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 Dr Avril Coghlan - Lecturer
Room 416, Food Science Building. ext. 3982

Research interests

  • Bioinformatics
  • Molecular evolution
  • Visit my research group's website
  • Visit the website of the MSc in Bioinformatics with Systems Biology
  • Visit my website of Irish bioinformatics jobs/PhD positions
  • A PhD position is available in my group (application deadline: 16th March 2010): Click here for more information

    E-mail: a.coghlan@ucc.ie
    Tel +353-21-4902743

    • 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, University College Cork

    Research Programme: Bioinformatics and molecular evolution

    We are a Bioinformatics research group situated in the Department of Microbiology in University College Cork. Research areas we are interested in are 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 group's website for more information.

    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.

    Haag, E. S., Chamberlin, H., Coghlan, A., Fitch, D. H. A., Peters, A. D. and Schulenburg, H. (2007) Evolutionary Biology of Caenorhabditis Nematodes: If They All Look Alike, You Aren.t Looking Hard Enough! Trends Genet. 23:101-4.

    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.

    Coghlan, A., Stajich, J. E. and Harris, T. W. (2006) Comparative Genomics in C. elegans, C. briggsae and Other Caenorhabditis Species. Methods Mol. Biol. 351:13-29. Book chapter.

    Coghlan, A., Eichler, E.E., Oliver, S., Paterson, A.H., Stein, L. (2005) Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet. 21:673-82.

    Coghlan, A. 2005. Nematode Genome Evolution. WormBook, ed. The C. elegans Research Community, WormBook, http://www.wormbook.org.

    Coghlan, A. and Wolfe, K.H. (2004) Origins of recently gained introns in Caenorhabditis. Proc. Natl. Acad. Sci. USA 101:11362-7.

    Stein, L., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M., Chen, J., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., Coulson, A., D'Eustachio, P., Fitch, D., Fulton, L., Fulton, R., Griffiths-Jones, S., Harris, T., Hillier, L., Kamath, R., Kuwabara, P., Mardis, E., Marra, M., Miner, T., Minx, P., Mullikin, J., Plumb, R., Rogers, J., Schein, J., Sohrmann, M., Spieth, J., Stajich, J., Wei, C., Willey, D., Wilson, R., Durbin, R., and Waterston, R. (2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biology 1:e45.

    Coghlan, A. and Wolfe, K. H. (2002) Fourfold Faster Rate of Genome Rearrangement in Nematodes than in Drosophila. Genome Res. 12:857-67.

    Coghlan, A., Mac Donaill, D. A. and Buttimore, N. H. (2001). Representation of amino acids as five-bit or three-bit patterns for filtering protein databases. Bioinformatics 17:676-85.

    Coghlan, A. and Wolfe, K. H. 2000. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae.

    Jobs in bioinformatics in Ireland

    Please visit my website on PhD positions and jobs in bioinformatics in my group and other groups in Ireland.

    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.