TY - JOUR AU - Matys, V. AU - Fricke, E. AU - Geffers, R. AU - Gössling, E. AU - Haubrock, M. AU - Hehl, R. AU - Hornischer, K. AU - Karas, D. AU - Kel, A. E. AU - Kel-Margoulis, O. V. AU - Kloos, D. U. AU - Land, S. AU - Lewicki-Potapov, B. AU - Michael, H. AU - Münch, R. AU - Reuter, I. AU - Rotert, S. AU - Saxel, H. AU - Scheer, M. AU - Thiele, S. AU - Wingender, E. PY - 2003 DA - 2003// TI - TRANSFAC: transcriptional regulation, from patterns to profiles JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg108 DO - 10.1093/nar/gkg108 ID - Matys2003 ER - TY - CHAP AU - Filkov, V. ED - Aluru, S. PY - 2005 DA - 2005// TI - Identifying Gene Regulatory Networks from Gene Expression Data BT - Handbook of Computational Molecular Biology ID - Filkov2005 ER - TY - JOUR AU - Hecker, M. AU - Lambeck, S. AU - Toepfer, S. AU - van Someren, E. P. AU - Guthke, R. PY - 2009 DA - 2009// TI - Gene regulatory network inference: Data integration in dynamic models – A review JO - Biosystems VL - 96 UR - https://doi.org/10.1016/j.biosystems.2008.12.004 DO - 10.1016/j.biosystems.2008.12.004 ID - Hecker2009 ER - TY - JOUR AU - Cho, K. H. AU - Choo, S. M. AU - Jung, S. H. AU - Kim, J. R. AU - Choi, H. S. AU - Kim, J. PY - 2007 DA - 2007// TI - Reverse engineering of gene regulatory networks JO - IET Syst Biol VL - 1 UR - https://doi.org/10.1049/iet-syb:20060075 DO - 10.1049/iet-syb:20060075 ID - Cho2007 ER - TY - JOUR AU - Werhli, A. V. AU - Husmeier, D. PY - 2007 DA - 2007// TI - Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge JO - Stat Appl Genet Mol Biol VL - 6 ID - Werhli2007 ER - TY - JOUR AU - Benson, M. AU - Breitling, R. PY - 2006 DA - 2006// TI - Network theory to understand microarray studies of complex diseases JO - Curr Mol Med VL - 6 UR - https://doi.org/10.2174/156652406778195044 DO - 10.2174/156652406778195044 ID - Benson2006 ER - TY - CHAP AU - Kavanaugh, A. F. AU - Lipsky, P. ED - Gallin, J. I. ED - Snyderman, R. PY - 1999 DA - 1999// TI - Rheumatoid arthritis BT - Inflammation: Basic Principles and Clinical Correlates PB - Wilkins CY - Philadelphia, PA, USA ID - Kavanaugh1999 ER - TY - JOUR AU - McInnes, I. B. AU - Schett, G. PY - 2007 DA - 2007// TI - Cytokines in the pathogenesis of rheumatoid arthritis JO - Nat Rev Immunol VL - 7 UR - https://doi.org/10.1038/nri2094 DO - 10.1038/nri2094 ID - McInnes2007 ER - TY - JOUR AU - Brennan, F. M. AU - Maini, R. N. AU - Feldmann, M. PY - 1998 DA - 1998// TI - Role of pro-inflammatory cytokines in rheumatoid arthritis JO - Springer Semin Immunopathol VL - 20 UR - https://doi.org/10.1007/BF00832003 DO - 10.1007/BF00832003 ID - Brennan1998 ER - TY - JOUR AU - Smolen, J. S. AU - Steiner, G. PY - 2003 DA - 2003// TI - Therapeutic strategies for rheumatoid arthritis JO - Nat Rev Drug Discov VL - 2 UR - https://doi.org/10.1038/nrd1109 DO - 10.1038/nrd1109 ID - Smolen2003 ER - TY - JOUR AU - Feldmann, M. AU - Maini, R. N. PY - 2003 DA - 2003// TI - Lasker Clinical Medical Research Award. TNF defined as a therapeutic target for rheumatoid arthritis and other autoimmune diseases JO - Nat Med VL - 9 UR - https://doi.org/10.1038/nm939 DO - 10.1038/nm939 ID - Feldmann2003 ER - TY - JOUR AU - Glocker, M. O. AU - Guthke, R. AU - Kekow, J. AU - Thiesen, H. J. PY - 2006 DA - 2006// TI - Rheumatoid arthritis, a complex