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Computational Biology

Modern biomedical research cannot endure without the most powerful tools from information science. Unfortunately, most bioinformatics tools are now developed by mathematicians and computer scientists lacking an understanding of the needs of biologists and biomedical researchers. The FfAME brings together both areas of expertise, often within a single scientist, to use informatics with evolutionary models to interpret experimental data, develop predictive models, and support planetary biology and medicine.

Naturally organized genome sequence databases were invented by scientists now working at FfAME, as were the first convincing tools to predict protein folds from primary sequence data, and some of the first tools to connect evolutionary sequence divergence to functional change in proteins. Ongoing work is developing better tools for evolutionary modeling, better software to visualize evolutionary events in the context of structural biolgy, and better strategies for predictive phylogenomics. Our goal is to enable scientific research and education by providing resources that effortlessly apply multiple lines of evidence from different scientific disciplines (for example molecular evolution, structural biology and paleontology) to illuminate problems in science and technology.

Molecular models of sequence evolution

The FfAME is developing advanced models for analyzing divergent evolution of proteins to join molecular evolution and structural biology to support functional analysis.


Predicting functional divergence in protein evolution by site-specific rate shifts
Gaucher, EA; Gu, X; Miyamoto, MM; Benner, SA
Trends Biochem. Sci. 27 (6) 315-321 (2002)


Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments
Chang, MSS; Benner, SA
J. Mol. Biol. 341 (2) 617-631 (2004)


A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous
Gaucher, EA; Miyamoto, MM
Mol. Phylogenet. Evol. 37 (3) 928-931 (2005)

Tools for visualization and analysis

The FfAME is developing better software to analyze, display and combine the results of molecular evolutionary analysis on proteins having biomedical significance. (NIH)

Developing new molecular dating tools

The FfAME is constructing a comprehensive model for vertebrate evolution using advanced dating tools. This groups genes that duplicated at about the same time and ties duplication events to the paleontological record.

Developing better databases for research

The FfAME is developing advanced databases for pharmacophylogenomics, allowing more rapid analysis of human disease (such as cancer, hypertension and inflammation) and to better understand vertebrate evolution


Functional inferences from reconstructed evolutionary biology involving rectified databases. An evolutionarily-grounded approach to functional genomics.
Benner, SA; Chamberlin, SG; Liberles, DA; Govindarajan, S; Knecht, L
Res. MicroBiol. 151 (2) 97-106 (2000)

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