Network modelling of gene regulation

Biophysics Reviews
Joshua W K Ho, Michael A Charleston

Abstract

Gene regulatory network (GRN) modelling has gained increasing attention in the past decade. Many computational modelling techniques have been proposed to facilitate the inference and analysis of GRN. However, there is often confusion about the aim of GRN modelling, and how a gene network model can be fully utilised as a tool for systems biology. The aim of the present article is to provide an overview of this rapidly expanding subject. In particular, we review some fundamental concepts of systems biology and discuss the role of network modelling in understanding complex biological systems. Several commonly used network modelling paradigms are surveyed with emphasis on their practical use in systems biology research.

References

Apr 1, 1973·Journal of Theoretical Biology·L Glass, S A Kauffman
Jun 17, 1998·Proceedings of the National Academy of Sciences of the United States of America·P J Goss, J Peccoud
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Jan 19, 2000·Nature·B D Strahl, C D Allis
Mar 31, 2000·Nature Genetics·A Wagner
Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·N FriedmanD Pe'er
Feb 24, 2001·Nature·D Endy, R Brent
Mar 22, 2001·Nature·S H Strogatz
Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hidde de Jong
Apr 23, 2002·Nature Genetics·Nabil GuelzimFrançois Képès
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
Jun 4, 2002·Nature Reviews. Molecular Cell Biology·Denis Noble
Jul 27, 2002·Trends in Genetics : TIG·Alberto de la FuentePedro Mendes
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Nov 5, 2002·Trends in Biotechnology·Paul BrazhnikPedro Mendes
Mar 19, 2003·Proceedings. Biological Sciences·Andreas Wagner
Jun 24, 2003·Nature Genetics·Gavin C Conant, Andreas Wagner
Jul 12, 2003·Bioinformatics·Maureen Heymans, Ambuj K Singh
Jun 17, 1961·Nature·W T ASTBURY
Sep 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·Brian P KelleyTrey Ideker
Oct 10, 2003·Bioinformatics·Pedro MendesKeying Ye
Oct 11, 2003·Science·John Quackenbush
Dec 4, 2003·Biochemical Society Transactions·J W PinneyG A McConkey
Dec 19, 2003·Nucleic Acids Research·Albin SandelinBoris Lenhard
Feb 7, 2004·Science·Amy Hin Yan TongCharles Boone
May 28, 2004·Briefings in Functional Genomics & Proteomics·Sui Huang
Jul 31, 2004·Bioinformatics·Alberto de la FuentePedro Mendes
Sep 17, 2004·Nature·Nicholas M LuscombeMark Gerstein
Mar 22, 2005·Nature Genetics·Katia BassoAndrea Califano
Dec 13, 2005·The FEBS Journal·Carlos Rodriguez-CasoRicard V Solé
Feb 16, 2006·PLoS Computational Biology·Ala TrusinaJ Barry Egan
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Irit Gat-ViksRon Shamir
Apr 8, 2006·Nature Biotechnology·Roded Sharan, Trey Ideker

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

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.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

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.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation 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.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.