University Directory

John M. Braverman, PhD

Associate Professor and Director of Environmental Science and Sustainability Studies Program

Department

Department of Biology

Environmental Science Program

Office

Science Center 127

Phone

610-660-1894

Contact

Dr. Braverman is an associate professor in the Department of Biology and the director of the Environmental Science and Sustainability Studies Program.

Dr. Braverman's active areas of inquiry fall in the general framework of evolutionary biology. In particular, he looks at evolutionary genetics, namely, how evolutionary change occurs at the DNA sequence level. This pertains to the new field of genomics. For instance, working with the Genomics Education Partnership (GEP), based at Washington University, he has conducted fine-scale annotation of genomes with the goal of understanding evolutionary changes among the genes discovered. Because annotation (location of genes and other features in a new genome sequence) requires careful checking by investigators, it can be laborious. The students in his Bioinformatics course have been able to assist in this process through a systematic and multi-school division of labor. Some of the publications below reflect the results they obtained for several species of Drosophila (fruit flies).

His other research considers evolutionary rates in different species, again at the DNA sequence level. It is logical that species with shorter generation times incur more mutations per year through the multiple replication events, in contrast to species with longer generation times. These mutations accumulate as substitutions (changes) in genes between different taxa. This hypothesis (the Generation Time Hypothesis or GTH) has been affirmed in many animal species. In his current research, he is testing the GTH in plants. What makes this interesting is that natural selection is not necessary to explain evolutionary changes, even though people commonly think that selection is responsible for everything.

A number of active collaborations with colleagues in the biology department involve the assembly, annotation, and discovery of variation in taxa ranging from bacteria to fungi to nematode worms.

- AB (1989) Princeton University
- PhD (1995) University of California, Davis
- MA (2003) Loyola University Chicago
- MDiv (2009) Jesuit School of Theology, Berkeley
- STL (2014) Jesuit School of Theology, Berkeley, of Santa Clara University
- Associate Professor (2016-present) 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
Cangren, P., Bertrand, Y. J. K., Braverman, J. M., Gilfillan, G. D., Hamilton, M. B., & Oxelman, B. (2024). A dataset of 40 assembled and annotated transcriptomes from 34 species in Silene and related genera. Data in Brief, 111094. https://doi.org/10.1016/j.dib.2024.111094
Winkler, A., Pivonka, A., Conry-Murray, A., Petruconis, C., Patterne, I., Bergman, B., Binder, E., Blackley, J., Brown, R., Commale, K., Costello, E., Cromer, T., Davila, J., DeSanto, O., Dunn, M. A., Duong, D., Feingold, S., Flanders, K., Frattara, M., Fryczynski, T., Givvines, L., Glavin, D., Hartman, R., Iacovella, J., Koestler, K., Kominick, C., Lam, A., Mashkovich, S., McCarthy, J., Merlino, C., Mihaita, A., Moulton, K., Nguyen, T., Niblock, D., Paoli, I., Rodriguez, S., Stefanic, I., Stoneroad, J., Teague, C., Tort-Umpierre, F., Varano, A., Vlahovic, A., Braverman, J., King-Smith, C., & Lee-Soety, J. Y. (2022). Genome Sequences and Characteristics of Six Cluster B1 Mycobacteriophages Discovered at Saint Joseph’s University. Microbiology Resource Announcements, 11(10), e00754-22. https://doi.org/10.1128/mra.00754-22
Lopatto, D., Rosenwald, A. G., Burgess, R. C., Silver Key, C., Van Stry, M., Wawersik, M., DiAngelo, J. R., Hark, A. T., Skerritt, M., Allen, A. K., Alvarez, C., Anderson, S., Arrigo, C., Arsham, A., Barnard, D., Bedard, J. E. J., Bose, I., Braverman, J. M., Burg, M. G., Croonquist, P., Du, C., Dubowsky, S., Eisler, H., Escobar, M. A., Foulk, M., Giarla, T., Glaser, R. L., Goodman, A. L., Gosser, Y., Haberman, A., Hauser, C., Hays, S., Howell, C. E., Jemc, J., Jones, C. J., Kadlec, L., Kagey, J. D., Keller, K. L., Kennell, J., Kleinschmit, A. J., Kleinschmit, M., Kokan, N. P., Kopp, O. R., Laakso, M. M., Leatherman, J., Long, L. J., Manier, M., Martinez-Cruzado, J. C., Matos, L. F., McClellan, A. J., McNeil, G., Merkhofer, E., Mingo, V., Mistry, H., Mitchell, E., Mortimer, N. T., Myka, J. L., Nagengast, A., Overvoorde, P., Paetkau, D., Paliulis, L., Parrish, S., Toering Peters, S., Preuss, M. L., Price, J. V., Pullen, N. A., Reinke, C., Revie, D., Robic, S., Roecklein-Canfield, J. A., Rubin, M. R., Sadikot, T., Sanford, J. S., Santisteban, M., Saville, K., Schroeder, S., Shaffer, C. D., Sharif, K. A., Sklensky, D. E., Small, C., Smith, S., Spokony, R., Sreenivasan, A., Stamm, J., Sterne-Marr, R., Teeter, K. C., Thackeray, J., Thompson, J. S., Velazquez-Ulloa, N., Wolfe, C., Youngblom, J., Yowler, B., Zhou, L., Brennan, J., Buhler, J., Leung, W., Elgin, S. C. R., & Reed, L. K. (2022). Student Attitudes Contribute to the Effectiveness of a Genomics CURE. Journal of Microbiology & Biology Education, 23(2), e00208-21.
Lopatto, D., Rosenwald, A. G., DiAngelo, J. R., Hark, A. T., Skerritt, M., Wawersik, M., Allen, A. K., Alvarez, C., Anderson, S., Arrigo, C., Arsham, A., Barnard, D., Bazinet, C., Bedard, J. E. J., Bose, I., Braverman, J. M., et al. 2020. Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience. Journal of Microbiology & Biology Education 21(1).
Leung, Wilson, Christopher D. Shaffer, Elizabeth J. Chen, Thomas J. Quisenberry, Kevin Ko, John M. Braverman, et al. 2017. “Retrotransposons Are the Major Contributors to the Expansion of the Drosophila Ananassae Muller F Element.” G3: Genes|Genomes|Genetics, 7(8): 2439-2460. doi:10.1016/j.tig.2016.11.004
Elgin, Sarah C. R., Charles Hauser, Teresa M. Holzen, Christopher Jones, Adam Kleinschmit, Judith Leatherman, Anna Allen, Consuelo Alvarez, Sara Anderson, Gaurav Arora, Cindy Arrigo, Andrew Arsham, Cheryl Bailey, Daron Barnard, Ana Maria Barral, Chris Bazinet, Dale Beach, James E. J. Bedard, April Bednarski, John Braverman, et al. 2017. The GEP: Crowd-Sourcing Big Data Analysis with Undergraduates. Trends in Genetics. 33(2): 81-85. http://dx.doi.org/10.1016/j.tig.2016.11.004
Braverman, John M., Matthew B. Hamilton, Brent A. Johnson. 2016. Patterns of Substitution Rate Variation at Many Nuclear Loci in Two Species Trios in the Brassicaceae Partitioned with ANOVA. Journal of Molecular Evolution. 83(3-4):97-109. doi:10.1007/s00239-016-9752-x
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): 110-116. 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(1): 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.