Desmond G. Higgins

Desmond G. Higgins's AcademicInfluence.com Rankings

Desmond G. Higgins

Biology

#1220

World Rank

#2076

Historical Rank

Bioinformatics

World Rank

Historical Rank

biology Degrees

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Biology

Why Is Desmond G. Higgins Influential?

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According to Wikipedia, Desmond Gerard Higgins is a Professor of Bioinformatics at University College Dublin, widely known for CLUSTAL, a series of computer programs for performing multiple sequence alignment. According to Nature, Higgins' papers describing CLUSTAL are among the top ten most highly cited scientific papers of all time.

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Desmond G. Higgins's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. (1994) (64052)
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. (1997) (39059)
Clustal W and Clustal X version 2.0 (2007) (25261)
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega (2011) (11978)
T-Coffee: A novel method for fast and accurate multiple sequence alignment. (2000) (6860)
Multiple sequence alignment with the Clustal series of programs (2003) (5031)
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. (1988) (3453)
Multiple sequence alignment with Clustal X. (1998) (2656)
CLUSTAL V: improved software for multiple sequence alignment (1992) (2406)
Multiple Sequence Alignment Using ClustalW and ClustalX (2003) (2332)
Using CLUSTAL for multiple sequence alignments. (1996) (1638)
Fast and sensitive multiple sequence alignments on a microcomputer (1989) (1275)
Clustal Omega, accurate alignment of very large numbers of sequences. (2014) (957)
Clustal Omega for making accurate alignments of many protein sequences (2018) (952)
M-Coffee: combining multiple sequence alignment methods with T-Coffee (2006) (575)
SAGA: sequence alignment by genetic algorithm. (1996) (574)
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. (1988) (572)
"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. (1988) (545)
Clustal Omega (2014) (470)
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data (2006) (396)
MADE4: an R package for multivariate analysis of gene expression data (2005) (350)
3DCoffee: combining protein sequences and structures within multiple sequence alignments. (2004) (350)
Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor (2011) (344)
Finding flexible patterns in unaligned protein sequences (1995) (335)
Getting better with bifidobacteria (2005) (330)
Improved sensitivity of profile searches through the use of sequence weights and gap excision (1994) (328)
CLUSTAL V: multiple alignment of DNA and protein sequences. (1994) (313)
COFFEE: an objective function for multiple sequence alignments (1998) (270)
Between-group analysis of microarray data (2002) (237)
Multireplicon genome architecture of Lactobacillus salivarius. (2006) (226)
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods (2007) (212)
GWIPS-viz: development of a ribo-seq genome browser (2013) (210)
Molecular evidence for the inclusion of cetaceans within the order Artiodactyla. (1994) (170)
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis (2003) (161)
RAGA: RNA sequence alignment by genetic algorithm. (1997) (150)
Influence of acute phytochemical intake on human urinary metabolomic profiles. (2007) (133)
Multiple sequence alignments. (2005) (128)
Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival (2009) (123)
Co-regulation of Gremlin and Notch signalling in diabetic nephropathy. (2008) (116)
Regulation of the Hypoxic Response in Candida albicans (2010) (116)
Sequence embedding for fast construction of guide trees for multiple sequence alignment (2010) (114)
R-Coffee: a method for multiple alignment of non-coding RNA (2008) (112)
CENP‐F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer (2007) (109)
Comparative Proteomics Profiling of a Phospholamban Mutant Mouse Model of Dilated Cardiomyopathy Reveals Progressive Intracellular Stress Responses*S (2008) (106)
Altered Cytoplasmic-to-Nuclear Ratio of Survivin Is a Prognostic Indicator in Breast Cancer (2008) (99)
Comparative Phenotypic Analysis of the Major Fungal Pathogens Candida parapsilosis and Candida albicans (2014) (97)
Hepatitis B virus subgenotyping: history, effects of recombination, misclassifications, and corrections. (2013) (95)
Structural and functional properties of genes involved in human cancer (2006) (91)
