Roni Rosenfeld

Research in Computational Molecular Biology / BioLinguistics

• Statistical-Computational Models of Molecular Evolution (looking for 1 new PhD student in this area).  Molecular evolution is a stochastic computational process that has been running on massively parallel hardware for some 10¹⁷ seconds now, and which has resulted in many amazing local maxima along the way.  The rapidly growing DNA and protein databases present a historic opportunity to model evolution at an unprecedented quantitative level, with enormous impact on medicine as well as on our fundamental understanding of life.  In this project we combine statistical and computational methods to derive biological explanations and pharmacological predictions.

• Viruses, vaccines, and digital life (looking for 1 new PhD student in this area).  Viruses are the simplest known self-replicating computational systems.  They also happen to be the leading emerging threat to humanity in the 21^st century. Fortunately, the new understanding of life in general and viruses in particular as digital programs opens the door to computational methods of defending against these threats.  This is a new project launched in collaboration with virologists at the University of Pittsburgh whose aim is to combine biological analysis with statistical learning methods to better understand viral evolution and accelerate vaccine development.

• Multi-species gene-expression analysis.  Micro arrays provide a plethora of information about gene activity in specific cell types and at specific cellular stages, and are used to help determine the function of many genes and gene products.  However, the data coming out of micro array experiments is notoriously noisy.  In this project we derive a computational framework to combine gene-expression measurements from multiple species with inferred functional relationships among orthologous and paralogous genes.