Bibliography
- Novichkova S, Egorov S, Daraselia N. MedScan, a natural language processing engine for MEDLINE abstracts. Bioinformatics 2003;19(13):1699-706
- Sivachenko A, Yuryev A. Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism. Expert Opin Ther Targets 2007;11(3):411-21
- Daraselia N, Yuryev A, Egorov S, Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. BMC Bioinformatics 2007;8(1):243
- Blaschke C, Leon EA, Krallinger M, Valencia A. Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics 2005;6(Suppl 1):S16
- Available from: http://www.drugbank.ca
- Available from: http://matadorembl.de
- Available from: http://insilico.charite.de/supertarget
- Available from: http://bidd.nus.edu.sg/group/cjttd/TTD_ns.asp
- Available from: http://pubchem.ncbi.nlm.nih.gov
- Available from: http://chembank.broad.harvard.edu
- Available from: http://sideeffects.embl.de/
- Available from: http://www.accessdata.fda.gov/Scripts/cder/DrugsatFDA
- http://clinicaltrials.gov
- Available from: http://www.genego.com/metadrug.php
- Available from: http://www.ingenuity.com/products/ipa-tox.html
- Available from: http://www.camcellnet.com
- Available from: http://www.gvkbio.com/informatics.html
- Sivachenko AY, Yuryev A, Daraselia N, Mazo I. Molecular networks in microarray analysis. J Bioinform Comput Biol 2007;5(2B):429-56
- Subramanian A, Tamayo P, Mootha VK, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005;102(43):15545-50
- Rothstein JD, Patel S, Regan MR, Beta-lactam antibiotics offer neuroprotection by increasing glutamate transporter expression. Nature 2005;433:73-7
- Kruger EA, Figg WD. TNP-470: an angiogenesis inhibitor in clinical development for cancer. Expert Opin Investig Drugs 2000;9:1383-96
- Guerin PJ, Olliaro P, Nosten F, Malaria: current status of control, diagnosis, treatment, and a proposed agenda for research and development. Lancet Infect Dis 2002;2:564-73
- Fang J, Chen SJ, Tong JH, Treatment of acute promyelocytic leukemia with ATRA and As2O3: a model of molecular target-based cancer therapy. Cancer Biol Ther 2002;1:614-20
- Chong CR, Sullivan DJ. New uses for old drugs. Nature 2007;448(7154):645-6
- Wong ML, Kaye AH, Hovens CM. Targeting malignant glioma survival signalling to improve clinical outcomes. J Clin Neurosci 2007;21:301-8
- Tuettenberg J, Friedel C, Vajkoczy P. Angiogenesis in malignant glioma–a target for antitumor therapy? Crit Rev Oncol Hematol 2006;59(3):181-93
- Ziegler DS, Wright RD, Kesari S, Resistance of human glioblastoma multiform cells to growth factor inhibitors is overcome by blockade of inhibitor of apoptosis proteins. J Clin Invest 2008;118(9):3109-22
- Ohgaki H, Kleihues P. Genetic pathways to primary and secondary glioblastoma. Am J Pathol 2007;170(5):1445-53
- Ohgaki H. Genetic pathways to glioblastomas. Neuropathology 2005;25(1):1-7
- Mueller W, Nutt CL, Ehrich M, Downregulation of RUNX3 and TES by hypermethylation in glioblastoma. Oncogene 2007;26(4):583-93
- Xie D, Yin D, Tong X, Cyr61 is overexpressed in gliomas and involved in integrin-linked kinase-mediated Akt and beta-catenin-TCF/Lef signaling pathways. Cancer Res 2004;64:1987-96
- Babic AM, Kireeva ML, Kolesnikova TV, Lau LF. Cyr61, a product of a growth factor-inducible immediate early gene, promotes angiogenesis and tumor growth. Proc Natl Acad Sci USA 1998;95:6355-60
- Jin Y, Kim HP, Ifedigbo E, Cyr61 protects against hyperoxia-induced cell death via Akt pathway in pulmonary epithelial cells. Am J Respir Cell Mol Biol 2005;33(3):297-302