Correlation between Biofilm Formation and the Hypoxic Response in Candida parapsilosis (2009) (85)
The Clustal Omega Multiple Alignment Package. (2021) (81)
Global MYCN Transcription Factor Binding Analysis in Neuroblastoma Reveals Association with Distinct E-Box Motifs and Regions of DNA Hypermethylation (2009) (80)
The Birth and Death of Olfactory Receptor Gene Families in Mammalian Niche Adaptation (2018) (78)
Evaluation of iterative alignment algorithms for multiple alignment (2005) (78)
A multivariate analysis approach to the integration of proteomic and gene expression data (2007) (78)
Analysis and Comparison of Benchmarks for Multiple Sequence Alignment (2006) (76)
miR-187 Is an Independent Prognostic Factor in Breast Cancer and Confers Increased Invasive Potential In Vitro (2012) (75)
The copper regulon of the human fungal pathogen Cryptococcus neoformans H99 (2011) (72)
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis (2011) (72)
GSK3 Inhibitors Regulate MYCN mRNA Levels and Reduce Neuroblastoma Cell Viability through Multiple Mechanisms, Including p53 and Wnt Signaling (2013) (72)
R-Coffee: a web server for accurately aligning noncoding RNA sequences (2008) (70)
Hypoxia selectively activates the CREB family of transcription factors in the in vivo lung. (2008) (65)
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments (2003) (65)
Prophage-Like Elements in Bifidobacteria: Insights from Genomics, Transcription, Integration, Distribution, and Phylogenetic Analysis (2005) (64)
Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets (1992) (64)
Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response (2005) (62)
Identification of fungi in shotgun metagenomics datasets (2018) (61)
Molecular evolution of immunoglobulin and fibronectin domains in titin and related muscle proteins. (1999) (61)
Making automated multiple alignments of very large numbers of protein sequences (2013) (61)
Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species (2016) (53)
Bioinformatics : sequence, structure, and databanks (2000) (53)
ProViz—a web-based visualization tool to investigate the functional and evolutionary features of protein sequences (2016) (52)
Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis. (2012) (50)
A Complete Analysis of HA and NA Genes of Influenza A Viruses (2010) (50)
Temporal change in gene expression in the rat dentate gyrus following passive avoidance learning (2007) (48)
Overlapping Antisense Transcription in the Human Genome (2002) (44)
OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity (1992) (43)
Integrating transcription factor binding site information with gene expression datasets (2007) (43)
Detecting microRNA activity from gene expression data (2010) (40)
Protein multiple sequence alignment benchmarking through secondary structure prediction (2017) (40)
The salmon gene encoding apolipoprotein A-I: cDNA sequence, tissue expression and evolution. (1991) (40)
Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification (2009) (39)
Simple chained guide trees give high-quality protein multiple sequence alignments (2014) (38)
Molecular phylogeny of the subgenus Sophophora of Drosophila derived from large subunit of ribosomal RNA sequences (2004) (36)
OD-seq: outlier detection in multiple sequence alignments (2015) (36)
Recombination in Hepatitis C Virus: Identification of Four Novel Naturally Occurring Inter-Subtype Recombinants (2012) (36)
Multiple sequence alignment. (2000) (34)
Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma (2015) (31)
An Integrated Global Analysis of Compartmentalized HRAS Signaling. (2019) (29)
Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance (2017) (29)
Subgenotyping of Genotype C Hepatitis B Virus: Correcting Misclassifications and Identifying a Novel Subgenotype (2012) (28)
Loss of Olfactory Receptor Function in Hominin Evolution (2014) (28)
Wnt signalling is a bi-directional vulnerability of cancer cells (2016) (27)
The Cu regulon of the human fungal pathogen Cryptococcus neoformans H99: Cuf1 activates distinct genes in response to both Cu excess and deficiency (2011) (26)
Subgenotype reclassification of genotype B hepatitis B virus (2012) (26)
Prolyl hydroxylase-1 regulates hepatocyte apoptosis in an NF-κB-dependent manner. (2016) (26)
Supervised multivariate analysis of sequence groups to identify specificity determining residues (2007) (26)
Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments (2015) (25)
GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content (1992) (24)
Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis (2014) (23)
Instability in progressive multiple sequence alignment algorithms (2015) (23)
Bioinformatics: Sequence, Structure, and Databanks: A Practical Approach (2000) (23)
Inhibition of the Pim1 Oncogene Results in Diminished Visual Function (2012) (22)
Gene Expression, Intron Density, and Splice Site Strength in Drosophila and Caenorhabditis (2007) (21)
TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida (2018) (21)
Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data (2010) (19)
High DNA melting temperature predicts transcription start site location in human and mouse (2009) (18)
Using Illumina next generation sequencing technologies to sequence multigene families in de novo species (2013) (18)
Sequence analysis of DNA randomly amplified from the Saccharomyces cerevisiae genome. (1998) (18)
Mind the gaps: progress in progressive alignment. (2005) (18)
mab21l2 transgenics reveal novel expression patterns of mab21l1 and mab21l2, and conserved promoter regulation without sequence conservation (2011) (16)
Distinct Patterns in the Regulation and Evolution of Human Cancer Genes (2008) (15)
BACILLUS SUBTILIS GENE SEQUENCES (1990) (15)
The evolution of titin and related giant muscle proteins (1994) (14)
Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification. (2015) (12)
Interfacing similarity search software with the sequence retrieval system ACNUC (1987) (12)
Systematic exploration of guide-tree topology effects for small protein alignments (2014) (11)
An intrinsically disordered proteins community for ELIXIR (2019) (11)
Scoring Function for Pattern Discovery Programs Taking Into Account Sequence Diversity (1996) (11)
QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction (2019) (10)
Multiple sequence alignment using Clustal Omega (2015) (10)
Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments (2015) (9)
A SAT-Based Approach to Multiple Sequence Alignment (2003) (8)
Identification of Non-Coding RNAs in the Candida parapsilosis Species Group (2016) (7)
Optimization of ribosomal RNA profile alignments (1998) (7)
Empirical estimation of the reliability of ribosomal RNA alignments (1998) (6)
MyD88 is an essential component of retinoic acid-induced differentiation in human pluripotent embryonal carcinoma cells (2017) (5)
Fast embedding methods for clustering tens of thousands of sequences (2008) (5)
Ensemble approach combining multiple methods improves human transcription start site prediction (2010) (4)
9 – Multiple Sequence Alignment (1997) (3)
Pseudo-Boolean Multiple Sequence Alignment (2000) (3)
Maternally and Paternally Silenced Imprinted Genes Differ in Their Intron Content (2004) (3)
The Phylogenetic Handbook: Multiple sequence alignment (2009) (3)
MIAH: automatic alignment of eukaryotic SSU rRNAs (1999) (2)
Abstract 4049: MiR-187 is a marker of poor prognosis in estrogen receptor-positive breast cancer (2010) (1)
Amino acid-based phylogeny and alignment. (2000) (1)
Abstract 2878: The tumor-permissive role of KHSRP in colorectal cancer: Mechanistic insights from a gene expression study (2016) (1)
APDB: a web server to evaluate the accuracy of sequence alignments using structural information (2006) (1)
An intrinsically disordered proteins community for ELIXIR [version 1; peer review: 2 approved] (2020) (1)
Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis (2014) (1)
ProViz - protein interactive exploration tool (2016) (1)
EMBLSCAN: fast approximate DNA database searches on compact disc (1992) (1)
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 (2013) (0)
ProViz - APC/C activator protein CDC20 - CDC20 - P26309 (2016) (0)
Book Review: Dictionary of Bioinformatics and Computational Biology. By Hancock, John M. and Zvelebil, Marketa J. (Eds) (2005) (0)
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 (2014) (0)
ProViz - Histone deacetylase 4 - HDAC4 - P56524 (2016) (0)
Systematic exploration of guide-tree topology effects for small protein alignments (2014) (0)
05.02 Differentiating patient responses in rheumatoid arthritis – systems analysis of key molecular networks (2017) (0)
ProViz - Mitotic checkpoint serine/threonine-protein kinase BUB1 - BUB1 - O43683 (2016) (0)
ProViz - Putative cyclin-A3-1 - CYCA3-1 - Q9FMH5 (2016) (0)
