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List of works by Desmond G. Higgins

"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons

scientific article

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

scientific article published in July 2004

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

scientific article

A multivariate analysis approach to the integration of proteomic and gene expression data

scientific article

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.

scientific article

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

scientific article published on October 2006

Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer

scientific article

Amino acid-based phylogeny and alignment

scientific article

Analysis and comparison of benchmarks for multiple sequence alignment

article

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

scientific article published on May 2009

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

scientific article

Between-group analysis of microarray data

scientific article

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

scientific article published on April 2007

CLUSTAL V: improved software for multiple sequence alignment ⬇️

scientific article (publication date: April 1992)

CLUSTAL V: multiple alignment of DNA and protein sequences

scientific article published in January 1994

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

scientific article

COFFEE: an objective function for multiple sequence alignments

scientific article

Clustal

software for multiple sequence alignment

Clustal Omega for making accurate alignments of many protein sequences

scientific article published on 7 September 2017

Clustal Omega, accurate alignment of very large numbers of sequences

scientific article published in January 2014

Clustal W and Clustal X version 2.0

scientific article (publication date: November 2007)

Clustal omega

2014 scientific article

Co-regulation of Gremlin and Notch signalling in diabetic nephropathy

scientific article published on 11 October 2007

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

scientific article

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

scientific article

Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses

scientific article

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

scientific article

Correlation between biofilm formation and the hypoxic response in Candida parapsilosis

scientific article published on 16 January 2009

Detecting microRNA activity from gene expression data

scientific article

Distinct patterns in the regulation and evolution of human cancer genes

article

EMBLSCAN: fast approximate DNA database searches on compact disc

scientific article published in April 1992

Empirical estimation of the reliability of ribosomal RNA alignments

scientific article published in January 1998

Ensemble approach combining multiple methods improves human transcription start site prediction

scientific article

Evaluation of iterative alignment algorithms for multiple alignment

scientific article published on 25 November 2004

Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen

scientific article

Evolutionary relatedness of some primate models of Plasmodium

scientific article published in July 1993

Fast embedding methods for clustering tens of thousands of sequences

scientific article published on 26 March 2008

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

scientific article (publication date: 11 October 2011)

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

scientific article

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

scientific article

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

scientific article published on 26 November 2013

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

scientific article published on 31 October 2013

Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis

scientific article published in September 2007

Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis

scientific article

Getting better with bifidobacteria

scientific article

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

scientific article published on 26 March 2013

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

scientific article published on December 2009

Hypoxia selectively activates the CREB family of transcription factors in the in vivo lung

scientific article published on 8 August 2008

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

scientific article

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

scientific article published on 27 February 2012

Improved sensitivity of profile searches through the use of sequence weights and gap excision

scientific article published in February 1994

Influence of acute phytochemical intake on human urinary metabolomic profiles

scientific article

Inhibition of the Pim1 oncogene results in diminished visual function

scientific article

Instability in progressive multiple sequence alignment algorithms

scientific article

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

scientific article

Integrating transcription factor binding site information with gene expression datasets

scientific article published on 24 November 2006

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

scientific article published on 11 December 2015

Loss of olfactory receptor function in hominin evolution

scientific article (publication date: 2014)

M-Coffee: combining multiple sequence alignment methods with T-Coffee

scientific article

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

scientific article

MIAH: automatic alignment of eukaryotic SSU rRNAs

scientific article published on 01 April 1999

Making automated multiple alignments of very large numbers of protein sequences

scientific article published on 21 February 2013

Malarial proteinase?

scientific article published in Nature

Maternally and paternally silenced imprinted genes differ in their intron content

scientific article published on January 2004

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

scientific article published on 8 September 2015

Mind the gaps: progress in progressive alignment

scientific article

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

scientific article published on 01 May 1999

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

scientific article

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

scientific article (publication date: November 2016)

Multiple Sequence Alignment

article

Multiple sclerosis and molecular mimicry

scientific article published on 01 April 1990

Multiple sequence alignment with the Clustal series of programs

scientific article

Multireplicon genome architecture of Lactobacillus salivarius

scholarly article

Non-muscle and smooth muscle myosin light chain kinases: no end in sight

scientific article published on January 1993

OD-seq: outlier detection in multiple sequence alignments

scientific article published on 25 August 2015

Optimization of ribosomal RNA profile alignments

scientific article published in January 1998

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

scientific article published on April 1991

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

scientific article

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

scientific article published on 26 April 2016

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

scientific article

RAGA: RNA sequence alignment by genetic algorithm

scientific article

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

scientific article

Regulation of the hypoxic response in Candida albicans

scientific article published on 24 September 2010

Replication and segregational stability of Bacillus plasmid pBAA1

scientific article

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

scientific article published on 6 January 2015

SAGA: sequence alignment by genetic algorithm

scientific article

Sequence analysis of DNA randomly amplified from the Saccharomyces cerevisiae genome

scientific article

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

scientific article published on 14 May 2010

Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets ⬇️

scientific article published on February 1, 1992

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

scientific article

Structural and functional properties of genes involved in human cancer

scientific article

Subgenotype reclassification of genotype B hepatitis B virus.

scientific article

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

scientific article

Supervised multivariate analysis of sequence groups to identify specificity determining residues

scientific article

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

scientific article

T-Coffee: A novel method for fast and accurate multiple sequence alignment

scientific article (publication date: 8 September 2000)

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

scientific article published on 31 May 2018

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

scientific article published on 9 February 2007

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

scientific article published on 24 January 2010

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

scientific article published in December 1997

The EMBL Data Library

scientific article

The EMBL data library

scientific article published on 01 July 1993

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

scientific article published on 25 May 2007

The Phylogeny of malaria: a useful study

scientific article published in July 1993

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

scientific article published on 23 August 2011

The evolution of titin and related giant muscle proteins

scientific article published on 01 April 1994

The relative evolution of Plasmodium.

scientific article published in January 1991

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

scientific article

Using CLUSTAL for multiple sequence alignments

scientific article (publication date: 1996)

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

scientific article published on 9 March 2013

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

scientific article

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

scientific article

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

scientific article

Wnt signalling is a bi-directional vulnerability of cancer cells

scientific article published on 11 August 2016

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

scientific article published on 28 February 2011

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

scientific article

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