Can Bioinformatics Be Considered as an Experimental Biological Science?
[1]
Olaf Ilzins, Institute of Advanced Studies (IDEA), Hoyo de la Puerta, Baruta, Venezuela.
[2]
Raul Isea, Institute of Advanced Studies (IDEA), Hoyo de la Puerta, Baruta, Venezuela.
[3]
Johan Hoebeke, Institute of Advanced Studies (IDEA), Hoyo de la Puerta, Baruta, Venezuela.
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an experimental science. These examples show how the development of theoretical biological models generates experimentally verifiable computer hypotheses, which necessarily must be validated by experiments in vitro or in vivo.
Bioinformatics, Hypothesis, Experimental, Biological, Computer
[1]
Hogeweg P. The Roots of Bioinformatics in Theoretical Biology. PLoS Comput Biol. 2011; 7(3): e1002021.
[2]
Luscombe NM, Greenbaum D, Gerstein M. What is bioinformatics? A proposed definition and overview of the field. Methods Inf Med. 2001; 40(4):346-58.
[3]
Huerta, M. 2000. NIH working definition of bioinformatics and computational biology. Available from http://www.bisti.nih.gov/docs/compubiodef.pdf [cited: 1 Dec 2014].
[4]
Offerman JD, Rychlik W. Oligo Primer Analysis Software in Introduction to bioinformatics: a theoretical and practical approach. Ed. Stephen A. Krawetz and David D. Womble; Humana Press Inc., Totowa, NJ. (2003), pp. 345-361.
[5]
Rychlik W, Rhoads RE. A Computer Program for Choosing Optimal Oligonucleotides for Filter Hybridization, Sequencing and in vitro Amplification of DNA. Nucleic Acids Res 1989; 17:8543-51.
[6]
Rychlik W, Spencer WJ, and Rhoads RE. Optimization of the Annealing Temperature for DNA Amplification in Vitro. Nucleic Acids Res.1990; 18:6409-12.
[7]
Notomi T, Okayama H, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000; 28: E63.
[8]
Ghasmian M, Gharavi MJ, Akhlaghi L, Moheball M, Meamar AR, Aryan E and Oormazdi H. Development and Assessment of Loop-Mediated Isothermal Amplification (LAMP) Assay for the Diagnosis of Human Visceral Leishmaniasis in Iran. Iran J Parasitol. 2014; 9(1): 50–9.
[9]
Cook J, Aydin-Schmidt B, González IJ, Bell D, Edlund E, Nassor MH, et al. Loop-mediated isothermal amplification (LAMP) for point-of-care detection of asymptomatic low-density malaria parasite carriers in Zanzibar. Malaria Journal. 2015; 14: 43.
[10]
Isea R, Aponte C, Cipriani R. Can the RNA of the Cowpea Chlorotic Mottle Virus be released through a channel by means of free diffusion? A Test in silico". Biophysical Chemistry. 2004; 107 (1-2): 101-6.
[11]
Schmier S, Mostafa A, Haarmann T, Bannert N, Ziebuhr J, Veljkovic V, et al. In Silico Prediction and Experimental Confirmation of HA Residues Conferring Enhanced Human Receptor Specificity of H5N1 Influenza A Viruses. Sci Rep. 2015; 5: 11434.
[12]
Engelbrecht, Andries P. (2007) Computational Intelligence: An Introduction, 2nd Edition. John Wiley & Sons, Ltd.
[13]
Huard J, Mueller S, et al. An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes. FEBS Journal 2012; 279: 3290–313
[14]
Tymoshenko S, Oppenheim RD, Agren R, Nielsen J, Soldati-Favre D, Hatzimanikatis V. Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. PLoS Comput Biol 2015; 11(5): e1004261.
[15]
Levine JH, Simonds EF, et al. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell 2015; 184–97.
