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Desmond Gerard Higgins

Full Professor of Bioinformatics

School Of Medicine
Conway Institute
Belfield
Dublin 4

Tel: +353 1 7166833
Email: des.higgins@ucd.ie

Biography

Our laboratory works on Bioinformatics. The main focus is on the development and maintenance of the Clustal package for multiple sequence alignment. This is one of the most widely used bioinformatics applications and was originally written by me in 1988. We also work on transcriptomics and proteomics data analysis and I am a PI in Systems Biology Ireland.

Professional

Honours and Awards

Year: 2016.
Title: Motoo Kimura award for molecular phylogenetics, Tokyo, Japan
       

Conference Contributions

61. 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. [Invited Oral Presentation], European Biomarkers Summit/Proteomics Europe, Amsterdam , 04-SEP-07 - 05-SEP-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. ; (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:
         

Publications

 

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. , pp.557-569 [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

Fitzpatrick SF, F¿¿bi¿¿n Z;Schaible B;Lenihan CR;Schwarzl T;Rodriguez J;Zheng X;Li Z;Tambuwala MM;Higgins DG;O'Meara Y;Slattery C;Manresa MC;Fraisl P;Bruning U;Baes M;Carmeliet P;Doherty G;von Kriegsheim A;Cummins EP;Taylor CT (2016) 'Prolyl hydroxylase-1 regulates hepatocyte apoptosis in an NF-¿¿B-dependent manner'. Biochemical and Biophysical Research Communications, . [DOI] [Details]
Fox G, Sievers F;Higgins DG (2016) 'Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments'. Bioinformatics, 32 (6):814-820. [DOI] [Details]
Jehl P, Manguy J;Shields DC;Higgins DG;Davey NE (2016) 'ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences'. Nucleic Acids Research, . [DOI] [Details]
Boyce, K. and Sievers, F. and Higgins, D.G. (2015) 'Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments'. Proceedings of the National Academy of Sciences of the United States of America, 112 (2):E101. Available Online [DOI] [Details]
Boyce K, Sievers F;Higgins DG (2015) 'Instability in progressive multiple sequence alignment algorithms'. Algorithms for Molecular Biology, 10 . [DOI] Link to full text [Details]
Duffy DJ, Krstic A;Halasz M;Schwarzl T;Fey D;Iljin K;Mehta JP;Killick K;Whilde J;Turriziani B;Haapa-Paananen S;Fey V;Fischer M;Westermann F;Henrich KO;Bannert S;Higgins DG;Kolch W (2015) 'Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma'. Oncotarget, 6 (41):43182-43201. [DOI] [Details]
Schwarzl T, Higgins DG;Kolch W;Duffy DJ (2015) 'Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification'. Molecular Biology, 427 (21):3368-3374. [DOI] [Details]
Jehl P, Sievers F;Higgins DG (2015) 'OD-seq: outlier detection in multiple sequence alignments'. BMC Bioinformatics, 16 . [DOI] Link to full text [Details]
Duffy, D.J. and Krstic, A. and Schwarzl, T. and Higgins, D.G. and Kolch, W. (2014) 'GSK3 inhibitors regulate MYCN mRNA levels and reduce neuroblastoma cell viability through multiple mechanisms, including p53 and Wnt signaling'. Molecular Cancer Therapeutics, 13 (2):454-467. Available Online [DOI] [Details]
Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM, Mullan JP, Donohue CA, Higgins DG, Baranov PV (2014) 'GWIPS-viz: development of a ribo-seq genome browser'. Nucleic Acids Research, 42 (Database issue):1-64. [DOI] [Details]
Sievers F, Higgins DG (2014) 'Clustal Omega, accurate alignment of very large numbers of sequences'. Methods, 1079 :105-116. [DOI] [Details]
Boyce K, Sievers F, Higgins DG (2014) 'Simple chained guide trees give high-quality protein multiple sequence alignments'. Proceedings of the National Academy of Sciences of the United States of America, 111 (29):10556-10561. [DOI] [Details]
Holland LM, Schröder MS, Turner SA, Taff H, Andes D, Grózer Z, Gácser A, Ames L, Haynes K, Higgins DG, Butler G (2014) 'Comparative phenotypic analysis of the major fungal pathogens Candida parapsilosis and Candida albicans'. PLoS Pathogens, 10 (9). [DOI] [Details]
Yin J, Morrissey ME, Shine L, Kennedy C, Higgins DG, Kennedy BN (2014) 'Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis'. BMC Genomics, 15 (1). [DOI] [Details]
Sievers F, Hughes GM, Higgins DG. (2014) 'Systematic exploration of guide-tree topology effects for small protein alignments'. BMC Bioinformatics, . [Details]
Hughes, G.M. and Teeling, E.C. and Higgins, D.G. (2014) 'Loss of olfactory receptor function in hominin evolution'. PLoS ONE, 9 (1). Available Online [DOI] [Details]
Hughes G.M., Gang L., Murphy W.J., Higgins D.G., Teeling E.C. (2013) 'Using Illumina Next Generation Sequencing Technologies to Sequence Multigene Families in de novo Species'. Molecular Ecology Resources, 13 (3):510-512. [Details]
Shi W, Zhang Z, Ling C, Zheng W, Zhu C, Carr MJ, Higgins DG. (2013) 'Hepatitis B virus subgenotyping: history, effects of recombination, misclassifications, and corrections'. Infection Genetics And Evolution, . [Details]
Sievers, F,Dineen, D,Wilm, A,Higgins, DG (2013) 'Making automated multiple alignments of very large numbers of protein sequences'. Bioinformatics, 29 :989-995. [DOI] [Details]
Mulrane L, Madden SF, Brennan DJ, Gremel G, McGee SF, McNally S, Martin F, Crown JP, Jirström 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, . [Details]
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]
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. (2012) 'Temporal dysregulation of cortical gene expression in the isolation reared Wistar rat'. Neurochemistry, . Available Online [Details]
