Michael J Dunn

University College Dublin, Dublin, Leinster, Ireland

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Publications (482)2078.82 Total impact

  • Michael J. Dunn · Hans-Joachim Kraus

    No preview · Article · Jan 2016 · PROTEOMICS

  • No preview · Conference Paper · Sep 2015
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    ABSTRACT: The qualitative and quantitative capabilities of 2-D electrophoresis and its use in widespread proteome analysis have been revolutionized over the past decade with the introduction of differential gel electrophoresis commonly known as DIGE. This highly sensitive CyDye protein labeling technique now attempts to advance conventional western blotting by the combination of DIGE labeling with ECL Plex CyDye conjugated secondary antibodies. The ability of this method to simultaneously visualize the total protein expression profile as well as the specific immunodetection of an individual protein species will significantly aid protein validation following 2-D gel separation by confirming the exact location of proteins of interest. This simple, rapid, and reproducible technique is demonstrated by 1-D and 2-D electrophoresis through the detection of the small 27 kDa heat shock protein (hsp 27), a protein known to be expressed in the human heart, from a complex cardiac protein extract.
    No preview · Article · Jul 2015 · Methods in molecular biology (Clifton, N.J.)
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    ABSTRACT: Psoriatic arthritis (PsA) can be treated using biologic therapies targeting biomolecules such as tumour necrosis factor alpha, interleukins (IL)-17 and IL-23. Whilst 70% PsA patients respond well to therapy, 30% patients show no or limited clinical improvement. Biomarkers that predict response to therapy would help to avoid unnecessary use of expensive biologics in non-responding patients and enable alternative treatments to be explored. Patient synovial-tissue samples from two clinical studies were analysed using Difference In-Gel Electrophoresis based proteomics to identify protein expression differences in response to anti-TNF-α treatment. Subsequent multiplexed multiple-reaction-monitoring (MRM) measurements were used to verify potential biomarkers. A total of 119 proteins were differentially expressed (p<0.05) in response to anti-TNF-α treatment and 25 proteins were differentially expressed (p<0.05) between "good responders" and "poor responders". From these differentially expressed proteins, MRM assays were developed for 4 proteins to explore their potential as treatment predictive biomarkers. Gel-based proteomics strategy has demonstrated differential protein expression in synovial tissue of PsA patients, in response to anti-TNF-α treatment. Development of multiplex MRM assays to these differentially expressed proteins has the potential to predict response to therapy and allow alternative, more effective treatments to be explored sooner. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Full-text · Article · Jun 2015 · PROTEOMICS - CLINICAL APPLICATIONS
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    ABSTRACT: The International Plant Proteomics Organization (INPPO) is a global platform of the plant proteomics community or, more generally, the scientific community that uses proteomics to address plant biology. Organizing an international conference is one of its initiatives to promote plant proteomics by involving and gathering scientists/researchers/students and by disseminating the acquired knowledge. In this fourth INPPO Highlights, the first INPPO World Congress 2014 (INPPO2014) is described and discussed. The INPPO2014 was held at the University of Hamburg (Germany) with the title "Plant Proteomics: Methodology to Biology" under the leadership of Sabine Lüthje (Germany). Participants (around 150) from 38 nations attended this congress covering all continents. The four-day scientific program comprised 52 lectures and 61 poster presentations in a highly professional and friendly atmosphere on mass spectrometry and gel-based proteomics. Two round-table open discussions deliberated on plant proteomics, its associated international organizations/initiatives and future INPPO perspectives. The Second INPPO World Congress 2016 (INPPO2016) "The Quest for Tolerant Varieties-Phenotyping at Plant and Cellular Level" is planned to be organized in Bratislava (Slovakia) under the leadership of Martin Hajduch (Slovak Republic) and Sébastien Carpentier (Belgium) and cosponsored by the COST action FA1306. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    No preview · Article · Apr 2015 · Proteomics
