de Jong H: Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 2002, 9(1):67–103. 10.1089/10665270252833208
Article
CAS
PubMed
Google Scholar
Lockhart DJ, Winzeler EA: Genomics, gene expression and DNA arrays. Nature 2000, 405(6788):827–836. 10.1038/35015701
Article
CAS
PubMed
Google Scholar
Bussemaker HJ, Li H, Siggia ED: Regulatory element detection using correlation with expression. Nat Genet 2001, 27(2):167–171. 10.1038/84792
Article
CAS
PubMed
Google Scholar
Conlon EM, Liu XS, Lieb JD, Liu JS: Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A 2003, 100(6):3339–3344. 10.1073/pnas.0630591100
Article
PubMed Central
CAS
PubMed
Google Scholar
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, Szustakowki J, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ: Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860–921. 10.1038/35057062
Article
CAS
PubMed
Google Scholar
Thompson W, Palumbo MJ, Wasserman WW, Liu JS, Lawrence CE: Decoding human regulatory circuits. Genome Res 2004, 14(10A):1967–1974. 10.1101/gr.2589004
Article
PubMed Central
CAS
PubMed
Google Scholar
Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ: The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31(1):51–54. 10.1093/nar/gkg129
Article
PubMed Central
CAS
PubMed
Google Scholar
Gupta M, Liu JS: Discovery of Conserved Sequence Patterns Using a Stochastic Dictionary Model. In Journal of the American Statistical Association. Volume 461. 98 ; 2003.
Grad YH, Roth FP, Halfon MS, Church GM: Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics 2004, 20(16):2738–2750. 10.1093/bioinformatics/bth320
Article
CAS
PubMed
Google Scholar
Sharan R, Ovcharenko I, Ben-Hur A, Karp RM: CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics 2003, 19 Suppl 1: i283–91. 10.1093/bioinformatics/btg1039
Article
PubMed
Google Scholar
Keles S, van der Laan M, Eisen MB: Identification of regulatory elements using a feature selection method. Bioinformatics 2002, 18(9):1167–1175. 10.1093/bioinformatics/18.9.1167
Article
CAS
PubMed
Google Scholar
Xu Y, Selaru FM, Yin J, Zou TT, Shustova V, Mori Y, Sato F, Liu TC, Olaru A, Wang S, Kimos MC, Perry K, Desai K, Greenwald BD, Krasna MJ, Shibata D, Abraham JM, Meltzer SJ: Artificial neural networks and gene filtering distinguish between global gene expression profiles of Barrett's esophagus and esophageal cancer. Cancer Res 2002, 62(12):3493–3497.
CAS
PubMed
Google Scholar
Vincenti MP, Brinckerhoff CE: Early response genes induced in chondrocytes stimulated with the inflammatory cytokine interleukin-1beta. Arthritis Res 2001, 3(6):381–388. 10.1186/ar331
Article
PubMed Central
CAS
PubMed
Google Scholar
Heller RA, Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW: Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci U S A 1997, 94(6):2150–2155. 10.1073/pnas.94.6.2150
Article
PubMed Central
CAS
PubMed
Google Scholar
Elliott SF, Coon CI, Hays E, Stadheim TA, Vincenti MP: Bcl-3 is an interleukin-1-responsive gene in chondrocytes and synovial fibroblasts that activates transcription of the matrix metalloproteinase 1 gene. Arthritis Rheum 2002, 46(12):3230–3239. 10.1002/art.10675
Article
CAS
PubMed
Google Scholar
Chadjichristos C, Ghayor C, Kypriotou M, Martin G, Renard E, Ala-Kokko L, Suske G, de Crombrugghe B, Pujol JP, Galera P: Sp1 and Sp3 transcription factors mediate interleukin-1 beta down-regulation of human type II collagen gene expression in articular chondrocytes. J Biol Chem 2003, 278(41):39762–39772. 10.1074/jbc.M303541200
Article
CAS
PubMed
Google Scholar
Francois M, Richette P, Tsagris L, Raymondjean M, Fulchignoni-Lataud MC, Forest C, Savouret JF, Corvol MT: Peroxisome proliferator-activated receptor-gamma down-regulates chondrocyte matrix metalloproteinase-1 via a novel composite element. J Biol Chem 2004, 279(27):28411–28418. 10.1074/jbc.M312708200
Article
CAS
PubMed
Google Scholar
Imamura T, Imamura C, Iwamoto Y, Sandell LJ: Transcriptional Co-activators CREB-binding protein/p300 increase chondrocyte Cd-rap gene expression by multiple mechanisms including sequestration of the repressor CCAAT/enhancer-binding protein. J Biol Chem 2005, 280(17):16625–16634. 10.1074/jbc.M411469200
Article
CAS
PubMed
Google Scholar
Gardner TS, di Bernardo D, Lorenz D, Collins JJ: Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003, 301(5629):102–105. 10.1126/science.1081900
Article
CAS
PubMed
Google Scholar
Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB: Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17(6):520–525. 10.1093/bioinformatics/17.6.520
Article
CAS
PubMed
Google Scholar
Chuang HYH, Chen L: Efficient Computation of the Singlular Value Decomposition on Cube Connected SIMD Machine: Reno. ; 1989:276–282.