Shi, WF,Carr, MJ,Dunford, L,Zhu, CD,Hall, WW,Higgins, DG (2012) 'Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis'. Virology, 427 :51-59. [DOI] [Details]
Shi, WF,Freitas, IT,Zhu, CD,Zheng, W,Hall, WW,Higgins, DG (2012) 'Recombination in Hepatitis C Virus: Identification of Four Novel Naturally Occurring Inter-Subtype Recombinants'. PLoS ONE, 7 . [DOI] [Details]
Shi, WF,Zhu, CD,Zheng, WM,Zheng, W,Ling, C,Carr, MJ,Higgins, DG,Zhang, Z (2012) 'Subgenotyping of Genotype C Hepatitis B Virus: Correcting Misclassifications and Identifying a Novel Subgenotype'. PLoS ONE, 7 . [DOI] [Details]
Yin, J,Shine, L,Raycroft, F,Deeti, S,Reynolds, A,Ackerman, KM,Glaviano, A,O'Farrell, S,O'Leary, O,Kilty, C,Kennedy, C,McLoughlin, S,Rice, M,Russell, E,Higgins, DG,Hyde, DR,Kennedy, BN (2012) 'Inhibition of the Pim1 Oncogene Results in Diminished Visual Function'. PLoS ONE, 7 . [DOI] [Details]
Sievers, F,Wilm, A,Dineen, D,Gibson, TJ,Karplus, K,Li, WZ,Lopez, R,McWilliam, H,Remmert, M,Soding, J,Thompson, JD,Higgins, DG (2011) 'Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega'. Molecular Systems Biology, 7 . [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]
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]
Cederlund ML, Vendrell V, Morrissey ME, Yin J, Gaora Pÿ, Smyth VA, Higgins DG, Kennedy BN (2011) '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, 240 (4):745-754. [DOI] [Details]
Guida, A,Lindstadt, 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 . [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]
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]
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'. Neurochemistry, 113 :601-614. [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] Link to full text [Details]
Blackshields, G,Sievers, F,Shi, WF,Wilm, A,Higgins, DG; (2010) 'Sequence embedding for fast construction of guide trees for multiple sequence alignment'. Algorithms for Molecular Biology, 5 . [DOI] [Details]
Madden, SF,Carpenter, SB,Jeffery, IB,Bjorkbacka, H,Fitzgerald, KA,O'Neill, LA,Higgins, DG; (2010) 'Detecting microRNA activity from gene expression data'. BMC Bioinformatics, 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]
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, . [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]
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'. Journal of Cancer, 100 :1452-1464. [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]
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, 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]
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 and Cellular Proteomics, 7 (3):519-533. [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]
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]
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]
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]
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]
Wallace, IM, Higgins, DG, ; (2007) 'Supervised multivariate analysis of sequence groups to identify specificity determining residues'. BMC Bioinformatics, 8 . [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, 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]
Gibney MJ, Walsh MC, Brennan L, Pujos-Guillot E, Sébédio 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]
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]
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]
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]
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]
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 :3. [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]
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, IM,Orla, O,Higgins, DG; (2005) 'Evaluation of iterative alignment algorithms for multiple alignment'. Bioinformatics, 21 :1408-1414. [DOI] [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; Blackshields, G; Higgins, DG; ; (2005) 'Multiple sequence alignments'. Current Opinion in Structural Biology, 15 (3):261-266. [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]
Leahy, SC; Higgins, DG; Fitzgerald, GF; van Sinderen, D; ; (2005) 'Getting better with bifidobacteria'. Journal of Applied Microbiology, 98 (6):1303-1315. [Details]
Wallace, IM; Orla, O; Higgins, DG; ; (2005) 'Evaluation of iterative alignment algorithms for multiple alignment'. Bioinformatics, 21 (8):1408-1414. [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]
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]
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; Suhre, K; Abergel, C; Higgins, DG; Notredame, C; ; (2004) '3DCoffee: Combining protein sequences and structures within multiple sequence alignments'. Molecular Biology, 340 (2):385-395. [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]
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]
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]
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]
Shields, D. C., Higgins, D. G., Sharp, P. M. (1992) 'GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content'. Comput Appl Biosci, 8 (5):521-3. Available Online [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]
Sharp, P. M., Cowe, E., Higgins, D. G., Shields, D. C., Wolfe, K. H., Wright, F. (1988) '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 (17):8207-11. Available Online [Details]
Shields, D. C., Sharp, P. M., Higgins, D. G., Wright, F. (1988) 'Silent sites in Drosophila genes are not neutral: evidence of selection among synonymous codons'. Mol Biol Evol, 5 (6):704-16. Available Online [Details]
 

Conference Publications

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,Gallaghe, WM (2008) CLINICAL CANCER RESEARCH Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer , pp.2681-2689 [DOI] [Details]
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]
Leahy, SC,Higgins, DG,Fitzgerald, GF,van Sinderen, D (2005) JOURNAL OF APPLIED MICROBIOLOGY Getting better with bifidobacteria , pp.1303-1315 [DOI] [Details]
                                                                                         

Research

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.

UCD Medicine Research Centre: Bioinformatics 

Research Projects

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
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 : 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 : 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 : Science Foundation Ireland (SFI)
Title : Multiple alignment method for the Genome ERA
Start Date / End Date : 01-DEC-03 / 31-MAY-09
Sponsor : Health Research Board (HRB)
Title : Mining the human genome for micro-RNAs
Start Date / End Date : 01-OCT-04 / 30-SEP-07
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 : Irish Research Council for Science Engineering and Technology (IRCSET)
Title : David Dineen IRCSET
Start Date / End Date : 01-OCT-06 / 30-SEP-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 : Les Laboratoires Servier, France
Title : PPAR Modulators and their role in therapeutic diabetes
Start Date / End Date : 01-SEP-07 / 31-AUG-09
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 : 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 : The Wellcome Trust (WT)
Title : Computational Infection Biology
Start Date / End Date : 01-OCT-11 / 31-JAN-16
Sponsor : Irish Cancer Society (ICS)
Title : Collaborative Cancer Research Centre: From population to patient: Leveraging systems medicine to personalise breast cancer treatment (ICS BREAST PREDICT)
Start Date / End Date : 01-OCT-13 / 30-SEP-18
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
 

Current Postgraduate Students

Paul Donovan, Doctor of Philosophy (PhD)   -   Thesis Co-Supervisor
Kieran Boyce, Doctor of Philosophy (PhD)   -   Thesis Supervisor
Izabella Krystkowiak, Doctor of Philosophy (PhD)   -   Thesis Supervisor
Gearoid Fox, Doctor of Philosophy (PhD)   -   Thesis Supervisor
Peter Jehl, Doctor of Philosophy (PhD)   -   Thesis Supervisor
Lucy Burkitt-Gray, Doctor of Philosophy (PhD)   -   Thesis Supervisor

Teaching

 

Modules Coordinated

201500   MDSA20210     Medicine Systems One: Molecules in Medicine 2