@article{Supper2009,
  author = {Supper, Jochen and Spangenberg, Luc\'{i}a and Planatscher, Hannes and
	Dr\"ager, Andreas and Schr\"oder, Adrian and Zell, Andreas},
  title = {{BowTieBuilder: modeling signal transduction pathways}},
  journal = {BMC Systems Biology},
  year = {2009},
  volume = {3},
  pages = {67},
  number = {1},
  month = jun,
  abstract = {Background: Sensory proteins react to changing environmental
    conditions by transducing signals into the cell. These signals are integrated
	into core proteins that activate downstream target proteins such
	as transcription factors (TFs). This structure is referred to as
	a bow tie, and allows cells to respond appropriately to complex environmental
	conditions. Understanding this cellular processing of information,
	from sensory proteins (e.g., cell-surface proteins) to target proteins
	(e.g., TFs) is important, yet for many processes the signaling pathways
	remain unknown.

	Results: Here, we present BowTieBuilder for inferring signal transduction
	pathways from multiple source and target proteins. Given protein-protein
	interaction (PPI) data signaling pathways are assembled without knowledge of
	the intermediate signaling proteins while maximizing the overall probability
	of the pathway. To assess the inference quality, BowTieBuilder and three
	alternative heuristics are applied to several pathways, and the resulting
	pathways are compared to reference pathways taken from KEGG. In addition,
	BowTieBuilder is used to infer a signaling pathway of the innate immune
	response in humans and a signaling pathway that potentially regulates an
	underlying gene regulatory network.

	Conclusions: We show that BowTieBuilder, given multiple source and/or target
	proteins, infers pathways with satisfactory recall and precision rates and
	detects the core proteins of each pathway.},
  doi = {10.1186/1752-0509-3-67},
  pdf = {https://www.biomedcentral.com/content/pdf/1752-0509-3-67.pdf},
  url = {https://www.biomedcentral.com/1752-0509/3/67}
}