DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models

PloS One
Alex GreenfieldRichard Bonneau


Current technologies have lead to the availability of multiple genomic data types in sufficient quantity and quality to serve as a basis for automatic global network inference. Accordingly, there are currently a large variety of network inference methods that learn regulatory networks to varying degrees of detail. These methods have different strengths and weaknesses and thus can be complementary. However, combining different methods in a mutually reinforcing manner remains a challenge. We investigate how three scalable methods can be combined into a useful network inference pipeline. The first is a novel t-test-based method that relies on a comprehensive steady-state knock-out dataset to rank regulatory interactions. The remaining two are previously published mutual information and ordinary differential equation based methods (tlCLR and Inferelator 1.0, respectively) that use both time-series and steady-state data to rank regulatory interactions; the latter has the added advantage of also inferring dynamic models of gene regulation which can be used to predict the system's response to new perturbations. Our t-test based method proved powerful at ranking regulatory interactions, tying for first out of methods in the DREAM4 100-...Continue Reading


Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Jul 27, 2001·Proceedings of the National Academy of Sciences of the United States of America·M K Kerr, G A Churchill
Jun 21, 2002·Methods in Enzymology·Christine E Horak, Michael Snyder
Jul 23, 2002·Nature Genetics·Jan IhmelsNaama Barkai
Aug 10, 2002·Bioinformatics·Amos TanayRon Shamir
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Jan 10, 2003·Nucleic Acids Research·V MatysE Wingender
Apr 12, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Sven BergmannNaama Barkai
Oct 10, 2003·Bioinformatics·Pedro MendesKeying Ye
Mar 15, 2005·Nature Biotechnology·Diego di BernardoJames J Collins
Mar 22, 2005·Nature Genetics·Katia BassoAndrea Califano
Feb 15, 2007·Molecular Systems Biology·Mukesh BansalDiego di Bernardo
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Marc T FacciottiNitin S Baliga
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Aug 1, 2007·Nature Methods·Elaine R Mardis
Nov 30, 2007·Cell·Christoph D Schmid, Philipp Bucher
Jun 28, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Kuo-Ching Liang, Xiaodong Wang
Oct 22, 2008·Nature Chemical Biology·Richard Bonneau
Jan 20, 2009·Bio Systems·Michael HeckerReinhard Guthke
Feb 3, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Daniel MarbachDario Floreano
Feb 4, 2009·Bioinformatics·Brian C Haynes, Michael R Brent
Apr 8, 2009·Annals of the New York Academy of Sciences·Daniel MarbachDario Floreano
Dec 8, 2009·Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society·Aviv MadarRichard Bonneau
Dec 30, 2009·BMC Bioinformatics·Johanna MazurLars Kaderali
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
Sep 21, 2013·IEEE Transactions on Pattern Analysis and Machine Intelligence·Mauricio A ÁlvarezNeil D Lawrence


