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Early Career Researchers A-Z

Dr Marina Alamanou



Dr Luis Alvarez



Dr Anna Aulicino



Dr Azadeh Beizaei



Dr Maria Bengoechea



Dr Kevin Byrne

Keywords: Genomics, evolution, bioinformatics, model organisms, yeast, data visualisation

Kevin’s research is focused on using genomics to address biological and evolutionary questions in model organisms primarily employing bioinformatics approaches. Yeasts have been a system of particular interest. The visualization and analysis of complex data is a key aspect of his work (for example see ygob.ucd.ie)


Dr Federico Cerrone

Keywords: Biorefining, polyhydroxyalkanoates, biocatalysis, high cell density fermentation, smart biopolymers, bioscaffolding

My research focuses on renewable resource conversion into biodegradable polymers through high cell density fermentation. A follow-up of this biopolymers production is to find an application into the biomedical sector, in particular as “smart” bioscaffolds for nerve cell regeneration. I am also involved in lactic acid production from food waste.


Dr Anthony Chubb

Keywords: Cheminformatics, molecular modelling, drug discovery, malaria, TB, distributed computation, molecular biology, structural biology

My pre-doctoral training is in molecular and cellular biology while my post-doctoral training includes structural biology, cheminformatics and computer-aided drug design. At present I am focusing on target discovery in malaria using a massively distributed computation to dock all lead compounds into all available model structures from the malaria proteome. My goal is to discover and develop at least one novel therapeutic drug.


Dr Aoife Cooke

Keywords: Inflammation, drug development, novel therapies

My project is a collaboration with Helsinn investigating the potential anti-inflammatory effect of an established class of drugs. My work aims to establish whether these drugs which are currently in clinical testing for palliative cancer therapy may have a broader range of applications in inflammatory disease.


Dr Gordon Cooke

Keywords: Translational medicine, microbiology, cell culture, molecular biology

My research to date has focused on translational medicine. I have worked on and published in the following areas: cancer (Barretts Metaplasia), respiratory disease (Sarcoidosis, Idiopathic Pulmonary Fibrosis and Cystic Fibrosis) and microbiology (gut flora of breast and formula fed new born babies)


Dr Sudipto Das



Dr Reeta Davis

Keywords: Biocatalysis, polyhydroxyalkanoates, high cell density, fermentation, biomass conversion

My research focuses on the conversion of non-food, renewable agricultural waste to value added products such as biodegradable plastic through bacterial fermentations. In addition, I am using purified enzymes as biocatalyst for the synthesis of small molecules that have uses as drugs or drug precursor.


Dr Eugene Dempsey



Dr Eugene Dillion



Dr Maciej Dobrzy?ski

Keywords: Systems biology, signalling pathways, modelling, heterogeneity, stochasticity, live-imaging, flow cytometry, FRET/FLIM imaging

I focus on mathematical modelling and experimental validation of cell fate decision-making by mammalian signal transduction pathways. In particular, I’m interested in molecular mechanisms behind the emergence of drug resistance of cancer cells.


Dr Emma Dorris



Dr Jane English



Dr Yue Fan



Dr Paul Fitzpatrick



Dr Brian Flatley

Keywords: Mass spectrometry; proteomics; prostate cancer;

The focus of my research is mass spectrometry based proteomics. The application of the technique is multifaceted including in-depth proteomic analysis of biological samples for identification of potential biomarkers or the quantitative measurement of target biomarkers using more high- throughput systems.


Dr Cristina Gamba



Dr Katherine Gaynor

Keywords: Fibrotic lung disease, Gremlin, idiopathic pulmonary fibrosis, sarcoidosis

My research involves investigating key mechanisms in the development and progression of fibrotic lung diseases and developing assays to monitor disease progression in a clinical setting.


Dr Nadezhda Glezeva



Dr Jill Guyonnet

Keywords: Atomic force microscopy, piezoelectricity, ferroelectricity, collagen

My research interests revolve around probing mechanical and electronic properties of matter at the nanoscale via atomic force microscopy. With past experience on ferroelectric thin films in ambient and ultrahigh vacuum conditions, my current research addresses piezoelectric properties of self-assembled collagen matrices in ambient and liquid environments.


Dr Melinda Halasz

Keywords: Neuroblastoma, cell signalling, proteomics, Zebrafish

My goal is to analyse the signalling and transcriptional networks that drive highly aggressive embryonal tumours by using -omics and systems biology approaches.


Dr Stephen Hammel



Dr Sara Hanson

Keywords: Yeast, genomics, genetics, evolution, mating type

My research examines the evolution of sexual reproduction and mating systems in eukaryotes. In particular, my work focuses on the origin of mating type switching mechanisms in ascomycete yeasts using molecular biology and classical genetics techniques. 


