D. Higgins

D. Higgins, Chaodong Zhu, M. Carr, 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

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

D. Higgins, Chaodong Zhu, W. Hall, 2012, Virology.

Detecting microRNA activity from gene expression data

Ian B. Jeffery, Desmond G. Higgins, Stephen F. Madden, 2010, BMC Bioinformatics.

Distinct Patterns in the Regulation and Evolution of Human Cancer Genes

Desmond G. Higgins, Stephen F. Madden, Simon J. Furney, 2008, Silico Biol..

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

Desmond G. Higgins, Audrey M. Michel, James P. A. Mullan, 2013, Nucleic Acids Res..

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

D. Higgins, G. Butler, M. Berriman, 2011, BMC Genomics.

Correlation between Biofilm Formation and the Hypoxic Response in Candida parapsilosis

D. Higgins, G. Butler, A. Guida, 2009, Eukaryotic Cell.

GSK3 Inhibitors Regulate MYCN mRNA Levels and Reduce Neuroblastoma Cell Viability through Multiple Mechanisms, Including p53 and Wnt Signaling

David J. Duffy, D. Higgins, W. Kolch, 2013, Molecular Cancer Therapeutics.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods

C. V. Jongeneel, Desmond G. Higgins, Iain M. Wallace, 2007, Nucleic Acids Res..

Loss of Olfactory Receptor Function in Hominin Evolution

Desmond G. Higgins, Emma C. Teeling, Graham M. Hughes, 2014, PloS one.

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

Fabian Sievers, Desmond G Higgins, D. Higgins, 2014, Methods in molecular biology.

The Birth and Death of Olfactory Receptor Gene Families in Mammalian Niche Adaptation

Graham M. Hughes, D. Higgins, W. Murphy, 2018, Molecular biology and evolution.

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

David J. Duffy, D. Higgins, W. Kolch, 2017, Genome Medicine.

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

David J. Duffy, D. Higgins, F. Westermann, 2015, Oncotarget.

Cancer Biology and Signal Transduction GSK 3 Inhibitors Regulate MYCN mRNA Levels and Reduce Neuroblastoma Cell Viability through Multiple Mechanisms , Including p 53 and Wnt Signaling

David J. Duffy, D. Higgins, W. Kolch, 2014 .

GSK3 inhibitors regulate MYCN mRNA levels and reduce neuroblastoma cell viability through multiple mechanisms including p53 and Wnt signalling Running title: GSK3 Inhibitors, Potential Neuroblastoma Therapeutic Agents

David J. Duffy, D. Higgins, T. Schwarzl, 2013 .

3DCoffee: combining protein sequences and structures within multiple sequence alignments.

Cédric Notredame, Orla O'Sullivan, Karsten Suhre, 2004, Journal of molecular biology.

Global MYCN Transcription Factor Binding Analysis in Neuroblastoma Reveals Association with Distinct E-Box Motifs and Regions of DNA Hypermethylation

Raymond L. Stallings, Kenneth Bryan, D. Higgins, 2009, PloS one.

Molecular evolution of immunoglobulin and fibronectin domains in titin and related muscle proteins.

D. Higgins, D G Higgins, P A Kenny, 1999, Gene.

Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis

D. Higgins, Jun Yin, B. Kennedy, 2014, BMC Genomics.

The Clustal Omega Multiple Alignment Package.

Fabian Sievers, Desmond G Higgins, D. Higgins, 2021, Methods in molecular biology.

MADE4: an R package for multivariate analysis of gene expression data

Guy Perrière, Aedín C. Culhane, Jean Thioulouse, 2005, Bioinform..

Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival

D. Higgins, M. O'sullivan, R. Stallings, 2009, PloS one.

QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction

Fabian Sievers, Desmond G Higgins, D. Higgins, 2019, Bioinform..

Integrating transcription factor binding site information with gene expression datasets

Ian B. Jeffery, Guy Perrière, Aedín C. Culhane, 2007, Bioinform..

Molecular evidence for the inclusion of cetaceans within the order Artiodactyla.

D. Higgins, D. Graur, Desmond G. Higgins, 1994, Molecular biology and evolution.

CLUSTAL V: multiple alignment of DNA and protein sequences.

D G Higgins, D. Higgins, D G Higgins, 1994, Methods in molecular biology.

The salmon gene encoding apolipoprotein A-I: cDNA sequence, tissue expression and evolution.

D. Higgins, P. Sharp, F. Gannon, 1991, Gene.

Transcriptional profiling of early differentiation of primary human mesenchymal stem cells into chondrocytes

D. Higgins, W. Kolch, G. Shaw, 2021, bioRxiv.

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

Desmond G. Higgins, Pádraig Cunningham, Andreas Wilm, 2009, Nucleic acids research.

Sequence analysis of DNA randomly amplified from the Saccharomyces cerevisiae genome.

D. Higgins, T. McCarthy, A. McGrath, 1998, Molecular and cellular probes.

The evolution of titin and related giant muscle proteins

D. Higgins, T. Gibson, M. Gautel, 1994, Journal of Molecular Evolution.

GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content

Desmond G. Higgins, Denis C. Shields, P. M. Sharp, 1992, Comput. Appl. Biosci..

Temporal change in gene expression in the rat dentate gyrus following passive avoidance learning

K. J. Murphy, D. Higgins, C. Regan, 2007, Journal of neurochemistry.

Between-group analysis of microarray data

Guy Perrière, Aedín C. Culhane, Desmond G. Higgins, 2002, Bioinform..

OD-seq: outlier detection in multiple sequence alignments

Desmond G. Higgins, Fabian Sievers, Peter Jehl, 2015, BMC Bioinformatics.

