John Kececioglu | Workshop Two for a Tango - 4th Edition

Workshop Metabolism and mathematical models: Two for a tango | 4th Edition
November 19-20, 2024 | ONLINE WORKSHOP
John Kececioglu (The University of Arizona, USA)
Title talk: Inferring pathways in metabolic networks via optimal factories and hyperpaths.
Short abstract: Fundamental to systems and synthetic biology is the task of inferring pathways of reactions in metabolic networks. Two key models for pathway inference are factories and hyperpaths: systems of reactions that ultimately produce target substances, starting from the available source compounds. Factories take into account the stoichiometries of reactions to produce the targets while conserving or not depleting intermediate metabolites; hyperpaths ignore stoichiometry, and yield an ordered cascade of reactions in which the input reactants to each reaction are produced as output products of prior reactions; finding optimal factories and hyperpaths are both NP-complete. We present recent results on the first practical exact algorithms for optimal factories and hyperpaths, which are fast in practice (as demonstrated through comprehensive experiments over the standard pathway databases in the literature), and freely available in the tools Freeia and Mmunin.
This is joint work with Spencer Krieger, published in RECOMB 2023, RECOMB 2024, and their special issues in the Journal of Computational Biology.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences - Inria Associated Team Capoeira - and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg - H2020 Twinning Project Olissipo.