multifactorial disease: on the way toward individualized medicine JO - Med Res Rev VL - 26 UR - https://doi.org/10.1002/med.20045 DO - 10.1002/med.20045 ID - Glocker2006 ER - TY - JOUR AU - Koczan, D. AU - Drynda, S. AU - Hecker, M. AU - Drynda, A. AU - Guthke, R. AU - Kekow, J. AU - Thiesen, H. J. PY - 2008 DA - 2008// TI - Molecular discrimination of responders and nonresponders to anti-TNFalpha therapy in rheumatoid arthritis by etanercept JO - Arthritis Res Ther VL - 10 UR - https://doi.org/10.1186/ar2419 DO - 10.1186/ar2419 ID - Koczan2008 ER - TY - JOUR AU - Fernald, G. H. AU - Knott, S. AU - Pachner, A. AU - Caillier, S. J. AU - Narayan, K. AU - Oksenberg, J. R. AU - Mousavi, P. AU - Baranzini, S. E. PY - 2007 DA - 2007// TI - Genome-wide network analysis reveals the global properties of IFN-beta immediate transcriptional effects in humans JO - J Immunol VL - 178 UR - https://doi.org/10.4049/jimmunol.178.8.5076 DO - 10.4049/jimmunol.178.8.5076 ID - Fernald2007 ER - TY - JOUR AU - Ferrari, F. AU - Bortoluzzi, S. AU - Coppe, A. AU - Sirota, A. AU - Safran, M. AU - Shmoish, M. AU - Ferrari, S. AU - Lancet, D. AU - Danieli, G. A. AU - Bicciato, S. PY - 2007 DA - 2007// TI - Novel definition files for human GeneChips based on GeneAnnot JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-446 DO - 10.1186/1471-2105-8-446 ID - Ferrari2007 ER - TY - JOUR AU - Dai, M. AU - Wang, P. AU - Boyd, A. D. AU - Kostov, G. AU - Athey, B. AU - Jones, E. G. AU - Bunney, W. E. AU - Myers, R. M. AU - Speed, T. P. AU - Akil, H. AU - Watson, S. J. AU - Meng, F. PY - 2005 DA - 2005// TI - Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gni179 DO - 10.1093/nar/gni179 ID - Dai2005 ER - TY - JOUR AU - Boissier, M. C. AU - Assier, E. AU - Biton, J. AU - Denys, A. AU - Falgarone, G. AU - Bessis, N. PY - 2009 DA - 2009// TI - Regulatory T cells (Treg) in rheumatoid arthritis JO - Joint Bone Spine VL - 76 UR - https://doi.org/10.1016/j.jbspin.2008.08.002 DO - 10.1016/j.jbspin.2008.08.002 ID - Boissier2009 ER - TY - JOUR AU - Peng, G. AU - Guo, Z. AU - Kiniwa, Y. AU - Voo, K. S. AU - Peng, W. AU - Fu, T. AU - Wang, D. Y. AU - Li, Y. AU - Wang, H. Y. AU - Wang, R. F. PY - 2005 DA - 2005// TI - Toll-like receptor 8-mediated reversal of CD4+ regulatory T cell function JO - Science VL - 309 UR - https://doi.org/10.1126/science.1113401 DO - 10.1126/science.1113401 ID - Peng2005 ER - TY - JOUR AU - Akira, S. AU - Isshiki, H. AU - Sugita, T. AU - Tanabe, O. AU - Kinoshita, S. AU - Nishio, Y. AU - Nakajima, T. AU - Hirano, T. AU - Kishimoto, T. PY - 1990 DA - 1990// TI - A nuclear factor for IL-6 expression (NF-IL6) is a member of a C/EBP family JO - EMBO J VL - 9 ID - Akira1990 ER - TY - JOUR AU - Yang, C. AU - Bolotin, E. AU - Jiang, T. AU - Sladek, F. M. AU - Martinez, E. PY - 2007 DA - 2007// TI - Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters JO - Gene VL - 389 UR - https://doi.org/10.1016/j.gene.2006.09.029 DO - 10.1016/j.gene.2006.09.029 ID - Yang2007 ER - TY - JOUR AU - D'haeseleer, P. AU - Wen, X. AU - Fuhrman, S. AU - Somogyi, R. PY - 1999 DA - 1999// TI - Linear modeling of mRNA expression levels during CNS development and injury JO - Pac Symp Biocomput VL - 4 ID - D'haeseleer1999 ER - TY - JOUR AU - van Someren, E. P. AU - Vaes, B. L. AU - Steegenga, W. T. AU - Sijbers, A. M. AU - Dechering, K. J. AU - Reinders, M. J. PY - 2006 DA - 2006// TI - Least absolute regression network analysis of the murine osteoblast differentiation network JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/bti816 DO - 10.1093/bioinformatics/bti816 ID - van Someren2006 ER - TY - CHAP AU - Yong-A-Poi, J. PY - 2008 DA - 2008// TI - Adaptive least absolute regression network analysis improves genetic network reconstruction by employing prior knowledge BT - Master's thesis PB - Delft University of Technology CY - Department of Mediamatics ID - Yong-A-Poi2008 ER - TY - JOUR AU - Thorsson, V. AU - Hörnquist, M. AU - Siegel, A. F. AU - Hood, L. PY - 2005 DA - 2005// TI - Reverse engineering galactose regulation in yeast through model selection JO - Stat Appl Genet Mol Biol VL - 4 ID - Thorsson2005 ER - TY - JOUR AU - Guthke, R. AU - Möller, U. AU - Hoffmann, M. AU - Thies, F. AU - Töpfer, S. PY - 2005 DA - 2005// TI - Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti226 DO - 10.1093/bioinformatics/bti226 ID - Guthke2005 ER - TY - JOUR AU - Tibshirani, R. PY - 1996 DA - 1996// TI - Regression shrinkage and selection via the lasso JO - J Royal Statist Soc B VL - 58 ID - Tibshirani1996 ER - TY - JOUR AU - Efron, B. AU - Hastie, T. AU - Johnstone, I. AU - Tibshirani, R. PY - 2004 DA - 2004// TI - Least angle regression JO - Ann Statist VL - 32 UR - https://doi.org/10.1214/009053604000000067 DO - 10.1214/009053604000000067 ID - Efron2004 ER - TY - CHAP AU - van Someren, E. P. AU - Wessels, L. F. A. AU - Reinders, M. J. T. AU - Backer, E. ED - Zhang, W. ED - Shmulevich, I. PY - 2002 DA - 2002// TI - Regularization and noise injection for improving genetic network models BT - Computational And Statistical Approaches To Genomics PB - Kluwer Acadmic Publishers CY - Boston, MA, USA ID - van Someren2002 ER - TY - JOUR AU - Gustafsson, M. AU - Hörnquist, M. AU - Lombardi, A. PY - 2005 DA - 2005// TI - Constructing and analyzing a large-scale gene-to-gene regulatory network – lasso-constrained inference and biological validation JO - IEEE/ACM Trans Comput Biol Bioinform VL - 2 UR - https://doi.org/10.1109/TCBB.2005.35 DO - 10.1109/TCBB.2005.35 ID - Gustafsson2005 ER - TY - JOUR AU - Zou, H. PY - 2006 DA - 2006// TI - The adaptive lasso and its oracle properties JO - J Am Stat Assoc VL - 101 UR - https://doi.org/10.1198/016214506000000735 DO - 10.1198/016214506000000735 ID - Zou2006 ER - TY - BOOK AU - Kitano, H. PY - 2001 DA - 2001// TI - Foundations of Systems Biology PB - MIT Press CY - Cambridge, MA, USA ID - Kitano2001 ER - TY - JOUR AU - Basso, K. AU - Margolin, A. A. AU - Stolovitzky, G. AU - Klein, U. AU - Dalla-Favera, R. AU - Califano, A. PY - 2005 DA - 2005// TI - Reverse engineering of regulatory networks in human B cells JO - Nat Genet VL - 37 UR - https://doi.org/10.1038/ng1532 DO - 10.1038/ng1532 ID - Basso2005 ER - TY - JOUR AU - Jordan, I. K. AU - Mariño-Ramírez, L. AU - Wolf, Y. I. AU - Koonin, E. V. PY - 2004 DA - 2004// TI - Conservation and coevolution in the scale-free human gene coexpression network JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh222 DO - 10.1093/molbev/msh222 ID - Jordan2004 ER - TY - CHAP AU - Clauset, A. AU - Shalizi, C. R. AU - Newman, M. E. J. PY - 2007 DA - 2007// BT - Power-law distributions