Professor Des Higgins

Research

Professor Desmond Gerard Higgins B.A.(Mod), PhD.

Contact Details

Title	Professor of Bioinformatics
Address	School of Medicine & Medical Science Conway Institute Belfield Dublin 4
Telephone:	Ext. 6833
Email:	ei.dcu@sniggih.sed

Biography:

Research Interests

Research in my laboratory centres on developing new bioinformatics and statistical tools for evolutionary biologists. The laboratory collaborates on the widely used Clustal and T-Coffee programs for multiple sequence alignment, researches the use of multivariate statistical methods for analysis of microarray data sets and addresses molecular evolutionary questions using bioinformatics approaches: for example, the evolution of promoters, of introns and of noncoding RNA genes.

Research Projects

Sponsor : Science Foundation Ireland (SFI)
Title : Clustal Omega and the future of multiple sequence alignment
Start Date / End Date : 01-JUL-12 / 01-JUL-17

Sponsor : University College Dublin (UCD)
Title : Data mining of miRNA expression from retinal gene expression microarray
Start Date / End Date : 17-MAY-10 / 16-NOV-11

Sponsor : Science Foundation Ireland (SFI)
Title : Multiple Alignment Methods for the Post Genome Era.
Start Date / End Date : 01-JUL-08 / 30-JUN-12

Sponsor : Les Laboratoires Servier, France
Title : PPAR Modulators and their role in therapeutic diabetes
Start Date / End Date : 01-SEP-07 / 31-AUG-09

Sponsor : Health Research Board (HRB)
Title : Identification and functional interrogation of Gene Regulatory Pathways in Breast Cancer Progression
Start Date / End Date : 01-OCT-07 / 30-SEP-10

Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET) Title : David Dineen IRCSET Start Date / End Date : 01-OCT-06 / 30-SEP-09
Sponsor : Wellcome Trust Sanger Institute Title : Setting up an orthologue database for nematode genomes Start Date / End Date : 01-OCT-04 / 30-SEP-05
Sponsor : Health Research Board (HRB) Title : Mining the human genome for micro-RNAs Start Date / End Date : 01-OCT-04 / 30-SEP-07
Sponsor : Science Foundation Ireland (SFI) Title : Multiple alignment method for the Genome ERA Start Date / End Date : 01-DEC-03 / 31-MAY-09
Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET) Title : Bioinformatics for the integration of gene expression and proteomics data in cancer Start Date / End Date : 01-OCT-03 / 30-SEP-06
Sponsor : Health Research Board (HRB) Title : Computer - aided cancer identification from gene expression profile data Start Date / End Date : 01-OCT-03 / 30-SEP-05
Sponsor : Health Research Board (HRB) Title : Application of multivariate methods to the analysis of a compendium of gene expression profiles of Leukaemia Start Date / End Date : 01-OCT-06 / 30-SEP-09
Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET) Title : Bioinformatic Analysis of MIRNA data from disease data set Start Date / End Date : 01-OCT-05 / 30-SEP-08
Hide

Show All

Book Chapters

Sharp, P.M., D.G. Higgins, D.C. Shields, and K.M. Devine; (1990) 'Protein-coding genes: DNA sequence database and codon usage' In: Harwood, C.R. & Cutting, S.M (eds). Molecular Biological Methods for Bacillus. *: John Wiley and Sons. [Details]

Sharp, P.M., D.G. Higgins, D.C. Shields, K.M. Devine, and J.A. Hoch; (1990) 'Bacillus subtilis gene sequences' In: Zukowski M.M., Ganesan, A.T. & Hoch, J.A (eds). Genetics and Biotechnology of Bacilli, Vol. III. San Diego: Academic Press. [Details]

Peer Reviewed Journals

Shi W, Zhu C, Zheng W, Carr MJ, Higgins DG, Zhang Z (2012) 'Subgenotype reclassification of genotype B hepatitis B virus'. BMC gastroenterology, 12 (1). [DOI] [Details]

