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The birth and death of olfactory receptor gene families in mammalian niche adaptation.

Hughes GM, Boston EM, Finarelli JA, Murphy WJ, Higgins DG, Teeling EC.

Mol Biol Evol. 2018 Mar 19. doi: 10.1093/molbev/msy028. [Epub ahead of print]


Identification of fungi in shotgun metagenomics datasets.

Donovan PD, Gonzalez G, Higgins DG, Butler G, Ito K.

PLoS One. 2018 Feb 14;13(2):e0192898. doi: 10.1371/journal.pone.0192898. eCollection 2018.


MyD88 is an essential component of retinoic acid-induced differentiation in human pluripotent embryonal carcinoma cells.

Sulaiman G, Cooke A, Ffrench B, Gasch C, Abdullai OA, O'Connor K, Elbaruni S, Blackshields G, Spillane C, Keegan H, McEneaney V, Knittel R, Rogers A, Jeffery IB, Doyle B, Bates M, d'Adhemar C, Lee MY, Campbell EL, Moynagh PN, Higgins DG, O'Toole S, O'Neill L, O'Leary JJ, Gallagher MF.

Cell Death Differ. 2017 Nov;24(11):1975-1986. doi: 10.1038/cdd.2017.124. Epub 2017 Sep 8.


Clustal Omega for making accurate alignments of many protein sequences.

Sievers F, Higgins DG.

Protein Sci. 2018 Jan;27(1):135-145. doi: 10.1002/pro.3290. Epub 2017 Oct 30.


Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance.

Duffy DJ, Krstic A, Halasz M, Schwarzl T, Konietzny A, Iljin K, Higgins DG, Kolch W.

Genome Med. 2017 Feb 10;9(1):15. doi: 10.1186/s13073-017-0407-3.


Protein multiple sequence alignment benchmarking through secondary structure prediction.

Le Q, Sievers F, Higgins DG.

Bioinformatics. 2017 May 1;33(9):1331-1337. doi: 10.1093/bioinformatics/btw840.


Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species.

Schröder MS, Martinez de San Vicente K, Prandini TH, Hammel S, Higgins DG, Bagagli E, Wolfe KH, Butler G.

PLoS Genet. 2016 Nov 2;12(11):e1006404. doi: 10.1371/journal.pgen.1006404. eCollection 2016 Nov.


Identification of Non-Coding RNAs in the Candida parapsilosis Species Group.

Donovan PD, Schröder MS, Higgins DG, Butler G.

PLoS One. 2016 Sep 22;11(9):e0163235. doi: 10.1371/journal.pone.0163235. eCollection 2016.


Wnt signalling is a bi-directional vulnerability of cancer cells.

Duffy DJ, Krstic A, Schwarzl T, Halasz M, Iljin K, Fey D, Haley B, Whilde J, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W.

Oncotarget. 2016 Sep 13;7(37):60310-60331. doi: 10.18632/oncotarget.11203.


Prolyl hydroxylase-1 regulates hepatocyte apoptosis in an NF-κB-dependent manner.

Fitzpatrick SF, Fábián 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.

Biochem Biophys Res Commun. 2016 Jun 3;474(3):579-586. doi: 10.1016/j.bbrc.2016.04.085. Epub 2016 Apr 27.


ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences.

Jehl P, Manguy J, Shields DC, Higgins DG, Davey NE.

Nucleic Acids Res. 2016 Jul 8;44(W1):W11-5. doi: 10.1093/nar/gkw265. Epub 2016 Apr 16.


Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma.

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.

Oncotarget. 2015 Dec 22;6(41):43182-201. doi: 10.18632/oncotarget.6568.


Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments.

Fox G, Sievers F, Higgins DG.

Bioinformatics. 2016 Mar 15;32(6):814-20. doi: 10.1093/bioinformatics/btv592. Epub 2015 Nov 14.


Instability in progressive multiple sequence alignment algorithms.

Boyce K, Sievers F, Higgins DG.

Algorithms Mol Biol. 2015 Oct 9;10:26. doi: 10.1186/s13015-015-0057-1. eCollection 2015.


Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification.

Schwarzl T, Higgins DG, Kolch W, Duffy DJ.

J Mol Biol. 2015 Oct 23;427(21):3368-74. doi: 10.1016/j.jmb.2015.09.006. Epub 2015 Sep 9.


OD-seq: outlier detection in multiple sequence alignments.

Jehl P, Sievers F, Higgins DG.

