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Desmond Higgins
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Research Profile (preview)
Procedures
Activities & Behaviors
Concepts & Ideas
Genes & Molecular Sequences
Chemicals & Drugs
Occupations
Devices
Physiology
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Network (preview)
10
Notredame, Cédric
9
Wallace, Iain
9
Culhane, Aedín
9
Gibson, Toby
6
Thompson, Julie
6
Sharp, Paul
5
Blackshields, Gordon
4
Perrière, Guy
4
Fagan, Ailís
3
O'Sullivan, Orla
3
Fuchs, Rainer
3
O'Brien, EA
3
McGettigan, Paul
2
McGrath, A
2
Jeffery, Ian
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Geonetwork of Desmond Higgins (preview)
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All Publications
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2009: Smith M J; Culhane A C; Donovan M; Coffey J C; Barry B D; Kelly M A; Higgins D G; Wang J H; Kirwan W O; Cotter T G; Redmond H P
Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification.
British journal of cancer 2009;100(9):1452-64.
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2008: Leonard Martin O; Howell Katherine; Madden Stephen F; Costello Christine M; Higgins Desmond G; Taylor Cormac T; McLoughlin Paul
Hypoxia selectively activates the CREB family of transcription factors in the in vivo lung.
American journal of respiratory and critical care medicine 2008;178(9):977-83.
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2008: Blackshields Gordon; Larkin Mark; Wallace Iain M; Wilm Andreas; Higgins Desmond G
Fast embedding methods for clustering tens of thousands of sequences.
Computational biology and chemistry 2008;32(4):282-6.
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2008: Wilm Andreas; Higgins Desmond G; Notredame Cédric
R-Coffee: a method for multiple alignment of non-coding RNA.
Nucleic acids research 2008;36(9):e52.
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2008: Walsh David W; Roxburgh Sarah A; McGettigan Paul; Berthier Celine C; Higgins Desmond G; Kretzler Matthias; Cohen Clemens D; Mezzano Sergio; Brazil Derek P; Martin Finian
Co-regulation of Gremlin and Notch signalling in diabetic nephropathy.
Biochimica et biophysica acta 2008;1782(1):10-21.
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2007: Walsh Marianne C; Brennan Lorraine; Pujos-Guillot Estelle; Sébédio Jean-Louis; Scalbert Augustin; Fagan Ailís; Higgins Desmond G; Gibney Michael J
Influence of acute phytochemical intake on human urinary metabolomic profiles.
The American journal of clinical nutrition 2007;86(6):1687-93.
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2007: Larkin M A; Blackshields G; Brown N P; Chenna R; McGettigan P A; McWilliam H; Valentin F; Wallace I M; Wilm A; Lopez R; Thompson J D; Gibson T J; Higgins D G
Clustal W and Clustal X version 2.0.
Bioinformatics (Oxford, England) 2007;23(21):2947-8.
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2007: Fahey Marie E; Higgins Desmond G
Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis.
Journal of molecular evolution 2007;65(3):349-57.
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2007: Moretti Sebastien; Armougom Fabrice; Wallace Iain M; Higgins Desmond G; Jongeneel Cornelius V; Notredame Cedric
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
Nucleic acids research 2007;35(Web Server issue):W645-8.
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2007: Fagan Ailís; Culhane Aedín C; Higgins Desmond G
A multivariate analysis approach to the integration of proteomic and gene expression data.
Proteomics 2007;7(13):2162-71.
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2007: O'Sullivan Niamh C; McGettigan Paul A; Sheridan Graham K; Pickering Mark; Conboy Lisa; O'Connor John J; Moynagh Paul N; Higgins Desmond G; Regan Ciaran M; Murphy Keith J
Temporal change in gene expression in the rat dentate gyrus following passive avoidance learning.
Journal of neurochemistry 2007;101(4):1085-98.
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2007: O'Brien Sallyann L; Fagan Ailís; Fox Edward J P; Millikan Robert C; Culhane Aedín C; Brennan Donal J; McCann Amanda H; Hegarty Shauna; Moyna Siobhan; Duffy Michael J; Higgins Desmond G; Jirström Karin; Landberg Göran; Gallagher William M
CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer.
International journal of cancer. Journal international du cancer 2007;120(7):1434-43.
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2007: Jeffery Ian B; Madden Stephen F; McGettigan Paul A; Perrière Guy; Culhane Aedín C; Higgins Desmond G
Integrating transcription factor binding site information with gene expression datasets.
Bioinformatics (Oxford, England) 2007;23(3):298-305.
