An in silico bioinformatics laboratory manual for bioscience departments: ‘prediction of glycosylation sites in phosphoethanolamine transferases’

References

• Adamczyk, B., T. Tharmalingam, and P. M. Rudd. 2012. “Glycans as Cancer Biomarkers.” Biochimica et Biophysica Acta 1820: 1347–1353.
   PubMed Web of Science ®Google Scholar
• Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. “Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs.” Nucleic Acids Research 25: 3389–3402.
   PubMed Web of Science ®Google Scholar
• Angata, T., R. Fujinawa, A. Kurimoto, K. Nakajima, M. Kato, S. Takamatsu, H. Korekane, et al. 2012. “Integrated Approach Toward the Discovery of Glyco-Biomarkers of Inflammation-Related Diseases.” Annals of the New York Academy of Sciences 1253: 159–169.
   PubMed Web of Science ®Google Scholar
• Artimo, P., M. Jonnalagedda, K. Arnold, D. Baratin, G. Csardi, E. de Castro, S. Duvaud, V. Flegel, A. Fortier, E. Gasteiger, A. Grosdidier, C. Hernandez, V. Ioannidis, D. Kuznetsov, R. Liechti, S. Moretti, K. Mostaguir, N. Redaschi, G. Rossier, I. Xenarios, and H. Stockinger. 2012. “ExPASy: SIB Bioinformatics Resource Portal.” Nucleic Acids Research 40 (W1): W597–W603.
   PubMed Web of Science ®Google Scholar
• Bansal, K. 2005. “Bioinformatics in Microbial Biotechnology – A Mini Review.” Microbial Cell Factories 4: 19.
   PubMed Web of Science ®Google Scholar
• Benson, D. A., I. Karsch-Mizrachi, K. Clark, D. J. Lipman, J. Ostell, and E. W. Sayers. 2012. “GenBank.” Nucleic Acids Research 40: D48–D53.
   PubMed Web of Science ®Google Scholar
• Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. “The Protein Data Bank.” Nucleic Acids Research 28: 235–242.
   PubMed Web of Science ®Google Scholar
• Blom, N., T. Sicheritz-Ponten, R. Gupta, S. Gammeltoft, and S. Brunak. 2004. “Prediction of Post-translational Glycosylation and Phosphorylation of Proteins from the Amino Acid Sequence.” Proteomics 4 (6): 1633–1649.
   PubMed Web of Science ®Google Scholar
• Bosch, D., and A. Schots. 2010. “Plant Glycans: Friend or Foe in Vaccine Development?” Expert Review of Vaccines 9: 835–842.
   PubMed Web of Science ®Google Scholar
• Boyle, J. A. 2004. “Bioinformatics in Undergraduate Education.” Biochemistry and Molecular Biology Education 32: 236–238.
   PubMed Web of Science ®Google Scholar
• Camacho, C., G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos, K. Bealer, and T. L. Madden. 2008. “BLAST+: Architecture and applications.” BMC Bioinformatics 10: 421.
   Web of Science ®Google Scholar
• Feig, A. L., and E. Jabri. 2002. “Incorporation of Bioinformatics Exercises into the Undergraduate Biochemistry Curriculum.” Biochemistry and Molecular Biology Education 30: 224–231.
   Web of Science ®Google Scholar
• Flanagan-Steet, H., and R. Steet. 2013. “‘Casting’ Light on the Role of Glycosylation During Embryonic Development: Insights from Zebrafish.” Glycoconjugate Journal 30: 33–40.
   PubMed Web of Science ®Google Scholar
• Furukawa, K., Y. Ohkawa, Y. Yamauchi, K. Hamamura, Y. Ohmi, and K. Furukawa. 2012. “Fine Tuning of Cell Signals by Glycosylation.” Journal of Biochemistry 151: 573–578.
   PubMed Web of Science ®Google Scholar
• Garwood, K., C. Garwood, C. Hedeler, T. Griffiths, N. Swainston, S. G. Oliver, and N. W. Paton. 2006. “Model-Driven User Interfaces for Bioinformatics Data Resources: Regenerating the Wheel as an Alternative to Reinventing It.” BMC Bioinformatics 7: 532.