Shi W, Freitas IT, Zhu C, Zheng W, Hall WW, Higgins DG (2012) 'Recombination in hepatitis C virus: identification of four novel naturally occurring inter-subtype recombinants'. PLoS ONE, 7 (7). [DOI] [Details]

Mulrane L, Madden SF, Brennan DJ, Gremel G, McGee SF, McNally S, Martin F, Crown JP, Jirstrom K, Higgins DG, Gallagher WM, O'Connor DP (2012) '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, . [DOI] [Details]

Shi W, Carr MJ, Dunford L, Zhu C, Hall WW, Higgins DG (2012) 'Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis'. Virology, 427 (1):51-59. [DOI] [Details]

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.; (2011) 'Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega'. Molecular systems biology, 7 . [Details]

Motherway, MO,Zomer, A,Leahy, SC,Reunanen, J,Bottacini, F,Claesson, MJ,O'Brien, F,Flynn, K,Casey, PG,Munoz, JAM,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; (2011) '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, 108 :11217-11222. [DOI] [Details]
Ding, C,Yin, J,Tovar, EMM,Fitzpatrick, DA,Higgins, DG,Thiele, DJ; (2011) 'The copper regulon of the human fungal pathogen Cryptococcus neoformans H99'. Molecular microbiology, 81 :1560-1576. [DOI] [Details]
Guida A, Lindstaedt C, Maguire SL, Ding C, Higgins DG, Corton NJ, Berriman M, Butler G; (2011) 'Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis'. BMC Genomics, 12 . [Details]
Murphy KJ, ter Horst JPF, Cassidy AW, DeSouza IEJ, 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, William T. O'Connor WT, Ring RH, von Schack D, Regan CM; (2010) 'Temporal dysregulation of cortical gene expression in the isolation reared Wistar rat'. Journal of neurochemistry, 113 :601-614. [Details]
Higgins DG, Yin J, McLoughlin S, Jeffery IB, Glaviano A, Kennedy B, ; (2010) 'Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data'. BMC Genomics, 11 . [DOI] [Details]
Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG.; (2010) 'Sequence embedding for fast construction of guide trees for multiple sequence alignment'. 5 . [Details]
Shi W, Lei F, Zhu C, Sievers F, Higgins DG; (2010) 'A complete analysis of HA and NA genes of influenza A viruses'. PLoS ONE, 5 (12). [DOI] [Details]
Dineen, DG,Schroder, M,Higgins, DG,Cunningham, P; (2010) 'Ensemble approach combining multiple methods improves human transcription start site prediction'. BMC Genomics, 11 . [DOI] [Details]
Synnott, JM,Guida, A,Mulhern-Haughey, S,Higgins, DG,Butler, G; (2010) 'Regulation of the Hypoxic Response in Candida albicans'. Eukaryotic Cell, 9 :1734-1746. [DOI] [Details]
Rossignol, T,Ding, C,Guida, A,d'Enfert, C,Higgins, DG,Butler, G; (2009) 'Correlation between Biofilm Formation and the Hypoxic Response in Candida parapsilosis'. Eukaryotic Cell, 8 :550-559. [DOI] [Details]
Smith, MJ,Culhane, AC,Donovan, M,Coffey, JC,Barry, BD,Kelly, MA,Higgins, DG,Wang, JH,Kirwan, WO,Cotter, TG,Redmond, HP; (2009) 'Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification'. Cancer, 100 :1452-1464. [DOI] [Details]
Murphy, DM,Buckley, PG,Bryan, K,Das, S,Alcock, L,Foley, NH,Prenter, S,Bray, I,Watters, KM,Higgins, D,Stallings, RL; (2009) 'Global MYCN Transcription Factor Binding Analysis in Neuroblastoma Reveals Association with Distinct E-Box Motifs and Regions of DNA Hypermethylation'. PLoS ONE, 4 . [DOI] [Details]
Dineen, DG,Wilm, A,Cunningham, P,Higgins, DG; (2009) 'High DNA melting temperature predicts transcription start site location in human and mouse'. Nucleic Acids Research, 37 :7360-7367. [DOI] [Details]
Blackshields, G., Larkin, M., Wallace, I. M., Wilm, A., Higgins, D. G., ; (2008) 'Fast embedding methods for clustering tens of thousands of sequences'. Computational Biology and Chemistry, 32 (4):282-286. [Details]
