Maximum likelihood reconstruction of ancestral networks by integer linear programming.

ABSTRACT:

Motivation

The study of the evolutionary history of biological networks enables deep functional understanding of various bio-molecular processes. Network growth models, such as the Duplication-Mutation with Complementarity (DMC) model, provide a principled approach to characterizing the evolution of protein-protein interactions (PPIs) based on duplication and divergence. Current methods for model-based ancestral network reconstruction primarily use greedy heuristics and yield sub-optimal solutions.

Results

We present a new Integer Linear Programming (ILP) solution for maximum likelihood reconstruction of ancestral PPI networks using the DMC model. We prove the correctness of our solution that is designed to find the optimal solution. It can also use efficient heuristics from

SUBMITTER: Rajan V 

PROVIDER: S-EPMC8599758 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature