Professor Des Higgins

Research

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

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:

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]

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]

Shi, WF,Lei, FM,Zhu, CD,Sievers, F,Higgins, DG (2010) 'A Complete Analysis of HA and NA Genes of Influenza A Viruses'. PLoS ONE, 5 . [DOI] [Details]

Cederlund ML, Vendrell V, Morrissey ME, Yin J, Gaora PÓ, 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. [Details]

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 (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 (27):11217-11222. [DOI] [Details]

Ding C, Yin J, Tovar EM, Fitzpatrick DA, Higgins DG, Thiele DJ (2011) 'The copper regulon of the human fungal pathogen Cryptococcus neoformans H99'. Molecular microbiology, 81 (6):1560-1576. [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]
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]
Madden SF, Carpenter SB, Jeffery IB, Björkbacka H, Fitzgerald KA, O'Neill LA, Higgins DG. (2010) 'Detecting microRNA activity from gene expression data'. BMC Bioinformatics, 11 . [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]
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]
Dineen, D., Schröder, M., Higgins, D.G., 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]
Synnott JM, Guida A, Mulhern-Haughey S, Higgins DG, Butler G. (2010) 'Regulation of the hypoxic response in Candida albicans'. Eukaryotic Cell, . [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]
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]
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]
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]
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]
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]
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]
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]
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]
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 . [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]
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]
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]
Wallace, IM,Orla, O,Higgins, DG (2005) 'Evaluation of iterative alignment algorithms for multiple alignment'. Bioinformatics, 21 :1408-1414. [DOI] [Details]
Sharp, P.M., Lloyd, A.T., and Higgins D.G (1991) 'Coelocanth relationships'. Nature, 353 :218-219. [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 & Cellular Proteomics, 7 (3):519-533. [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]
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]
Wallace, IM, Higgins, DG, (2007) 'Supervised multivariate analysis of sequence groups to identify specificity determining residues'. BMC Bioinformatics, 8 . [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]
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]
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]
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]
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'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]
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]
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]
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]
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]
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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]