Integrating fragmented software applications into holistic solutions: focus on drug discovery

Bibliography

• Altschul SF, Gish W, Miller W, Basic local alignment search tool. J Mol Biol 1990;215:403-10
   PubMed Web of Science ®Google Scholar
• Kent WJ. BLAT -the BLAST-like alignment tool. Genome Res 2002;12:656-64
   PubMed Web of Science ®Google Scholar
• Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 2002;30:2478-83
   PubMed Web of Science ®Google Scholar
• Wallace IM, Blackshields G, Higgins DG. Multiple sequence alignments. Curr Opin Struct Biol 2005;15:261-6
   PubMed Web of Science ®Google Scholar
• Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Curr Protocol Bioinformatics 2002; Chapter 2 unit 2.3: Published Online: 1 August 2002, doi: 10.1002/0471250953.bi0203s00
   Google Scholar
• SantaLucia J Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 1998;95:1460-5
   PubMed Web of Science ®Google Scholar
• Picardi E, Pesole G. Computational methods for ab initio and comparative gene finding. Methods Mol Biol 2010;609:269-84
   Google Scholar
• Zhang Y, Skolnick J. The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 2005;102:1029-34
   PubMed Web of Science ®Google Scholar
• Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-70
   PubMed Web of Science ®Google Scholar
• Dearden JC. In silico prediction of drug toxicity. J Comput Aided Mol Des 2003;17:119-27
   PubMed Web of Science ®Google Scholar
• Tong W, Hong H, Xie Q, Assessing QSAR limitations – a regulatory perspective. Curr Comput Aided Drug Des 2005;1:195-205
   Web of Science ®Google Scholar
• Sun H, Scott DO. Structure-based drug metabolism predictions for drug design. Chem Biol Drug Des 2010;75:3-17
   PubMed Web of Science ®Google Scholar
• Jeanmougin M, de Reynies A, Marisa L, Should we abandon the t-test in the analysis of gene expression microarray data: a comparison of variance modeling strategies? PLoS One 2010;5:e12336
   PubMedGoogle Scholar
• Broberg P. A comparative review of estimates of the proportion unchanged genes and the false discovery rate. BMC Bioinformatics 2005;6:199
   PubMedGoogle Scholar
• Yuryev A, Kotelnikova E, Daraselia N. Ariadne's ChemEffect and pathway studio knowledge base. Expert Opin Drug Discov 2009;4:1307-18
   PubMed Web of Science ®Google Scholar
• Kotelnikova E, Yuryev A, Mazo I, Daraselia N. Computational approaches for drug repositioning and combination therapy design. J Bioinform Comput Biol 2010;8:593-606
   PubMedGoogle Scholar
• Korcsmaros T, Farkas IJ, Szalay MS, Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery. Bioinformatics 2010;26:2042-50
   PubMed Web of Science ®Google Scholar
• Ekins S, Nikolsky Y, Bugrim A, Pathway mapping tools for analysis of high content data. Methods Mol Biol 2007;356:319-50
   PubMedGoogle Scholar
• Novichkova S, Egorov S, Daraselia N. MedScan, a natural language processing engine for MEDLINE abstracts. Bioinformatics 2003;19:1699-706
   PubMed Web of Science ®Google Scholar
• Aranda B, Achuthan P, Alam-Faruque Y, The intact molecular interaction database in 2010. Nucleic Acids Res 2010;38:D525-31
   PubMed Web of Science ®Google Scholar
• Rohl C, Price Y, Fischer TB, Cataloging the relationships between proteins: a review of interaction databases. Mol Biotechnol 2006;34:69-93
   PubMedGoogle Scholar
• 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;102:15545-50
   PubMed Web of Science ®Google Scholar
• Yi M, Stephens RM. SLEPR: a sample-level enrichment-based pathway ranking method – seeking biological themes through pathway-level consistency. PLoS One 2008;3:e3288
   PubMed Web of Science ®Google Scholar
• Dinu I, Potter JD, Mueller T, Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics 2007;8:242
   PubMedGoogle Scholar
• Goeman JJ, Buhlmann P. Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 2007;23:980-7
   PubMed Web of Science ®Google Scholar
• Liu Q, Dinu I, Adewale AJ, Comparative evaluation of gene-set analysis methods. BMC Bioinformatics 2007;8:43
   PubMedGoogle Scholar
• Bonchev D, Buck GA. From molecular to biological structure and back. J Chem Inf Model 2007;47:909-17
   PubMed Web of Science ®Google Scholar
• Ideker T. A systems approach to discovering signaling and regulatory pathways – or, how to digest large interaction networks into relevant pieces. Adv Exp Med Biol 2004;547:21-30
   PubMed Web of Science ®Google Scholar
• Sivachenko AY, Yuryev A, Daraselia N, Mazo I. Molecular networks in microarray analysis. J Bioinform Comput Biol 2007;5:429-56
   PubMed Web of Science ®Google Scholar
• Kitano HH. Biological robustness. Nat Rev Genet 2004;5:826-37
   PubMed Web of Science ®Google Scholar
• Csermely P, Agoston V, Pongor S. The efficiency of multi-target drugs: the network approach might help drug design. Trends Pharmacol Sci 2005;26:178-82
   PubMed Web of Science ®Google Scholar
• Hopkins AL. Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 2008;4:682-90
   PubMed Web of Science ®Google Scholar
• Spiro Z, Kovacs IA, Csermely P. Drug-therapy networks and the prediction of novel drug targets. J Biol 2008;7(6):20
   PubMedGoogle Scholar
• Goutsias J, Lee NH. Computational and experimental approaches for modeling gene regulatory networks. Curr Pharm Des 2007;13:1415-36
   PubMed Web of Science ®Google Scholar
• Li H, Xuan J, Wang Y, Zhan M. Inferring regulatory networks. Front Biosci 2008;13:263-75
   PubMed Web of Science ®Google Scholar
• Li H, Sun Y, Zhan M. Exploring pathways from gene co-expression to network dynamics. Methods Mol Biol 2009;541:249-67
   PubMedGoogle Scholar
• Davies K. Running tranSMART for the Drug Development Marathon. Bio-IT World, 2010. Available from: http://www.bio-itworld.com/issues/2010/jan/transmart.html [Last accessed 24 January 2011]
   Google Scholar
• PNasonwade conference, Boston, September 28 2010. Available from: http://www.allconferences.com/conferences/2030/20300928171754/
   Google Scholar