Google Scholar
Alter O, Brown PO, Botstein D: Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 2000, 97(18):10101–10106. 10.1073/pnas.97.18.10101
Article
PubMed Central
CAS
PubMed
Google Scholar
Liu Y, Sun HB, Yokota H: Regulating gene expression using optimal control theory. Proc 3rd IEEE Sym Bioinfo Bioeng 2003, 1–3.
Google Scholar
Holter NS, Mitra M, Maritan A, Cieplak M, Banavar JR, Fedoroff NV: Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc Natl Acad Sci U S A 2000, 97(15):8409–8414. 10.1073/pnas.150242097
Article
PubMed Central
CAS
PubMed
Google Scholar
Holland JH: Adaptation in natural and artificial systems. Ann Arbor , The University of Michigan Press; 1975.
Google Scholar
Li L, Weinberg CR, Darden TA, Pedersen LG: Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method. Bioinformatics 2001, 17(12):1131–1142. 10.1093/bioinformatics/17.12.1131
Article
CAS
PubMed
Google Scholar
Grether-Beck S, Buettner R, Krutmann J: Ultraviolet A radiation-induced expression of human genes: molecular and photobiological mechanisms. Biol Chem 1997, 378(11):1231–1236.
CAS
PubMed
Google Scholar
Eastman Q, Grosschedl R: Regulation of LEF-1/TCF transcription factors by Wnt and other signals. Curr Opin Cell Biol 1999, 11(2):233–240. 10.1016/S0955-0674(99)80031-3
Article
CAS
PubMed
Google Scholar
Tan L, Peng H, Osaki M, Choy BK, Auron PE, Sandell LJ, Goldring MB: Egr-1 mediates transcriptional repression of COL2A1 promoter activity by interleukin-1beta. J Biol Chem 2003.
Google Scholar
Philipsen S, Suske G: A tale of three fingers: the family of mammalian Sp/XKLF transcription factors. Nucleic Acids Res 1999, 27(15):2991–3000. 10.1093/nar/27.15.2991
Article
PubMed Central
CAS
PubMed
Google Scholar
Vincenti MP, Coon CI, Brinckerhoff CE: Nuclear factor kappaB/p50 activates an element in the distal matrix metalloproteinase 1 promoter in interleukin-1beta-stimulated synovial fibroblasts. Arthritis Rheum 1998, 41(11):1987–1994. Publisher Full Text 10.1002/1529-0131(199811)41:11%3C;1987::AID-ART14%3E;3.0.CO;2-8
Article
CAS
PubMed
Google Scholar
Ding GJ, Fischer PA, Boltz RC, Schmidt JA, Colaianne JJ, Gough A, Rubin RA, Miller DK: Characterization and quantitation of NF-kappaB nuclear translocation induced by interleukin-1 and tumor necrosis factor-alpha. Development and use of a high capacity fluorescence cytometric system. J Biol Chem 1998, 273(44):28897–28905. 10.1074/jbc.273.44.28897
Article
CAS
PubMed
Google Scholar
Barnes PJ, Karin M: Nuclear factor-kappaB: a pivotal transcription factor in chronic inflammatory diseases. N Engl J Med 1997, 336(15):1066–1071. 10.1056/NEJM199704103361506
Article
CAS
PubMed
Google Scholar
Sun HB, Malacinski GM, Yokota H: Promoter competition assay for analyzing gene regulation in joint tissue engineering. Front Biosci 2002, 7: a169–74.
CAS
PubMed
Google Scholar
Sun HB, Liu Y, Qian L, Yokota H: Model-based analysis of matrix metalloproteinase expression under mechanical shear. Ann Biomed Eng 2003, 31(2):171–180. 10.1114/1.1540635
Article
PubMed
Google Scholar
Collins FS, Green ED, Guttmacher AE, Guyer MS: A vision for the future of genomics research. Nature 2003, 422(6934):835–847. 10.1038/nature01626
Article
CAS
PubMed
Google Scholar
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X: The sequence of the human genome. Science 2001, 291(5507):1304–1351. 10.1126/science.1058040
Article
CAS
PubMed
Google Scholar
Davuluri RV, Grosse I, Zhang MQ: Computational identification of promoters and first exons in the human genome. Nat Genet 2001, 29(4):412–417. 10.1038/ng780
Article
CAS
PubMed
Google Scholar
Liu Y, Yokota H: Modelling and idenification of transcription-factor binding motifs in human chondrogenesis. Systems Biology 2004, 1(1):85–92. 10.1049/sb:20045012
Article
CAS
PubMed
Google Scholar
Qian L, Liu Y, Sun HB, Yokota H: Systems analysis of matrix metalloproteinase mRNA expression in skeletal tissues. Front Biosci 2002, 7: a126–34.
Article
PubMed
Google Scholar
Akaike H: A new look at the statistical model identification. IEEE Transactions on Automatic Control 1974, AC-19: 716–723. 10.1109/TAC.1974.1100705
Article
Google Scholar
Liu Y, Yokota H: Modelling and identification of transcription-factor binding motifs in human chondrogenesis. Systems Biology 2004, 1(1):85–92. 10.1049/sb:20045012
Article
CAS
PubMed
Google Scholar
Wingender E, Dietze P, Karas H, Knuppel R: TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 1996, 24(1):238–241. 10.1093/nar/24.1.238
Article
PubMed Central
CAS
PubMed
Google Scholar