Des Higgins, PhD - Publications

Affiliations: 
Conway Institute University College Dublin, Dublin, County Dublin, Ireland 
Area:
Bioinformatics

108 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 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, ... ... Higgins DG, et al. Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma. Oncotarget. PMID 26673823 DOI: 10.18632/oncotarget.6568  0.96
2015 Boyce K, Sievers F, Higgins DG. Instability in progressive multiple sequence alignment algorithms. Algorithms For Molecular Biology : Amb. 10: 26. PMID 26457114 DOI: 10.1186/s13015-015-0057-1  0.96
2015 Schwarzl T, Higgins DG, Kolch W, Duffy DJ. Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification. Journal of Molecular Biology. 427: 3368-74. PMID 26362006 DOI: 10.1016/j.jmb.2015.09.006  0.96
2015 Jehl P, Sievers F, Higgins DG. OD-seq: outlier detection in multiple sequence alignments. Bmc Bioinformatics. 16: 269. PMID 26303676 DOI: 10.1186/s12859-015-0702-1  0.96
2015 Boyce K, Sievers F, Higgins DG. 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: E101. PMID 25564671 DOI: 10.1073/pnas.1419351112  0.96
2014 Sievers F, Higgins DG. Clustal omega. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 48: 3.13.1-3.13.16. PMID 25501942 DOI: 10.1002/0471250953.bi0313s48  0.96
2014 Sievers F, Hughes GM, Higgins DG. Systematic exploration of guide-tree topology effects for small protein alignments. Bmc Bioinformatics. 15: 338. PMID 25282640 DOI: 10.1186/1471-2105-15-338  0.96
2014 Yin J, Morrissey ME, Shine L, Kennedy C, Higgins DG, Kennedy BN. Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis. Bmc Genomics. 15: 825. PMID 25266257 DOI: 10.1186/1471-2164-15-825  0.96
2014 Holland LM, Schröder MS, Turner SA, Taff H, Andes D, Grózer Z, Gácser A, Ames L, Haynes K, Higgins DG, Butler G. Comparative phenotypic analysis of the major fungal pathogens Candida parapsilosis and Candida albicans. Plos Pathogens. 10: e1004365. PMID 25233198 DOI: 10.1371/journal.ppat.1004365  0.96
2014 Boyce K, Sievers F, Higgins DG. 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: 10556-61. PMID 25002495 DOI: 10.1073/pnas.1405628111  0.96
2014 Hughes GM, Teeling EC, Higgins DG. Loss of olfactory receptor function in hominin evolution. Plos One. 9: e84714. PMID 24392153 DOI: 10.1371/journal.pone.0084714  0.96
2014 Duffy DJ, Krstic A, Schwarzl T, Higgins DG, Kolch W. GSK3 inhibitors regulate MYCN mRNA levels and reduce neuroblastoma cell viability through multiple mechanisms, including p53 and Wnt signaling. Molecular Cancer Therapeutics. 13: 454-67. PMID 24282277 DOI: 10.1158/1535-7163.MCT-13-0560-T  0.96
2014 Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM, Mullan JP, Donohue CA, Higgins DG, Baranov PV. GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Research. 42: D859-64. PMID 24185699 DOI: 10.1093/nar/gkt1035  0.96
2014 Sievers F, Higgins DG. Clustal Omega, accurate alignment of very large numbers of sequences. Methods in Molecular Biology (Clifton, N.J.). 1079: 105-16. PMID 24170397 DOI: 10.1007/978-1-62703-646-7_6  0.96
2013 Shi W, Zhang Z, Ling C, Zheng W, Zhu C, Carr MJ, Higgins DG. Hepatitis B virus subgenotyping: history, effects of recombination, misclassifications, and corrections. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 16: 355-61. PMID 23538336 DOI: 10.1016/j.meegid.2013.03.021  0.96
2013 Hughes GM, Gang L, Murphy WJ, Higgins DG, Teeling EC. Using Illumina next generation sequencing technologies to sequence multigene families in de novo species. Molecular Ecology Resources. 13: 510-21. PMID 23480365 DOI: 10.1111/1755-0998.12087  0.96