   PubMed Web of Science ®Google Scholar
• Gasteiger, E., C. Hoogland, A. Gattiker, S. Duvaud, M. R. Wilkins, R. D. Appel, and A. Bairoch. 2005. “Protein Identification and Analysis Tools on the ExPASy Server.” In The Proteomics Protocols Handbook, edited by J. M. Walker, 571–607. New Jersey: Humana Press.
   Google Scholar
• Goujon, M., H. McWilliam, W. Li, F. Valentin, S. Squizzato, J. Paern, and R. Lopez. 2010. “A New Bioinformatics Analysis Tools Framework at EMBL-EBI.” Nucleic Acids Research 38 (Suppl): W695–699.
   PubMedGoogle Scholar
• Gupta, R., and S. Brunak. 2002. “Prediction of Glycosylation across the Human Proteome and the Correlation to Protein Function.” Pacific Symposium Biocomputing 7: 310–22.
   Google Scholar
• Howard, D. R., J. A. Miskowski, S. K. Grunwald, and M. L. Abler. 2007. “Assessment of a Bioinformatics Across Life Science Curricula Initiative.” Biochemistry and Molecular Biology Education 35: 16–23.
   PubMed Web of Science ®Google Scholar
• Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, and D. G. Higgins. 2007. “Clustal W and Clustal X version 2.0.” Bioinformatics 23: 2947–2948.
   PubMed Web of Science ®Google Scholar
• Lieth, C. W., T. Lütteke, and M. Frank. 2006. “The Role of Informatics in Glycobiology Research with Special Emphasis on Automatic Interpretation of MS Spectra.” Biochimica et Biophysica Acta 1760: 568–577.
   PubMed Web of Science ®Google Scholar
• Liu, C. C., and X. S. Ye. 2012. “Carbohydrate-Based Cancer Vaccines: Target Cancer with Sugar Bullets.” Glycoconjugate Journal 29: 259–271.
   PubMed Web of Science ®Google Scholar
• Maloney, M., J. Parker, M. LeBlanc, C. T. Woodard, M. Glackin, and M. Hanrahan. 2010. “Bioinformatics and the Undergraduate Curriculum.” CBE–Life Sciences. Education 9: 172–174.
   PubMed Web of Science ®Google Scholar
• Marchal, I., G. Golfier, O. Dugas, and M. Majed. 2003. “Bioinformatics in Glycobiology.” Biochimie 85: 75–81.
   PubMed Web of Science ®Google Scholar
• Menon, A. K. 2009. “Split Topology of GPI Biosynthesis.” In Glycosylphosphatidylinositol (GPI) Anchoring of Proteins, edited by A. K. Menon, T. Kinoshita, P. Orlean and F. Tamanoi, 151–158. New York, NY: Academic Press.
   Google Scholar
• Ojo, O. O., and M. Omabe. 2011. “Incorporating Bioinformatics into Biological Science Education in Nigeria: Prospects and Challenges.” Infection, Genetics and Evolution 11: 784–787.
   PubMed Web of Science ®Google Scholar
• Sato, S., M. Ouellet, C. St-Pierre, and M. J. Tremblay. 2012. “Glycans, Galectins, and HIV-1 Infection.” Annals of the New York Academy of Sciences 1253: 133–148.
   PubMed Web of Science ®Google Scholar
• Sutcliffe, I. C., and S. P. Cummings. 2007. “Making Bioinformatics Projects a Meaningful Experience in an Undergraduate Biotechnology or Biomedical Science Programme”. Bioscience Education 10.
   Google Scholar
• Taniguchi, N., and H. Korekane. 2011. “Branched N-Glycans and Their Implications for Cell Adhesion, Signaling and Clinical Applications for Cancer Biomarkers and in Therapeutics.” BMB Reports 44: 772–781.
   PubMed Web of Science ®Google Scholar
• Voet, D., and J. G. Voet. 2011. Biochemistry. 4th ed. New York: Wiley.
   Google Scholar