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Desmond Higgins

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Publications

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Graham M Hughes; William J Murphy; Li Gang; Desmond G Higgins; Emma C Teeling
Using Illumina next generation sequencing technologies to sequence multigene families in de novo species.
Fabian Sievers; Andreas Wilm; David Dineen; Desmond G Higgins
Making automated multiple alignments of very large numbers of protein sequences.
Laoighse Mulrane; Donal J Brennan; John P Crown; William M Gallagher; Gabriela Gremel; Desmond G Higgins; Karin Jirström; Stephen F Madden; Finian Martin; Sharon F McGee; Sara McNally; Darran P O'Connor
miR-187 is an independent prognostic factor in breast cancer and confers increased invasive potential in vitro.

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All Publications

2013: Graham M Hughes; William J Murphy; Li Gang; Desmond G Higgins; Emma C Teeling
Using Illumina next generation sequencing technologies to sequence multigene families in de novo species.
Molecular ecology resources 2013;13(3):510-21.
2013: Fabian Sievers; Andreas Wilm; David Dineen; Desmond G Higgins
Making automated multiple alignments of very large numbers of protein sequences.
Bioinformatics (Oxford, England) 2013;29(8):989-95.
2012: Laoighse Mulrane; Donal J Brennan; John P Crown; William M Gallagher; Gabriela Gremel; Desmond G Higgins; Karin Jirström; Stephen F Madden; Finian Martin; Sharon F McGee; Sara McNally; Darran P O'Connor
miR-187 is an independent prognostic factor in breast cancer and confers increased invasive potential in vitro.
Clinical cancer research : an official journal of the American Association for Cancer Research 2012;18(24):6702-13.
2012: Weifeng Shi; Chaodong Zhu; Michael J Carr; linda maria dunford; William W Hall; Desmond G Higgins
Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis.
Virology 2012;427(1):51-9.
2012: Jun Yin; Kristin M Ackerman; Sudhakar Deeti; Antonino Glaviano; Desmond G Higgins; David R Hyde; Ciaran Kennedy; Claire Kilty; Sarah McLoughlin; Sean O'Farrell; Olivia O'Leary; Francis Raycroft; Alison Reynolds; Megan Rice; Eileen Russell; Lisa Shine; Breandán N Kennedy
Inhibition of the Pim1 oncogene results in diminished visual function.
PloS one 2012;7(12):e52177.
2012: Weifeng Shi; Wei Zheng; Chaodong Zhu; Ines T Freitas; William W Hall; Desmond G Higgins
Recombination in hepatitis C virus: identification of four novel naturally occurring inter-subtype recombinants.
PloS one 2012;7(7):e41997.
2011: Mary O'Connell-Motherway; Marco Ventura; Aldert L Zomer; José Antonio Moreno Muñoz; Francesca Bottacini; Pat G Casey; Marcus J Claesson; Willem M de Vos; Gerald F Fitzgerald; Kiera Flynn; Desmond G Higgins; Aileen M Houston; Breda Kearney; Sinead Leahy; Frances O'Brien; Caitlin O'Mahony; Paul W O'Toole; Airi Palva; Justus Reunanen; Fergus Shanahan; Douwe van Sinderen
Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(27):11217-22.
2011: Maria L Cederlund; Victor Vendrell; Maria E Morrissey; Jun Yin; Peadar Ó Gaora; Vincent A Smyth; Desmond G Higgins; Breandán N Kennedy
mab21l2 transgenics reveal novel expression patterns of mab21l1 and mab21l2, and conserved promoter regulation without sequence conservation.
Developmental dynamics : an official publication of the American Association of Anatomists 2011;240(4):745-54.
2011: Alessandro Guida; Desmond G Higgins; Claudia Lindstädt; Sarah L Maguire; Matthew Berriman; Nicola J Corton; Chen Ding; Geraldine Butler
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis.
BMC genomics 2011;12():628.
2011: Fabian Sievers; Johannes Söding; Julie D Thompson; Andreas Wilm; Kevin Karplus; Weizhong Li; Rodrigo Lopez; Hamish McWilliam; Michael Remmert; David Dineen; Toby J Gibson; Desmond G Higgins
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Molecular systems biology 2011;7():539.
2010: John M Synnott; Alessandro Guida; Siobhan Mulhern-Haughey; Desmond G Higgins; Geraldine Butler
Regulation of the hypoxic response in Candida albicans.
Eukaryotic cell 2010;9(11):1734-46.
2010: Weifeng Shi; Fumin Lei; Chaodong Zhu; Fabian Sievers; Desmond G Higgins
A complete analysis of HA and NA genes of influenza A viruses.