Dr Debra Higgins

Keywords: Kidney disease, fibrosis, hypoxia, hypoxia inducible factor (HIF), renal biomarker, diagnostic and prognostic biomarkers, inflammation, diabetic nephropathy, gene expression

Investigating the role of hypoxia through HIF-mediated pathways in development and progression of kidney disease and exploiting this knowledge to develop novel diagnostic and treatment strategies for kidney disease.


Dr Thérèse Holton

Keywords: Bioinformatics, milk, peptides, food for health

Thérèse is a bioinformatician with a PhD in eukaryote phylogenomics. Her research focuses on the computational analysis of potentially bioactive peptides in milk as part of the Food for Health Ireland consortium. She is also interested in the evolution of milk proteins and the enzymes associated with their digestion.


Dr Daniel Jones



Dr Rosemary Kane



Dr Susan Kennedy

Keywords: Protein-protein interactions, EGFR network, colorectal cancer, systems biology

I am part of the PRIMES team in SBI. My work focuses on protein-protein interactions in the EGFR network in relation to colorectal cancer. I am using a variety of proteomic techniques and Mass Spectrometry to analyse interactions which occur in the hope of identifying novel therapeutic targets.


Dr Kate Killick



Dr Devrim Kilinc

Keywords: Neuroscience; microfludics; magnetic tweezers; nanorods

I am interested in the mechanisms with which cells especially neurons interact with the physical environment they are in and mechanical cues they receive. To this end I develop microfluidic culture devices to control the chemical environment and apply external forces via the magnetic tweezers method.


Dr Rut Klinger



Dr Lidija Kovacic



Dr Gosia Kubica



Dr Stefanie Kuhns



Dr Henriette Laursen



Dr Lili Li



Dr Bartlomiej Lukasz



Dr Iain MacAulay



Dr Ashwini Maratha



Dr Alexandre Martos



Dr Lorraine McGill



Dr Katey McKayed

Keywords: High-content screening and automated image analysis, cytoskeletal and focal adhesion dynamics, mechanobiology

My research focuses on the mechanoresponse of cells to their environment. Specifically, how the cytoskeleton responds and adapts to novel biomaterials and how the cell is affected in terms of adherence morphology motility and toxicity. RNA interference, advanced light microscopy, high content screening (HCS) and cell-based assays are used to identify critical cytoskeletal proteins in this response.


Dr Sophie Meillon



Dr Jai Prakash Mehta

Keywords: Next-generation sequencing, neuroblastoma, MYCN

Neuroblastoma is a childhood cancer which arises from the developing sympathetic nervous system. Previous studies have shown MYCN to be associated with the most aggressive form of the cancer. Currently we are using Next Generation Sequencing to sequence the RNA at various time points after MYCN expression. The aim is to build regulatory networks from various high-throughput omics data generated from sequencing and proteomics experiments. We are also looking at fusion genes on various Neuroblastoma cell lines using paired end RNA-sequencing.


Dr Aleksandra Miranda-CasoLuengo

Keywords: Infection biology, virulence, regulation of gene expression, host-pathogen interactions

My research focuses on understanding bacterial adaptation to pathogenic lifestyle. I am particularly interested in studying a multi-level regulation of gene expression that facilitates colonization of and survival within a host as well as metabolic pathways that bacteria use to acquire nutrients from their host. To unveil the molecular interplay between both organisms I also investigate host – pathogen interactions during infection.


Dr Raul Miranda-CasoLuengo

Keywords: Infection biology, microbial ecology, microbiome, reproductive tract endometritis, host-pathogen interaction, transcriptional regulation, iron acquisition.

  1. Understanding Rhodococcus equi adaptation as intracellular pathogen of macrophages;
  2. Analysis of the structure and dynamics of microbial assemblages associated to mucosal surfaces to understand animal disorders that cannot be explained by a single etiologic agent such as in bovine postpartum endometritis.


Dr Marco Monopoli



Dr Therese Montgomery



Dr Eamonn Mulvaney



Dr Nayla Munawar



Dr Lisa Murphy



Dr Tanja Narancic

Keywords: Microbiology, green technology, biodegradable plastic, polyhydroxyalkanoate, polyhydroxybutyrate, proteomics, metabolomics, syngas, upcycling, waste transformation, biocatalysis, enzyme technology, protein engineering, directed evolution

My resarch focuses on biotechnological conversion of municipal waste to biodegradable polymers – polyhydroxyalkanoate; mass spectrometry based proteomics; metabolomics; biocatalysis; bioactive compounds and bacterial fermentations