Leonard MO, Howell K, Madden SF, Costello CM, Higgins DG, Taylor CT, McLoughlin P; (2008) 'Hypoxia selectively activates the CREB family of transcription factors in the in vivo lung'. American Journal of Respiratory and Critical Care Medicine, . [Details]
Walsh DW, Roxburgh SA, Gettigan P, Berthier CC, Higgins D, Kretzler M, Cohen CD, Mezzano S, Brazil DP and Martin F; (2008) 'Co-regulation of Gremlin and Notch signalling in diabetic nephropathy'. Biochimica Et Biophysica Acta, 1782 (NA):10-12. [DOI] [Details]
Blackshields, G,Larkin, M,Wallace, IM,Wilm, A,Higgins, DG; (2008) 'Fast embedding methods for clustering tens of thousands of sequences'. Computational Biology and Chemistry, 32 :282-286. [DOI] [Details]
Wilm, A,Higgins, DG,Notredame, C; (2008) 'R-Coffee: a method for multiple alignment of non-coding RNA'. Nucleic Acids Research, 36 . [DOI] [Details]
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; (2008) 'Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses'. Proteomics, 7 :519-533. [DOI] [Details]
Gramolini, A. O., Kislinger, T., Alikhani-Koopaei, R., Fong, V., Thompson, N. J., Isserlin, R., Sharma, P., Oudit, G. Y., Trivieri, M. G., Fagan, A., Kannan, A., Higgins, D. G., Huedig, H., Hess, G., Arab, S., Seidman, J. G., Seidman, C. E., Frey, B., Perry, M., Backx, P. H., Liu, P. P., MacLennan, D. H., Emili, A., ; (2008) 'Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses'. Molecular & Cellular Proteomics, 7 (3):519-533. [Details]
Brennan, D. J., Rexhepaj, E., O'Brien, S. L., McSherry, E., O'Connor, D. P., Fagan, A., Culhane, A. C., Higgins, D. G., Jirstrom, K., Millikan, R. C., Landberg, G., Duffy, M. J., Hewitt, S. M., Gallaghe, W. M., ; (2008) 'Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer'. Clinical Cancer Research, 14 (9):2681-2689. [Details]
O'Brien SL, Fagan A, Fox EJ, Millikan RC, Culhane AC, Brennan DJ, McCann AH,; (2007) 'CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer'. International Journal of Cancer, 120 (7):1434-1443. [Details]
Gibney MJ, Walsh MC, Brennan L, Pujos-Guillot E, SÃ©bÃ©dio JL, Scalbert A, Fagan A, Higgins DG, ; (2007) 'Influence of acute phytochemical intake on human urinary metabolomic profiles'. American Journal of Clinical Nutrition, 6 (NA):1687-1693. [Details]
Fagan A, Culhane AC, Higgins DG.; (2007) 'A multivariate analysis approach to the integration of proteomic and gene expression data'. Proteomics, 7 (13):2162-2171. [Details]
O'Sullivan NC, McGettigan PA, Sheridan GK, Pickering M, Conboy L, O'Connor JJ,; (2007) 'Temporal change in gene expression in the rat dentate gyrus following passive avoidance learning'. Journal of Neurochemistry, 101 (4):1085-1098. [Details]
Jeffery, IB, Madden, SF, McGettigan, PA, Perriere, G, Culhane, AC, Higgins, DG, ; (2007) 'Integrating transcription factor binding site information with gene expression datasets'. Bioinformatics, 23 :298-305. [Details]
Wallace, IM, Higgins, DG, ; (2007) 'Supervised multivariate analysis of sequence groups to identify specificity determining residues'. BMC Bioinformatics, 8 . [Details]
Fahey, ME,Higgins, DG; (2007) 'Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis'. Journal of Molecular Evolution, 65 :349-357. [DOI] [Details]
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; (2007) 'Clustal W and clustal X version 2.0'. Bioinformatics, 23 :2947-2948. [DOI] [Details]
Walsh DW, Roxburgh SA, Gettigan P, Berthier CC, Higgins D, Kretzler M, Cohen CD, Mezzano S, Brazil DP and Martin F ; (2007) 'Co-regulation of Gremlin and Notch signalling in diabetic nephropathy'. Biochima et Biophysica Acta - Molecular Cell Research, . [Details]
Furney, S., Madden, S., Higgins, D., Lopez-Bigas, N., ; (2007) 'Properties and prediction of proto-oncogenes and tumour suppressor genes'. FEBS Journal, 274 :171-171. [Details]
Jeffery, IB; Higgins, DG; Culhane, AC; ; (2006) 'Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data'. BMC Bioinformatics, 7 (NA). [Details]
