QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction. - Sievers, Fabian; Higgins, Desmond G. (Bioinform., 2020)

Protein multiple sequence alignment benchmarking through secondary structure prediction. - Le, Quan; Sievers, Fabian; Higgins, Desmond G. (Bioinform., 2017)

Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments. - Fox, Gearoid; Sievers, Fabian; Higgins, Desmond G. (Bioinform., 2016)

ProViz - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. - Jehl, Peter; Manguy, Jean; Shields, Denis C.; Higgins, Desmond G.; Davey, Norman E. (Nucleic Acids Res., 2016)

Instability in progressive multiple sequence alignment algorithms. - Boyce, Kieran; Sievers, Fabian; Higgins, Desmond G. (Algorithms Mol. Biol., 2015)

OD-seq: outlier detection in multiple sequence alignments. - Jehl, Peter; Sievers, Fabian; Higgins, Desmond G. (BMC Bioinform., 2015)

Systematic exploration of guide-tree topology effects for small protein alignments. - Sievers, Fabian; Hughes, Graham M.; Higgins, Desmond G. (BMC Bioinform., 2014)

GWIPS-viz: development of a ribo-seq genome browser. - Michel, Audrey M.; Fox, Gearoid; Kiran, Anmol M.; Bo, Christof De; O'Connor, Patrick B. F.; Heaphy, Stephen M.; Mullan, James P. A.; Donohue, Claire A.; Higgins, Desmond G.; Baranov, Pavel V. (Nucleic Acids Res., 2014)

Making automated multiple alignments of very large numbers of protein sequences. - Sievers, Fabian; Dineen, David; Wilm, Andreas; Higgins, Desmond G. (Bioinform., 2013)

Sequence embedding for fast construction of guide trees for multiple sequence alignment. - Blackshields, Gordon; Sievers, Fabian; Shi, Weifeng; Wilm, Andreas; Higgins, Desmond G. (Algorithms Mol. Biol., 2010)

Detecting microRNA activity from gene expression data. - Madden, Stephen F.; Carpenter, Susan B.; Jeffery, Ian B.; Björkbacka, Harry; Fitzgerald, Katherine A.; O'Neill, Luke A.; Higgins, Desmond G. (BMC Bioinform., 2010)

Fast embedding methods for clustering tens of thousands of sequences. - Blackshields, Gordon; Larkin, Mark A.; Wallace, Iain M.; Wilm, Andreas; Higgins, Desmond G. (Comput. Biol. Chem., 2008)

Distinct Patterns in the Regulation and Evolution of Human Cancer Genes. - Furney, Simon J.; Madden, Stephen F.; Kisiel, Tomasz A.; Higgins, Desmond G.; López-Bigas, Núria (Silico Biol., 2008)

R-Coffee: a web server for accurately aligning noncoding RNA sequences. - Moretti, Sébastien; Wilm, Andreas; Higgins, Desmond G.; Xenarios, Ioannis; Notredame, Cédric (Nucleic Acids Res., 2008)

Integrating transcription factor binding site information with gene expression datasets. - Jeffery, Ian B.; Madden, Stephen F.; McGettigan, Paul A.; Perrière, Guy; Culhane, Aedín C.; Higgins, Desmond G. (Bioinform., 2007)

Clustal W and Clustal X version 2.0. - Larkin, Mark A.; Blackshields, Gordon; Brown, Nigel P.; Chenna, R.; McGettigan, Paul A.; McWilliam, Hamish; Valentin, Franck; Wallace, Iain M.; Wilm, Andreas; Lopez, Rodrigo; Thompson, Julie Dawn; Gibson, Toby J.; et al. (Bioinform., 2007)

Supervised multivariate analysis of sequence groups to identify specificity determining residues. - Wallace, Iain M.; Higgins, Desmond G. (BMC Bioinform., 2007)

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. - Moretti, Sébastien; Armougom, Fabrice; Wallace, Iain M.; Higgins, Desmond G.; Jongeneel, C. Victor; Notredame, Cédric (Nucleic Acids Res., 2007)