- Kunz M, Moeller S, Koczan D, Mechanisms of hypoxic gene regulation of angiogenesis factor Cyr61 in melanoma cells. J Biol Chem 2003;278(46):45651-60
- Tsai MS, Bogart DF, Li P, Expression and regulation of Cyr61 in human breast cancer cell lines. Oncogene 2002;21(6):964-73
- Yen ML, Su JL, Chien CL, Diosgenin induces hypoxia-inducible factor-1 activation and angiogenesis through estrogen receptor-related phosphatidylinositol 3-kinase/Akt and p38 mitogen-activated protein kinase pathways in osteoblasts. Mol Pharmacol 2005;68(4):1061-73
- Bunone G, Briand PA, Miksicek RJ, Picard D. Activation of the unliganded estrogen receptor by EGF involves the MAP kinase pathway and direct phosphorylation. EMBO J 1996;15:2174-83
- Kato S, Endoh H, Masuhiro Y, Activation of the estrogen receptor through phosphorylation by mitogen-activated protein kinase. Science 1995;270:1491-4
- Wang R, Zhang QG, Han D, Inhibition of MLK3-MKK4/7-JNK1/2 pathway by Akt1 in exogenous estrogen-induced neuroprotection against transient global cerebral ischemia by a non-genomic mechanism in male rats. J Neurochem 2006;99(6):1543-54
- Vergote I, Abram P. Fulvestrant, a new treatment option for advanced breast cancer: tolerability versus existing agents. Ann Oncol 2006;17(2):200-4, [Epub 26 October 2005]
- Schneider SW, Ludwig T, Tatenhorst L, Glioblastoma cells release factors that disrupt blood-brain barrier features. Acta Neuropathol 2004;107(3):272-6, [Epub 17 January 2004]
- Boyer JL. New perspectives for the treatment of cholestasis: lessons from basic science applied clinically. J Hepatol 2007;46(3):365-71
- Miyata M, Tozawa A, Otsuka H, Role of farnesoid X receptor in the enhancement of canalicular bile acid output and excretion of unconjugated bile acids: a mechanism for protection against cholic acid-induced liver toxicity. J Pharmacol Exp Ther 2005;312(2):759-66
- Kliewer SA, Goodwin B, Willson TM. The nuclear pregnane X receptor: a key regulator of xenobiotic metabolism. Endocr Rev 2002;23(5):687-702
- Zollner G, Wagner M, Moustafa T, Coordinated induction of bile acid detoxification and alternative elimination in mice: role of FXR-regulated organic solute transporter-alpha/beta in the adaptive response to bile acids. Am J Physiol Gastrointest Liver Physiol 2006;290(5):G923-32
- Pascussi JM, Robert A, Nguyen M, Possible involvement of pregnane X receptor-enhanced CYP24 expression in drug-induced osteomalacia. J Clin Invest 2005;115(1):177-86
- Martínez-Jiménez CP, Gómez-Lechón MJ, Castell JV, Jover R. Transcriptional regulation of the human hepatic CYP3A4: identification of a new distal enhancer region responsive to CCAAT/enhancer-binding protein beta isoforms (liver activating protein and liver inhibitory protein). Mol Pharmacol 2005;67(6):2088-101
- Jigorel E, Le Vee M, Boursier-Neyret C, Differential regulation of sinusoidal and canalicular hepatic drug transporter expression by xenobiotics activating drug-sensing receptors in primary human hepatocytes. Drug Metab Dispos 2006;34(10):1756-63
- Staudinger JL, Madan A, Carol KM, Parkinson A. Regulation of drug transporter gene expression by nuclear receptors. Drug Metab Dispos 2003;31(5):523-7
- Song KH, Li T, Owsley E, Bile acids activate fibroblast growth factor 19 signaling in human hepatocytes to inhibit cholesterol 7alpha-hydroxylase gene expression. Hepatology 2009;49(1):297-305