A Boolean network inference from time-series gene expression data using a genetic algorithm

Shohag Barman, Yung-Keun Kwon


Inferring a gene regulatory network from time-series gene expression data is a fundamental problem in systems biology, and many methods have been proposed. However, most of them were not efficient in inferring regulatory relations involved by a large number of genes because they limited the number of regulatory genes or computed an approximated reliability of multivariate relations. Therefore, an improved method is needed to efficiently search more generalized and scalable regulatory relations. In this study, we propose a genetic algorithm-based Boolean network inference (GABNI) method which can search an optimal Boolean regulatory function of a large number of regulatory genes. For an efficient search, it solves the problem in two stages. GABNI first exploits an existing method, a mutual information-based Boolean network inference (MIBNI), because it can quickly find an optimal solution in a small-scale inference problem. When MIBNI fails to find an optimal solution, a genetic algorithm (GA) is applied to search an optimal set of regulatory genes in a wider solution space. In particular, we modified a typical GA framework to efficiently reduce a search space. We compared GABNI with four well-known inference methods through ext...Continue Reading


Mar 1, 1969·Journal of Theoretical Biology·S A Kauffman
Oct 16, 1999·Science·A L Barabasi, R Albert
Mar 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Fangting LiChao Tang
Oct 11, 2007·Annals of the New York Academy of Sciences·Gustavo StolovitzkyAndrea Califano
Feb 27, 2010·PloS One·Robert J PrillGustavo Stolovitzky
Mar 24, 2010·Proceedings of the National Academy of Sciences of the United States of America·Daniel MarbachGustavo Stolovitzky
Oct 12, 2010·PloS One·Vân Anh Huynh-ThuPierre Geurts
Nov 24, 2012·BMC Systems Biology·Anne-Claire HauryJean-Philippe Vert
Jan 1, 2015·PloS One·Shengtong HanXiaodan Fan

Related Concepts

Reproducibility of Results
Gene Expression
Gene Modules
Gene Expression
Genes, Regulator
Information Centers
Anatomical Space Structure
Gene Function

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.