PloS one 2010;5(12):e14454.
2010: David G Dineen; Markus Schröder; Desmond G Higgins; Pádraig Cunningham
Ensemble approach combining multiple methods improves human transcription start site prediction.
BMC genomics 2010;11():677.
2010: Stephen F Madden; Susan B Carpenter; Ian B Jeffery; Harry Björkbacka; Katherine A Fitzgerald; Luke A O'Neill; Desmond G Higgins
Detecting microRNA activity from gene expression data.
BMC bioinformatics 2010;11():257.
2010: Gordon Blackshields; Fabian Sievers; Weifeng Shi; Andreas Wilm; Desmond G Higgins
Sequence embedding for fast construction of guide trees for multiple sequence alignment.
Algorithms for molecular biology : AMB 2010;5():21.
2010: Jun Yin; Sarah McLoughlin; Ian B Jeffery; Antonino Glaviano; Breandan Kennedy; Desmond G Higgins
Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data.
BMC genomics 2010;11():50.
2009: David G Dineen; Andreas Wilm; Pádraig Cunningham; Desmond G Higgins
High DNA melting temperature predicts transcription start site location in human and mouse.
Nucleic acids research 2009;37(22):7360-7.
2009: myles smith; Aedín C Culhane; M Donovan; J C Coffey; BD Barry; M A Kelly; Desmond G Higgins; Jiang Huai Wang; William O Kirwan; Thomas G Cotter; H Paul Redmond
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.
2008: Martin O Leonard; Katherine Howell; Stephen F Madden; Christine M Costello; Desmond G Higgins; Cormac T Taylor; Paul McLoughlin
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.
2008: Gordon Blackshields; Mark Larkin; Iain M Wallace; Andreas Wilm; Desmond G Higgins
Fast embedding methods for clustering tens of thousands of sequences.
Computational biology and chemistry 2008;32(4):282-6.
2008: Andreas Wilm; Desmond G Higgins; Cédric Notredame
R-Coffee: a method for multiple alignment of non-coding RNA.
Nucleic acids research 2008;36(9):e52.
2008: David W Walsh; Sarah A Roxburgh; Paul McGettigan; Celine C Berthier; Desmond G Higgins; Matthias Kretzler; Clemens D Cohen; Sergio Mezzano; Derek Brazil; Finian Martin
Co-regulation of Gremlin and Notch signalling in diabetic nephropathy.
Biochimica et biophysica acta 2008;1782(1):10-21.
2007: Marianne C Walsh; Lorraine Brennan; Estelle Pujos-Guillot; Jean-Louis Sébédio; Augustin Scalbert; Ailís Fagan; Desmond G Higgins; Mike joseph Gibney
Influence of acute phytochemical intake on human urinary metabolomic profiles.
The American journal of clinical nutrition 2007;86(6):1687-93.
2007: M A Larkin; Gordon Blackshields; N P Brown; R Chenna; Paul A McGettigan; H McWilliam; F Valentin; Iain M Wallace; Andreas Wilm; R Lopez; julie thompson; Toby J Gibson; Desmond G Higgins
Clustal W and Clustal X version 2.0.
Bioinformatics (Oxford, England) 2007;23(21):2947-8.
2007: Marie E Fahey; Desmond G Higgins
Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis.
Journal of molecular evolution 2007;65(3):349-57.
2007: Sebastien Moretti; Fabrice Armougom; Iain M Wallace; Desmond G Higgins; Victor Jongeneel; Cédric Notredame
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.
2007: Ailís Fagan; Aedín C Culhane; Desmond G Higgins
A multivariate analysis approach to the integration of proteomic and gene expression data.
Proteomics 2007;7(13):2162-71.
2007: Niamh C O'Sullivan; Paul A McGettigan; Graham K Sheridan; Mark Pickering; Lisa Conboy; John J O'Connor; Paul N Moynagh; Desmond G Higgins; Ciaran M Regan; Keith J Murphy
Temporal change in gene expression in the rat dentate gyrus following passive avoidance learning.
Journal of neurochemistry 2007;101(4):1085-98.
2007: Sallyann L O'Brien; Ailís Fagan; Edward J P Fox; Robert C Millikan; Aedín C Culhane; Donal J Brennan; Amanda McCann; Shauna Hegarty; Siobhan Moyna; Michael J Duffy; Desmond G Higgins; Karin Jirström; Göran Landberg; William M Gallagher
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.
