Alon U. 2007. Network motifs: Theory and experimental approaches. Nat Rev Genet 8: 450-461. (Pubitemid 46789247)
Balázsi G, Barabási AL, Oltvai ZN. 2005. Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci 102: 7841-7846. (Pubitemid 40781025)
Bernard A, Hartemink AJ. 2005. Informative structure priors: Joint learning of dynamic regulatory networks from multiple types of data. Pac Symp Biocomput 2005: 459-470.
Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, et al. 2007. A predictive model for transcriptional control of physiology in a free living cell. Cell 131: 1354-1365. (Pubitemid 350297417)
Boorsma A, Lu X-J, Zakrzewska A, Klis FM, Bussemaker HJ. 2008. Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. PLoS ONE 3: e3112. doi: 10.1371/journal.pone.0003112.
Boulesteix AL, Strimmer K. 2005. Predicting transcription factor activities from combined analysis of microarray and ChIP data: A partial least squares approach. Theor Biol Med Model 2: 23. doi: 10.1186/1742-4682-2-23.
Bussemaker HJ, Foat BC, Ward LD. 2007. Predictive modeling of genomewide mRNA expression: From modules to molecules. Annu Rev Biophys Biomol Struct 36: 329-347. (Pubitemid 46998122)
Capaldi AP, Kaplan T, Liu Y, Habib N, Regev A, Friedman N, O'Shea EK. 2008. Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet 40: 1300-1306.
Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, et al. 2009. Unlocking the secrets of the genome. Nature 459: 927-930.
Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, et al. 2011. The transcriptional diversity of 25 Drosophila cell lines. Genome Res 21: 301-314.
Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG. 2009. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PLoS Comput Biol 5: e1000417. doi: 10.1371/journal.pcbi.1000417.
Costello JC, Dalkilic MM, Beason SM, Gehlhausen JR, Patwardhan R, Middha S, Eads BD, Andrews JR. 2009. Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function. Genome Biol 10: R97. doi: 10.1186/gb-2009-10-9-r97.
Drosophila 12 Genomes Consortium 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
The ENCODE Project Consortium. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046. doi: 10.1371/journal.pbio. 1001046.
Ernst J, Kellis M. 2010. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825.
Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z. 2008. A semisupervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol 4: e1000044. doi: 10.1371/journal.pcbi. 1000044.
Erwin DH, Davidson EH. 2009. The evolution of hierarchical gene regulatory networks. Nat Rev Genet 10: 141-148.
Estabrooks A, Jo T, Japkowicz N. 2004. A multiple resampling method for learning from imbalanced data sets. Comput Intell 20: 18-36.
Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muñiz-Rascado L, Martínez-Flores I, Salgado H, et al. 2008. Regulon DB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36: D120-D124. (Pubitemid 351149707)
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin J, Yang L, Artieri C, van Baren MJ, Booth BW, Brown JB, et al. 2010. The developmental transcriptome of Drosophila melanogaster. Nature 471: 473-479.
Greenfield A, Madar A, Ostrer H, Bonneau R. 2010. DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models. PLoS ONE 5: e13397. doi: 10.1371/journal.pone.0013397.
Guelzim N, Bottani S, Bourgine P, Kepes F. 2002. Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31: 60-63.
Gupta R, Stincone A, Antczak P, Durant S, Bicknell R, Bikfalvi A, Falciani F. 2011. A computational framework for gene regulatory network inference that combines multiplemethods and datasets. BMC Syst Biol 5: 52. doi: 10.1186/1752-0509-5-52.
Halfon MS, Gallo SM, Bergman CM. 2008. REDfly 2.0: An integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Res 36: D594-D598. (Pubitemid 351149791)
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104. (Pubitemid 39215116)
Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EEM, Bork P. 2007. Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Mol Syst Biol 3: 72. doi: 10.1038/msb4100112.
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL. 2000. The large-scale organization of metabolic networks. Nature 407: 651-654.
Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, et al. 2011. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471: 458-459.
Kheradpour P, Stark A, Roy S, Kellis M. 2007. Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res 17: 1919-1931. (Pubitemid 351360014)
Kummerfeld SK, Teichmann SA. 2006. DBD: A transcription factor prediction database. Nucleic Acids Res 1: D74-D81.