BMC Bioinformatics. 2015 Aug 25;16:269. doi: 10.1186/s12859-015-0702-1.


Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments.

Boyce K, Sievers F, Higgins DG.

Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):E101. doi: 10.1073/pnas.1419351112. Epub 2015 Jan 6. No abstract available.


Clustal omega.

Sievers F, Higgins DG.

Curr Protoc Bioinformatics. 2014 Dec 12;48:3.13.1-16. doi: 10.1002/0471250953.bi0313s48.


Systematic exploration of guide-tree topology effects for small protein alignments.

Sievers F, Hughes GM, Higgins DG.

BMC Bioinformatics. 2014 Oct 4;15:338. doi: 10.1186/1471-2105-15-338.


Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis.

Yin J, Morrissey ME, Shine L, Kennedy C, Higgins DG, Kennedy BN.

BMC Genomics. 2014 Sep 30;15:825. doi: 10.1186/1471-2164-15-825.


Comparative phenotypic analysis of the major fungal pathogens Candida parapsilosis and Candida albicans.

Holland LM, Schröder MS, Turner SA, Taff H, Andes D, Grózer Z, Gácser A, Ames L, Haynes K, Higgins DG, Butler G.

PLoS Pathog. 2014 Sep 18;10(9):e1004365. doi: 10.1371/journal.ppat.1004365. eCollection 2014 Sep.


Simple chained guide trees give high-quality protein multiple sequence alignments.

Boyce K, Sievers F, Higgins DG.

Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10556-61. doi: 10.1073/pnas.1405628111. Epub 2014 Jul 7.


Loss of olfactory receptor function in hominin evolution.

Hughes GM, Teeling EC, Higgins DG.

PLoS One. 2014 Jan 2;9(1):e84714. doi: 10.1371/journal.pone.0084714. eCollection 2014.


GSK3 inhibitors regulate MYCN mRNA levels and reduce neuroblastoma cell viability through multiple mechanisms, including p53 and Wnt signaling.

Duffy DJ, Krstic A, Schwarzl T, Higgins DG, Kolch W.

Mol Cancer Ther. 2014 Feb;13(2):454-67. doi: 10.1158/1535-7163.MCT-13-0560-T. Epub 2013 Nov 26.


GWIPS-viz: development of a ribo-seq genome browser.

Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM, Mullan JP, Donohue CA, Higgins DG, Baranov PV.

Nucleic Acids Res. 2014 Jan;42(Database issue):D859-64. doi: 10.1093/nar/gkt1035. Epub 2013 Oct 31.


Clustal Omega, accurate alignment of very large numbers of sequences.

Sievers F, Higgins DG.

Methods Mol Biol. 2014;1079:105-16. doi: 10.1007/978-1-62703-646-7_6.


Hepatitis B virus subgenotyping: history, effects of recombination, misclassifications, and corrections.

Shi W, Zhang Z, Ling C, Zheng W, Zhu C, Carr MJ, Higgins DG.

Infect Genet Evol. 2013 Jun;16:355-61. doi: 10.1016/j.meegid.2013.03.021. Epub 2013 Mar 26. Review.


Using Illumina next generation sequencing technologies to sequence multigene families in de novo species.

Hughes GM, Gang L, Murphy WJ, Higgins DG, Teeling EC.

Mol Ecol Resour. 2013 May;13(3):510-21. doi: 10.1111/1755-0998.12087. Epub 2013 Mar 9.


Making automated multiple alignments of very large numbers of protein sequences.

Sievers F, Dineen D, Wilm A, Higgins DG.

Bioinformatics. 2013 Apr 15;29(8):989-95. doi: 10.1093/bioinformatics/btt093. Epub 2013 Feb 21.


Inhibition of the Pim1 oncogene results in diminished visual function.

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.

PLoS One. 2012;7(12):e52177. doi: 10.1371/journal.pone.0052177. Epub 2012 Dec 26.


Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.

Shi W, Zhu C, Zheng W, Zheng W, Ling C, Carr MJ, Higgins DG, Zhang Z.

PLoS One. 2012;7(10):e47271. doi: 10.1371/journal.pone.0047271. Epub 2012 Oct 15.


miR-187 is an independent prognostic factor in breast cancer and confers increased invasive potential in vitro.

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.

Clin Cancer Res. 2012 Dec 15;18(24):6702-13. doi: 10.1158/1078-0432.CCR-12-1420. Epub 2012 Oct 11.


Subgenotype reclassification of genotype B hepatitis B virus.

