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Journal Articles
2007
2006
2005
2004
2003
2002
Pre-2002
Software
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Journal Articles
2007
Jeffery IB, Madden SF, McGettigan PA, Perrière G, Culhane AC, Higgins DG.
Integrating transcription factor binding site information with gene expression datasets.
Bioinformatics. 2007 Feb 1;23(3):298-305. Epub 2006 Nov 24. PMID: 17127681
Wallace IM, Higgins DG.
Supervised multivariate analysis of sequence groups to identify specificity determining residues.
BMC Bioinformatics. 2007 Apr 23;8:135. PMID: 17451607
Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W645-8. Epub 2007 May 25. PMID: 17526519
Fagan A, Culhane AC, Higgins DG.
A multivariate analysis approach to the integration of proteomic and gene expression data.
Proteomics. 2007 Jun;7(13):2162-71. PMID: 17549791
Fahey ME, Higgins DG.
Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis.
J Mol Evol. 2007 Sep;65(3):349-57. Epub 2007 Sep 1. PMID: 17763878
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.
Clustal W and Clustal X version 2.0.
Bioinformatics. 2007 Nov 1;23(21):2947-8. Epub 2007 Sep 10. PMID: 17846036
Walsh DW, Roxburgh SA, McGettigan P, Berthier CC, Higgins DG, Kretzler M, Cohen CD, Mezzano S, Brazil DP, Martin F.
Co-regulation of Gremlin and Notch signalling in diabetic nephropathy.
Biochim Biophys Acta. 2007 Oct 11, PMID: 17980714
O'Brien S. L., Fagan A., Fox E. J., Millikan R. C., Culhane A. C., Brennan D. J., McCann A. H., Hegarty S., Moyna S., Duffy M. J., Higgins D. G., Jirstrom K., Landberg G., Gallagher W. M., 2007
CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer.
Int J Cancer. Jan 4, [Epub ahead of print]
2006
Jeffery I. B., Madden S. F., McGettigan P. A., Perriere G., Culhane A. C., Higgins D. G., 2006
Integrating transcription factor binding site information with gene expression datasets.
Bioinformatics. Nov 24; [Epub ahead of print]
Armougom F., Poirot O., Moretti S., Higgins D.G., Bucher P., Keduas V.,Notredame C., 2006
APDB: a web server to evaluate the accuracy of sequence alignments using structural information.
Bioinformatics. 2006 Oct 1;22(19):2439-40.
Jeffery I. B., Higgins D. G., Culhane A. C., 2006
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data.
BMC Bioinformatics. Jul 26;7:359.
Blackshields, G. Wallace, I.M., Larkin, M., Higgins, D.G., 2006
Analysis and comparison of benchmarks for multiple sequence alignment.
In Silico Biol. 2006 Jun 8;6(4):0030
Claesson, M.J., Li, Y., Leahy, S., Canchaya, C., van Pijkeren,
J.P., Cerdeno-Tarraga, A. M., Parkhill, J., Flynn, S., O'sullivan, G. C., Collins, J. K., Higgins, D., Shanahan, F.,
Fitzgerald, G. F., van Sinderen, D. and O'toole, P.W., 2006
From the Cover: Multireplicon genome architecture of Lactobacillus salivarius.
Proc Natl Acad Sci U S A. Apr 25;103(17):6718-6723
Wallace, I.M., O'Sullivan, O., Higgins, D.G., Notredame, C., 2006
M-Coffee: combining multiple sequence alignment methods with T-Coffee
Nucleic Acids Res. 2006 Mar 23;34(6):1692-9..
Furney, S.J., Higgins, D.G., Ouzounis, C.A., Lopez-Bigas, N., 2006
Structural and functional properties of genes involved in human cancer
BMC Genomics. 2006 Jan 11;7:3.
