Gene regulatory network inference: an introductory survey

TL;DR

This survey introduces gene regulatory network inference, discussing its importance, historical development, and categorizing existing tools to provide a foundational understanding for further study.

Contribution

It offers a comprehensive overview and categorization of gene regulatory network inference methods, highlighting their strengths and foundational concepts.

Findings

Progress in network inference tools over two decades

Categorization of inference methods based on commonalities

Provides foundational knowledge for further research

Abstract

Gene regulatory networks are powerful abstractions of biological systems. Since the advent of high-throughput measurement technologies in biology in the late 90s, reconstructing the structure of such networks has been a central computational problem in systems biology. While the problem is certainly not solved in its entirety, considerable progress has been made in the last two decades, with mature tools now available. This chapter aims to provide an introduction to the basic concepts underpinning network inference tools, attempting a categorisation which highlights commonalities and relative strengths. While the chapter is meant to be self-contained, the material presented should provide a useful background to the later, more specialised chapters of this book.