-
Kitano H, Funahashi A, Matsuoka Y, Oda K: Using process diagrams for the graphical representation of biological networks.
Nat Biotechnol 2005, 23(8):961-966. PubMed Abstract | Publisher Full Text 
-
Kohn KW: Molecular interaction map of the mammalian cell cycle control and DNA repair systems.
Mol Biol Cell 1999, 10(8):2703-2734. PubMed Abstract | Publisher Full Text | PubMed Central Full Text 
-
Kohn KW, Aladjem MI, Weinstein JN, Pommier Y: Molecular interaction maps of bioregulatory networks: a general rubric for systems biology.
Mol Biol Cell 2006, 17(1):1-13. PubMed Abstract | Publisher Full Text | PubMed Central Full Text 
-
Systems Biology Graphical Notation
[http://sbgn.org/]

-
Oda K, Kimura T, Matsuoka Y, Funahashi A, Muramatsu M, Kitano H: Molecular interaction map of a macrophage.
AfCS Research Reports 2004, 2(14):12. 
-
Oda K, Kitano H: A comprehensive map of the toll-like receptor signaling network.
Mol Syst Biol 2006, 2:2006 0015. PubMed Abstract | Publisher Full Text | PubMed Central Full Text 
-
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Bioinformatics 2003, 19(4):524-531. PubMed Abstract | Publisher Full Text 
-
Takeda K, Akira S: Toll-like receptors in innate immunity.
Int Immunol 2005, 17(1):1-14. PubMed Abstract | Publisher Full Text 
-
Kagan JC, Medzhitov R: Phosphoinositide-mediated adaptor recruitment controls Toll-like receptor signaling.
Cell 2006, 125(5):943-955. PubMed Abstract | Publisher Full Text 
-
Fitzgerald KA, Chen ZJ: Sorting out Toll signals.
Cell 2006, 125(5):834-836. PubMed Abstract | Publisher Full Text 
-
Zhong B, Tien P, Shu HB: Innate immune responses: crosstalk of signaling and regulation of gene transcription.
Virology 2006, 352(1):14-21. PubMed Abstract | Publisher Full Text 
-
Levy DE, Kessler DS, Pine R, Reich N, Darnell JE Jr.: Interferon-induced nuclear factors that bind a shared promoter element correlate with positive and negative transcriptional control.
Genes Dev 1988, 2(4):383-393. PubMed Abstract | Publisher Full Text 
-
Darnell JE Jr., Kerr IM, Stark GR: Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins.
Science 1994, 264(5164):1415-1421. PubMed Abstract | Publisher Full Text 
-
Chen FE, Huang DB, Chen YQ, Ghosh G: Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA.
Nature 1998, 391(6665):410-413. PubMed Abstract | Publisher Full Text 
-
Cramer P, Larson CJ, Verdine GL, Muller CW: Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution.
Embo J 1997, 16(23):7078-7090. PubMed Abstract | Publisher Full Text | PubMed Central Full Text 
-
Ghosh G, van Duyne G, Ghosh S, Sigler PB: Structure of NF-kappa B p50 homodimer bound to a kappa B site.
Nature 1995, 373(6512):303-310. PubMed Abstract | Publisher Full Text 
-
Huang DB, Huxford T, Chen YQ, Ghosh G: The role of DNA in the mechanism of NFkappaB dimer formation: crystal structures of the dimerization domains of the p50 and p65 subunits.
Structure 1997, 5(11):1427-1436. PubMed Abstract | Publisher Full Text 
-
Kerr JF, Wyllie AH, Currie AR: Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics.
Br J Cancer 1972, 26(4):239-257. PubMed Abstract 
-
Butte AJ, Kohane IS: Creation and implications of a phenome-genome network.
Nat Biotechnol 2006, 24(1):55-62. PubMed Abstract | Publisher Full Text 
-
Singh A, Mai D, Kumar A, Steyn AJ: Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association.
Proc Natl Acad Sci U S A 2006, 103(30):11346-11351. PubMed Abstract | Publisher Full Text | PubMed Central Full Text 
-
Division of Pathway Medicine, University of Edinburgh
[http://www.pathwaymedicine.ed.ac.uk ]

-
yWorks - The Diagramming Company
[http://www.yworks.com/en/index.html]

