Francisco José Ayala

Research and Education

Present Neuroblast

1995 - 1998 Postdoctoral Research Fellow, Institute of Molecular Evolutionary Genetics.

1995 Ph.D. in Organismic and Evolutionary Biology, Harvard University.

1990 B.A. with Honors in Biochemistry, Harvard University.


U.S. Patent No. 7,546,170: A very easily-tuned and robust control algorithm for single- and multi-variable systems.

U.S. Patent No. 7,493,295: Method, System and Computer Program for Developing Cortical Algorithms.

U.S. Patent No. 7,139,740: System and Method for Developing Artificial Intelligence.

U.S. Patent No. 6,424,961: Adaptive Neural Learning System.


Morozov, P., T. Sitnikova, G. Churchill,  F. J. Ayala, and A. Rzhetsky. 2000.  A new method for characterizing replacement rate variation in molecular sequences: Application of the Fourier and wavelet models to Drosophila and Mammalian proteins.  Genetics 154: 381-395.

Rzhetsky, A., and F. J. Ayala. 1999.  The enigma of intron origins. Cell. Mol. Life Sci. 55: 3-6.

Ayala, F. J., A. Rzhetsky, and F. J. Ayala. 1999.  Molecular clocks and the origins of animals.  In S.P. Wasser (Ed.) Evolutionary theory and processes: Modern perspectives, pp. 151-169.

Ayala, F. J., A. Rzhetsky, and F. J. Ayala. 1998.  Origin of the metazoan phyla:  Molecular clocks confirm paleontological estimates. Proc. Natl. Acad. USA 95: 606-611.  See Research News article in Science, News and Views article in Nature, and Stephen J. Gould article in Natural History that cite this work.

Rzhetsky, A., F. J. Ayala, L. C. Hsu, C. Chang, and A. Yoshida. 1997.  Fitting models of intron evolution to aldehyde dehydrogenase data. In B. Mirkin, F. McMorris, F. Roberts, and A. Rzhetsky (Eds.) Mathematical hierarchies and biology, DIMACS series in discrete mathematics and theoretical computer science, pp. 95-110.

Rzhetsky, A., F. J. Ayala, L. C. Hsu, C. Chang, and A. Yoshida. 1997.  Exon/intron structure of aldehyde dehydrogenase genes supports the "introns-late" theory.  Proc. Natl. Acad. Sci. USA  94: 6820-6825.

Jasieński, M., F. J. Ayala, and F. A. Bazzaz. 1997.  Correlation of phenotypic plasticity and similarity of DNA among genotypes.  Heredity 78: 176-181.

Ayala, F. J., C. A. Campbell, and R. K. Selander. 1996.  Molecular population genetics of the alcohol dehydrogenase locus in the Hawaiian drosophilid D. mimica.  Mol. Biol. Evol. 13: 1363-1367.

Rzhetsky, F. J., J. Dopazo, E. Snyder, C. A. Dangler, and F. J. Ayala. 1996.  Assessing dissimilarity of genes by comparing their RNAse A mismatch cleavage patterns.  Genetics 144: 1975-1983.

Ayala, F. J., J. K. Wetterer, J. T. Longino, and D. L. Hartl. 1996.  Molecular phylogeny of Azteca ants (Hymenoptera: Formicidae) and the colonization of Cecropia trees.  Mol. Phyl. Evol. 5: 423-428.

Dorit, R. L., and F. J. Ayala. 1995.  ADH evolution and the phylogenetic footprint.  J. Mol. Evol. 40: 658-662.

Ayala, F. J., D. E. Krane, and D. L. Hartl. 1994.  Genetic variation in Inc1-ColIb plasmids.  J. Mol. Evol. 39: 129-133.

Ayala, F. J., B. S. W. Chang, and D. L. Hartl. 1993.  Molecular evolution of the Rh3 gene in Drosophila.  Genetica 92: 23-32.

Ayala, F. J., and D. L. Hartl. 1993.  Molecular drift of the Bride of Sevenless (boss) gene in Drosophila.  Mol. Biol. Evol. 10: 1030-1040.

Ochman, H., F. J. Ayala, and D. L. Hartl. 1993.  Use of polymerase chain reaction to amplify segments outside boundaries of known sequences.  Methods Enzymol. 218:  309-321.