Publications for the Higgins Lab, UCD


Fabian Sievers, Desmond G Higgins
The Clustal Omega Multiple Alignment Package
Multiple Sequence Alignment, pp3-16, Methods in Molecular Biology, vol 2231, Humana, New York


Fabian Sievers, Geoffrey J Barton, Desmond G Higgins
Multiple Sequence Alignment
Bioinformatics 227, pp 227-250, AD Baxevanis, GD Bader, DS Wishart (Eds)
ISBN: 978-1-119-33558-0


Fabian Sievers, Desmond G Higgins
QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction
Bioinformatics, btz552, July 2019, doi: 10.1093/bioinformatics/btz552


Fabian Sievers, Desmond G Higgins
Clustal Omega for making accurate alignments of many protein sequences
Tools for Protein Science, Volume 27, Issue 1, January 2018, Pages 135-145 . doi: 10.1002/pro.3290


Quan Le, Fabian Sievers, Desmond G Higgins
Protein Multiple Sequence Alignment Benchmarking through Secondary Structure Prediction
Bioinformatics, 2017 Jan 16. pii: btw840. doi: 10.1093/bioinformatics/btw840


Peter Jehl, J Manguy, Dennis C Shields, Desmond G Higgins, Norman E Davey
ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences
Nucleic Acids Res, Vol44, W1 ; 2016, doi: 10.1093/nar/gkw265


Gearoid Fox, Fabian Sievers, Desmond G Higgins
Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments
Bioinformatics ; 2015, doi: 10.1093/bioinformatics/btv592

Kieran Boyce, Fabian Sievers, Desmond G Higgins
Instability in progressive multiple sequence alignment algorithms
Algorithms for Molecular Biology ; 2015, 10:26, DOI: 10.1186/s13015-015-0057-1
Supplementary Material

UCD Research Repository

Peter Jehl, Fabian Sievers, Desmond G Higgins
OD-seq: Outlier detection in multiple sequence alignments
BMC Bioinformatics ; August 2015, 16:269, DOI: 10.1186/s12859-015-0702-1
Supplementary Material

UCD Research Repository

Kieran Boyce, Fabian Sievers, Desmond G Higgins
Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments
PNAS 2015 ; January 6, 2015, 10.1073/pnas.1419351112


Fabian Sievers, Desmond G Higgins.
Clustal Omega.
Current Protocols in Bioinformatics, December 2014, 48:1.25.1-1.25.33.
Supplementary Material

Fabian Sievers, Graham M Hughes, Desmond G Higgins
Systematic Exploration of Guide-Tree Topology Effects for Small Protein Alignments
BMC Bioinformatics, October 2014, 15:338 , doi:10.1186/1471-2105-15-338
Benchmark data and driver scripts

small trees

Kieran Boyce, Fabian Sievers, Desmond G Higgins
Simple chained guide trees give high-quality protein multiple sequence alignments
PNAS 2014 ; July 9, 2014, doi:10.1073/pnas.1405628111
Benchmark data and driver scripts

Fabian Sievers, Desmond G Higgins
Clustal Omega, accurate alignment of very large numbers of sequences
Methods in Molecular Biology, Multiple Sequence Alignments Methods II, pp 105-116, DOI 10.1007/978-1-62703-646-7_6

David J Duffy, Aleksandar Krstic, Thomas Schwarzl, Desmond G Higgins, Walter Kolch
GSK3 Inhibitors Regulate MYCN mRNA Levels and Reduce Neuroblastoma Cell Viability through Multiple Mechanisms, Including p53 and Wnt Signaling
doi: 10.1158/1535-7163.MCT-13-0560-T Mol Cancer Ther February 2014 13; 454

Graham M Hughes, Emma C Teeling, Desmond G Higgins
Loss of olfactory receptor function in hominin evolution
PLoS ONE 9(1): e84714. doi:10.1371/journal.pone.0084714

Audrey M Michel, Gearoid Fox, Anmol M Kiran, Christof De Bo, Patrick BF O’Connor, Stephen M Heaphy, James PA Mullan, Claire A Donohue, Desmond G Higgins, Pavel V Baranov
GWIPS-viz: development of a ribo-seq genome browser
Nucl. Acids Res. (1 January 2014) 42 (D1): D859-D864. doi: 10.1093/nar/gkt1035


Sievers F, Dineen D, Wilm A, Higgins DG.
Making automated multiple alignments of very large numbers of protein sequences.
Bioinformatics 29 (8), 989-995. doi: 10.1093/bioinformatics/btt093.
Benchmark Scripts

Weifeng Shi, Zhong Zhang, Cheng Ling, Weimin Zheng, Chaodong Zhu, Michael J Carr, Desmond G Higgins
Hepatitis B virus subgenotyping: history, effects of recombination, misclassifications, and corrections
Infection, Genetics and Evolution 16, p355-361

Graham M Hughes, Li Gang, William J Murphy, Desmond G Higgins, Emma C Teeling
Using Illumina Next Generation Sequencing technologies to sequence multigene families in de novo species
Molecular Ecology Resources, Volume 13, Issue 3, pages 510–521, May 2013, DOI: 10.1111/1755-0998.12087


Jun Yin, Lisa Shine, Francis Raycroft, Sudhakar Deeti, Alison Reynolds, Kristin M Ackerman, Antonino Glaviano, Sean O'Farrell, Olivia O'Leary, Claire Kilty, Ciaran Kennedy, Sarah McLoughlin, Megan Rice, Eileen Russell, Desmond G Higgins, David R Hyde, Breandan N Kennedy
Inhibition of the Pim1 oncogene results in diminished visual function
PLoS ONE 7(12): e52177. doi:10.1371/journal.pone.0052177

DP O'Connor, L Mulrane, DJ Brennan, S Madden, G Gremel, SF McGee, S McNally, FM Martin, JP Crown, K Jirstrom, DG Higgins, W Gallagher
miR-187 is an independent prognostic factor in lymph node-positive breast cancer patients.
Cancer Research: December 15, 2012; Volume 72, Issue 24, Supplement 3 doi: 10.1158/0008-5472.SABCS12-P4-09-06

Laoighse Mulrane, Stephen F Madden, Donal J Brennan, Gabriela Gremel, Sharon F McGee, Sara McNally, Finian Martin, John P Crown, Karin Jirström, Desmond G Higgins, William M Gallagher, Darran P O'Connor
miR-187 is an independent prognostic factor in breast cancer and confers increased invasive potential in vitro
Clin Cancer Res December 15, 2012 18; 6702 doi: 10.1158/1078-0432.CCR-12-1420

Weifeng Shi, Chaodong Zhu, Weimin Zheng, Wei Zheng, Cheng Ling, Michael J Carr, Desmond G Higgins, Zhong Zhang
Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype
PLoS ONE 7(10): e47271. doi:10.1371/journal.pone.0047271

Weifeng Shi, Chaodong Zhu, Wei Zheng, Michael J Carr, Desmond G Higgins, Zhong Zhang
Subgenotype reclassification of genotype B hepatitis B virus
BMC Gastroenterology 2012, 12:116 doi:10.1186/1471-230X-12-116

Weifeng Shi, Ines T Freitas, Chaodong Zhu, Wei Zheng, William W Hall, Desmond G Higgins
Recombination in hepatitis C virus: identification of four novel naturally occurring inter-subtype recombinants
PLoS ONE 7(7): e41997. doi:10.1371/journal.pone.0041997

Weifeng Shi, Michael J Carr, Linda Dunford, Chaodong Zhu, William W Hall, Desmond G Higgins
Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis
Virology 427(1), p51-59


Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Mol Syst Biol 7. 2011 Oct 11. doi: 10.1038/msb.2011.75.
HomFam Benchmark

UCD Research Repository

Alessandro Guida, Claudia Lindstädt, Sarah L Maguire, Chen Ding, Desmond G Higgins, Nicola J Corton, Matthew Berriman, 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 doi:10.1186/1471-2164-12-628

Ding C, Yin J, Tovar EM, Fitzpatrick DA, Higgins DG, Thiele DJ.
The copper regulon of the human fungal pathogen Cryptococcus neoformans H99.
Mol Microbiol. 2011 Aug 8. doi: 10.1111/j.1365-2958.2011.07794.x. [Epub ahead of print]

Motherway MO, Zomer A, Leahy SC, Reunanen J, Bottacini F, Claesson MJ, O'Brien F, Flynn K, Casey PG, Munoz JA, Kearney B, Houston AM, O'Mahony C, Higgins DG, Shanahan F, Palva A, de Vos WM, Fitzgerald GF, Ventura M, O'Toole PW, van Sinderen D.
Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.
Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11217-22. Epub 2011 Jun 20.

Cederlund ML, Vendrell V, Morrissey ME, Yin J, Gaora PO, Smyth VA, Higgins DG, Kennedy BN.
mab21l2 transgenics reveal novel expression patterns of mab21l1 and mab21l2, and conserved promoter regulation without sequence conservation.
Dev Dyn. 2011 Apr;240(4):745-54. doi: 10.1002/dvdy.22573. Epub 2011 Feb 28.


Shi W, Lei F, Zhu C, Sievers F, Higgins DG.
A complete analysis of HA and NA genes of influenza A viruses.
PLoS One. 2010 Dec 29;5(12):e14454.
UCD Research Repository

Dineen DG, Schroder M, Higgins DG, Cunningham P.
Ensemble approach combining multiple methods improves human transcription start site prediction.
BMC Genomics. 2010 Nov 30;11:677.

Synnott JM, Guida A, Mulhern-Haughey S, Higgins DG, Butler G.
Regulation of the hypoxic response in Candida albicans.
Eukaryot Cell. 2010 Sep 24.

Madden SF, Carpenter SB, Jeffery IB, Björkbacka H, Fitzgerald KA, O'Neill LA, Higgins DG.
Detecting microRNA activity from gene expression data.
BMC Bioinformatics. 2010 May 18;11:257.

Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG.
Sequence embedding for fast construction of guide trees for multiple sequence alignment.
Algorithms Mol Biol. 2010 May 14;5:21.
UCD Research Repository

Murphy KJ, Ter Horst JP, Cassidy AW, DeSouza IE, Morgunova M, Li C, Connole LM, O'Sullivan NC, Loscher JS, Brady AT, Rombach N, Connellan J, McGettigan PA, Scully D, Fedriani R, Lukasz B, Moran MP, McCabe OM, Wantuch CM, Hughes ZA, Mulvany SK, Higgins DG, Pangalos MN, Marquis KL, O'Connor WT, Ring RH, von Schack D, Regan CM.
Temporal dysregulation of cortical gene expression in the isolation reared Wistar rat.
J Neurochem. 2010 May;113(3):601-14.

Yin J, McLoughlin S, Jeffery IB, Glaviano A, Kennedy B, Higgins DG.
Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data.
BMC Genomics. 2010 Jan 20;11:50.


Bray I, Bryan K, Prenter S, Buckley PG, Foley NH, Murphy DM, Alcock L, Mestdagh P, Vandesompele J, Speleman F, London WB, McGrady PW, Higgins DG, O'Meara A, O'Sullivan M, Stallings RL.
Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.
PLoS One. 2009 Nov 16;4(11):e7850.

Dineen DG, Wilm A, Cunningham P, Higgins DG.
High DNA melting temperature predicts transcription start site location in human and mouse.
Nucleic Acids Res. 2009 Oct 9.

Smith MJ, Culhane AC, Donovan M, Coffey JC, Barry BD, Kelly MA, Higgins DG, Wang JH, Kirwan WO, Cotter TG, Redmond HP.
Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification.
Br J Cancer. 2009 May 5;100(9):1452-64.

Correlation between biofilm formation and the hypoxic response in Candida parapsilosis.
Rossignol T, Ding C, Guida A, d'Enfert C, Higgins DG, Butler G.
Eukaryot Cell. 2009 Apr;8(4):550-9. Epub 2009 Jan 16.


Leonard MO, Howell K, Madden SF, Costello CM, Higgins DG, Taylor CT, McLoughlin P.
Hypoxia selectively activates the CREB family of transcription factors in the in vivo lung.
Am J Respir Crit Care Med. 2008 Nov 1;178(9):977-83. Epub 2008 Aug 8.

Furney SJ, Madden SF, Kisiel TA, Higgins DG, Lopez-Bigas N.
Distinct patterns in the regulation and evolution of human cancer genes.
In Silico Biol. 2008;8(1):33-46.

Blackshields G, Larkin M, Wallace IM, Wilm A, Higgins DG.
Fast embedding methods for clustering tens of thousands of sequences.
Comput Biol Chem. 2008 Aug; 32(4):282-6

Brennan DJ, Rexhepaj E, O'Brien SL, McSherry E, O'Connor DP, Fagan A, Culhane AC, Higgins DG, Jirstrom K, Millikan RC, Landberg G, Duffy MJ, Hewitt SM, Gallagher WM.
Altered Cytoplasmic-to-Nuclear Ratio of Survivin Is a Prognostic Indicator in Breast Cancer
Clin Cancer Res. 2008 May 1;14(9):2681-9.