R-Coffee: a web server for accurately aligning noncoding RNA sequences

Ioannis Xenarios, Desmond G. Higgins, Andreas Wilm, 2008, Nucleic Acids Res..

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

D. Higgins, Jun Yin, B. Kennedy, 2011, Developmental dynamics : an official publication of the American Association of Anatomists.

Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response

D. Higgins, M. Duffy, A. Culhane, 2005, Expert opinion on biological therapy.

BACILLUS SUBTILIS GENE SEQUENCES

Desmond G. Higgins, Denis C. Shields, D. Higgins, 1990 .

Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data

Ian B. Jeffery, Aedín C. Culhane, Desmond G. Higgins, 2006, BMC Bioinformatics.

COFFEE: an objective function for multiple sequence alignments

Liisa Holm, Desmond G. Higgins, Cédric Notredame, 1998, Bioinform..

Molecular phylogeny of the subgenus Sophophora of Drosophila derived from large subunit of ribosomal RNA sequences

D. Higgins, M. Solignac, M. Pélandakis, 2004, Genetica.

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

Fabian Sievers, Desmond G Higgins, Kieran Boyce, 2015, Proceedings of the National Academy of Sciences.

TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida

Desmond G Higgins, D. Higgins, G. Butler, 2018, PLoS genetics.

CENP‐F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer

Aedín C Culhane, Desmond G Higgins, Karin Jirström, 2007, International journal of cancer.

Cross-platform comparison and visualisation of gene expression data using co-inertia analysis

Guy Perrière, Aedín C. Culhane, Desmond G. Higgins, 2003, BMC Bioinformatics.

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

Desmond G. Higgins, Denis C. Shields, Norman E. Davey, 2016, Nucleic Acids Res..

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

Markus S. Schröder, D. Higgins, G. Butler, 2016, PLoS genetics.

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

D. Higgins, P. Carmeliet, A. von Kriegsheim, 2016, Biochemical and biophysical research communications.

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

David J. Duffy, D. Higgins, W. Kolch, 2017, Genome Medicine.

Analysis and Comparison of Benchmarks for Multiple Sequence Alignment

Desmond G. Higgins, Mark A. Larkin, Gordon Blackshields, 2006, Silico Biol..

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

D. Higgins, G. Blackshields, E. Campbell, 2017, Cell Death and Differentiation.

A Complete Analysis of HA and NA Genes of Influenza A Viruses

Desmond G. Higgins, Fumin Lei, Fabian Sievers, 2010, PloS one.

Instability in progressive multiple sequence alignment algorithms

D. Higgins, Fabian Sievers, Kieran Boyce, 2015, Algorithms for Molecular Biology.

Inhibition of the Pim1 Oncogene Results in Diminished Visual Function

Alison L. Reynolds, D. Higgins, D. Hyde, 2012, PloS one.

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

Desmond G. Higgins, Gordon Blackshields, Andreas Wilm, 2010, Algorithms for Molecular Biology.

Evaluation of iterative alignment algorithms for multiple alignment

Desmond G. Higgins, Iain M. Wallace, Orla O'Sullivan, 2005, Bioinform..

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

Desmond G. Higgins, Fabian Sievers, Gearoid Fox, 2015, Bioinform..

Supporting Online Material Materials and Methods Figs. S1 to S13 Tables S1 to S3 References Label-free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy

Mortazavi, D. Higgins, X. Xie, 2022 .

Supervised multivariate analysis of sequence groups to identify specificity determining residues

Desmond G. Higgins, Iain M. Wallace, D. Higgins, 2007, BMC Bioinformatics.

Protein multiple sequence alignment benchmarking through secondary structure prediction

Quan Le, Desmond G. Higgins, Fabian Sievers, 2017, Bioinform..

Ensemble approach combining multiple methods improves human transcription start site prediction

Pádraig Cunningham, Markus Schröder, Desmond G Higgins, 2010, BMC Genomics.

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

Fabian Sievers, Desmond G Higgins, Kieran Boyce, 2014, Proceedings of the National Academy of Sciences.

Overlapping Antisense Transcription in the Human Genome

D. Higgins, T. Moore, M. E. Fahey, 2002, Comparative and functional genomics.

Plasmodium falciparum appears to have arisen as a result of lateral transfer between avian and human hosts.

D. Higgins, T. McCutchan, A. Waters, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Making automated multiple alignments of very large numbers of protein sequences

Desmond G. Higgins, Andreas Wilm, Fabian Sievers, 2013, Bioinform..

APDB: a web server to evaluate the accuracy of sequence alignments using structural information

Desmond G. Higgins, Fabrice Armougom, Sébastien Moretti, 2006, Bioinform..

Detecting microRNA activity from gene expression data

D. Higgins, I. Jeffery, S. Madden, 2010, BMC Bioinformatics.

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

David J. Duffy, D. Higgins, F. Westermann, 2015, Oncotarget.

Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data

D. Higgins, A. Culhane, I. Jeffery, 2006, BMC Bioinformatics.

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

D. Higgins, Fabian Sievers, Kieran Boyce, 2014, Proceedings of the National Academy of Sciences.

OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity

Jaap Heringa, Desmond G. Higgins, Hubert Sommerfeldt, 1992, Comput. Appl. Biosci..

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

D. Higgins, J. Wang, T. Cotter, 2009, British Journal of Cancer.

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

Desmond G. Higgins, Fabian Sievers, Graham M. Hughes, 2014, BMC Bioinformatics.

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

Audrey M. Michel, Claire A. Donohue, Patrick B. F. O'Connor, 2013, Nucleic Acids Res..