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, 7 . [Details]
Blackshields, G.,Wallace, I. M.,Larkin, M.,Higgins, D. G.; (2006) 'Analysis and comparison of benchmarks for multiple sequence alignment'. In Silico Biol, 6 (4):321-39. [Details]
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, 22 (19):2439-40. [Details]
Claesson, MJ,Li, Y,Leahy, S,Canchaya, C,van Pijkeren, JP,Cerdeno-Tarraga, AM,Parkhill, J,Flynn, S,O'Sullivan, GC,Collins, JK,Higgins, D,Shanahan, F,Fitzgerald, GF,van Sinderen, D,O'Toole, PW; (2006) 'Multireplicon genome architecture of Lactobacillus salivarius'. Proceedings of the National Academy of Sciences of the United States of America, 103 :6718-6723. [DOI] [Details]
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, 34 (6):1692-9. [Details]
Ventura, M., Lee, JH., Canchaya, C., Zink, R., Leahy, S., Moreno-Munoz, J.A., O'Connell-Motherway, M., Higgins, D., Fitzgerald, G.F., O'Sullivan, D.J. van Sinderen, D.; (2005) 'Prophage-Like Elements in Bifidobacteria: Insights from Genomics, Trnascription, Integration, Distribution and Phylogenetic'. Analysis Appliend and Environmental Microbiology, . [Details]
Wallace, IM; Orla, O; Higgins, DG; ; (2005) 'Evaluation of iterative alignment algorithms for multiple alignment'. Bioinformatics, 21 (8):1408-1414. [Details]
Wallace, IM,Orla, O,Higgins, DG; (2005) 'Evaluation of iterative alignment algorithms for multiple alignment'. Bioinformatics, 21 :1408-1414. [DOI] [Details]
Brennan, DJ; O'Brien, SL; Fagan, A; Culhane, AC; Higgins, DG; Duffy, MJ; Gallagher, WM; ; (2005) 'Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response'. Expert Opinion on Biological Therapy, 5 (8):1069-1083. [Details]
Higgins, DG, Blackshields, G, Wallace, IM, ; (2005) 'Mind the gaps: Progress in progressive alignment'. Proceedings of the National Academy of Sciences of the United States of America, 102 (30):10411-10412. [Details]
Culhane, AC; Thioulouse, J; Perriere, G; Higgins, DG; ; (2005) 'MADE4: an R package for multivariate analysis of gene expression data'. Bioinformatics, 21 (11):2789-2790. [Details]
Wallace, IM; Blackshields, G; Higgins, DG; ; (2005) 'Multiple sequence alignments'. Current Opinion in Structural Biology, 15 (3):261-266. [Details]
Leahy, SC; Higgins, DG; Fitzgerald, GF; van Sinderen, D; ; (2005) 'Getting better with bifidobacteria'. Journal of Applied Microbiology, 98 (6):1303-1315. [Details]
O'Sullivan, O; Suhre, K; Abergel, C; Higgins, DG; Notredame, C; ; (2004) '3DCoffee: Combining protein sequences and structures within multiple sequence alignments'. Journal of Molecular Biology, 340 (2):385-395. [Details]
Fahey, M. E., Mills, W., Higgins, D. G. and Moore, T. F.; (2004) 'Maternally and paternally silenced imprinted genes differ in their intron content'. Comparative and Functional Genomics, 5 :572-583. [Details]
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):1215-1221. [Details]
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 Research, (31):3497-3500. [Details]
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, . [Details]
Fahey, M. E., Moore, T. F. and Higgins, D. G.; (2002) 'Overlapping antisense transcription in the human genome'. Comp. Functional Genomics, (3):244-253. [Details]
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. [Details]
Notredame, C., Higgins, D. G. and Heringa, J; (2000) 'T-Coffee: A novel method for fast and accurate multiple sequence alignment'. Journal of Molecular Biology, (302):205-217. [Details]
Sharp, P.M., Lloyd, A.T., and Higgins D.G; (1991) 'Coelocanth relationships'. Nature, 353 :218-219. [Details]
ATKINS, GJ, DALY, EA, SHEAHAN, BJ, HIGGINS, DG, SHARP, PM, ; (1990) 'MULTIPLE-SCLEROSIS AND MOLECULAR MIMICRY'. Neuropathology and Applied Neurobiology, 16 (2):179-180. [DOI] [Details]
Hide