2007: Ian B Jeffery; Stephen F Madden; Paul A McGettigan; Guy Perrière; Aedín C Culhane; Desmond G Higgins
Integrating transcription factor binding site information with gene expression datasets.
Bioinformatics (Oxford, England) 2007;23(3):298-305.
2007: Iain M Wallace; Desmond G Higgins
Supervised multivariate analysis of sequence groups to identify specificity determining residues.
BMC bioinformatics 2007;8():135.
2006: Fabrice Armougom; Olivier Poirot; Sébastien Moretti; Desmond G Higgins; Phillip Bucher; Vladimir Keduas; Cédric Notredame
APDB: a web server to evaluate the accuracy of sequence alignments using structural information.
Bioinformatics (Oxford, England) 2006;22(19):2439-40.
2006: Gordon Blackshields; Iain M Wallace; Mark Larkin; Desmond G Higgins
Analysis and comparison of benchmarks for multiple sequence alignment.
In silico biology 2006;6(4):321-39.
2006: Ian B Jeffery; Desmond G Higgins; Aedín C Culhane
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data.
BMC bioinformatics 2006;7():359.
2006: Iain M Wallace; Orla O'Sullivan; Desmond G Higgins; Cédric Notredame
M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Nucleic acids research 2006;34(6):1692-9.
2005: Donal J Brennan; Sallyann L O'Brien; Ailís Fagan; Aedín C Culhane; Desmond G Higgins; Michael J Duffy; William M Gallagher
Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response.
Expert opinion on biological therapy 2005;5(8):1069-83.
2005: Desmond G Higgins; Gordon Blackshields; Iain M Wallace
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.
2005: Iain M Wallace; Gordon Blackshields; Desmond G Higgins
Multiple sequence alignments.
Current opinion in structural biology 2005;15(3):261-6.
2005: Aedín C Culhane; Jean Thioulouse; Guy Perrière; Desmond G Higgins
MADE4: an R package for multivariate analysis of gene expression data.
Bioinformatics (Oxford, England) 2005;21(11):2789-90.
2005: Iain M Wallace; Orla O'Sullivan; Desmond G Higgins
Evaluation of iterative alignment algorithms for multiple alignment.
Bioinformatics (Oxford, England) 2005;21(8):1408-14.
2005: Sinead Leahy; Desmond G Higgins; Gerald F Fitzgerald; Douwe van Sinderen
Getting better with bifidobacteria.
Journal of applied microbiology 2005;98(6):1303-15.
2004: Orla O'Sullivan; Karsten Suhre; Chantal Abergel; Desmond G Higgins; Cédric Notredame
3DCoffee: combining protein sequences and structures within multiple sequence alignments.
Journal of molecular biology 2004;340(2):385-95.
2004: Marie E Fahey; Walter Mills; Desmond G Higgins; Tom Moore
Maternally and paternally silenced imprinted genes differ in their intron content.
Comparative and functional genomics 2004;5(8):572-83.
2003: Aedín C Culhane; Guy Perrière; Desmond G Higgins
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis.
BMC bioinformatics 2003;4():59.
2003: Ramu Chenna; Hideaki Sugawara; Tadashi Koike; Rodrigo Lopez; Toby J Gibson; Desmond G Higgins; julie thompson
Multiple sequence alignment with the Clustal series of programs.
Nucleic acids research 2003;31(13):3497-500.
2002: Aedín C Culhane; Guy Perrière; Elizabeth C Considine; Thomas G Cotter; Desmond G Higgins
Between-group analysis of microarray data.
Bioinformatics (Oxford, England) 2002;18(12):1600-8.
2002: M E Fahey; T F Moore; Desmond G Higgins
Overlapping antisense transcription in the human genome.
Comparative and functional genomics 2002;3(3):244-53.
2000: Cédric Notredame; Desmond G Higgins; Jaap Heringa
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Journal of molecular biology 2000;302(1):205-17.
2000: Desmond G Higgins; W R Taylor
Multiple sequence alignment.
Methods in molecular biology (Clifton, N.J.) 2000;143():1-18.
2000: Desmond G Higgins
Amino acid-based phylogeny and alignment.
Advances in protein chemistry 2000;54():99-135.
1999: Paraic Kenny; E M Liston; Desmond G Higgins
Molecular evolution of immunoglobulin and fibronectin domains in titin and related muscle proteins.
Gene 1999;232(1):11-23.
1999: P Thébault; P Monestié; A McGrath; Desmond G Higgins
MIAH: automatic alignment of eukaryotic SSU rRNAs.
Bioinformatics (Oxford, England) 1999;15(4):341-2.
