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2011

 

Collison, M., Hirt, R.P., Wipat, A., Nakjang, S., Sanseau, P., and Brown. J. (2011). Data Mining the Human Gut Microbiota for Therapeutic Targets. Briefings in Bioinformatics. Accepted for publication.

Stadler L, Hoffmann T, Tomlinson D, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner S, Knowles M, Davis J, Ko Ferrigno P. (2011). Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and Applications of the SQT variant PEDS (in press).

Alcaraz N, Kucuk H, Weile J, Wipat A, Baumbach J (2011) KeyPathwayMiner - Detecting case-specific biological pathways by using expression data. Int. Math. (in press).

Weile, J., Pocock, M. Cockell, S. J., Lord, P., Dewar, J. M., Holstein, E., Wilkinson, D., Lydall, D., Hallinan, J. S. & Wipat, A. (2011). Customisable views on semantically integrated networks for systems biology. Bioinformatics 27(9): 1299 - 1306.

Misirli, G., Hallinan, J. S., Yu, T., Lawson, J. R., Wimalaratne, S. M., Cooling, M. T. & Wipat, A. (2011). Model annotation for synthetic biology: Automated model to sequence conversion. Bioinformatics. 2011 Apr 1;27(7):973-9.

Addinall SG, Holstein EM, Lawless C, Yu M, Chapman K, Banks AP, Ngo HP, Maringele L, Taschuk M, Young A, Ciesiolka A, Lister AL, Wipat A, Wilkinson DJ, Lydall D. (2011). Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects. PLoS Genet. 2011 Apr;7(4):e1001362. Epub 2011 Apr 7.

Misirli, G., Pocock, M. Cockell, S. J., Lord, P., Dewar, J. M., Holstein, E., Wilkinson, D., Lydall, D., Hallinan, J. S. & Wipat, A. (2011). Customisable views on semantically integrated networks for systems biology. Bioinformatics 27(9): 1299 - 1306.

2010

Fuellen G, Adjaye J, de Grey A, Lepperdinger G, de Magalhães JP, Sühnel J, Wipat A. (2011) Bioinformatics in aging research: a workshop report. Rejuvenation Res. 2010 Dec;13(6):763-7.

Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR. (2010) The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative. Proteomics. Jul 19. PMID: 20677327.

Lister AL, Lord P, Pocock M, Wipat A. (2010). Annotation of SBML models through rule-based semantic integration. J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S3.PMID: 20626923

Hallinan, JS, Misirli, G and Wipat A. (2010). Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. IEEE Eng Med Biol Soc. 2010:768-774.

Cockell, S. J., Weile, J., Lord, P., Wipat, C., Andriychenko, D., Pocock, M., Wilkinson, D., Young, M. and Wipat., A. (2010). An integrated dataset for in silico drug discovery. J. Integrative Bioinformatics. Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-116.PMID: 20375448

Passos, J., Nelson, G., Wang, C., Richter, T., Simillion, C., Proctor, C. J., Miwa, S., Olijslagers, S., Hallinan, J., Wipat, A., Saretski, G., Rudolph, K. L., Kirkwood, T. B. L. & von Zglinicki, T. (2010). A feedback loop between p21 and reactive oxygen production is necessary for establishment of cell senescence. Molecular Systems Biology 6(347).

M. T. Cooling, Rouilly, V., Misirli, G., Lawson, L., Yu, T., Hallinan, J. and Wipat, A.. (2010). Standard Virtual Biological Parts: A Repository of Modular Modelling Components for Synthetic Biology. Bioinformatics Apr 1;26(7):925-31.

Passos, J. F., Simillion, C., Hallinan, J., Wipat, A. & von Zglinicki, T. (2010). Cellular senescence: Unravelling complexity. Age. 31(4):353 - 363. 

 Weatherhead S, Hallinan J, Wipat A, Farr P, Reynolds N. (2010). Development of a dynamic mathematical model of epidermis reveals critical importance of increasing the proportion of both cycling stem and transient amplifying cells, in the development of psoriatic plaques. Journal of Investigative Dermatology: 40th Annual Meeting of the European Society for Dermatological Research.Helsinki, Finland:Nature Publishing Group.