Name: Dr. Avril Coghlan
Position: Lecturer
T: 353 (0)21 4903982
F: 353 (0)21 4903101
E: a.coghlan@ucc.ie
Biography
Academic Career
1999 BA (Mod), Genetics, Trinity College Dublin
2003 PhD Bioinformatics, Trinity College Dublin
2003-2005 Post-doctoral Fellow, University College Dublin
2005-2008 Post-doctoral Fellow, Wellcome Trust Sanger Institute, Cambridge, UK
2008- present, Lecturer, Bioinformatics, Department of Microbiology, UCC
Teaching areas
- Bioinformatics
- Molecular Evolution
- Computational Systems Biology
Research interests and expertise
- Bioinformatics
- Molecular Evolution
- Computational Systems Biology
Research
Research Overview
I am a bioinformatician situated in the Department of Microbiology in University College Cork. Research areas that I am interested in include annotation and evolutionary analyses of nematode and schistosome genomes, development of gene prediction algorithms, identification of orthologs and paralogs and gene family evolution, and the evolution of microsatellite and other genomic repeats in eukaryotic genomes. Please visit my research website at http://www.ucc.ie/microbio/avrilcoghlan for more information.
Selected Recent Publications
Berriman, M., Haas, B., LoVerde, P., Wilson, R., Dillon, G., Cerqueira, G., Mashiyama, S., Al- Lazikani, B., Andrade, L., Ashton, P., Aslett, M., Bartolomeu, D., Blandin, G., Caffrey, C., Coghlan, A., Day, T., Delcher, A., De Marco, R., Djikeng, A., Eyre, T., Gamble, J., Ghedin, E., Gu, Y., Hertz-Fowler, C., Hirai, H., Hirai, Y., Houston, R., Ivens, A., Johnston, D., Lacerda, D., Macedo, C., Neto, A., Ning, Z., Oliveira, G., Overington, J., Parkhill, J., Pertea, M., Protasio, A., Quail, M., Rogers, J., Sajid, M., Salzberg, S., Stanke, M., Tivey, A., White, O., Williams, D., Wortman, J., Wu, W., Zamanian, M., Fraser-Liggett, C., Barrell, B., and El-Sayed, N. 2009. The genome of the blood fluke Schistosoma mansoni. (2009) Nature. 460:352-358 (Open Access).
Coghlan, A. , Fiedler, T.J., McKay, S., Flicek, P., Harris, T.W., Blasiar, D., and Stein, L. nGASP - the nematode genome annotation assessment project. (2008) BMC Bioinformatics. 9:549.
Ruan, J., Li, H., Chen, Z., Coghlan, A., Coin, L. J. M., Guo, Y., Heriche, J.-K., Hu, Y., Kristiansen, K., Li, R., Liu, T., Moses, A., Qin, J., Vang, S., Vilella, A. J., Ureta-Vidal, A., Bolund, L., Wang, J. and Durbin, R. (2008) TreeFam: 2008 Update. Nucleic Acids Res. 36:D735-40.
Coghlan, A. and Durbin, R. (2007) Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure. Bioinformatics 23:1468-75.
Li, H., Coghlan, A. (joint first author), Ruan, J., Coin, L., Heriche, J.-K., Osmotherly, L., Li, R., Liu, T., Zhang, Z., Bolund, L., Wong, G. K.-S., Zheng, W., Dehal, P., Wang, J. and Durbin, R. (2006) TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34:D572-80.
Research funding and grants
Science Foundation Ireland, Research Frontiers Award, October 2009-present
PhD
positions and jobs in my group
A PhD position is available in my group (application deadline: 16th March 2010): see http://www.ucc.ie/microbio/avrilcoghlan/ for more information.
MSc in Bioinformatics with Systems Biology
For information on the one-year MSc in Bioinformatics with Systems Biology that I am involved in teaching, see the MSc in Bioinformatics with Systems Biology website http://www.ucc.ie/microbio/MScBioinf/