from the Mediterranean and Red Seas. Environmental Microbiology, 5: 842-849.

Bielawski, J. P. and Z. Yang. (2003) Maximum likelihood methods for detecting adaptive evolution after gene duplication. Journal of structural and Functional Genomics, 3: 201-212.

Yang, W., J. P. Bielawski, Z. Yang. (2003) Widespread adaptive evolution in the human immunodeficiency virus type-1 genome. Journal of Molecular Evolution, 57:212-221.

Bielawski, J. P. and Z. Yang. (2003) Maximum likelihood methods for detecting adaptive evolution in gene families. In: Genome Evolution: Gene and Genome Duplications and the Origin of Novel Gene Function. A. Meyer and Y. Van De Peer (eds).

Ward, T. J., J. P. Bielawski, H. C. Corby-Kistler, E. Sullivan, and K. O'Donnell. 2002. Ancient polymorphism and adaptive evolution in the trichothecene gene cluster of phytopathogenic Fusarium. PNAS 99:9278-9283.

Bielawski, J. P. 2002. Phylogenetic inference: an overview. In: Oxford Encyclopaedia of Evolution. M. Pagel (eds) Oxford University Press, Oxford. Pp. 891-895.

Bielawski, J. P. and J. R Gold. 2002. Mutation patterns of mitochondrial H- and L-strand DNA in closely related cyprinid fishes. Genetics 161:1589-1597.

Bielawski, J. P., A. C. Brault, and J. R Gold. 2002. Phylogenetic relationships within genus Pimephales (Cyprinidae: Teleostei). Journal of Fish Biology 61: 293-297.

Anisimova, M., J. P. Bielawski, and Z. Yang. 2002. Evaluation of the Bayesian approach to detecting codon sites under positive Darwinian selection. Molecular Biology and Evolution 19:950-958.

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