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Systems biology of regulatory motifs and networks – towards understanding gene expression from the DNA sequence
The regulation of gene expression in response to developmental or environmental stimuli is central to all organisms. Transcription is regulated by trans-acting transcription factors that recognize cis-regulatory DNA elements (CRMs or enhancers) and function in a combinatorial fashion. We use both bioinformatics and molecular biology methods to gain a systematic understanding of enhancer structure and function. Our goal is to “crack” the regulatory code, predict enhancer activity from the DNA sequence, and to understand how transcriptional networks define cellular and developmental programs.
Zeitlinger, J., Stark, A. (2010). Developmental gene regulation in the era of genomics.
Dev Biol. 339(2):230-9
(abstract)
2009
Meireles-Filho, AC., Stark, A. (2009). Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information.
Curr Opin Genet Dev. 19(6):565-70
(abstract)
2007
Stark, A., Lin, MF., Kheradpour, P., Pedersen, JS., Parts, L., Carlson, JW., Crosby, MA., Rasmussen, MD., Roy, S., Deoras, AN., Ruby, JG., Brennecke, J., Hodges, E., Hinrichs, AS., Caspi, A., Paten, B., Park, SW., Han, MV., Maeder, ML., Polansky, BJ., Robson, BE., Aerts, S., van Helden, J., Hassan, B., Gilbert, DG., Eastman, DA., Rice, M., Weir, M., Hahn, MW., Park, Y., Dewey, CN., Pachter, L., Kent, WJ., Haussler, D., Lai, EC., Bartel, DP., Hannon, GJ., Kaufman, TC., Eisen, MB., Clark, AG., Smith, D., Celniker, SE., Gelbart, WM., Kellis, M. (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Nature. 450(7167):219-32
(abstract)
Zeitlinger, J., Zinzen, RP., Stark, A., Kellis, M., Zhang, H., Young, RA., Levine, M. (2007). Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.
Genes Dev. 21(4):385-90
(abstract)
2005
Stark, A., Brennecke, J., Bushati, N., Russell, RB., Cohen, SM. (2005). Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution.
Cell. 123(6):1133-46
(abstract)