Moretti S, Wilm A, Higgins DG, Xenarios I, Notredame C.
R-Coffee: a web server for accurately aligning noncoding RNA sequences
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W10-3

Wilm A, Higgins DG, Notredame C
R-Coffee: a method for multiple alignment of non-coding RNA
Nucleic Acids Res. 2008 May;36(9):e52.

Gramolini AO, Kislinger T, Alikhani-Koopaei R, Fong V, Thompson NJ, Isserlin R, Sharma P, Oudit GY, Trivieri MG, Fagan A, Kannan A, Higgins DG, Huedig H, Hess G, Arab S, Seidman JG, Seidman CE, Frey B, Perry M, Backx PH, Liu PP, MacLennan DH, Emili A.
Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses
Mol Cell Proteomics. 2008 Mar;7(3):519-33

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. 2008 Jan;1782(1):10-21


O'Sullivan NC, McGettigan PA, Sheridan GK, Pickering M, Conboy L, O'Connor JJ, Moynagh PN, Higgins DG, Regan CM, Murphy KJ.
Temporal change in gene expression in the rat dentate gyrus following passive avoidance learning
J Neurochem. 2007 Feb 7; PMID: 17298388

Walsh MC, Brennan L, Pujos-Guillot E, Sébédio J-L, Augustin S, Fagan A, Higgins, DG, Gibney, MJ
Influence of acute phytochemical intake on human urinary metabolomic profiles
Am. Journal of Clinical Nutrition, 2007 Dec;86(6):1687-93

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.
CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer
Int J Cancer. Jan 2007,


Jeffery I. B., Madden S. F., McGettigan P. A., Perriere G., Culhane A. C., Higgins D. G.
Integrating transcription factor binding site information with gene expression datasets
Bioinformatics. Nov 24

Armougom F., Poirot O., Moretti S., Higgins D.G., Bucher P., Keduas V.,Notredame C.
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.
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.
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.
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.
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.
Structural and functional properties of genes involved in human cancer
BMC Genomics. 2006 Jan 11;7:3.


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.
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.
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.
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.
Application of DNA Microarray Technology in Determining Breast Cancer Prognosis and Therapeutic Response
Expert Opinion on Biological Therapy Aug;5(8):1069-83

Leahy, S. C., Higgins, D. G., Fitzgerald, G. F. and van Sinderen, D.
Getting better with bifidobacteria
J. Appl. Microbiol.98(6):2303-1315.

Culhane, A. C., Thioulouse, J., Perriere, G. and Higgins, D. G.
MADE4: an R package for multivariate analysis of gene expression data

Wallace, I. M., Blackshields, G. and Higgins, D. G.
Multiple sequence alignments. Curr. Opin. Struct. Biol. Jun;15(3):261-6.
Curr. Opin. Struct. Biol. Jun;15(3):261-6.

Fahey, M. E., Mills, W., Higgins, D. G. and Moore, T. F.
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.
Evaluation of iterative alignment algorithms for multiple alignment
Bioinformatics 21:1408


Kapushesky, M., Kemmeren, P., Culhane, A. C., Durinck, S., Ihmels, J., Korner, C., Kull, M., Torrente, A., Sarkans, U., Vilo, J. and Brazma, A.
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.
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.
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.
3DCoffee: combining protein sequences and structures within multiple sequence alignments
J. Mol. Biol. 340:385-395


Prestwich, S., Higgins, D. and O'Sullivan, O.
Approach to multiple sequence alignment
Lect. Notes Comput. Sci. 2833:940-944
Culhane, A. C., Perriere, G. and Higgins, D. G.
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.
Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497-3500
Nucleic Acids Res. 31:3497-3500.