Maternally and paternally silenced imprinted genes differ in their intron content: Research Papers (2004) (0)
ProViz - Putative histone deacetylase - LMJF_08_1090 - Q4QI60 (2016) (0)
ProViz - Replication protein E1 - E1 - P03116 (2016) (0)
Book Review: Introduction to Mathematical Methods in Bioinformatics. By Alexander Isaev (2005) (0)
ProViz - Envelope small membrane protein - E - P0DTC4 (2016) (0)
ProViz - Histone deacetylase superfamily - Caur_0342 - A9WD24 (2016) (0)
ProViz - Securin - PTTG1 - O95997 (2016) (0)
Multiple alignments get faster and better: Speech recognition and sequences (2004) (0)
193 MiR-187 is an Independent Prognostic Factor in Breast Cancer (2012) (0)
ProViz - Serine/threonine-protein kinase Haspin homolog ALK1 - ALK1 - P43633 (2016) (0)
Title Fast , scalable generation of high-quality protein multiplesequence alignments using Clustal Omega (2017) (0)
ProViz - Filament protein FIN1 - FIN1 - Q03898 (2016) (0)
ProViz - Cell division control protein 6 homolog - CDC6 - Q99741 (2016) (0)
Abstract P4-09-06: miR-187 is an independent prognostic factor in lymph node-positive breast cancer patients. (2012) (0)
ProViz - Origin recognition complex subunit 1 - Orc1 - O16810 (2016) (0)
ProViz - Aurora kinase B - AURKB - Q96GD4 (2016) (0)
ProViz - Cyclin-dependent kinase inhibitor 1B - CDKN1B - P46527 (2016) (0)
ProViz - BRCA1-associated RING domain protein 1 - BARD1 - Q99728 (2016) (0)
ResearchSequence embedding for fast construction of guide trees for multiple sequence alignment (0)
Author's response to reviews Title: Subgenotype reclassification of genotype B hepatitis B virus Authors: (2012) (0)
ProViz - ORF9b protein - 9b - P0DTD2 (2016) (0)
ProViz - Protein mes1 - mes1 - P41005 (2016) (0)
Demystifying the net, Simon R. Swindell, R. Russell Miller, Garry S.A. Myers (Eds.), in: Internet for the Molecular Biologist. Horizon Scientific Press (1996), 187, UK£19.99, ISBN: 1 898486 02 6 (1996) (0)
ProViz - Uncharacterized protein slr0245 - slr0245 - P72702 (2016) (0)
ProViz - Securin - cut2 - P21135 (2016) (0)
ProViz - 3-oxoacyl-[acyl-carrier-protein] reductase Oar2 - SJAG_03198 - B6K3K8 (2016) (0)
ProViz - Histone-lysine N-methyltransferase EHMT1 - EHMT1 - Q9H9B1 (2016) (0)
Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance (2017) (0)
Title OD-seq : outlier detection in multiple sequence alignments (2017) (0)
ProViz - Proto-oncogene tyrosine-protein kinase Src - SRC - P12931 (2016) (0)
ProViz - Signal transducing adapter molecule 2 - STAM2 - O75886 (2016) (0)
UNIT 3 . 13 Clustal Omega (2014) (0)
ProViz - Spike glycoprotein - S - P0DTC2 (2016) (0)
ProViz - Protein POLYCHOME - PYM - O48533 (2016) (0)
ProViz - Hyaluronan mediated motility receptor - HMMR - O75330 (2016) (0)
Instability in progressive multiple sequence alignment algorithms (2015) (0)
Su2021 The Tumor-Permissive Role of KHSRP as a Target for the Polyphenol Resveratrol: Potential Tumor-Suppressive Effects in a Pre-Clinical Model of Colorectal Cancer (2016) (0)
OD-seq: outlier detection in multiple sequence alignments (2015) (0)
ProViz - Cell division cycle protein 20 homolog - CDC20 - Q12834 (2016) (0)
ProViz - Acetoin utilization protein - acuC2 - O67877 (2016) (0)
ProViz - Cell cycle serine/threonine-protein kinase CDC5/MSD2 - CDC5 - P32562 (2016) (0)
Building Optimal Score Computation (1998) (0)
New center to study environmental impacts on reproductive risk. (1996) (0)
Transcriptional profiling of early differentiation of primary human mesenchymal stem cells into chondrocytes (2021) (0)
ProViz - Serine/threonine-protein kinase Nek2 - NEK2 - P51955 (2016) (0)
ProViz - Protein non-structural 7b - - P0DTD8 (2016) (0)
ProViz - S-phase entry cyclin-5 - CLB5 - P30283 (2016) (0)
ProViz - Non-structural protein 6 - 6 - P0DTC6 (2016) (0)
Systematic validation of novel breast cancer progression-associated biomarkers via high-throughput antibody generation and application of tissue microarray technology (2007) (0)
ProViz - Transcription factor NRM1 - NRM1 - P53718 (2016) (0)
ProViz - Membrane protein - - P0DTC5 (2016) (0)
P28: Advanced image analysis of immunohistochemistry on tumour specimens (2009) (0)
Table of Contents (1994) (0)
ProViz - Cell division cycle-associated protein 3 - CDCA3 - Q99618 (2016) (0)
ProViz - Ras GTPase-activating-like protein IQG1 - IQG1 - Q12280 (2016) (0)

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Desmond G. Higgins's Academic­Influence.com Rankings