Shi W, Zhu C, Zheng W, Carr MJ, Higgins DG, Zhang Z.

BMC Gastroenterol. 2012 Aug 27;12:116. doi: 10.1186/1471-230X-12-116.


Recombination in hepatitis C virus: identification of four novel naturally occurring inter-subtype recombinants.

Shi W, Freitas IT, Zhu C, Zheng W, Hall WW, Higgins DG.

PLoS One. 2012;7(7):e41997. doi: 10.1371/journal.pone.0041997. Epub 2012 Jul 24.


Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis.

Shi W, Carr MJ, Dunford L, Zhu C, Hall WW, Higgins DG.

Virology. 2012 May 25;427(1):51-9. doi: 10.1016/j.virol.2012.01.030. Epub 2012 Feb 27.


Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis.

Guida A, Lindstädt C, Maguire SL, Ding C, Higgins DG, Corton NJ, Berriman M, Butler G.

BMC Genomics. 2011 Dec 22;12:628. doi: 10.1186/1471-2164-12-628.


Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.

Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75.


The copper regulon of the human fungal pathogen Cryptococcus neoformans H99.

Ding C, Yin J, Tovar EM, Fitzpatrick DA, Higgins DG, Thiele DJ.

Mol Microbiol. 2011 Sep;81(6):1560-76. doi: 10.1111/j.1365-2958.2011.07794.x. Epub 2011 Aug 23.


Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.

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, Palva A, de Vos WM, Fitzgerald GF, Ventura M, O'Toole PW, van Sinderen D.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11217-22. doi: 10.1073/pnas.1105380108. Epub 2011 Jun 20.


mab21l2 transgenics reveal novel expression patterns of mab21l1 and mab21l2, and conserved promoter regulation without sequence conservation.

Cederlund ML, Vendrell V, Morrissey ME, Yin J, Gaora PÓ, Smyth VA, Higgins DG, Kennedy BN.

Dev Dyn. 2011 Apr;240(4):745-54. doi: 10.1002/dvdy.22573. Epub 2011 Feb 28.


A complete analysis of HA and NA genes of influenza A viruses.

Shi W, Lei F, Zhu C, Sievers F, Higgins DG.

PLoS One. 2010 Dec 29;5(12):e14454. doi: 10.1371/journal.pone.0014454.


Ensemble approach combining multiple methods improves human transcription start site prediction.

Dineen DG, Schröder M, Higgins DG, Cunningham P.

BMC Genomics. 2010 Nov 30;11:677. doi: 10.1186/1471-2164-11-677.


Regulation of the hypoxic response in Candida albicans.

Synnott JM, Guida A, Mulhern-Haughey S, Higgins DG, Butler G.

Eukaryot Cell. 2010 Nov;9(11):1734-46. doi: 10.1128/EC.00159-10. Epub 2010 Sep 24.


Detecting microRNA activity from gene expression data.

Madden SF, Carpenter SB, Jeffery IB, Björkbacka H, Fitzgerald KA, O'Neill LA, Higgins DG.

BMC Bioinformatics. 2010 May 18;11:257. doi: 10.1186/1471-2105-11-257.


Sequence embedding for fast construction of guide trees for multiple sequence alignment.

Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG.

Algorithms Mol Biol. 2010 May 14;5:21. doi: 10.1186/1748-7188-5-21.


Temporal dysregulation of cortical gene expression in the isolation reared Wistar rat.

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.

J Neurochem. 2010 May;113(3):601-14. doi: 10.1111/j.1471-4159.2010.06617.x. Epub 2010 Jan 24.


Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data.

Yin J, McLoughlin S, Jeffery IB, Glaviano A, Kennedy B, Higgins DG.

BMC Genomics. 2010 Jan 20;11:50. doi: 10.1186/1471-2164-11-50.


Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

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.

PLoS One. 2009 Nov 16;4(11):e7850. doi: 10.1371/journal.pone.0007850.


High DNA melting temperature predicts transcription start site location in human and mouse.

Dineen DG, Wilm A, Cunningham P, Higgins DG.

Nucleic Acids Res. 2009 Dec;37(22):7360-7. doi: 10.1093/nar/gkp821.


Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification.

Smith MJ, Culhane AC, Donovan M, Coffey JC, Barry BD, Kelly MA, Higgins DG, Wang JH, Kirwan WO, Cotter TG, Redmond HP.

Br J Cancer. 2009 May 5;100(9):1452-64. doi: 10.1038/sj.bjc.6604931.

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