User:Avril Coghlan
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I am a new member of OpenWetWare!
Contact Info
- Avril Coghlan
- Department of Microbiology
- University College Cork
- Cork, Ireland
- Email me through OpenWetWare
I work in the Department of Microbiology at University College Cork. I learned about OpenWetWare from Noel O'Boyle, and I've joined because I am involved in a scientific collaboration with two other groups, and would like to put data and results on the web for them to see and comment on. It will also help me record what I have done on our collaborative project.
Education
- 2003, PhD, Bioinformatics, Trinity College Dublin
- 1999, BA (Mod), Genetics, Trinity College Dublin
Research interests
- Bioinformatics
- Molecular Evolution
- Computational Systems Biology
Research projects
- Computational modelling of propanediol metabolism in the metabolosome organelles of enteric bacteria
Publications
- Coghlan A and Wolfe KH. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast. 2000 Sep 15;16(12):1131-45. DOI:10.1002/1097-0061(20000915)16:12<1131::AID-YEA609>3.0.CO;2-F |
- Coghlan A, Mac Dónaill DA, and Buttimore NH. Representation of amino acids as five-bit or three-bit patterns for filtering protein databases. Bioinformatics. 2001 Aug;17(8):676-85. DOI:10.1093/bioinformatics/17.8.676 |
- Coghlan A and Wolfe KH. Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res. 2002 Jun;12(6):857-67. DOI:10.1101/gr.172702 |
- Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, and Waterston RH. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 2003 Nov;1(2):E45. DOI:10.1371/journal.pbio.0000045 |
- Coghlan A and Wolfe KH. Origins of recently gained introns in Caenorhabditis. Proc Natl Acad Sci U S A. 2004 Aug 3;101(31):11362-7. DOI:10.1073/pnas.0308192101 |
- Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, and Durbin R. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D572-80. DOI:10.1093/nar/gkj118 |
- Coghlan A and Durbin R. Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure. Bioinformatics. 2007 Jun 15;23(12):1468-75. DOI:10.1093/bioinformatics/btm133 |
- Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta-Vidal A, Bolund L, Wang J, and Durbin R. TreeFam: 2008 Update. Nucleic Acids Res. 2008 Jan;36(Database issue):D735-40. DOI:10.1093/nar/gkm1005 |
- Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, nGASP Consortium, and Stein LD. nGASP--the nematode genome annotation assessment project. BMC Bioinformatics. 2008 Dec 19;9:549. DOI:10.1186/1471-2105-9-549 |
- Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, Coulson R, Day TA, Delcher A, DeMarco R, Djikeng A, Eyre T, Gamble JA, Ghedin E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D, Macedo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ, Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR, White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell BG, and El-Sayed NM. The genome of the blood fluke Schistosoma mansoni. Nature. 2009 Jul 16;460(7253):352-8. DOI:10.1038/nature08160 |
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