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John M. Braverman, S.J., Ph.D.

Associate Professor
Office: Science Center 127
Research Lab: Science Center 109
Phone: 610-660-1894
Fax: 610-660-1832


  • A.B. (1989) Princeton University
  • Ph.D. (1995) University of California, Davis
  • M.A. (2003) Loyola University Chicago
  • M.Div. (2009) Jesuit School of Theology, Berkeley
  • S.T.L. (2014) Jesuit School of Theology, Berkeley, of Santa Clara University 

Professional Experience

  • Associate Professor (as of August 2016) of Biology, Saint Joseph's University
  • Assistant Professor (2010-2016) of Biology, Saint Joseph’s University
  • Visiting Assistant Professor (2003-2006) Department of Biology, Georgetown University

Courses Taught

Bioinformatics • Genetic and Evolutionary Biology • Evolution • Genome Science • God and Evolution


Robinson, Lauren M., Joseph R. Boland, and John M. Braverman. 2016. Revisiting a Classic Study of the Molecular Clock. Journal of Molecular Evolution, 82(3). doi:10.1007/s00239-016-9728-x.

Leung, W., et al, including Braverman, J.M.  2015.  Drosophila Muller F elements maintain a distinct set of genomic properties over 40 million years of evolution. G3: Genes|Genomes|Genetics 5(5): 719-740.

Lopatto, D., Hauser, C., Jones, C.J., Paetkau, D., Chandrasekaran, V., Dunbar, D., MacKinnon, C., Stamm, J., Alvarez, C., Barnard, D., Bedard, J.E.J., Bednarski, A.E., Bhalla, S., Braverman, J.M., Burg, M., Chung, H.-M., DeJong, R.J., DiAngelo, J.R., Du, C., Eckdahl, T.T., Emerson, J., Frary, A., Frohlich, D., Goodman, A.L., Gosser, Y., Govind, S., Haberman, A., Hark, A.T., Hoogewerf, A., Johnson, D., Kadlec, L., Kaehler, M., Key, S.C.S., Kokan, N.P., Kopp, O.R., Kuleck, G.A., Lopilato, J., Martinez-Cruzado, J.C., McNeil, G., Mel, S., Nagengast, A., Overvoorde, P.J., Parrish, S., Preuss, M.L., Reed, L.D., Regisford, E.G., Revie, D., Robic, S., Roecklien-Canfield, J.A., Rosenwald, A.G., Rubin, M.R., Saville, K., Schroeder, S., Sharif, K.A., Shaw, M., Skuse, G., Smith, C.D., Smith, M., Smith, S.T., Spana, E.P., Spratt, M., Sreenivasan, A., Thompson, J.S., Wawersik, M., Wolyniak, M.J., Youngblom, J., Zhou, L., Buhler, J., Mardis, E., Leung, W., Shaffer, C.D., Threlfall, J., Elgin, S.C.R., 2014. A Central Support System Can Facilitate Implementation and Sustainability of a Classroom-Based Undergraduate Research Experience (CURE) in Genomics. CBE Life Sciences Education 13(4): 711–723.

Shaffer, C.D., Alvarez, C.J., Bednarski, A.E., Dunbar, D., Goodman, A.L., Reinke, C., Rosenwald, A.G., Wolyniak, M.J., Bailey, C., Barnard, D., Bazinet, C., Beach, D.L., Bedard, J.E.J., Bhalla, S., Braverman, J., Burg, M., Chandrasekaran, V., Chung, H.-M., Clase, K., DeJong, R.J., DiAngelo, J.R., Du, C., Eckdahl, T.T., Eisler, H., Emerson, J.A., Frary, A., Frohlich, D., Gosser, Y., Govind, S., Haberman, A., Hark, A.T., Hauser, C., Hoogewerf, A., Hoopes, L.L.M., Howell, C.E., Johnson, D., Jones, C.J., Kadlec, L., Kaehler, M., Key, S.C.S., Kleinschmit, A., Kokan, N.P., Kopp, O., Kuleck, G., Leatherman, J., Lopilato, J., MacKinnon, C., Martinez-Cruzado, J.C., McNeil, G., Mel, S., Mistry, H., Nagengast, A., Overvoorde, P., Paetkau, D.W., Parrish, S., Peterson, C.N., Preuss, M., Reed, L.K., Revie, D., Robic, S., Roecklein-Canfield, J., Rubin, M.R., Saville, K., Schroeder, S., Sharif, K., Shaw, M., Skuse, G., Smith, C.D., Smith, M.A., Smith, S.T., Spana, E., Spratt, M., Sreenivasan, A., Stamm, J., Szauter, P., Thompson, J.S., Wawersik, M., Youngblom, J., Zhou, L., Mardis, E.R., Buhler, J., Leung, W., Lopatto, D., Elgin, S.C.R., 2014. A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time. CBE Life Sciences Education 13(1): 111–130.