Show All

Conference Publications

O'Sullivan NC, McGettigan PA, Croydon L, Sheridan GK, Pickering M, Ring RH, von Schack D, Higgins DG, Regan CM, Murphy KJ ; (2007) Cell type- and region-specific regulation of nuclear factor kappa-B p65 activity in the hippocampus during consolidation of an avoidance conditioning task Society for Neuroscience Annual Meeting 2007 [Details]

Conference Contributions

Brennan, D. J., Rexhepaj, E., Jirstrom, K., Kronblad, A., Fagan, A., Culhane, A. C., Millikan, R. C., Landberg, G., Duffy, M. J., Rydén, L., Higgins, D. G., O'Brien, S. L., and Gallagher, W. M. ; (2007) Validation of novel breast cancer biomarkers arising from re-analysis of publicly available 'omic datasets via tissue microarrays and automated quantitative scoring models for immunohistochemistry. [Oral Presentation], Oncogenomics 2007: Dissecting Cancer Through Genome Research,, Phoenix, AZ , 31-JAN-07 - 03-FEB-07.

Brennan, D. J., Rexhepaj, E., Jirstrom, K., Kronblad, A., Fagan, A., Culhane, A. C., Millikan, R. C., Landberg, G., Duffy, M. J., Rydén, L., Higgins, D. G., O'Brien, S. L., and Gallagher, W. M. ; (2006) Validation of novel breast cancer biomarkers arising from re-analysis of publicly available 'omic datasets via tissue microarrays and automated quantitative scoring models for immunohistochemistry. [Invited Lecture], International Cancer Biomarker Consortium Member Meeting, Singapore , 02-DEC-06 - 03-DEC-06.

Zachariadis, O., Cassidy,J.P., Jeffery,I.B., Culhane, A.C., Higgins,D.G., Morgan, K.T., Wojke, M., Jayyosi, Z., Brady,J. and Mahon, B.P. ; (2005) Gamma-delta T Cells Regulate The Early Inflammatory Response To Bacterial Infection In The Respiratory Tract. [Non Refereed Paper/Abstract Presented at Conference], European Society of Veterinary Pathology Annual meeting, Naples, Italy, Naples, Italy , 31-AUG-05 - 02-SEP-05.

Education

Year 1988 Institution: Trinity College Dublin
Qualification: PhD Subject:

Year 1981 Institution: Trinity College Dublin
Qualification: BA Subject:

Modules Coordinated

201200 MDSA20220 Medicine Systems One: Molecules in Medicine 2 (PMC)

201200 MDSA20210 Medicine Systems One: Molecules in Medicine 2