Publications

Whitney, P.H., Shrestha, B., Xiong, J, Zhang, T, and Rushlow, C.A. (2022). Differential integration of activation and repression signals in a multi-enhancer system. bioRxiv https://biorxiv.org/10.1101/2022.05.12.491703.

Huang, S-K., Dutta, S., Whitney, P.H., Shvartsman, S., and Rushlow, C.A. (2021). Spatial Organization of transcribing loci during early genome activation in Drosophila. Current Biology Sep 29, S0960-9822 (21). Online ahead of print.

Huang, S-K., Dutta, S., Whitney, P.H., Shvartsman, S., and Rushlow, C.A. (2021). An “individualist model of an actve genome in a developing embryo. bioRxiv https://doi.org/10.1101/2021.01.08.425929

Yamada, S.*, Whitney, P.H.*, Huang, S-H., Eck, E.C., Garcia, H.G., and Rushlow, C.A. (2019). The Drosophila pioneer factor Zelda modulates the nuclear microenvironment of a Dorsal target enhancer to potentiate transcriptional output. Curr. Biol. 29, 1387-1393. *contributed equally.

Djabrayan, N. J-V., Smits, C. M., Krajnc, M., Stern, T., Yamada S, Lemon, W. C., Keller, P. J., Rushlow, C.A., and Shvartsman S. Y. (2019). Metabolic Regulation of Developmental Cell Cycles and Zygotic Transcription. Curr. Biol. 29, 1193-1198.

Yamada, S., Whitney, P.H., Huang, S-H., Eck, E.C., Garcia, H.G., and Rushlow, C.A. (2018). The Drosophila pioneer factor Zelda modulates the nuclear microenvironment of a Dorsal target enhancer to potentiate transcriptional output. bioRxiv 471029; doi: https://doi.org/10.1101/471029

Madaan U, Yzeiraj E, Meade M, Clark JF, Rushlow, C., Savage-Dunn C. (2018). BMP Signaling Determines Body Size via Transcriptional Regulation of Collagen Genes in Caenorhabditis elegans. Genetics 210, 1355-1367.

Samee, H., Lim, B., Samper, N., Lu, H., Rushlow, CA., Jiménez, G., Shvartsman, S. and Sinha, S. (2015). A systematic ensemble approach to thermodynamic modeling of gene expression from sequence data. Cell Systems 1: 396-407.

Sun*, Y., Nien, C.Y.*, Chen, K., Liu, H. Y., Johnston, J., Zeitlinger, J.**, and Rushlow, C.A.** (2015). Zelda lowers the intrinsic nucleosome barrier at enhancers during zygotic genome activation in Drosophila. Genome Research 25, 1703-1714 PMID: 26335633. *contributed equally, **co-corresponding authors.

Foo* , S. M., Sun, Y.*, Lim, B., Ziukaite, R., O’Brien, K., Nien, C-Y., Kirov, N.,  Shvartsman, S., and Rushlow, C.A. (2014). Zelda potentiates morphogen activity by increasing chromatin accessibility. Curr. Biol. 24, 1341-6. PMID: 24909324. *contributed equally.

Fu, S., Nien, C-Y., Liang, H-L., and Rushlow, C. (2014). Co-activation of microRNAs by Zelda is essential for early Drosophila development. Development 141, 2108-2118. PMID:24764079.

Lim, B., Samper, N., Lu, H., Rushlow, C, Jiminez, G., and Shvarstman, SY. (2013). Kinetics of gene derepression by ERK signaling. PNAS 110, 10330-10335. PMID:23733957.

Rushlow, C. A. and Shvarstman, S.Y. (2012). Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient. Curr Opin in Genet Dev 22, 542-6. PMID:22981910.

Siegal, M. and Rushlow, C. (2012). Pausing on the path to robustness. Dev Cell 22, 905-6. PMID:22595664.

Liang, H., Xu, M., Chuang, Y., and Rushlow, C. (2012). Response to the BMP gradient requires highly combinatorial inputs from multiple patterning systems in the Drosophila embryo. Development 139, 1956-1964. PMID:22513375.

Kanodia, J. S., Liang, H-L., Kim, Y., Lim, B., Zhan, M., Lu, H., Rushlow, C. A.*, and Shvartsman, S. Y.* (2012). Pattern formation by graded and uniform signals: gene regulation by Dorsal and Zelda in the Drosophila embryo. Biophysical Journal 102, 427-33. *co-corresponding authors. PMID:22325264.

Nien, C.*, Liang, H.*, Butcher, S., Sun, Y., Fu, S., Gocha, T., Kirov, N., Manak, J., and Rushlow, C. (2011). Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PLoS Genetics 7, e1002339. PMID:22028675. *contributed equally.

Struffi P., Corado M., Kaplan L., Yu D., Rushlow C., Small S. (2011). Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer. Development 138, 4291-4299. PMID:21865322.

Liang, H.*, Nien, C.*, Liu, H., Metzstein, M., Kirov, N., and Rushlow, C. (2008). The zinc finger protein Zelda is a key activator of the early zygoti2017c genome in Drosophila. Nature 456, 400-405. PMID:18931655. *contributed equally.