The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

Genome Biology
Richard BonneauVesteinn Thorsson

Abstract

We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interactions, and apply the method to predict a large portion of the regulatory network of the archaeon Halobacterium NRC-1. The Inferelator uses regression and variable selection to identify transcriptional influences on genes based on the integration of genome annotation and expression data. The learned network successfully predicted Halobacterium's global expression under novel perturbations with predictive power similar to that seen over training data. Several specific regulatory predictions were experimentally tested and verified.

References

Oct 16, 1999·Science·A-L Barabási, R Albert
Jan 19, 2000·Proceedings of the National Academy of Sciences of the United States of America·H NymeyerJ N Onuchic
Jul 26, 2000·Nature·G von DassowG M Odell
Oct 4, 2000·Proceedings of the National Academy of Sciences of the United States of America·W V NgS DasSarma
Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nir FriedmanDana Pe'er
May 31, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·T IdekerLeroy Hood
Jul 27, 2001·Bioinformatics·E SegalDaphne Koller
Sep 26, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M Wahde, J Hertz
Dec 26, 2001·Nucleic Acids Research·Minoru KanehisaAkihiro Nakaya
Dec 26, 2001·Nucleic Acids Research·Joseph C MellorCharles DeLisi
Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hidde de Jong
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
Jul 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jonathan A BernsteinStanley N Cohen
Aug 8, 2002·Pharmacogenomics·E P van SomerenM J T Reinders
Aug 10, 2002·Bioinformatics·Amos TanayRon Shamir
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Oct 31, 2002·Proceedings of the National Academy of Sciences of the United States of America·Nitin S BaligaLeroy Hood
Mar 26, 2003·Bioinformatics·Jianxin Wang, Ping Liang
Apr 3, 2003·Genome Research·Yuval KlugerMark Gerstein
Apr 26, 2003·Trends in Biochemical Sciences·Thijs J G EttemaJohn van der Oost
May 3, 2003·Current Opinion in Structural Biology·Eric Alm, Adam P Arkin
Sep 10, 2003·Proceedings of the National Academy of Sciences of the United States of America·Ilya ShmulevichWei Zhang
Oct 10, 2003·Bioinformatics·Qizheng ShengBart De Moor
Oct 14, 2003·Nature Biotechnology·Ziv Bar-JosephDavid K Gifford
Dec 19, 2003·Nucleic Acids Research·Alex BatemanSean R Eddy
Feb 12, 2004·Bioinformatics·Ronaldo F HashimotoEdward R Dougherty
Feb 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Amos TanayRon Shamir
Apr 23, 2004·Current Opinion in Biotechnology·Markus J HerrgårdBernhard Ø Palsson
May 7, 2004·Genome Biology·Peter M BowersDavid Eisenberg
Aug 25, 2004·Physical Review Letters·Ilya Shmulevich, Stuart A Kauffman
Nov 10, 2004·Proceedings of the National Academy of Sciences of the United States of America·Debopriya DasMichael Q Zhang
Apr 27, 2005·The Analyst·Warwick B DunnHelen E Johnson
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Vesteinn ThorssonLeroy Hood
Oct 19, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Mika GustafssonAnna Lombardi
Feb 26, 2013·Algorithms for Molecular Biology : AMB·Beatriz PontesJesús S Aguilar-Ruiz
Apr 19, 2013·Bioinformatics·Samad LotiaAlexander R Pico