2005
Ventura, M., Lee, J. H., Canchaya, C., Zink, R., Leahy, S.,
Moreno-Munoz, J. A., O'Connell-Motherway, M., Higgins, D., Fitzgerald, G. F., O'Sullivan, D. J.
and van Sinderen, D.,2005
Prophage-Like Elements in Bifidobacteria: Insights from Genomics, Transcription,Integration, Distribution, and Phylogenetic Analysis
Applied and Environmental Microbiology, December 2005, p. 8692-8705, Vol. 71, No.1
Higgins D. G., Blackshields G., Wallace I. M., 2005
Mind the gaps: Progress in progressive alignment
Proc Natl Acad Sci U S A. Jul 26;102(30):10411-2
Gallagher W. M., Bergin O. E., Rafferty M., Kelly Z. D., Nolan I. M., Fox
E. J. P., Culhane A. C., McArdle L., Fraga M. F., Hughes L., Currid C. A., O'Mahony F.,
Byrne A., Murphy A. A., Moss C., McDonnell S., Stallings R. L., Plumb J. A.,
Esteller M., Brown R., Dervan P. A., Easty D. J. (2005)
Multiple Markers for
Melanoma Progression Regulated by DNA Methylation: Insights from
Transcriptomic Studies. Carcinogenesis. 2005 Nov;26(11):1856-67.
Duffy M. J., Kelly Z. D., Culhane A. C., O' Brien S., Gallagher W. M., 2005,
DNA
Microarray-Based Gene Expression Profiling in Cancer: Aiding Cancer
Diagnosis, Assessing Prognosis and Predicting Response to Therapy.
Current Pharmacogenomics 3(4), 289-304.
Brennan D., O' Brien S., Fagan A., Culhane A. C., Higgins D. G., Duffy M. J.,
Gallagher W. M. ,2005
Application of DNA Microarray Technology
in Determining Breast Cancer Prognosis and Therapeutic Response. Expert
Opinion on Biological Therapy Aug;5(8):1069-83
Brazma A., and Culhane A. C., 2005
Algorithms for gene
expression analysis. In Encyclopaedia of Genetics, Genomics, Proteomics
and Bioinformatics. Wiley. (In Press)
Leahy, S. C., Higgins, D. G., Fitzgerald, G. F. and van Sinderen, D., 2005
Getting better with bifidobacteria.
J. Appl. Microbiol.98(6):2303-1315.
Culhane, A. C., Thioulouse, J., Perriere, G. and Higgins, D. G., 2005
MADE4: an R package for multivariate analysis of gene expression data
Bioinformatics.21(11):2789-90 .
Wallace, I. M., Blackshields, G. and Higgins, D. G., 2005
Multiple sequence alignments. Curr. Opin. Struct. Biol. Jun;15(3):261-6.
Fahey, M. E., Mills, W., Higgins, D. G. and Moore, T. F., 2005
Maternally and paternally silenced imprinted genes differ in their intron content.
Comparative and Functional Genomics, Volume 5, Number 8, December 2004, pp. 572-583(12).
Wallace, I. M., O'Sullivan, O. and Higgins, D. G., 2005
Evaluation of iterative alignment algorithms for multiple alignment. Bioinformatics 21:1408.
2004
Kapushesky, M., Kemmeren, P., Culhane, A. C.,
Durinck, S., Ihmels, J., Korner, C., Kull, M., Torrente, A.,
Sarkans, U., Vilo, J. and Brazma, A., 2004
Expression profiler: next generation - an online platform
for analysis of microarray data. Nucleic Acids Res. 32:W465-W470.
Blackshields, G., Wallace, I. and Higgins, D., 2004
Multiple alignments get faster and better. The Biochemist 26:29-32.
McArdle, L., McDermott, M., Purcell, R., Grehan, D., O'Meara, A., Breatnach, F., Catchpoole, D., Culhane, A. C., Jeffery, I., Gallagher, W. M. and Stallings, R. L., 2004 Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q. Carcinogenesis 25(9):1599-1609.
O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D. G. and Notredame, C., 2004 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol. 340:385-395.
2003
Prestwich, S., Higgins, D. and O'Sullivan, O., 2003 A SAT-based
approach to multiple sequence alignment.
Lect. Notes Comput. Sci. 2833:940-944.