2013 Sievers F, Dineen D, Wilm A, Higgins DG. Making automated multiple alignments of very large numbers of protein sequences. Bioinformatics (Oxford, England). 29: 989-95. PMID 23428640 DOI: 10.1093/bioinformatics/btt093  0.96
2012 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, et al. Inhibition of the Pim1 oncogene results in diminished visual function. Plos One. 7: e52177. PMID 23300608 DOI: 10.1371/journal.pone.0052177  0.96
2012 Shi W, Zhu C, Zheng W, Zheng W, Ling C, Carr MJ, Higgins DG, Zhang Z. Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype. Plos One. 7: e47271. PMID 23077582 DOI: 10.1371/journal.pone.0047271  0.96
2012 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. 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. 18: 6702-13. PMID 23060431 DOI: 10.1158/1078-0432.CCR-12-1420  0.96
2012 Shi W, Zhu C, Zheng W, Carr MJ, Higgins DG, Zhang Z. Subgenotype reclassification of genotype B hepatitis B virus. Bmc Gastroenterology. 12: 116. PMID 22925657 DOI: 10.1186/1471-230X-12-116  0.96
2012 Shi W, Freitas IT, Zhu C, Zheng W, Hall WW, Higgins DG. Recombination in hepatitis C virus: identification of four novel naturally occurring inter-subtype recombinants. Plos One. 7: e41997. PMID 22911872 DOI: 10.1371/journal.pone.0041997  0.96
2012 Shi W, Carr MJ, Dunford L, Zhu C, Hall WW, Higgins DG. Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis. Virology. 427: 51-9. PMID 22374235 DOI: 10.1016/j.virol.2012.01.030  0.96
2011 Guida A, Lindstädt C, Maguire SL, Ding C, Higgins DG, Corton NJ, Berriman M, Butler G. Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. Bmc Genomics. 12: 628. PMID 22192698 DOI: 10.1186/1471-2164-12-628  0.96
2011 Sievers F, Wilm A, Dineen D, 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. Molecular Systems Biology. 7: 539. PMID 21988835 DOI: 10.1038/msb.2011.75  0.96
2011 Ding C, Yin J, Tovar EM, Fitzpatrick DA, Higgins DG, Thiele DJ. The copper regulon of the human fungal pathogen Cryptococcus neoformans H99. Molecular Microbiology. 81: 1560-76. PMID 21819456 DOI: 10.1111/j.1365-2958.2011.07794.x  0.96
2011 O'Connell Motherway M, 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, et al. 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: 11217-22. PMID 21690406 DOI: 10.1073/pnas.1105380108  0.96
2011 Cederlund ML, Vendrell V, Morrissey ME, Yin J, Gaora PÓ, Smyth VA, Higgins DG, Kennedy BN. 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: 745-54. PMID 21360786 DOI: 10.1002/dvdy.22573  0.96
2010 Shi W, Lei F, Zhu C, Sievers F, Higgins DG. A complete analysis of HA and NA genes of influenza A viruses. Plos One. 5: e14454. PMID 21209922 DOI: 10.1371/journal.pone.0014454  0.96
2010 Dineen DG, Schröder M, Higgins DG, Cunningham P. Ensemble approach combining multiple methods improves human transcription start site prediction. Bmc Genomics. 11: 677. PMID 21118509 DOI: 10.1186/1471-2164-11-677  0.96
2010 Synnott JM, Guida A, Mulhern-Haughey S, Higgins DG, Butler G. Regulation of the hypoxic response in Candida albicans. Eukaryotic Cell. 9: 1734-46. PMID 20870877 DOI: 10.1128/EC.00159-10  0.96
2010 Madden SF, Carpenter SB, Jeffery IB, Björkbacka H, Fitzgerald KA, O'Neill LA, Higgins DG. Detecting microRNA activity from gene expression data. Bmc Bioinformatics. 11: 257. PMID 20482775 DOI: 10.1186/1471-2105-11-257  0.96
2010 Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms For Molecular Biology : Amb. 5: 21. PMID 20470396 DOI: 10.1186/1748-7188-5-21  0.96