Dr Kevin O'Brien



Dr Seán O'Shea



Dr Maria Prencipe



Dr Cinzia Raso

Keywords: EGFR network reconstruction, interactome, PRIMES, mass spectrometry

Currently, I am a postdoctoral researcher (L2) in Systems Biology Ireland, involved in PRIMES (Protein Interaction Machines in EGFR Signalling) (FP7-HEALTH-2011-two-stage). PRIMES focuses on the role of protein interactions to assemble dynamic molecular machines that receive and process information to coordinate cellular responses. PRIMES investigates: (i) how protein interactions contribute to the generation of biological specificity in signalling (ii) how pathogenetic perturbations affect protein interaction networks and (iii) how we can exploit protein interactions as therapeutic targets. I was born in Cosenza, Italy, have completed two Ph.D. programmes: Animal Pharmacology & Toxicology and Biomedical & Computer Engineering and spent 7 months as a visiting scientist in John Yates laboratory at Scripps Research Institute, San Diego, California, to improve my knowledge about mass spectrometry and MudPIT techniques.


Dr Jens Rauch

Keywords: Cancer, systems biology, signalling pathways, A-Raf

I am currently investigating the role of Raf signalling in cancer differentiation and metabolism. More specifically Raf kinases are found at different localisations within a cell and I want to understand what kind of specific function is associated with this spatial and temporal regulation of signalling and which factors are involved.


Dr Nora Rauch

Keywords: EGFR network, MAPK signalling, Raf kinases

My project with Systems Biology Ireland is part of the EU framework 7 program PRIMES. We are interested in protein-protein interactions in the oncogenic EGFR signalling network. My work deals with the functional characterization of critical interactions in particular their usefulness as drug targets.


Dr Helen Reid



Dr Alison Reynolds



Dr Aisling Robinson



Dr Peadar Rooney

Keywords: Diabetes, insulin, drug delivery

I am currently investigating the delivery of insulin for diabetic patients, through encapsulation in nano-hydrogels, the key elements in overcoming this is the degradation and limited crossing of insulin from the digestive system into the bloodstream. We are designed a drug delivery system that protects the insulin from degradation and increases insulin permeation. 


Dr Colm Ryan

Keywords: network-biology; epistasis; gwas; genetic-interactions

Colm J. Ryan is the ICON Newman Fellow in Genomics. He is interested in understanding how network context may be used to understand the connection between genotype and phenotype. During his PhD he studied large scale genetic-interaction networks in yeast and currently he is applying related ideas to the analysis of complex disease.


Dr Silke Ryan

Keywords: Obstructive sleep apnoea, intermittent hypoxia, cardiovascular disease, inflammation

Obstructive sleep apnoea (OSA) is a highly prevalent disease and associated with significant cardiovascular morbidity and mortality. My research focuses on the understanding of the mechanisms of this association. In particular, using a true translational approach, I investigate the role of intermittent hypoxia, a hallmark feature of sleep apnoea in promoting inflammatory pathway activation and its interaction with adipose tissue in this process.


Dr Anna Salvati



Dr Bettina Schaible



Dr Robert Schwamborn

Keywords: Cell signalling, microfluidics, live cell imaging

I am currently establishing a microfluidic chip in collaboration with Devrim Kilinc from Gil Lee’s laboratory. The chip exposes cells to orthogonal gradients of drugs which allows us to screen drug combinations for the optimal concentrations. Our current models involve synergistic induction of cell death in cancer cells. I analyse the cells via life cell imaging, flow cytometry, immunohistochemistry.


Dr Michael Sharkey



Dr Fabian Sievers



Dr Craig Slattery

Keywords: Kidney disease, diabetic nephropathy, toxicology, toxicogenomics

My research focuses on cellular mechanisms underlying development of a variety of kidney disorders including diabetic nephropathy drug-induced kidney damage and renal cancers. I employ a range of approaches from cell culture models to in vivo models and human clinical samples. I am also hugely interested in science education and outreach.


Dr Lisa Staunton

Keywords: Prostate cancer, proteomics, biomarker

My project aims to identify the protein expression profiles of morphologically discrete foci in prostate cancer using a clinically focused strategy for discovery of biomarkers. My project is focused on distinct regions of cancer foci in tissue from patients which are isolated by laser capture microdissection and proteomic profiling by label-free LC-MS/MS to identify differential expression both between regions and patient groups followed by multiplexed measurement of proteins of interest by MRM mass spectrometry.


Dr Ilias Stavropoulos



Dr Marta Terrile



Dr Chris Watson



Dr Suisheng Zhang

Keywords: Probiotics, Reactive Oxygen Species (ROS), antioxidants, inflammation.

My research is genetic modification of lactic acid bacteria which express antioxidant enzymes such as catalase or superoxide dismutase (SOD) as therapy of inflammatory diseases such as inflammatory bowel disease (IBD).


Dr Veranika Zobnina



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