Culhane, A. C., Perriere, G. and Higgins, D. G., 2003 Cross platform
comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics.
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G. and Thompson, J. D., 2003
Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497-3500.
O'Sullivan, O., Zehnder, M., Higgins, D., Bucher, P., Grosdidier, A. and Notredame, C., 2003
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics 19 Suppl 1:I215-I221.
2002
Culhane, A. C., Perriere, G., Considine, E. C., Cotter, T. G. and Higgins, D. G., 2002
Between-group analysis of microarray data. Bioinformatics 18:1600-1608.
Fahey, M. E., Moore, T. F. and Higgins, D. G., 2002
Overlapping antisense transcription in the human genome.
Comp. Functional Genomics 3:244-253.
Pre-2002
Notredame, C., Higgins, D. G. and Heringa, J., 2000
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
J. Mol. Biol. 302:205-217.
Higgins, D. G. and Taylor, W. R., 2000
Multiple sequence alignment. Methods Mol. Biol. 143:1-18.
Higgins, D. G., 2000
Amino acid-based phylogeny and alignment. Adv. Protein Chem. 54:99-135.
Kenny, P. A., Liston, E. M. and Higgins, D. G., 1999
Molecular evolution of immunoglobulin and fibronectin domains in titin and related muscle proteins.
Gene 232:11-23.
Thebault, P., Monestie, P., McGrath, A. and Higgins, D. G., 1999
MIAH: automatic alignment of eukaryotic SSU rRNAs.
Bioinformatics 15:341-342.
O'Brien, E. A. and Higgins, D. G., 1998
Empirical estimation of the reliability of ribosomal RNA alignments. Bioinformatics 14:830-838.
Notredame, C., Holm, L. and Higgins, D. G., 1998
COFFEE: an objective function for multiple sequence alignments.
Bioinformatics. 14:407-422.
McGrath, A., Higgins, D. G. and McCarthy, T. V., 1998
Sequence analysis of DNA randomly amplified from the Saccharomyces cerevisiae genome.
Mol. Cell. Probes 12:397-405.
O'Brien, E. A., Notredame, C. and Higgins, D. G., 1998
Optimization of ribosomal RNA profile alignments. Bioinformatics 14:332-341.
Jeanmougin, F., Thompson, J. D., Gouy, M., Higgins, D. G. and Gibson, T. J., 1998
Multiple sequence alignment with Clustal X. Trends Biochem Sci. 23(10):403-405.
Notredame, C., O'Brien, E. A. and Higgins, D. G., 1997
RAGA: RNA sequence alignment by genetic algorithm.
Nucleic Acids Res. 25:4570-4580.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. and Higgins, D. G., 1997
The CLUSTAL_X windows interface: flexible strategies for multiple sequence
alignment aided by quality analysis tools.
Nucleic Acids Res. 25:4876-4882.
Notredame, C. and Higgins, D. G., 1996
SAGA: sequence alignment by genetic algorithm.
Nucleic Acids Res. 24:1515-1524.
Higgins, D. G., Thompson, J. D. and Gibson, T. J., 1996
Using CLUSTAL for multiple sequence alignments.
Methods Enzymol. 266:383-402.
 Jonassen, I., Collins, J. F. and Higgins, D. G., 1995
Finding flexible patterns in unaligned protein sequences.
Protein Sci. 4(8):1587-1595.
Thompson, J. D., Higgins, D. G. and Gibson, T. J., 1994
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic Acids Res. 22:4673-4680.
Castresana, J., Lubben, M., Saraste, M. and Higgins, D. G., 1994
Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen.
EMBO J. 13:2516-2525.
Higgins, D. G., Labeit, S., Gautel, M. and Gibson, T. J., 1994
The evolution of titin and related giant muscle proteins.
J. Mol. Evol. 38:395-404.
Thompson, J. D., Higgins, D. G. and Gibson, T. J., 1994
Improved sensitivity of profile searches through the use of sequence weights and gap excision.
Comput. Appl. Biosci. 10:19-29.
Higgins, D. G., 1994
CLUSTAL V: multiple alignment of DNA and protein sequences.
