Stark Group

Alexander Stark (Group Leader)

(Email)

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 a crucial mechanism in 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. Enhancers retain their activity even when placed in artificial contexts (e.g. in reporter gene assays), but the exact requirements for enhancer function, i.e. a regulatory code, remains unknown and enhancer activity cannot be predicted from the DNA sequence.

Selected Publications

  • Arnold, CD., Gerlach, D., Stelzer, C., Boryn, LM., Rath, M., Stark, A. (2013). Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq. Science. (abstract)
  • Kvon, EZ., Stampfel, G., Yáñez-Cuna, JO., Dickson, BJ., Stark, A. (2012). HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev. 26(9):908-13 (abstract)
  • Yáñez-Cuna, JO., Dinh, HQ., Kvon, EZ., Shlyueva, D., Stark, A. (2012). Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding. Genome Res. 22(10):2018-30 (abstract)
  • Yáñez-Cuna, JO., Kvon, EZ., Stark, A. (2012). Deciphering the transcriptional cis-regulatory code. Trends Genet. (abstract)
  • 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)

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