Citations

Dec 8, 2007·Functional & Integrative Genomics·Enrico Capobianco
Jul 16, 2013·Nature Biotechnology·Soheil FeiziManolis Kellis
Jul 19, 2012·Nature Reviews. Genetics·Ziv Bar-JosephItamar Simon
Sep 2, 2010·Nature Reviews. Microbiology·Riet De Smet, Kathleen Marchal
Oct 30, 2010·IET Systems Biology·Sushmita RoyT Lane
Jan 24, 2009·Proceedings of the National Academy of Sciences of the United States of America·David R LorenzJames J Collins
Mar 24, 2010·Proceedings of the National Academy of Sciences of the United States of America·Daniel MarbachGustavo Stolovitzky
Mar 17, 2010·Proceedings of the National Academy of Sciences of the United States of America·Debashis SahooDavid L Dill
Oct 1, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sriram ChandrasekaranGene E Robinson
Aug 19, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·T M Murali, Corban G Rivera
Feb 4, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Thomas SakoparnigNiko Beerenwinkel
May 7, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Andreas TjärnbergErik L L Sonnhammer
Aug 4, 2009·Omics : a Journal of Integrative Biology·Yong WangLuonan Chen
Jun 27, 2008·Briefings in Functional Genomics & Proteomics·Leroy HoodJohn D Aitchison
Jan 12, 2010·Briefings in Bioinformatics·Teresa M PrzytyckaDonna K Slonim
Dec 7, 2007·Bioinformatics·David J ReissNitin S Baliga
Jul 1, 2008·Bioinformatics·T A KnijnenburgM J T Reinders
Dec 29, 2012·Bioinformatics·Liming WangMichael S Samoilov
Feb 4, 2009·Nucleic Acids Research·Javier CarreraAlfonso Jaramillo
Feb 11, 2012·Nucleic Acids Research·Elizabeth G WilbanksMarc T Facciotti
Dec 12, 2012·Interface Focus·Christopher A Penfold, David L Wild
Dec 7, 2013·Journal of the Royal Society, Interface·Alejandro F Villaverde, Julio R Banga
Jun 19, 2008·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Fernando OrtegaFrancesco Falciani
May 3, 2013·Genome Research·Brian C HaynesMichael R Brent
Jun 6, 2006·Genome Research·Amardeep KaurNitin S Baliga
Sep 6, 2007·Genome Research·Amy K SchmidNitin S Baliga
Jul 19, 2008·Annual Review of Analytical Chemistry·L Hood
Jan 6, 2010·Statistical Methods in Medical Research·Ning Sun, Hongyu Zhao
Feb 13, 2013·BMC Bioinformatics·Nguyen Xuan VinhPramod P Wangikar
Oct 2, 2007·BMC Bioinformatics·Florian Markowetz, Rainer Spang
Jun 28, 2011·Source Code for Biology and Medicine·Koji KyodaShuichi Onami
May 7, 2009·BMC Research Notes·Eugene Novikov, Emmanuel Barillot
Sep 25, 2012·BMC Research Notes·Johannes D Stigter, Jaap Molenaar
Jan 31, 2009·PLoS Computational Biology·Debopriya DasJoe W Gray
Feb 4, 2010·PLoS Computational Biology·Shakti GuptaShankar Subramaniam
May 11, 2010·PLoS Computational Biology·Xuejing LiChristina Leslie
Oct 17, 2012·PLoS Computational Biology·Jason E McDermottAntonio Sanfilippo
May 30, 2013·PLoS Computational Biology·Xiaodong CaiGeorgios B Giannakis
Dec 25, 2013·PLoS Computational Biology·Evan J MolinelliChris Sander
Aug 28, 2009·PloS One·Scott ChristleyXiaohui Xie
Feb 27, 2010·PloS One·Robert J PrillGustavo Stolovitzky
Oct 12, 2010·PloS One·Vân Anh Huynh-ThuPierre Geurts
Dec 15, 2010·PloS One·Adrian SchröderAndreas Zell
Jan 4, 2013·PloS One·Michael BaitalukJulia Ponomarenko
May 12, 2010·Gene Regulation and Systems Biology·Xiaosheng Wang, Osamu Gotoh
Apr 16, 2014·PloS One·James Henderson, George Michailidis
