title: Signaling hypergraphs.
abstract: Signaling pathways function as the information-passing mechanisms of cells. A number of databases with extensive manual curation represent the current knowledge base for signaling pathways. These databases motivate the development of computational approaches for prediction and analysis. Such methods require an accurate and computable representation of signaling pathways. Pathways are often described as sets of proteins or as pairwise interactions between proteins. However, many signaling mechanisms cannot be described using these representations. In this opinion, we highlight a representation of signaling pathways that is underutilized: the hypergraph. We demonstrate the usefulness of hypergraphs in this context and discuss challenges and opportunities for the scientific community.
authors.affiliation: Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Ritz
authors.affiliation: Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
authors.forename: Allison N
authors.initials: AN
authors.lastname: Tegge
authors.affiliation: Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
authors.forename: Hyunju
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Poirel
authors.affiliation: Department of Computer Science, Virginia Tech, Blacksburg, VA, USA; ICTAS Center for Systems Biology of Engineered Tissues, Virginia Tech, Blacksburg, VA, USA. Electronic address: murali@cs.vt.edu.
authors.forename: T M
authors.initials: TM
authors.lastname: Murali
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016208:Databases, Factual; D005786:Gene Expression Regulation; D008954:Models, Biological; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D011506:Proteins
keywords: graphs; hypergraphs; signaling pathways