APDB: a web server to evaluate the accuracy of sequence alignments using structural information. - Armougom, Fabrice; Poirot, Olivier; Moretti, Sébastien; Higgins, Desmond G.; Bucher, Phillip; Keduas, Vladimir; Notredame, Cédric (Bioinform., 2006)

Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. - Jeffery, Ian B.; Higgins, Desmond G.; Culhane, Aedín C. (BMC Bioinform., 2006)

Analysis and Comparison of Benchmarks for Multiple Sequence Alignment. - Blackshields, Gordon; Wallace, Iain M.; Larkin, Mark A.; Higgins, Desmond G. (Silico Biol., 2006)

Evaluation of iterative alignment algorithms for multiple alignment. - Wallace, Iain M.; O'Sullivan, Orla; Higgins, Desmond G. (Bioinform., 2005)

MADE4: an R package for multivariate analysis of gene expression data. - Culhane, Aedín C.; Thioulouse, Jean; Perrière, Guy; Higgins, Desmond G. (Bioinform., 2005)

Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. - Culhane, Aedín C.; Perrière, Guy; Higgins, Desmond G. (BMC Bioinform., 2003)

Multiple sequence alignment with the Clustal series of programs. - Ramu, Chenna; Sugawara, Hideaki; Koike, Tadashi; Lopez, Rodrigo; Gibson, Toby J.; Higgins, Desmond G.; Thompson, Julie Dawn (Nucleic Acids Res., 2003)

A SAT-Based Approach to Multiple Sequence Alignment. - Prestwich, Steven D.; Higgins, Desmond G.; O'Sullivan, Orla (2003)

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. - O'Sullivan, Orla; Zehnder, Mark; Higgins, Desmond G.; Bucher, Philipp; Grosdidier, Aurélien; Notredame, Cédric (2003)

Between-group analysis of microarray data. - Culhane, Aedín C.; Perrière, Guy; Considine, Elizabeth C.; Cotter, Thomas G.; Higgins, Desmond G. (Bioinform., 2002)

MIAH: automatic alignment of eukaryotic SSU rRNAs. - Thébault, Patricia; Monestie, Pierre; McGrath, Annette; Higgins, Desmond G. (Bioinform., 1999)

Optimization of ribosomal RNA profile alignments. - O'Brien, Emmet A.; Notredame, Cédric; Higgins, Desmond G. (Bioinform., 1998)

COFFEE: an objective function for multiple sequence alignments. - Notredame, Cédric; Holm, Liisa; Higgins, Desmond G. (Bioinform., 1998)

Empirical estimation of the reliability of ribosomal RNA alignments. - O'Brien, Emmet A.; Higgins, Desmond G. (Bioinform., 1998)

Improved sensitivity of profile searches through the use of sequence weights and gap excision. - Thompson, Julie Dawn; Higgins, Desmond G.; Gibson, Toby J. (Comput. Appl. Biosci., 1994)

The EMBL data library. - Rice, Catherine M.; Fuchs, Rainer; Higgins, Desmond G.; Stoehr, Peter; Cameron, Graham (Nucleic Acids Res., 1993)

Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets. - Higgins, Desmond G. (Comput. Appl. Biosci., 1992)

EMBLSCAN: fast approximate DNA database searches on compact disc. - Higgins, Desmond G.; Stoehr, Peter (Comput. Appl. Biosci., 1992)

CLUSTAL V: improved software for multiple sequence alignment. - Higgins, Desmond G.; Bleasby, Alan J.; Fuchs, Rainer (Comput. Appl. Biosci., 1992)

GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content. - Shields, Denis C.; Higgins, Desmond G.; Sharp, P. M. (Comput. Appl. Biosci., 1992)

OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. - Heringa, Jaap; Sommerfeldt, Hubert; Higgins, Desmond G.; Argos, Patrick (Comput. Appl. Biosci., 1992)

Fast and sensitive multiple sequence alignments on a microcomputer. - Higgins, Desmond G.; Sharp, P. M. (Comput. Appl. Biosci., 1989)

Interfacing similarity search software with the sequence retrieval system ACNUC. - Higgins, Desmond G.; Gouy, Manolo (Comput. Appl. Biosci., 1987)