2010 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, ... ... Higgins DG, et al. Temporal dysregulation of cortical gene expression in the isolation reared Wistar rat. Journal of Neurochemistry. 113: 601-14. PMID 20096092 DOI: 10.1111/j.1471-4159.2010.06617.x  0.96
2010 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. 11: 50. PMID 20089164 DOI: 10.1186/1471-2164-11-50  0.96
2009 Murphy DM, Buckley PG, Bryan K, Das S, Alcock L, Foley NH, Prenter S, Bray I, Watters KM, Higgins D, Stallings RL. Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation. Plos One. 4: e8154. PMID 19997598 DOI: 10.1371/journal.pone.0008154  0.96
2009 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, et al. Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival. Plos One. 4: e7850. PMID 19924232 DOI: 10.1371/journal.pone.0007850  0.96
2009 Dineen DG, Wilm A, Cunningham P, Higgins DG. High DNA melting temperature predicts transcription start site location in human and mouse. Nucleic Acids Research. 37: 7360-7. PMID 19820114 DOI: 10.1093/nar/gkp821  0.96
2009 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. British Journal of Cancer. 100: 1452-64. PMID 19401702 DOI: 10.1038/sj.bjc.6604931  0.96
2009 Rossignol T, Ding C, Guida A, d'Enfert C, Higgins DG, Butler G. Correlation between biofilm formation and the hypoxic response in Candida parapsilosis. Eukaryotic Cell. 8: 550-9. PMID 19151323 DOI: 10.1128/EC.00350-08  0.96
2008 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. American Journal of Respiratory and Critical Care Medicine. 178: 977-83. PMID 18689465 DOI: 10.1164/rccm.200712-1890OC  0.96
2008 Moretti S, Wilm A, Higgins DG, Xenarios I, Notredame C. R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Research. 36: W10-3. PMID 18483080 DOI: 10.1093/nar/gkn278  0.96
2008 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. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 14: 2681-9. PMID 18451232 DOI: 10.1158/1078-0432.CCR-07-1760  0.96
2008 Blackshields G, Larkin M, Wallace IM, Wilm A, Higgins DG. Fast embedding methods for clustering tens of thousands of sequences. Computational Biology and Chemistry. 32: 282-6. PMID 18450519 DOI: 10.1016/j.compbiolchem.2008.03.005  0.96
2008 Furney SJ, Madden SF, Kisiel TA, Higgins DG, Lopez-Bigas N. Distinct patterns in the regulation and evolution of human cancer genes. In Silico Biology. 8: 33-46. PMID 18430988  0.96
2008 Wilm A, Higgins DG, Notredame C. R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Research. 36: e52. PMID 18420654 DOI: 10.1093/nar/gkn174  0.96
2008 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, et al. Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses. Molecular & Cellular Proteomics : McP. 7: 519-33. PMID 18056057 DOI: 10.1074/mcp.M700245-MCP200  0.96
2008 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. Biochimica Et Biophysica Acta. 1782: 10-21. PMID 17980714 DOI: 10.1016/j.bbadis.2007.09.005  0.96
2007 Walsh MC, Brennan L, Pujos-Guillot E, Sébédio JL, Scalbert A, Fagan A, Higgins DG, Gibney MJ. Influence of acute phytochemical intake on human urinary metabolomic profiles American Journal of Clinical Nutrition. 86: 1687-1693. PMID 18065587  0.96
2007 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 (Oxford, England). 23: 2947-8. PMID 17846036 DOI: 10.1093/bioinformatics/btm404  0.96
2007 Fahey ME, Higgins DG. Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis Journal of Molecular Evolution. 65: 349-357. PMID 17763878 DOI: 10.1007/s00239-007-9015-y  0.96