in empirical data ID - Clauset2007 ER - TY - JOUR AU - Ishibashi, K. AU - Kuwahara, M. AU - Gu, Y. AU - Tanaka, Y. AU - Marumo, F. AU - Sasaki, S. PY - 1998 DA - 1998// TI - Cloning and functional expression of a new aquaporin (AQP9) abundantly expressed in the peripheral leukocytes permeable to water and urea, but not to glycerol JO - Biochem Biophys Res Commun VL - 244 UR - https://doi.org/10.1006/bbrc.1998.8252 DO - 10.1006/bbrc.1998.8252 ID - Ishibashi1998 ER - TY - JOUR AU - Strubin, M. AU - Newell, J. W. AU - Matthias, P. PY - 1995 DA - 1995// TI - OBF-1, a novel B cell-specific coactivator that stimulates immunoglobulin promoter activity through association with octamer-binding proteins JO - Cell VL - 80 UR - https://doi.org/10.1016/0092-8674(95)90500-6 DO - 10.1016/0092-8674(95)90500-6 ID - Strubin1995 ER - TY - JOUR AU - Rey, M. AU - Vicente-Manzanares, M. AU - Viedma, F. AU - Yáñez-Mó, M. AU - Urzainqui, A. AU - Barreiro, O. AU - Vázquez, J. AU - Sánchez-Madrid, F. PY - 2002 DA - 2002// TI - Cutting edge: association of the motor protein nonmuscle myosin heavy chain-IIA with the C terminus of the chemokine receptor CXCR4 in T lymphocytes JO - J Immunol VL - 169 UR - https://doi.org/10.4049/jimmunol.169.10.5410 DO - 10.4049/jimmunol.169.10.5410 ID - Rey2002 ER - TY - JOUR AU - O'Hara, R. AU - Murphy, E. P. AU - Whitehead, A. S. AU - FitzGerald, O. AU - Bresnihan, B. PY - 2000 DA - 2000// TI - Acute-phase serum amyloid A production by rheumatoid arthritis synovial tissue JO - Arthritis Res VL - 2 UR - https://doi.org/10.1186/ar78 DO - 10.1186/ar78 ID - O'Hara2000 ER - TY - JOUR AU - Ogura, Y. AU - Inohara, N. AU - Benito, A. AU - Chen, F. F. AU - Yamaoka, S. AU - Nunez, G. PY - 2000 DA - 2000// TI - Nod2, a Nod1/Apaf-1 family member that is restricted to monocytes and activates NF-kappaB JO - J Biol Chem VL - 276 UR - https://doi.org/10.1074/jbc.M008072200 DO - 10.1074/jbc.M008072200 ID - Ogura2000 ER - TY - JOUR AU - Salmi, M. AU - Koskinen, K. AU - Henttinen, T. AU - Elima, K. AU - Jalkanen, S. PY - 2004 DA - 2004// TI - CLEVER-1 mediates lymphocyte transmigration through vascular and lymphatic endothelium JO - Blood VL - 104 UR - https://doi.org/10.1182/blood-2004-01-0222 DO - 10.1182/blood-2004-01-0222 ID - Salmi2004 ER - TY - JOUR AU - Qian, F. AU - Kruse, U. AU - Lichter, P. AU - Sippel, A. E. PY - 1995 DA - 1995// TI - Chromosomal localization of the four genes (NFIA, B, C, and X) for the human transcription factor nuclear factor I by FISH JO - Genomics VL - 28 UR - https://doi.org/10.1006/geno.1995.1107 DO - 10.1006/geno.1995.1107 ID - Qian1995 ER - TY - JOUR AU - Goertsches, R. H. AU - Hecker, M. AU - Zettl, U. K. PY - 2008 DA - 2008// TI - Monitoring of multiple sclerosis immunotherapy: From single candidates to biomarker networks JO - J Neurol VL - 255 UR - https://doi.org/10.1007/s00415-008-6010-1 DO - 10.1007/s00415-008-6010-1 ID - Goertsches2008 ER - TY - JOUR AU - Stolovitzky, G. AU - Monroe, D. AU - Califano, A. PY - 2007 DA - 2007// TI - Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference JO - Ann N Y Acad Sci VL - 1115 UR - https://doi.org/10.1196/annals.1407.021 DO - 10.1196/annals.1407.021 ID - Stolovitzky2007 ER - TY - JOUR AU - Stolovitzky, G. AU - Prill, R. J. AU - Califano, A. PY - 2009 DA - 2009// TI - Lessons