Feb 12, 2014·Omics : a Journal of Integrative Biology·Konstantina DimitrakopoulouAnastasios Bezerianos
Nov 5, 2013·Nucleic Acids Research·Samuel A DanzigerJohn D Aitchison
Feb 11, 2010·Future Microbiology·Gwendoline KintSigrid C J De Keersmaecker
Jan 23, 2014·Nature Immunology·Brian A KiddJoel T Dudley
Aug 30, 2012·Briefings in Bioinformatics·Zhong WangRongling Wu
May 12, 2012·Journal of Biomedicine & Biotechnology·Jianlong QiGregory Butler
Mar 28, 2013·Archaea : an International Microbiological Journal·Pallavee Srivastava, Meenal Kowshik
Jan 29, 2014·Journal of Bioinformatics and Computational Biology·Peter Gennemark, Dag Wedelin
Feb 22, 2014·Current Opinion in Biotechnology·Derek N MacklinMarkus W Covert
Jun 17, 2014·Bioinformatics·Matthew StudhamErik L L Sonnhammer
Apr 15, 2014·Journal of Theoretical Biology·Y X Rachel Wang, Haiyan Huang
Oct 25, 2011·Theoretical Biology & Medical Modelling·Fadhl M AlakwaaYasser M Kadah
Oct 22, 2008·Nature Chemical Biology·Richard Bonneau
May 20, 2009·IET Systems Biology·A JuliusG J Pappas
Jun 30, 2009·Molecular BioSystems·Javier CarreraAlfonso Jaramillo
Jun 24, 2011·Molecular BioSystems·Jason E McDermottLouis A Sherman
Nov 26, 2013·Nucleic Acids Research·Serdar TurkarslanNitin S Baliga
Dec 17, 2014·Proceedings of the National Academy of Sciences of the United States of America·Ann C BabtieMichael P H Stumpf
Mar 8, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Daniel LoboMichael Levin
Sep 4, 2008·Molecular Systems Biology·Sven NelanderChris Sander
Jun 19, 2009·Molecular Systems Biology·Tie KoideNitin S Baliga
Jul 29, 2010·Molecular Systems Biology·Amardeep KaurNitin S Baliga
Jul 17, 2015·Bioinformatics·Daniel Trejo BanosGuido Sanguinetti
Feb 24, 2015·Frontiers in Microbiology·Sylvie SchulzeJörg Linde
Jul 30, 2014·Frontiers in Genetics·Miguel A Hernández-PrietoMatthias E Futschik
Oct 9, 2014·Bioinformatics·Erhan BilalLeonidas G Alexopoulos
May 26, 2016·Nature Communications·David SchnoerrGuido Sanguinetti
Dec 19, 2014·PLoS Computational Biology·Siddhartha JainZiv Bar-Joseph
Feb 28, 2015·PLoS Computational Biology·Saheed ImamTimothy J Donohue
May 8, 2015·PLoS Computational Biology·Zachary D KurtzRichard Bonneau
Jul 29, 2016·PLoS Computational Biology·Chuan GaoBarbara E Engelhardt
Aug 8, 2007·Current Opinion in Biotechnology·Nathan D Price, Ilya Shmulevich
Oct 31, 2016·Nucleic Acids Research·Alireza Fotuhi Siahpirani, Sushmita Roy
Nov 5, 2016·Proceedings of the National Academy of Sciences of the United States of America·Drew G MichaelMichael R Brent
Nov 13, 2015·Science Translational Medicine·Mika GustafssonMikael Benson
Feb 13, 2016·Scientific Reports·Nooshin OmranianZoran Nikoloski
Mar 16, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Doaa AltarawyLenwood S Heath
Jan 20, 2009·Bio Systems·Michael HeckerReinhard Guthke
Dec 7, 2016·PLoS Computational Biology·Kari Y LamRichard Bonneau
Feb 7, 2017·PLoS Computational Biology·David HenriquesJulio R Banga
Apr 6, 2017·Bioinformatics·Sabrina RashidZiv Bar-Joseph
Jun 10, 2015·Integrative Biology : Quantitative Biosciences From Nano to Macro·Mark F CiaccioNeda Bagheri
Jun 24, 2017·PLoS Computational Biology·Rasmus MagnussonMika Gustafsson
Dec 1, 2017·Bioinformatics·Phan Nguyen, Rosemary Braun
Nov 28, 2017·Annual Review of Genetics·Mar Martinez-PastorAmy K Schmid
Dec 10, 2017·Scientific Reports·Jigar S DesaiColleen J Doherty