2007 Fagan A, Culhane AC, Higgins DG. A multivariate analysis approach to the integration of proteomic and gene expression data Proteomics. 7: 2162-2171. PMID 17549791 DOI: 10.1002/pmic.200600898  0.96
2007 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 Research. 35: W645-8. PMID 17526519 DOI: 10.1093/nar/gkm333  0.96
2007 Wallace IM, Higgins DG. Supervised multivariate analysis of sequence groups to identify specificity determining residues Bmc Bioinformatics. 8. PMID 17451607 DOI: 10.1186/1471-2105-8-135  0.96
2007 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. Journal of Neurochemistry. 101: 1085-98. PMID 17298388 DOI: 10.1111/j.1471-4159.2006.04418.x  0.96
2007 O'Brien SL, Fagan A, Fox EJ, Millikan RC, Culhane AC, Brennan DJ, McCann AH, Hegarty S, Moyna S, Duffy MJ, Higgins DG, Jirström K, Landberg G, Gallagher WM. CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer. International Journal of Cancer. Journal International Du Cancer. 120: 1434-43. PMID 17205517 DOI: 10.1002/ijc.22413  0.96
2007 Jeffery IB, Madden SF, McGettigan PA, Perrière G, Culhane AC, Higgins DG. Integrating transcription factor binding site information with gene expression datasets. Bioinformatics (Oxford, England). 23: 298-305. PMID 17127681 DOI: 10.1093/bioinformatics/btl597  0.96
2006 Armougom F, Poirot O, Moretti S, Higgins DG, Bucher P, Keduas V, Notredame C. APDB: a web server to evaluate the accuracy of sequence alignments using structural information. Bioinformatics (Oxford, England). 22: 2439-40. PMID 17032685 DOI: 10.1093/bioinformatics/btl404  0.96
2006 Blackshields G, Wallace IM, Larkin M, Higgins DG. Analysis and comparison of benchmarks for multiple sequence alignment In Silico Biology. 6: 321-339. PMID 16922695  0.96
2006 Jeffery IB, Higgins DG, Culhane AC. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data Bmc Bioinformatics. 7. PMID 16872483 DOI: 10.1186/1471-2105-7-359  0.96
2006 Claesson MJ, Li Y, Leahy S, Canchaya C, van Pijkeren JP, Cerdeño-Tárraga AM, Parkhill J, Flynn S, O'Sullivan GC, Collins JK, Higgins D, Shanahan F, Fitzgerald GF, van Sinderen D, O'Toole PW. Multireplicon genome architecture of Lactobacillus salivarius. Proceedings of the National Academy of Sciences of the United States of America. 103: 6718-23. PMID 16617113 DOI: 10.1073/pnas.0511060103  0.96
2006 Wallace IM, O'Sullivan O, Higgins DG, Notredame C. M-Coffee: Combining multiple sequence alignment methods with T-Coffee Nucleic Acids Research. 34: 1692-1699. PMID 16556910 DOI: 10.1093/nar/gkl091  0.96
2006 Furney SJ, Higgins DG, Ouzounis CA, López-Bigas N. Structural and functional properties of genes involved in human cancer. Bmc Genomics. 7: 3. PMID 16405732 DOI: 10.1186/1471-2164-7-3  0.96
2005 Ventura M, Lee JH, Canchaya C, Zink R, Leahy S, Moreno-Munoz JA, O'Connell-Motherway M, Higgins D, Fitzgerald GF, O'Sullivan DJ, van Sinderen D. Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution, and phylogenetic analysis. Applied and Environmental Microbiology. 71: 8692-705. PMID 16332864 DOI: 10.1128/AEM.71.12.8692-8705.2005  0.96
2005 Brennan DJ, O'Brien SL, Fagan A, Culhane AC, Higgins DG, Duffy MJ, Gallagher WM. Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response. Expert Opinion On Biological Therapy. 5: 1069-83. PMID 16050784 DOI: 10.1517/14712598.5.8.1069  0.96
2005 Higgins DG, Blackshields G, Wallace IM. Mind the gaps: Progress in progressive alignment Proceedings of the National Academy of Sciences of the United States of America. 102: 10411-10412. PMID 16027352 DOI: 10.1073/pnas.0504801102  0.96