-
Freeman T.C. GL Brosch M., van Dongen S., Mazière P., Grocock R.J, Freilich S., Thornton J. and Enright A.J.: Construction, Visualisation and Clustering of Transcription Networks from Microarray Expression Data.
PLoS Computational Biology 2007, in press. 
-
Bioconductor open source software for bioinformatics
[http://www.bioconductor.org/]

-
van Dongen S: Graph clustering by flow simulation.
[PhD dissertation] Utrecht (The Netherlands): University of Utrecht 2000, 169. 
-
Moodie SL SA Goryanin I, Ghazal P: A Graphical Notation to Describe the Logical Interactions of Biological Pathways.
Journal of Integrative Bioinformatics 2006, 3(2):11. 
-
Chaudhary PM, Eby M, Jasmin A, Bookwalter A, Murray J, Hood L: Death receptor 5, a new member of the TNFR family, and DR4 induce FADD-dependent apoptosis and activate the NF-kappaB pathway.
Immunity 1997, 7(6):821-830. PubMed Abstract | Publisher Full Text 
-
Gil MP, Bohn E, O'Guin AK, Ramana CV, Levine B, Stark GR, Virgin HW, Schreiber RD: Biologic consequences of Stat1-independent IFN signaling.
Proc Natl Acad Sci U S A 2001, 98(12):6680-6685. PubMed Abstract | Publisher Full Text | PubMed Central Full Text 
-
Alexander WS, Hilton DJ: The role of suppressors of cytokine signaling (SOCS) proteins in regulation of the immune response.
Annu Rev Immunol 2004, 22:503-529. PubMed Abstract | Publisher Full Text 
-
Kubo M, Hanada T, Yoshimura A: Suppressors of cytokine signaling and immunity.
Nat Immunol 2003, 4(12):1169-1176. PubMed Abstract | Publisher Full Text 
-
Huang YH, Wu JY, Zhang Y, Wu MX: Synergistic and opposing regulation of the stress-responsive gene IEX-1 by p53, c-Myc, and multiple NF-kappaB/rel complexes.
Oncogene 2002, 21(44):6819-6828. PubMed Abstract | Publisher Full Text 
-
Charles CH, Yoon JK, Simske JS, Lau LF: Genomic structure, cDNA sequence, and expression of gly96, a growth factor-inducible immediate-early gene encoding a short-lived glycosylated protein.
Oncogene 1993, 8(3):797-801. PubMed Abstract 
-
Navarro L, Mowen K, Rodems S, Weaver B, Reich N, Spector D, David M: Cytomegalovirus activates interferon immediate-early response gene expression and an interferon regulatory factor 3-containing interferon-stimulated response element-binding complex.
Mol Cell Biol 1998, 18(7):3796-3802. PubMed Abstract | Publisher Full Text | PubMed Central Full Text 
-
Ohki R, Yamamoto K, Mano H, Lee RT, Ikeda U, Shimada K: Identification of mechanically induced genes in human monocytic cells by DNA microarrays.
J Hypertens 2002, 20(4):685-691. PubMed Abstract | Publisher Full Text 
-
Pietzsch A, Buchler C, Aslanidis C, Schmitz G: Identification and characterization of a novel monocyte/macrophage differentiation-dependent gene that is responsive to lipopolysaccharide, ceramide, and lysophosphatidylcholine.
Biochem Biophys Res Commun 1997, 235(1):4-9. PubMed Abstract | Publisher Full Text 
-
Li H, Zhu H, Xu CJ, Yuan J: Cleavage of BID by caspase 8 mediates the mitochondrial damage in the Fas pathway of apoptosis.
Cell 1998, 94(4):491-501. PubMed Abstract | Publisher Full Text 
-
Wen J, Ramadevi N, Nguyen D, Perkins C, Worthington E, Bhalla K: Antileukemic drugs increase death receptor 5 levels and enhance Apo-2L-induced apoptosis of human acute leukemia cells.
Blood 2000, 96(12):3900-3906. PubMed Abstract | Publisher Full Text 
-
Yin XM: Signal transduction mediated by Bid, a pro-death Bcl-2 family proteins, connects the death receptor and mitochondria apoptosis pathways.
Cell Res 2000, 10(3):161-167. PubMed Abstract | Publisher Full Text 
-
STRING: functional protein association networks
[http://string.embl.de/]

-
Ingenuity Pathway Analysis Software
[http://www.ingenuity.com]