1998: A McGrath; Desmond G Higgins; Tommie V McCarthy
Sequence analysis of DNA randomly amplified from the Saccharomyces cerevisiae genome.
Molecular and cellular probes 1998;12(6):397-405.
1998: F Jeanmougin; julie thompson; M Gouy; Desmond G Higgins; Toby J Gibson
Multiple sequence alignment with Clustal X.
Trends in biochemical sciences 1998;23(10):403-5.
1998: Cédric Notredame; L Holm; Desmond G Higgins
COFFEE: an objective function for multiple sequence alignments.
Bioinformatics (Oxford, England) 1998;14(5):407-22.
1998: EA O'Brien; Desmond G Higgins
Empirical estimation of the reliability of ribosomal RNA alignments.
Bioinformatics (Oxford, England) 1998;14(10):830-8.
1998: EA O'Brien; Cédric Notredame; Desmond G Higgins
Optimization of ribosomal RNA profile alignments.
Bioinformatics (Oxford, England) 1998;14(4):332-41.
1997: julie thompson; Toby J Gibson; Frédéric Plewniak; F Jeanmougin; Desmond G Higgins
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
Nucleic acids research 1997;25(24):4876-82.
1997: Cédric Notredame; EA O'Brien; Desmond G Higgins
RAGA: RNA sequence alignment by genetic algorithm.
Nucleic acids research 1997;25(22):4570-80.
1996: Cédric Notredame; Desmond G Higgins
SAGA: sequence alignment by genetic algorithm.
Nucleic acids research 1996;24(8):1515-24.
1996: Desmond G Higgins; julie thompson; Toby J Gibson
Using CLUSTAL for multiple sequence alignments.
Methods in enzymology 1996;266():383-402.
1994: julie thompson; Desmond G Higgins; Toby J Gibson
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.
1994: Jose Castresana; M Lübben; Matti Saraste; Desmond G Higgins
Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen.
The EMBO journal 1994;13(11):2516-25.
1994: Desmond G Higgins; Siegfried Labeit; Mathias Gautel; Toby J Gibson
The evolution of titin and related giant muscle proteins.
Journal of molecular evolution 1994;38(4):395-404.
1994: julie thompson; Desmond G Higgins; Toby J Gibson
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.
1994: Desmond G Higgins
CLUSTAL V: multiple alignment of DNA and protein sequences.
Methods in molecular biology (Clifton, N.J.) 1994;25():307-18.
1993: C M Rice; Rainer Fuchs; Desmond G Higgins; P J Stoehr; G N Cameron
The EMBL data library.
Nucleic acids research 1993;21(13):2967-71.
1993: Toby J Gibson; Desmond G Higgins
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.
1992: D C Shields; Desmond G Higgins; Paul M Sharp
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.
1992: Desmond G Higgins; Rainer Fuchs; P J Stoehr; G N Cameron
The EMBL Data Library.
Nucleic acids research 1992;20 Suppl():2071-4.
1992: Desmond G Higgins; A J Bleasby; Rainer Fuchs
CLUSTAL V: improved software for multiple sequence alignment.
Computer applications in the biosciences : CABIOS 1992;8(2):189-91.
1992: Desmond G Higgins; P Stoehr
EMBLSCAN: fast approximate DNA database searches on compact disc.
Computer applications in the biosciences : CABIOS 1992;8(2):137-9.
1992: Desmond G Higgins
Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets.
Computer applications in the biosciences : CABIOS 1992;8(1):15-22.
1989: Desmond G Higgins; D J McConnell; Paul M Sharp
Malarial proteinase?
Nature 1989;340(6235):604.
1989: Desmond G Higgins; Paul M Sharp
Fast and sensitive multiple sequence alignments on a microcomputer.
Computer applications in the biosciences : CABIOS 1989;5(2):151-3.
1989: K M Devine; S T Hogan; Desmond G Higgins; D J McConnell
Replication and segregational stability of Bacillus plasmid pBAA1.
Journal of bacteriology 1989;171(2):1166-72.
1988: Desmond G Higgins; Paul M Sharp
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.
Gene 1988;73(1):237-44.
1988: D C Shields; Paul M Sharp; Desmond G Higgins; F Wright
"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons.
Molecular biology and evolution 1988;5(6):704-16.
1988: Paul M Sharp; E Cowe; Desmond G Higgins; D C Shields; Kenneth H Wolfe; F Wright
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.
1987: Desmond G Higgins; M Gouy
Interfacing similarity search software with the sequence retrieval system ACNUC.
Computer applications in the biosciences : CABIOS 1987;3(3):239-41.