2005 Wallace IM, Blackshields G, Higgins DG. Multiple sequence alignments Current Opinion in Structural Biology. 15: 261-266. PMID 15963889 DOI: 10.1016/j.sbi.2005.04.002  0.96
2005 Leahy SC, Higgins DG, Fitzgerald GF, Van Sinderen D. Getting better with bifidobacteria Journal of Applied Microbiology. 98: 1303-1315. PMID 15916644 DOI: 10.1111/j.1365-2672.2005.02600.x  0.96
2005 Culhane AC, Thioulouse J, Perrière G, Higgins DG. MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics (Oxford, England). 21: 2789-90. PMID 15797915 DOI: 10.1093/bioinformatics/bti394  0.96
2005 Wallace IM, O'Sullivan O, Higgins DG. Evaluation of iterative alignment algorithms for multiple alignment Bioinformatics. 21: 1408-1414. PMID 15564300 DOI: 10.1093/bioinformatics/bti159  0.96
2004 Fahey ME, Mills W, Higgins DG, Moore T. Maternally and paternally silenced imprinted genes differ in their intron content. Comparative and Functional Genomics. 5: 572-83. PMID 18629181 DOI: 10.1002/cfg.437  0.96
2004 O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C. 3DCoffee: Combining protein sequences and structures within multiple sequence alignments Journal of Molecular Biology. 340: 385-395. PMID 15201059 DOI: 10.1016/j.jmb.2004.04.058  0.96
2003 Culhane AC, Perrière G, Higgins DG. Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. Bmc Bioinformatics. 4: 59. PMID 14633289 DOI: 10.1186/1471-2105-4-59  0.96
2003 O'Sullivan O, Zehnder M, Higgins D, Bucher P, Grosdidier A, Notredame C. APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics (Oxford, England). 19: i215-21. PMID 12855461 DOI: 10.1093/bioinformatics/btg1029  0.96
2003 Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research. 31: 3497-500. PMID 12824352 DOI: 10.1093/nar/gkg500  0.96
2003 Prestwich S, Higgins D, O'Sullivan O. A SAT-Based approach to multiple sequence alignment Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2833: 940-944.  0.96
2002 Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 2.3. PMID 18792934 DOI: 10.1002/0471250953.bi0203s00  0.96
2002 Fahey ME, Moore TF, Higgins DG. Overlapping antisense transcription in the human genome. Comparative and Functional Genomics. 3: 244-53. PMID 18628857 DOI: 10.1002/cfg.173  0.96
2002 Culhane AC, Perrière G, Considine EC, Cotter TG, Higgins DG. Between-group analysis of microarray data. Bioinformatics (Oxford, England). 18: 1600-8. PMID 12490444 DOI: 10.1093/bioinformatics/18.12.1600  0.96
2000 Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology. 302: 205-17. PMID 10964570 DOI: 10.1006/jmbi.2000.4042  0.96
2000 Higgins DG. Amino acid-based phylogeny and alignment Advances in Protein Chemistry. 54: 99-135. PMID 10829226  0.96
1999 Kenny PA, Liston EM, Higgins DG. Molecular evolution of immunoglobulin and fibronectin domains in titin and related muscle proteins Gene. 232: 11-23. PMID 10333517 DOI: 10.1016/S0378-1119(99)00122-5  0.96
1999 Thébault P, Monestié P, McGrath A, Higgins DG. MIAH: Automatic alignment of eukaryotic SSU rRNAs Bioinformatics. 15: 341-342. PMID 10320403 DOI: 10.1093/bioinformatics/15.4.341  0.96
1998 O'Brien EA, Higgins DG. Empirical estimation of the reliability of ribosomal RNA alignments Bioinformatics. 14: 830-838. PMID 9927711 DOI: 10.1093/bioinformatics/14.10.830  0.96
1998 McGrath A, Higgins DG, McCarthy TV. Sequence analysis of DNA randomly amplified from the Saccharomyces cerevisiae genome Molecular and Cellular Probes. 12: 397-405. PMID 9843657 DOI: 10.1006/mcpr.1998.0199  0.96
1998 Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences. 23: 403-5. PMID 9810230 DOI: 10.1016/S0968-0004(98)01285-7  0.96