O'Sullivan, O., Zehnder, M., Higgins, D., Bucher, P., Grosdidier, A. and Notredame, C.
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments
Bioinformatics 19 Suppl 1:I215-I221

earlier publications

Culhane, A. C., Perriere, G., Considine, E. C., Cotter, T. G. and Higgins, D. G.
Between-group analysis of microarray data
Bioinformatics 18:1600-1608

Fahey, M. E., Moore, T. F. and Higgins, D. G.
Overlapping antisense transcription in the human genome
Comp. Functional Genomics 3:244-253

Notredame, C., Higgins, D. G. and Heringa, J.
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.
Multiple sequence alignment
Methods Mol. Biol. 143:1-18
Higgins, D. G.
Amino acid-based phylogeny and alignment.
Adv. Protein Chem. 54:99-135

Kenny, P. A., Liston, E. M. and Higgins, D. G.
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.
MIAH: automatic alignment of eukaryotic SSU rRNAs.
Bioinformatics 15:341-342.
O'Brien, E. A. and Higgins, D. G.
Empirical estimation of the reliability of ribosomal RNA alignments
Bioinformatics 14:830-838
Notredame, C., Holm, L. and Higgins, D. G.
COFFEE: an objective function for multiple sequence alignments.
Bioinformatics. 14:407-422.
McGrath, A., Higgins, D. G. and McCarthy, T. V.
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.
Optimization of ribosomal RNA profile alignments.
Bioinformatics 14:332-341
Jeanmougin, F., Thompson, J. D., Gouy, M., Higgins, D. G. and Gibson, T. J.
Multiple sequence alignment with Clustal X.
Trends Biochem Sci. 23(10):403-405.
Notredame, C., O'Brien, E. A. and Higgins, D. G.
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.
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.
SAGA: sequence alignment by genetic algorithm
Nucleic Acids Res. 24:1515-1524.
Higgins, D. G., Thompson, J. D. and Gibson, T. J.
Using CLUSTAL for multiple sequence alignments
Methods Enzymol. 266:383-402.
Jonassen, I., Collins, J. F. and Higgins, D. G.
Finding flexible patterns in unaligned protein sequences
Protein Sci. 4(8):1587-1595
Thompson, J. D., Higgins, D. G. and 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 Res. 22:4673-4680
Castresana, J., Lubben, M., Saraste, M. and Higgins, D. G.
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.
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.
Improved sensitivity of profile searches through the use of sequence weights and gap excision
Comput. Appl. Biosci. 10:19-29
Higgins, D. G.
CLUSTAL V: multiple alignment of DNA and protein sequences
Methods Mol. Biol. 25:307-18
Graur, D. and Higgins, D. G.
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.
The EMBL data library
Nucleic Acids Res. 21:2967-2971
Waters, A. P., Higgins, D. G. and McCutchan, T. F.
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.
The phylogeny of malaria - a useful study
The phylogeny of malaria - a useful study
Higgins, D. G., Bleasby, A. J. and Fuchs, R.
CLUSTAL V: improved software for multiple sequence alignment
Comput. Appl. Biosci. 8:189-191
Higgins, D. G. and Stoehr, P.
EMBLSCAN: fast approximate DNA database searches on compact disc
Comput. Appl. Biosci. 8:137-139
Higgins, D. G.
Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets
Comput. Appl. Biosci. 1992 Feb;8(1):15-22
Heringa, J., Sommerfeldt, H., Higgins, D. and Argos, P.
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.
The EMBL Data Library
Nucleic Acids Res. 20 Suppl:2071-2074
Shields, D. C., Higgins, D. G. and Sharp, P. M.
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.
Pelandakis, M., Higgins, D. G., and Solignac, M.
Genetica 84(2):87-94
Powell, R., Higgins, D. G., and Wolff, J.
The salmon gene encoding apolipoprotein-AI - cDNA sequence, tissue expression and evolution
Gene 104(2):155-161
Pelandakis, M., Higgins, D. G., and Solignac, M.
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.
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.
Coelacanths relationships
Nature 353:218-219
Waters, A. P., Higgins, D. G., and McCutchan, T. F.
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.
Multiple-sclerosis and molecular mimicry
Neuropath. Appl. Neuro. 16(2):179-180
Higgins, D. G. and Sharp, P. M.
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
Malarial proteinase
Nature 340:604.
Devine, K. M., Hogan ST, Higgins DG, McConnell DJ
Replication and segregational stability of Bacillus plasmid pBAA1
J. Bacteriol. 171:1166-1172
Higgins, D. G. and Sharp, P. M.
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.
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.
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.
Interfacing similarity search software with the sequence retrieval system ACNUC.
Comput. Appl. Biosci. 3:239-241.