Bibliography
- Drews J. Drug discovery: a historical perspective. Science 2000;287:1960-4
- Henney AM. System biology: a new hope for drug discovery. Expert Opin Drug Discov 2006;1:653-61
- Kitchen DB, Decornez H, FURR Jr, et al. Docking and scoring in virtual screening for drug discovery: methods and applications. Nature 2004;3:935-49
- Dobson CM. Chemical space and biology. Nature 2004;432:824-8
- Loging W, Harland L, Bryn WJ. High-throughput electronic biology: mining information for drug discovery. Nature 2007;6:220-30
- Augen J. Bioinformatics and information technology: reshaping the drug discovery process. Drug Discov Today 2002;7:39-40
- Chen YPP, editor. Bioinformatics Technologies. New York: Springer; 2005
- Jennings A, Tennant M. Discovery strategies in a pharmaceutical setting: the application of computational techniques. Expert Opin Drug Discov 2006;1:709-21
- Roos DS. Computational biology: bioinformatics–trying to swim in a sea of data. Science 2001;291:1260-1
- Jorgensen WL. The many roles of computation in drug discovery. Science 2004;303:1813-7
- Pollock S, Safer H. Bioinformatics in the drug discovery process. Ann Rep Med Chem 2001;1-9
- Ratti E, Trist D. Continuing evolution of the drug discovery process in the pharmaceutical industry. Pure Appl Chem 2001;73:67-75
- Kumble KD. An update on using protein microarrays in drug discovery. Expert Opin Drug Discov 2007;2:1477-6
- Russ AP, Grosse J. Mouse genetics in drug target discovery and validation: no simple answers to complex problems. Expert Opin Drug Discov 2007;2:1379-87
- Blundell TL, Sibanda BL, Montalvao RW, et al. Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery. Phil Trans R Soc B 2006;361:413-423
- Habeman AB. Strategies to move beyond target validation. Genet Eng News 2005;25:36
- Terstappen GC, schilupen C, Raggiaschi R, et al. Target deconvolution strategies in drug discovery. Nature 2007;6:891-903
- Warmuth MK, Ratsch C, Mathieson M, et al. Active learning in the drug discovery process. Adv Neural Inf Process Syst 2002;1449-56
- Warmuth MK, Liao J, Ratsch G, et al. Support vector machines for active learning in the drug discovery process. J Chem Inf Sci 2003;43:667-73
- Schreiber SL. Target-oriented and diversity-oriented organic synthesis in drug discovery. Science 2000;287:1964-8
- Gibbs JB. Mechanism-based target identifiation and drug discovery in cancer research. Science 2000;287:1969-73
- Attwood TK. Genomics: the babel of bioinformatics. Science 2000;290:471-3
- Li J, Liu H, Downing Jr, et al. Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients. Bioinformatics 2003;19:71-8
- Gond G, Li J. Efficient mining of emerging patterns: discovering trends and differences. Proc Int Conf Knowledge Discov Data Arch 1999:43-52
- Knapp K, Chen YPP. An evaluation of contemporary hidden markov model gene finders with a predicted exon taxonomy. Nucleic Acids Res 2007;35:317-24
- Horesh Y, Amir A, Michaeli S. A rapid method for detection of putative RNAi target genes in genomic data. Bioinformatics 2003;19:1173-80
- Dieterich C, Herwig R, Vingron M. Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites. Bioinformatics 2003;19:1150-6
- Nahar J, Ali S, Chen YPP. Microarray data classification using automatic SVM kernel selection. DNA Cell Biol 2007;10:707-12
- Szuromi P, Vinson V, Marshall E. Rethinking drug discovery. Science 2004;303:1795
- Mann S, Li J, Chen YPP. A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts. Nucleic Acids Res 2007;35:e121-7
- Novak BA, Jain AN. Pathway recognition and augmentation by computational analysis of microarray expression data. Bioinformatics 2006;22:233-41
- Pinter RY, Rokhlenko O, Esti YL. Alignment of metabolic pathways. Bioinformatics 2005;21:3401-8
- Stevens RC, Yokoyama S, Wilson LA. Global efforts in structural genomics. Science 2001;294:89-92
- Dixit SB, Beveridge DL. Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction. Bioinformatics 2006;22:1007-9
- Oyama T, Kitano K, Satou K, et al. Extraction of knowledge on protein-protein interaction by association rule discovery. Bioinformatics 2002;18:705-14
- Chen Q, Chen YPP. Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle. BMC Bioinform 2007;7:394. Published online 30 August 2006, doi:10.1186/1471-2105-7-394
- Joung JG, Hwang KB, Nam JW, et al. Discovery of microRNA-mRNA modules via population-based probabilistic learning. Bioinformatics 2007;23:1141-7
- Yousef M, Jung S, Kossenkov AV, et al. Naïve bayes for microRNA target predictions–machine learning for microRNA targets. Bioinformatics 2007;23:2987-92
- Hede K. Studies define role of microRNA in cancer. J Natl Cancer Inst 2005;97:1114-5
- Shell S, Park SM, Radjabi AR, et al. Let-7 expression defines two differentiation stages of cancer. Proc Natl Acad Sci USA 2007;27:11400-5
- Zheng Y, Kwoh CK. Cancer classification with microRNA expression patterns found by an information theory approach. J Comput 2006;1:30-9
- Bo XC, Wang SQ. TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA. Bioinformatcis 2005;21:1401-2
- Holford M, Li N, Nadkarni P, et al. VitaPad: visualization tools for the analysis of pathway data. Bioinformatics 2005;21:1596-602
- Krishnamurthy L, Nadeau J, Ozsoyoglu G, et al. Pathways database system: an integrated system for biological pathways. Bioinformatics 2003;19:930-7
- Makarenkov V, Zentilli P, Kevorkov D, et al. An efficient method for the detection and elimination of systematic error in high-throughput screening. Bioinformatics 2007;23:1648-57
- Zhang M, White RA, Wang LQ. Improving conformational searches by geometric screening. Bioinformatics 2005;21:624-30
- Makarehkov V, Kevorkov D, Zentilli P. HTS-Corrector: software for the statistical analysis and correction of experimental high-throughput screening data. Bioinformatics 2006;22:1408-9
- Holler TP, Evdokimov AG, Narasimhan L. Structural biology approaches to antibacterial drug discovery. Expert Opin Drug Discov 2007;2:1085-101
- Grunberg R, Nilges M, Leckner J. Biskit – a software platform for structural bioinformatics. Bioinformatics 2007;23:769-70
- Available from: http://www.ebi.ac.uk/embl/index.html
- Available from: http://www.Ncbi.nlm.nih.gov/Genbank
- Available from: http://www.ddbj.nig.ac.jp/Welcome-e.html
- Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. Nat Genet 2000;25:25-9
- Pfizer TBS. Advances in knowledge management for pharmaceutical research and development. Curr Opin Drug Discov Dev 2005;8:316-22
- Neumann EK, Quan D. BioDash: a semantic web dashboard for drug development. Pac Symp Biocomput 2006;11:176-87
- Available from: http://www.targetscan.org/
- Kennedy D. Drug discovery. Science 2004;303:1729