1998 Notredame C, Holm L, Higgins DG. COFFEE: An objective function for multiple sequence alignments Bioinformatics. 14: 407-422. PMID 9682054  0.96
1998 O'Brien EA, Notredame C, Higgins DG. Optimization of ribosomal RNA profile alignments Bioinformatics. 14: 332-341. PMID 9632828  0.96
1997 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research. 25: 4876-82. PMID 9396791 DOI: 10.1093/nar/25.24.4876  0.96
1997 Notredame C, O'Brien EA, Higgins DG. RAGA: RNA sequence alignment by genetic algorithm Nucleic Acids Research. 25: 4570-4580. PMID 9358168  0.96
1996 Higgins DG, Thompson JD, Gibson TJ. Using CLUSTAL for multiple sequence alignments. Methods in Enzymology. 266: 383-402. PMID 8743695 DOI: 10.1016/S0076-6879(96)66024-8  0.96
1996 Notredame C, Higgins DG. SAGA: Sequence alignment by genetic algorithm Nucleic Acids Research. 24: 1515-1524. PMID 8628686 DOI: 10.1093/nar/24.8.1515  0.96
1995 Jonassen I, Collins JF, Higgins DG. Finding flexible patterns in unaligned protein sequences Protein Science. 4: 1587-1595. PMID 8520485  0.96
1994 Graur D, Higgins DG. Molecular evidence for the inclusion of cetaceans within the order Artiodactyla. Molecular Biology and Evolution. 11: 357-64. PMID 8015431  0.96
1994 Castresana J, Lübben M, Saraste M, Higgins DG. Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen Embo Journal. 13: 2516-2525. PMID 8013452  0.96
1994 Higgins DG. CLUSTAL V: multiple alignment of DNA and protein sequences Methods in Molecular Biology (Clifton, N.J.). 25: 307-318. PMID 8004173  0.96
1994 Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research. 22: 4673-80. PMID 7984417 DOI: 10.1093/nar/22.22.4673  0.96
1993 Gibson TJ, Higgins DG. Non-muscle and smooth muscle myosin light chain kinases: no end in sight. Dna Sequence : the Journal of Dna Sequencing and Mapping. 3: 333-5. PMID 8400365 DOI: 10.3109/10425179309020833  0.96
1993 Rice CM, Fuchs R, Higgins DG, Stoehr PJ, Cameron GN. The EMBL data library. Nucleic Acids Research. 21: 2967-71. PMID 8332519  0.48
1992 Higgins DG, Fuchs R, Stoehr PJ, Cameron GN. The EMBL Data Library. Nucleic Acids Research. 20: 2071-4. PMID 1598236  0.48
1992 Shields DC, Higgins DG, Sharp PM. GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content. Computer Applications in the Biosciences : Cabios. 8: 521-3. PMID 1422886  0.96
1991 Powell R, Higgins DG, Wolff J, Byrnes L, Stack M, Sharp PM, Gannon F. The salmon gene encoding apolipoprotein A-I: cDNA sequence, tissue expression and evolution. Gene. 104: 155-61. PMID 1916288 DOI: 10.1016/0378-1119(91)90245-7  0.96
1990 Atkins GJ, Daly EA, Sheahan BJ, Higgins DG, Sharp PM. Multiple sclerosis and molecular mimicry. Neuropathology and Applied Neurobiology. 16: 179-80. PMID 1693178  0.96
1989 Higgins DG, Sharp PM. Fast and sensitive multiple sequence alignments on a microcomputer. Computer Applications in the Biosciences : Cabios. 5: 151-3. PMID 2720464  0.96
1989 Higgins DG, McConnell DJ, Sharp PM. Malarial proteinase? Nature. 340: 604. PMID 2671749 DOI: 10.1038/340604a0  0.96
1988 Higgins DG, Sharp PM. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 73: 237-44. PMID 3243435 DOI: 10.1016/0378-1119(88)90330-7  0.96
1988 Shields DC, Sharp PM, Higgins DG, Wright F. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Molecular Biology and Evolution. 5: 704-16. PMID 3146682  0.96
1988 Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH, 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 Research. 16: 8207-11. PMID 3138659  0.96
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