Freda, P., and J.M. Braverman.  2013. Drosophila suzukii, or Spotted Wing Drosophila, Recorded in Southeastern Pennsylvania. Entomological News, 123(1): 71–75.

Soria-Hernanz, D.F., O. Fiz-Palacios, J.M. Braverman, and M.B. Hamilton. 2008. Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms. BMC Evolutionary Biology. 8: 344ff.

Soria-Hernanz, D.F., J.M. Braverman, and M.B. Hamilton. 2008.    Parallel rate heterogeneity in chloroplast and mitochondrial genomes of Brazil nut trees (Lecythidaceae) is consistent with lineage effects. Molecular Biology and Evolution 25: 1282-1296.

Teodorovic, S., J.M. Braverman, and H.G. Elmendorf. 2007. Unusually low levels of genetic variation among Giardia lamblia isolates. Eukaryotic Cell 6: 1421-1430.

Lohmueller, K.E., M.M. Mauney, D. Reich, and J.M. Braverman. 2006. Variants associated with common diseases are not unusually differentiated in frequency across populations. American Journal of Human Genetics 78: 130-136.

Braverman, J.M., B.P. Lazzaro, M. Aguadé, and C.H. Langley. 2005. DNA sequence polymorphism and divergence at the erect wing and suppressor of sable loci of Drosophila melanogaster and D. simulans. Genetics 170: 1153-1165.

Hamilton, M. B., J.M. Braverman, and D.F. Soria-Hernanz. 2003. Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in new world species of the Lecythidaceae. Molecular Biology and Evolution 20: 1710-1721.

Langley, C.H., B.P. Lazzaro, W. Phillips, E. Heikkinen, and J.M. Braverman. 2000. Linkage disequilibria and the site frequency spectra in the su(s) and su(wa) regions of the Drosophila melanogaster X chromosome. Genetics 156: 1837-1852.

Parsch, J., J.M. Braverman, and W. Stephan. 2000. Comparative sequence analysis and patterns of covariation in RNA secondary structures. Genetics 154: 909-921.

Chen, Y., D.B. Carlini, J.F. Baines, J. Parsch, J.M. Braverman, S. Tanda, and W. Stephan. 1999. RNA secondary structure and compensatory evolution. Genes & Genetic Systems 74: 271-286.

Stephan, W., L. Xing, D.A. Kirby, and J.M. Braverman. 1998. A test of the background selection hypothesis based on nucleotide data from Drosophila ananassae. Proceedings of the National Academy of Sciences USA 95: 5649-5654.

Braverman, J.M., R.H. Hudson, N. Kaplan, C.H. Langley, and W. Stephan. 1995. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140: 783-796.

Braverman, J.M., B. Goñi, and H.A. Orr. 1992. Loss of a paternal chromosome causes developmental anomalies among Drosophila hybrids. Heredity 69:416-422.

Book Reviews

Braverman, John M. “Science and Faith: A New Introduction by John F. Haught.” Theology Today 72, no. 2 (July 1, 2015): 236–237.
Braverman, John M. “G. Auletta, M. Leclerc, and R.A. Martínez, Eds. Biological Evolution: Facts and Theories. A Critical Appraisal 150 Years After The Origin of Species.” Theology and Science 10, no. 3 (2012): 333–334.



My main areas of research are: population genetics, molecular evolution, and bioinformatics. My goal is to characterize and explain genetic variation observed within natural populations and among species. I use empirical (field collection and laboratory) and computer modeling and DNA sequencing to test models of natural selection and their alternatives. I study rates and patterns of molecular divergence to test the molecular clock and identify the processes responsible. I design software to answer evolutionary questions about large genomic datasets. My study organisms range from Drosophila melanogaster and D. simulans (two species of fruit fly) to tropical trees.