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2007: Wallace Iain M; Higgins Desmond G
Supervised multivariate analysis of sequence groups to identify specificity determining residues.
BMC bioinformatics 2007;8():135.
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2006: Armougom Fabrice; Poirot Olivier; Moretti Sébastien; Higgins Desmond G; Bucher Phillip; Keduas Vladimir; Notredame Cedric
APDB: a web server to evaluate the accuracy of sequence alignments using structural information.
Bioinformatics (Oxford, England) 2006;22(19):2439-40.
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2006: Blackshields Gordon; Wallace Iain M; Larkin Mark; Higgins Desmond G
Analysis and comparison of benchmarks for multiple sequence alignment.
In silico biology 2006;6(4):321-39.
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2006: Jeffery Ian B; Higgins Desmond G; Culhane Aedín C
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data.
BMC bioinformatics 2006;7():359.
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2006: Wallace Iain M; O'Sullivan Orla; Higgins Desmond G; Notredame Cedric
M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Nucleic acids research 2006;34(6):1692-9.
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2005: Brennan Donal J; O'Brien Sallyann L; Fagan Ailís; Culhane Aedín C; Higgins Desmond G; Duffy Michael J; Gallagher William M
Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response.
Expert opinion on biological therapy 2005;5(8):1069-83.
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2005: Higgins D G; Blackshields G; Wallace I M
Mind the gaps: progress in progressive alignment.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(30):10411-2.
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2005: Wallace Iain M; Blackshields Gordon; Higgins Desmond G
Multiple sequence alignments.
Current opinion in structural biology 2005;15(3):261-6.
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2005: Culhane Aedín C; Thioulouse Jean; Perrière Guy; Higgins Desmond G
MADE4: an R package for multivariate analysis of gene expression data.
Bioinformatics (Oxford, England) 2005;21(11):2789-90.
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2005: Wallace Iain M; O'Sullivan Orla; Higgins Desmond G
Evaluation of iterative alignment algorithms for multiple alignment.
Bioinformatics (Oxford, England) 2005;21(8):1408-14.
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2005: Leahy S C; Higgins D G; Fitzgerald G F; van Sinderen D
Getting better with bifidobacteria.
Journal of applied microbiology 2005;98(6):1303-15.
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2004: O'Sullivan Orla; Suhre Karsten; Abergel Chantal; Higgins Desmond G; Notredame Cédric
3DCoffee: combining protein sequences and structures within multiple sequence alignments.
Journal of molecular biology 2004;340(2):385-95.
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2004: Fahey Marie E; Mills Walter; Higgins Desmond G; Moore Tom
Maternally and paternally silenced imprinted genes differ in their intron content.
Comparative and functional genomics 2004;5(8):572-83.
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2003: Culhane Aedín C; Perrière Guy; Higgins Desmond G
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis.
BMC bioinformatics 2003;4():59.
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2003: Chenna Ramu; Sugawara Hideaki; Koike Tadashi; Lopez Rodrigo; Gibson Toby J; Higgins Desmond G; Thompson Julie D
Multiple sequence alignment with the Clustal series of programs.
Nucleic acids research 2003;31(13):3497-500.
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2002: Culhane Aedín C; Perrière Guy; Considine Elizabeth C; Cotter Thomas G; Higgins Desmond G
Between-group analysis of microarray data.
Bioinformatics (Oxford, England) 2002;18(12):1600-8.
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2002: Fahey M E; Moore T F; Higgins D G
Overlapping antisense transcription in the human genome.
Comparative and functional genomics 2002;3(3):244-53.
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2000: Notredame C; Higgins D G; Heringa J
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Journal of molecular biology 2000;302(1):205-17.
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2000: Higgins D G; Taylor W R
Multiple sequence alignment.
Methods in molecular biology (Clifton, N.J.) 2000;143():1-18.
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2000: Higgins D G
Amino acid-based phylogeny and alignment.
Advances in protein chemistry 2000;54():99-135.
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1999: Kenny P A; Liston E M; Higgins D G
Molecular evolution of immunoglobulin and fibronectin domains in titin and related muscle proteins.
Gene 1999;232(1):11-23.
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1999: Thébault P; Monestié P; McGrath A; Higgins D G
MIAH: automatic alignment of eukaryotic SSU rRNAs.
Bioinformatics (Oxford, England) 1999;15(4):341-2.
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1998: McGrath A; Higgins D G; McCarthy T V
Sequence analysis of DNA randomly amplified from the Saccharomyces cerevisiae genome.
Molecular and cellular probes 1998;12(6):397-405.