Sep 14, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Lucas B EdelmanNathan D Price
Dec 6, 2014·European Journal of Immunology·Fuyan WangHaiming Wei
Sep 13, 2014·PloS One·Miriam Kolog GulkoDieter Oesterhelt
Aug 15, 2018·Environmental Microbiology·Anne E OtwellNitin S Baliga
Nov 18, 2018·The Plant Journal : for Cell and Molecular Biology·Maricris L ZaidemMichael D Purugganan
Jan 17, 2007·Molecular Systems Biology·Jason ErnstZiv Bar-Joseph
Jan 19, 2019·Non-coding RNA·Irena Misiewicz-KrzeminskaNorma C Gutiérrez
Jan 25, 2019·PLoS Computational Biology·Dayanne M CastroRichard Bonneau
Nov 23, 2007·Journal of Cellular and Molecular Medicine·Nathan D PriceQiang Tian
Oct 4, 2014·BMC Systems Biology·Jesse C J van DamMaría Suárez-Diez
Jan 6, 2009·Immunological Reviews·Daniel E Zak, Alan Aderem
Apr 8, 2009·Annals of the New York Academy of Sciences·John WatkinsonDimitris Anastassiou
Apr 8, 2009·Annals of the New York Academy of Sciences·Tom MichoelYves Van de Peer
Feb 5, 2019·Bioinformatics·Yannis Pantazis, Ioannis Tsamardinos
Feb 15, 2007·Molecular Systems Biology·Boris HayeteJames J Collins
Feb 15, 2007·Molecular Systems Biology·Mukesh BansalDiego di Bernardo
Oct 22, 2010·Environmental Toxicology and Chemistry·Edward J PerkinsAlexandre Loguinov
Apr 23, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xiao LiangKa Yee Yeung
Oct 17, 2012·Nature Reviews. Microbiology·Nicholas K PriestRuth C Massey
Aug 21, 2013·Immunological Reviews·Vineet D Menachery, Ralph S Baric
Nov 19, 2015·Molecular Systems Biology·Mario L Arrieta-OrtizPatrick Eichenberger
Mar 28, 2018·Molecular Systems Biology·Seth A AmentNathan D Price
Mar 23, 2017·Molecular Systems Biology·Serdar TurkarslanNitin S Baliga
Jul 17, 2014·Molecular Systems Biology·Aaron N BrooksNitin S Baliga
Feb 23, 2018·Scientific Reports·Vân Anh Huynh-Thu, Pierre Geurts
Jan 7, 2020·Bioinformatics·Rasmus Magnusson, Mika Gustafsson
Mar 24, 2016·BMC Systems Biology·Jovan TanevskiSašo Džeroski
Mar 10, 2020·PLoS Computational Biology·Sanjana GuptaJames R Faeder
Nov 3, 2018·PloS One·M Umut CaglarClaus O Wilke
Oct 21, 2016·Genome Biology·Kevin A McGoffJohn L Harer
Apr 28, 2018·Scientific Reports·Shayan Tabe-BordbarSaurabh Sinha
Mar 19, 2019·Experimental Biology and Medicine·Anders B Dohlman, Xiling Shen
Jul 25, 2019·Nature Microbiology·Manish KumarJens Nielsen
Aug 28, 2020·Scientific Reports·Daniel MorganErik L L Sonnhammer
Jun 20, 2013·Plant, Cell & Environment·Joost J B KeurentjesBas J Zwaan
Jan 31, 2017·Computational and Mathematical Methods in Medicine·Yue FanQinke Peng
Jul 30, 2020·MSystems·Adrián López García de LomanaNitin S Baliga
Feb 14, 2017·PLoS Computational Biology·Miguel FribourgVladimir Brezina
May 3, 2019·BMC Bioinformatics·Chen WangXiaodong Cai
Jul 14, 2020·Bioinformatics·Torsten Gross, Nils Blüthgen
Jun 4, 2020·MSystems·Lars Barquist
Jul 24, 2019·Nature Ecology & Evolution·Jordi van GestelAndreas Wagner
Nov 11, 2020·NPJ Systems Biology and Applications·Deniz SeçilmişErik L L Sonnhammer
Dec 17, 2020·Frontiers in Bioengineering and Biotechnology·Abhinav AdhikariJeffrey D Varner
Jan 16, 2021·Nucleic Acids Research·Maxwell L NealJohn D Aitchison
Sep 2, 2020·Cell Systems·Payam Dibaeinia, Saurabh Sinha
Jan 30, 2021·PLoS Computational Biology·Jonathan LuBarbara E Engelhardt
Aug 24, 2018·Yi ZhangJinze Liu

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