Research Interests

Regulation of gene expression

We are interested in understanding fundamental mechanisms that coordinate and compartmentalize the transcription of genes as a function of their positions in the genome. We have found that the effects of genome position vary across cell types indicating that genome position effects are plastic. To study the mechanisms and consequences of genome plasticity we use the fruit fly Drosophila melanogaster where we develop transgenic probes, disease models, chemical assays and bioinformatics tools.

Representative Publications

Markstein, M. 2013. Colorectal cancer as a three-dimensional disease in a dish: the case for drug screening using organoids, zebrafish, and flies. Drug Discovery Today, in press.

Roti, G., Carlton, A., Ross, K.N., Markstein, M., Pajcini, K., Su, A.H., Perrimon, N., Pear, W.S., Kung, A.L., Blacklow, S.C., Aster, J.C., Stegmaier, K. 2013. Complementary Genomic Screens Identify SERCA as a Therapeutic Target in NOTCH1 Mutated Cancer. Cancer Cell, in press.

Ni, J. Q., Liu, L. P., Binari, R., Hardy, R., Shim, H. S., Cavallaro, A., Booker, M., Pfeiffer, B. D., Markstein, M., Wang, H., Villalta, C., Laverty, T. R., Perkins, L. A., and Perrimon, N. 2009. A Drosophila resource of transgenic RNAi lines for neurogenetics. Genetics, 182: 1089-1100.

Markstein, M., Pitsouli, C., Villalta, C., Celniker, S. E., and Perrimon, N. 2008. Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nature Genetics, 40: 476-483.
Featured in Nature Methods and Harvard Focus Magazine.

Ni, J. Q.*, Markstein, M.*, Binari, R.*, Pfeiffer, B., Liu, L. P., Villalta, C., Booker, M., Perkins, L., and Perrimon, N. 2008. Vector and parameters for targeted transgenic RNA interference in Drosophila melanogaster. *Contributed equally. Nature Methods, 5: 49-51.

Markstein, M.*, Zinzen, R.*, Markstein, P., Yee, K. P., Erives, A., Stathopoulos, A., and Levine, M. 2004. A regulatory code for neurogenic gene expression in the Drosophila embryo. *Contributed equally. Development, 131: 2387-2394.

Senger, K., Armstrong, G. W., Rowell, W. J., Kwan, J. M., Markstein, M., and Levine, M. 2004. Immunity regulatory DNAs share common organizational features in Drosophila. Molecular Cell, 13: 19-32.

Stathopoulos, A., Van Drenth, M., Erives, A., Markstein, M., and Levine, M. 2002. Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell, 111: 687-701.

Markstein, M. and Levine, M. 2002. Decoding cis-regulatory DNAs in the Drosophila genome. Current Opinion in Genetics and Development, 12: 601-606.

Markstein, M., Markstein, P., Markstein, V., and Levine, M. S. 2002. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. PNAS, 99: 763-768.