from the DREAM2 Challenges JO - Ann N Y Acad Sci VL - 1158 UR - https://doi.org/10.1111/j.1749-6632.2009.04497.x DO - 10.1111/j.1749-6632.2009.04497.x ID - Stolovitzky2009 ER - TY - JOUR AU - Karopka, T. AU - Fluck, J. AU - Mevissen, H. T. AU - Glass, A. PY - 2006 DA - 2006// TI - The Autoimmune Disease Database: a dynamically compiled literature-derived database JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-325 DO - 10.1186/1471-2105-7-325 ID - Karopka2006 ER - TY - JOUR AU - Kinne, R. W. AU - Bräuer, R. AU - Stuhlmüller, B. AU - Palombo-Kinne, E. AU - Burmester, G. R. PY - 2000 DA - 2000// TI - Macrophages in rheumatoid arthritis JO - Arthritis Res VL - 2 UR - https://doi.org/10.1186/ar86 DO - 10.1186/ar86 ID - Kinne2000 ER - TY - JOUR AU - Faith, J. J. AU - Hayete, B. AU - Thaden, J. T. AU - Mogno, I. AU - Wierzbowski, J. AU - Cottarel, G. AU - Kasif, S. AU - Collins, J. J. AU - Gardner, T. S. PY - 2007 DA - 2007// TI - Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles JO - PLoS Biol VL - 5 UR - https://doi.org/10.1371/journal.pbio.0050008 DO - 10.1371/journal.pbio.0050008 ID - Faith2007 ER - TY - JOUR AU - Margolin, A. A. AU - Nemenman, I. AU - Basso, K. AU - Wiggins, C. AU - Stolovitzky, G. AU - Dalla Favera, R. AU - Califano, A. PY - 2006 DA - 2006// TI - ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-S1-S7 DO - 10.1186/1471-2105-7-S1-S7 ID - Margolin2006 ER - TY - JOUR AU - Opgen-Rhein, R. AU - Strimmer, K. PY - 2007 DA - 2007// TI - From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data JO - BMC Syst Biol VL - 1 UR - https://doi.org/10.1186/1752-0509-1-37 DO - 10.1186/1752-0509-1-37 ID - Opgen-Rhein2007 ER - TY - JOUR AU - Luscombe, N. M. AU - Babu, M. M. AU - Yu, H. AU - Snyder, M. AU - Teichmann, S. A. AU - Gerstein, M. PY - 2004 DA - 2004// TI - Genomic analysis of regulatory network dynamics reveals large topological changes JO - Nature VL - 431 UR - https://doi.org/10.1038/nature02782 DO - 10.1038/nature02782 ID - Luscombe2004 ER - TY - JOUR AU - Chalifa-Caspi, V. AU - Shmueli, O. AU - Benjamin-Rodrig, H. AU - Rosen, N. AU - Shmoish, M. AU - Yanai, I. AU - Ophir, R. AU - Kats, P. AU - Safran, M. AU - Lancet, D. PY - 2003 DA - 2003// TI - GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia JO - Brief Bioinform VL - 4 UR - https://doi.org/10.1093/bib/4.4.349 DO - 10.1093/bib/4.4.349 ID - Chalifa-Caspi2003 ER - TY - JOUR AU - Yang, I. V. AU - Chen, E. AU - Hasseman, J. P. AU - Liang, W. AU - Frank, B. C. AU - Wang, S. AU - Sharov, V. AU - Saeed, A. I. AU - White, J. AU - Li, J. AU - Lee, N. H. AU - Yeatman, T. J. AU - Quackenbush, J. PY - 2002 DA - 2002// TI - Within the fold: assessing differential expression measures and reproducibility in microarray assays JO - Genome Biol VL - 3 ID - Yang2002 ER - TY - STD TI - Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ: The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 2009, (37 Database):D755–761. 10.1093/nar/gkn875 ID - ref53 ER - TY - JOUR PY - 2007 DA - 2007// TI - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project JO - Nature VL - 447 UR - https://doi.org/10.1038/nature05874 DO - 10.1038/nature05874 ID - ref54 ER - TY - JOUR AU - Mallows, C. PY - 1973 DA - 1973// TI - Some comments on cp JO - Technometrics VL - 15 ID - Mallows1973 ER -