Desmond G. Higgins

University College Dublin

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Papers

Citation

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i-10 index

Research Trends

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Document Type

Co-Authors

Peter Jehl

Food for Health Ireland

Jean Manguy

University College Dublin

Norman E. Davey

Institute of Cancer Research

Denis C. Shields

University College Dublin

Walter Kölch

University College Dublin

Donal J. Brennan

University College Dublin

William M. Gallagher

University College Dublin

Karin Jirström

Lund University

Aleksandar Krstić

University College Dublin

David J. Duffy

University of Florida

Cooperative Institutions

University College Dublin

187

Trinity College Dublin

University College Cork

European Bioinformatics Institute

National University of Ireland

Royal College of Surgeons in Ireland

Conway School of Landscape Design

Centre National de la Recherche Scientifique

St. Vincent's University Hospital

St. James's Hospital

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

Supplementary Figure 5 from miR-187 Is an Independent Prognostic Factor in Breast Cancer and Confers Increased Invasive Potential In Vitro

Laoighse Mulrane Stephen F. Madden Donal J. Brennan Gabriela Gremel Sharon F. McGee

PDF file - 47K, miR187 expression and patient outcome stratified according to ER status

10.1158/1078-0432.22451441

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Citations (0)

The copper regulon of the human fungal pathogen Cryptococcus neoformans H99

Molecular Microbiology (2011)

Chen Ding Jun Yin Edgar Mauricio Medina Tovar David Fitzpatrick Desmond G. Higgins

Cryptococcus neoformans is a human fungal pathogen that is the causative agent of cryptococcosis and fatal meningitis in immuno-compromised hosts. Recent studies suggest that copper (Cu) acquisition plays an important role in C. neoformans virulence, as mutants that lack Cuf1, which activates the Ctr4 high affinity Cu importer, are hypo-virulent in mouse models. To understand the constellation of Cu-responsive genes in C. neoformans and how their expression might contribute to virulence, we determined the transcript profile of C. neoformans in response to elevated Cu or Cu deficiency. We identified two metallothionein genes (CMT1 and CMT2), encoding cysteine-rich Cu binding and detoxifying proteins, whose expression is dramatically elevated in response to excess Cu. We identified a new C. neoformans Cu transporter, CnCtr1, that is induced by Cu deficiency and is distinct from CnCtr4 and which shows significant phylogenetic relationship to Ctr1 from other fungi. Surprisingly, in contrast to other fungi, we found that induction of both CnCTR1 and CnCTR4 expression under Cu limitation, and CMT1 and CMT2 in response to Cu excess, are dependent on the CnCuf1 Cu metalloregulatory transcription factor. These studies set the stage for the evaluation of the specific Cuf1 target genes required for virulence in C. neoformans.

Regulon

Efflux

10.1111/j.1365-2958.2011.07794.x

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Citations (105)

MIAH: automatic alignment of eukaryotic SSU rRNAs.

Bioinformatics (1999)

P Th√©bault P Monesti√©Annette McGrath Desmond G. Higgins

Abstract SUMMARY: MIAH is a WWW server for the automatic alignment of new eukaryotic SSU rRNA sequences to an existing alignment of 1500 sequences. AVAILABILITY: http://chah.ucc.ie/MIAH Contact :

10.1093/bioinformatics/15.4.341

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Citations (2)

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

Nucleic Acids Research (2007)

Sébastien Moretti Fabrice Armougom Iain M. Wallace Desmond G. Higgins C. Victor Jongeneel

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205–217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692–1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

Sequence (biology)

Multiple sequence alignment

R package

Alignment-free sequence analysis

10.1093/nar/gkm333

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Citations (228)

Supplementary Figure 4 from GSK3 Inhibitors Regulate MYCN mRNA Levels and Reduce Neuroblastoma Cell Viability through Multiple Mechanisms, Including p53 and Wnt Signaling

David J. Duffy Aleksandar Krstić Thomas Schwarzl Desmond G. Higgins Walter Kölch

PDF - 78K, Figure S4. Additional PFTalpha and GSK3 inhibitor co-treatment viability data. A. Attempted p53 mediated rescue of GSK3 inhibitor cell death phenotype across three cell lines as measured by MTS viability assay after 24h and 48h of treatment. Only BIO treatment in IMR32 and KCNR showed partial rescue upon PFTalpha co-treatment.