Apr 16, 2014·PloS One·James Henderson, George Michailidis
Nov 5, 2013·Nucleic Acids Research·Samuel A DanzigerJohn D Aitchison
Mar 29, 2014·BMC Systems Biology·Paola Vera-LiconaReinhard Laubenbacher
Nov 28, 2013·PLoS Computational Biology·Takeshi HaseHiroaki Kitano
Dec 7, 2013·Journal of the Royal Society, Interface·Alejandro F Villaverde, Julio R Banga
Oct 25, 2011·Journal of Clinical Bioinformatics·Konstantina DimitrakopoulouAnastasios Bezerianos
Sep 25, 2012·BMC Research Notes·Johannes D Stigter, Jaap Molenaar
Dec 12, 2012·Interface Focus·Christopher A Penfold, David L Wild
Feb 15, 2012·Cellular and Molecular Life Sciences : CMLS·Floriane Nicol-BenoîtDenis Michel
Jul 16, 2013·Nature Biotechnology·Soheil FeiziManolis Kellis
Jul 17, 2012·Nature Methods·Daniel MarbachGustavo Stolovitzky
Aug 29, 2012·Integrative and Comparative Biology·Antje H L Fischer, Joel Smith
Feb 7, 2016·Seminars in Cell & Developmental Biology·Narsis A KianiJesper Tegnér
Sep 3, 2014·Journal of Biomedical Informatics·Emmanuel S AdaborFrancis T Oduro
Jun 20, 2013·Plant, Cell & Environment·Joost J B KeurentjesBas J Zwaan
Jan 3, 2012·Current Opinion in Biotechnology·Justin AshworthNitin S Baliga
Jun 15, 2015·Bioinformatics·Francesca PetraliaZhidong Tu
Jan 13, 2015·Bioinformatics·Vân Anh Huynh-Thu, Guido Sanguinetti
Apr 29, 2015·Frontiers in Microbiology·Saliha DurmuşReinhard Guthke
Oct 2, 2012·Cell·Maria CiofaniDan R Littman
Mar 16, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Doaa AltarawyLenwood S Heath
Jan 1, 2013·Cells·Alejandro F VillaverdeJulio R Banga
Mar 2, 2016·PloS One·Hyunghoon ChoJian Peng
Sep 1, 2018·Bioinformatics·Daniel MorganErik L L Sonnhammer
May 24, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Hong-Li ZengHamed Mahmoudi
Nov 19, 2015·Molecular Systems Biology·Mario L Arrieta-OrtizPatrick Eichenberger
Jul 6, 2014·Molecular Systems Biology·Javier CarreraIlias Tagkopoulos
Sep 13, 2019·Bioinformatics·Torsten GrossNils Blüthgen
Feb 23, 2018·Scientific Reports·Vân Anh Huynh-Thu, Pierre Geurts
Jul 12, 2019·Protein & Cell·Pengcheng YangLe Kang
Jan 29, 2020·Molecular Informatics·Wenchao LiJianming Zhang
Jul 12, 2019·Journal of Bioinformatics and Computational Biology·Shuhei KimuraMariko Okada
Oct 17, 2019·Journal of Bioinformatics and Computational Biology·Luowen Liu, Jing Liu
Dec 12, 2019·Proceedings of the National Academy of Sciences of the United States of America·Ye Yuan, Ziv Bar-Joseph
Apr 10, 2020·Emerging Topics in Life Sciences·Montgomery BlencoweXia Yang
Apr 24, 2020·Scientific Reports·Jacopo CirroneDennis E Shasha
Jun 30, 2019·Frontiers in Genetics·Johann S HaweMatthias Heinig
Jul 2, 2020·NPJ Systems Biology and Applications·Zahra Razaghi-Moghadam, Zoran Nikoloski
Jul 15, 2020·Nature Communications·Atte AaltoJorge Gonçalves
Jul 16, 2020·BMC Bioinformatics·Dandan CheLifei Chen
Nov 11, 2020·Briefings in Bioinformatics·Giulia MuzioKarsten Borgwardt
Nov 26, 2018·IET Systems Biology·Wei ZhangNing Wang
Oct 4, 2020·Computers in Biology and Medicine·Emmanuel S Adabor, George K Acquaah-Mensah
Feb 13, 2018·Garima GuptaVartika Tewari

Methods Mentioned

gene knock-out
genetic knock-out
single-gene knock-out
gene knock-outs

Related Concepts

Likelihood Functions
Gene Modules
Experimental Design
Gene Knockout Techniques
Drug Interactions

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.

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.

The Tendon Seed Network

Tendons are rich in the extracellular matrix and are abundant throughout the body providing essential roles including structure and mobility. The transcriptome of tendons is being compiled to understand the micro-anatomical functioning of tendons. Discover the latest research pertaining to the Tendon Seed Network here.

Myocardial Stunning

Myocardial stunning is a mechanical dysfunction that persists after reperfusion of previously ischemic tissue in the absence of irreversible damage including myocardial necrosis. Here is the latest research.

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.


Incretins are metabolic hormones that stimulate a decrease in glucose levels in the blood and they have been implicated in glycemic regulation in the remission phase of type 1 diabetes. Here is the latest research.

Chromatin Regulation and Circadian Clocks

The circadian clock plays an important role in regulating transcriptional dynamics through changes in chromatin folding and remodelling. Discover the latest research on Chromatin Regulation and Circadian Clocks here.

Long COVID-19

“Long Covid-19” describes illness in patients who are reporting long-lasting effects of the SARS-CoV-19 infection, often long after they have recovered from acute Covid-19. Ongoing health issues often reported include low exercise tolerance and breathing difficulties, chronic tiredness, and mental health problems such as post-traumatic stress disorder and depression. This feed follows the latest research into Long Covid.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.