Lancichinetti A, Kivelä M, Saramäki J, Fortunato S. 2010. Characterizing the community structure of complex networks. PLoS ONE 5: e11976. doi: 10.1371/journal.pone.0011976.
Levine RB, Morton DB, Restifo LL. 1995. Remodeling of the insect nervous system. Curr Opin Neurobiol 5: 28-35.
Li X, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, et al. 2008. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6: e27. doi: 10.1371/journal.pbio.0060027.
MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keränen SV, et al. 2009. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol 10: R80. doi: 10.1186/gb-2009-10-7-r80.
MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. 2006. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7: 113. doi: 10.1186/1471-2105-7-113.
Macskassy SA, Provost F. 2005. Suspicion scoring based on guilt-by-association, collective inference, and focused data access. In Proceedings of the International Conference on Intelligence Analysis (IA '05).
Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G. 2010. Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci 107: 6286-6291.
Marbach D, Costello JC, Küffner R, Vega N, Prill RJ, Camacho DM, Allison KR, The DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G. 2012. Wisdom of crowds for robust gene network inference. Nat Methods (in press).
Mitchell T. 1997. Machine learning. McGraw-Hill, New York.
The modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Nègre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, et al. 2010. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787-97.
Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, et al. 2011. A cis-regulatory map of the Drosophila genome. Nature 471: 527-531.
Pacifico S, Liu G, Guest S, Parrish JR, Fotouhi F, Finley RL Jr. 2006. A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. BMC Bioinformatics 7: 195. doi: 10.1186/1471-2105-7-195.
Park CY, Hess DC, Huttenhower C, Troyanskaya OG. 2010. Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PLoS Comput Biol 6: e1001009. doi: 10.1371/journal.pcbi.1001009.
Potapov AP, Voss N, Sasse N, Wingender E. 2005. Topology of mammalian transcription networks. Genome Inform 16: 270-278.
Qian J, Lin J, Luscombe NM, Yu H, Gerstein M. 2003. Prediction of regulatory networks:Genome-wide identification of transcription factor targets from gene expression data. Bioinformatics 19: 1917-1926. (Pubitemid 37322335)
Ravasz E, Barabási A-L. 2003. Hierarchical organization in complex networks. Phys Rev E Stat Nonlin Soft Matter Phys 67: 026112.
Raveh-Sadka T, Levo M, Segal E. 2009. Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res 19: 1480-1496.
Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA, Walhout AJ. 2005. A compendium of Caenorhabditis elegans regulatory transcription factors: A resource for mapping transcription regulatory networks. Genome Biol 6: R110. doi: 10.1186/gb-2005-6-13-r110.
Roy S, Lane T, Werner-Washburne M. 2009. Learning structurally consistent undirected graphical models. Proc Int Conf Mach Learn 382: 905-912
Seok J, Kaushal A, Davis RW, Xiao W. 2010. Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships. BMC Bioinformatics 11: S8. doi: 10.1186/1471-2105-11-S1-S8.
Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G. 2012. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148: 458-472.
Sharan R, Ulitsky I, Shamir R. 2007. Network-based prediction of protein function. Mol Syst Biol 3: 88. doi: 10.1038/msb4100129.
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, et al. 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-232. (Pubitemid 350100553)
Stewart AJ, Seymour RM, Pomiankowski A. 2009. Degree dependence in rates of transcription factor evolution explains the unusual structure of transcription networks. Proc Biol Sci 276: 2493-2501.
Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, Celniker SE, Rubin GM. 2007. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol 8: R145. doi: 10.1186/gb-2007-8-7- r145.
Tsang J, Zhu J, van Oudenaarden A. 2007.MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 26: 753-767. (Pubitemid 46856248)
Wilczynski B, Furlong EEM. 2009. Challenges for modeling global gene regulatory networks during development: Insights from Drosophila. Dev Biol 340: 161-169.
Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo RY, Alon U, Margalit H. 2004. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci 101: 5934-5939. (Pubitemid 38520506)
Zdobnov EM, Apweiler R. 2001. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848. (Pubitemid 32970486)
Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M. 2007. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev 21: 385-390.
Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, et al. 2004. The functional landscape of mouse gene expression. J Biol 3: 21. doi: 10.1186/jbiol16.