Viability assay

10.1158/1535-7163.22500351.v1

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Citations (0)

The fluvial-to-marine transition within the post-rift Lower Cambrian Hardyston Formation, Eastern Pennsylvania, USA

Sedimentary Geology (2002)

Edward L. Simpson Kelly A. Dilliard Bruce Fenton Rowell Desmond G. Higgins

Conglomerate

Trough (economics)

Siliciclastic

10.1016/s0037-0738(01)00193-2

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Citations (35)

Identification of fungi in shotgun metagenomics datasets

PLoS ONE (2018)

Paul D. Donovan Gabriel González Desmond G. Higgins Geraldine Butler Kimihito Ito

Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets. We focus primarily on animal metagenomes, especially those from pig and mouse microbiomes. We identified fungi in 39 of 70 datasets comprising 71 fungal species. At least 11 pathogenic species with zoonotic potential were identified, including Candida tropicalis. We identified Pseudogymnoascus species from 13 Antarctic soil samples initially analyzed for the presence of bacteria capable of degrading diesel oil. We also show that Candida tropicalis and Candida loboi are likely the same species. In addition, we identify several examples where contaminating DNA was erroneously included in fungal genome assemblies.

Amplicon

Shotgun

10.1371/journal.pone.0192898

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Citations (93)

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

Nucleic Acids Research (2016)

Peter Jehl Jean Manguy Denis C. Shields Desmond G. Higgins Norman E. Davey

Low-throughput experiments and high-throughput proteomic and genomic analyses have created enormous quantities of data that can be used to explore protein function and evolution. The ability to consolidate these data into an informative and intuitive format is vital to our capacity to comprehend these distinct but complementary sources of information. However, existing tools to visualize protein-related data are restricted by their presentation, sources of information, functionality or accessibility. We introduce ProViz, a powerful browser-based tool to aid biologists in building hypotheses and designing experiments by simplifying the analysis of functional and evolutionary features of proteins. Feature information is retrieved in an automated manner from resources describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterization of functional regions. These features are mapped to evolutionary information from precomputed multiple sequence alignments. Data are displayed in an interactive and information-rich yet intuitive visualization, accessible through a simple protein search interface. This allows users with limited bioinformatic skills to rapidly access data pertinent to their research. Visualizations can be further customized with user-defined data either manually or using a REST API. ProViz is available at http://proviz.ucd.ie/.

Interface (matter)

Feature (linguistics)

10.1093/nar/gkw265

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Citations (77)

Four additions to the Irish spider (Araneae) fauna.

Irish Naturalists' Journal/Irish naturalists' journal (1990)

Desmond G. Higgins

Source

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Citations (1)

Comparative Proteomics Profiling of a Phospholamban Mutant Mouse Model of Dilated Cardiomyopathy Reveals Progressive Intracellular Stress Responses

Molecular & Cellular Proteomics (2007)

Anthony O. Gramolini Thomas Kislinger Rasoul Alikhani-Koopaei Vincent Fong Natalie J. Thompson

Defective mobilization of Ca2+ by cardiomyocytes can lead to cardiac insufficiency, but the causative mechanisms leading to congestive heart failure (HF) remain unclear. In the present study we performed exhaustive global proteomics surveys of cardiac ventricle isolated from a mouse model of cardiomyopathy overexpressing a phospholamban mutant, R9C (PLN-R9C), and exhibiting impaired Ca2+ handling and death at 24 weeks and compared them with normal control littermates. The relative expression patterns of 6190 high confidence proteins were monitored by shotgun tandem mass spectrometry at 8, 16, and 24 weeks of disease progression. Significant differential abundance of 593 proteins was detected. These proteins mapped to select biological pathways such as endoplasmic reticulum stress response, cytoskeletal remodeling, and apoptosis and included known biomarkers of HF (e.g. brain natriuretic peptide/atrial natriuretic factor and angiotensin-converting enzyme) and other indicators of presymptomatic functional impairment. These altered proteomic profiles were concordant with cognate mRNA patterns recorded in parallel using high density mRNA microarrays, and top candidates were validated by RT-PCR and Western blotting. Mapping of our highest ranked proteins against a human diseased explant and to available data sets indicated that many of these proteins could serve as markers of disease. Indeed we showed that several of these proteins are detectable in mouse and human plasma and display differential abundance in the plasma of diseased mice and affected patients. These results offer a systems-wide perspective of the dynamic maladaptions associated with impaired Ca2+ homeostasis that perturb myocyte function and ultimately converge to cause HF.

Phospholamban

Shotgun proteomics

ATF6

Dilated Cardiomyopathy

10.1074/mcp.m700245-mcp200

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Citations (104)