Methods Mol. Biol. 25:307-18.
Graur, D. and Higgins, D. G., 1994
Molecular evidence for the inclusion of cetaceans within the order Artiodactyla.
Mol. Biol. Evol. 11:357-364.
Rice, C. M., Fuchs, R., Higgins, D. G., Stoehr, P. J. and Cameron, G. N., 1993
The EMBL data library. Nucleic Acids Res. 21:2967-2971.
Waters, A. P., Higgins, D. G. and McCutchan, T. F., 1993
Evolutionary relatedness of some primate models of Plasmodium. Mol. Biol. Evol. 10(4):914-923.
Waters, A. P., Higgins, D. G., and McCutchan, T. F., 1993
The phylogeny of malaria - a useful study.
Parasitology Today 9(7):246-250.
Higgins, D. G., Bleasby, A. J. and Fuchs, R., 1992
CLUSTAL V: improved software for multiple sequence alignment.
Comput. Appl. Biosci. 8:189-191.
Higgins, D. G. and Stoehr, P., 1992
EMBLSCAN: fast approximate DNA database searches on compact disc.
Comput. Appl. Biosci. 8:137-139.
Higgins, D. G., 1992
Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets.
Comput. Appl. Biosci. 8:15-22.
Heringa, J., Sommerfeldt, H., Higgins, D. and Argos, P., 1992
OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity.
Comput. Appl. Biosci. 8:599-600.
Higgins, D. G., Fuchs, R., Stoehr, P. J. and Cameron, G. N., 1992
The EMBL Data Library.
Nucleic Acids Res. 20 Suppl:2071-2074.
Shields, D. C., Higgins, D. G. and Sharp, P. M., 1992
GCWIND: a microcomputer program for identifying open reading frames according to codon positional
G+C content. Comput. Appl. Biosci. 8:521-523.
Pelandakis, M., Higgins, D. G., and Solignac, M., 1991
Molecular phylogeny of the subgenus Sophophora of Drosophila derived from large subunit
of ribosomal-RNA sequences. Genetica 84(2):87-94.
Powell, R., Higgins, D. G., and Wolff, J., 1991
The salmon gene encoding apolipoprotein-AI - cDNA sequence, tissue expression and
evolution. Gene 104(2):155-161.
Sharp, P. M., Lloyd, A. T., and Higgins, D. G., 1991
Coelacanths relationships. Nature 353:218-219.
Waters, A. P., Higgins, D. G., and McCutchan, T. F., 1991
Plasmodium-falciparum appears to have arisen as a result of lateral transfer between
avian and human hosts. Proc. Natl. Acad. Sci. USA 88(8):3140-3144.
Atkins, G. J., Daly, E. A., Sheahan, B. J.,
Higgins, D. G., and Sharp, P. M., 1990
Multiple-sclerosis and molecular mimicry. Neuropath. Appl. Neuro. 16(2):179-180.
Higgins, D. G. and Sharp, P. M., 1989
Fast and sensitive multiple sequence alignments on a microcomputer.
Comput. Appl. Biosci. 5:151-153.
Higgins, D. G., McConnell, D. J. and Sharp, P. M, 1989
Malarial proteinase. Nature 340:604.
Devine, K. M., Hogan ST, Higgins DG, McConnell DJ., 1989
Replication and segregational stability of Bacillus plasmid pBAA1.
J. Bacteriol. 171:1166-1172.
Higgins, D. G. and Sharp, P. M., 1988
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.
Gene. 73:237-244.
Shields, D. C., Sharp, P. M., Higgins, D. G. and Wright, F., 1988
"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons.
Mol. Biol. Evol. 5:704-716.
Sharp, P. M., Cowe, E., Higgins, D. G., Shields, D. C., Wolfe, K.H. and
Wright, F., 1988
Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity.
Nucleic Acids Res. 16:8207-8211.
Higgins, D. G. and Gouy, M., 1987
Interfacing similarity search software with the sequence retrieval system ACNUC.
Comput. Appl. Biosci. 3:239-241.
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