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1998: Jeanmougin F; Thompson J D; Gouy M; Higgins D G; Gibson T J
Multiple sequence alignment with Clustal X.
Trends in biochemical sciences 1998;23(10):403-5.
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1998: Notredame C; Holm L; Higgins D G
COFFEE: an objective function for multiple sequence alignments.
Bioinformatics (Oxford, England) 1998;14(5):407-22.
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1998: O'Brien E A; Higgins D G
Empirical estimation of the reliability of ribosomal RNA alignments.
Bioinformatics (Oxford, England) 1998;14(10):830-8.
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1998: O'Brien E A; Notredame C; Higgins D G
Optimization of ribosomal RNA profile alignments.
Bioinformatics (Oxford, England) 1998;14(4):332-41.
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1997: Thompson J D; Gibson T J; Plewniak F; Jeanmougin F; Higgins D G
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
Nucleic acids research 1997;25(24):4876-82.
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1997: Notredame C; O'Brien E A; Higgins D G
RAGA: RNA sequence alignment by genetic algorithm.
Nucleic acids research 1997;25(22):4570-80.
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1996: Notredame C; Higgins D G
SAGA: sequence alignment by genetic algorithm.
Nucleic acids research 1996;24(8):1515-24.
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1996: Higgins D G; Thompson J D; Gibson T J
Using CLUSTAL for multiple sequence alignments.
Methods in enzymology 1996;266():383-402.
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1994: Thompson J D; Higgins D G; Gibson T J
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic acids research 1994;22(22):4673-80.
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1994: Castresana J; Lübben M; Saraste M; Higgins D G
Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen.
The EMBO journal 1994;13(11):2516-25.
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1994: Higgins D G; Labeit S; Gautel M; Gibson T J
The evolution of titin and related giant muscle proteins.
Journal of molecular evolution 1994;38(4):395-404.
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1994: Thompson J D; Higgins D G; Gibson T J
Improved sensitivity of profile searches through the use of sequence weights and gap excision.
Computer applications in the biosciences : CABIOS 1994;10(1):19-29.
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1994: Higgins D G
CLUSTAL V: multiple alignment of DNA and protein sequences.
Methods in molecular biology (Clifton, N.J.) 1994;25():307-18.
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1993: Rice C M; Fuchs R; Higgins D G; Stoehr P J; Cameron G N
The EMBL data library.
Nucleic acids research 1993;21(13):2967-71.
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1993: Gibson T J; Higgins D G
Non-muscle and smooth muscle myosin light chain kinases: no end in sight.
DNA sequence : the journal of DNA sequencing and mapping 1993;3(5):333-5.
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1992: Shields D C; Higgins D G; Sharp P M
GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content.
Computer applications in the biosciences : CABIOS 1992;8(5):521-3.
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1992: Higgins D G; Fuchs R; Stoehr P J; Cameron G N
The EMBL Data Library.
Nucleic acids research 1992;20 Suppl():2071-4.
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1992: Higgins D G; Bleasby A J; Fuchs R
CLUSTAL V: improved software for multiple sequence alignment.
Computer applications in the biosciences : CABIOS 1992;8(2):189-91.
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1992: Higgins D G; Stoehr P
EMBLSCAN: fast approximate DNA database searches on compact disc.
Computer applications in the biosciences : CABIOS 1992;8(2):137-9.
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1992: Higgins D G
Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets.
Computer applications in the biosciences : CABIOS 1992;8(1):15-22.
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1989: Higgins D G; McConnell D J; Sharp P M
Malarial proteinase?
Nature 1989;340(6235):604.
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1989: Higgins D G; Sharp P M
Fast and sensitive multiple sequence alignments on a microcomputer.
Computer applications in the biosciences : CABIOS 1989;5(2):151-3.
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1989: Devine K M; Hogan S T; Higgins D G; McConnell D J
Replication and segregational stability of Bacillus plasmid pBAA1.
Journal of bacteriology 1989;171(2):1166-72.
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1988: Higgins D G; Sharp P M
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.
Gene 1988;73(1):237-44.
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1988: Shields D C; Sharp P M; Higgins D G; Wright F
"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons.
Molecular biology and evolution 1988;5(6):704-16.
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1988: Sharp P M; Cowe E; Higgins D G; Shields D C; Wolfe K H; Wright F
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 research 1988;16(17):8207-11.
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1987: Higgins D G; Gouy M
Interfacing similarity search software with the sequence retrieval system ACNUC.
Computer applications in the biosciences : CABIOS 1987;3(3):239-41.
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