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    ABSTRACT: Electroconvulsive therapy (ECT) is the most acutely effective treatment available for severe depression. However, its mechanism of action is not fully understood. Elucidating the protein changes induced in the brain by ECT will enhance our understanding of this antidepressant therapy. Electroconvulsive stimulation (ECS), the animal analogue of ECT, was administered to rats to determine the proteomic changes induced in the hippocampus, a region of the brain implicated in the biology of depression and its treatment. Two-dimensional difference in gel electrophoresis (2D-DiGE) and liquid chromatography tandem mass spectrometry (LC-MS/MS) methods were applied to identify differentially expressed proteins following acute (×1 treatment), chronic (×10 treatments) or chronic+4 weeks (×10 treatments plus 4 weeks later) ECS. Administration of acute, chronic and chronic+4 weeks ECS induced significant changes in multiple DiGE gel protein spots. Interestingly, the largest number of differentially expressed protein spots was identified following chronic+4 weeks ECS. Following protein identification by LC-MS/MS, gene ontology analysis primarily implicated proteins with cytoskeletal and metabolism-related roles in the action of ECS. Immunoblotting confirmed the changes in abundance of the cytoskeletal protein actin following chronic+4 weeks ECS. Overall, chronic+4 weeks ECS was particularly effective at inducing longer-lasting changes in the abundance of hippocampal proteins with cytoskeletal and metabolism roles. These results suggest a role for persisting cytoskeletal-related neuroplastic changes in the action of ECS and may be informative as to the antidepressant mechanisms of ECT in patients with depression.
    No preview · Article · Oct 2014 · Brain Research
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    ABSTRACT: Electroconvulsive therapy (ECT) is an effective antidepressant treatment, but its molecular mechanisms of action remain to be fully elucidated. To better understand the effects of ECT, we conducted a proteomic study to characterize global changes in plasma protein abundance induced by electroconvulsive stimulation (ECS) in the animal model equivalent of ECT. Male Sprague-Dawley rats were administered a single or repeat (10 sessions) course of ECS, and compared with sham-ECS administered animals. Quantitative differential protein expression analysis was performed, using 2-dimensional difference in gel electrophoresis (2D DiGE), on immunodepleted plasma. Proteins were selected for identification by liquid chromatography tandem mass spectrometry (LC-MS/MS): 150 protein spots were significantly altered following a single ECS and 178, following repeated ECS. In total, 18 proteins were identified by LC-MS/MS. Many of these were acute-phase response proteins, previously reported to be increased in depressed patients. Changes in the abundance of two proteins of interest were confirmed by other measures. Repeat ECS was found to significantly reduce plasma levels of haptoglobin and apolipoprotein A-IV, although these changes were no longer evident 4 weeks after the repeated ECS. Our results implicate the immune system-induced acute phase protein response in ECS action while identifying potential plasma biomarkers for ECS.
    No preview · Article · Sep 2014 · Journal of Psychopharmacology
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    ABSTRACT: Prenatal stress influences the development of the fetal brain and so contributes to the risk of the development of psychiatric disorders in later life. The hippocampus is particularly sensitive to prenatal stress, and robust abnormalities have been described in the hippocampus in schizophrenia and depression. The aim of this study was to determine whether prenatal stress is associated with distinct patterns of differential protein expression in the hippocampus using a validated mouse model. We therefore performed a comparative proteomic study assessing female hippocampal samples from 8 prenatally stressed mice and 8 control mice. Differential protein expression was assessed using 2-dimensional difference in gel electrophoresis and subsequent mass spectrometry. The observed changes in a selected group of differentially expressed proteins were confirmed by Western blotting. In comparison to controls, 47 protein spots (38 individual proteins) were found to be differentially expressed in the hippocampus of prenatally stressed mice. Functional grouping of these proteins revealed that prenatal stress influenced the expression of proteins involved in brain development, cytoskeletal composition, stress response, and energy metabolism. Western blotting was utilized to validate the changes in calretinin, hippocalcin, profilin-1 and the signal-transducing adaptor molecule STAM1. Septin-5 could not be validated via Western blotting due to methodological issues. Closer investigation of the validated proteins also pointed to an interesting role for membrane trafficking deficits mediated by prenatal stress. Our findings demonstrate that prenatal stress leads to altered hippocampal protein expression, implicating numerous molecular pathways that may provide new targets for psychotropic drug development. © 2014 S. Karger AG, Basel.
    Full-text · Article · Aug 2014 · Developmental Neuroscience
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    ABSTRACT: International Plant Proteomics Organization (INPPO) outlined ten initiatives to promote plant proteomics in each and every country. With greater emphasis in developing countries, one of those was to “organize workshops at national and international levels to train manpower and exchange information”. This third INPPO highlights covers the workshop organized for the very first time in a developing country, India, at the Department of Botany in University of Delhi on December 26–30, 2013 titled – “1st Plant Proteomics Workshop / Training Program” under the umbrella of INPPO India-Nepal chapter. Selected 20 participants received on-hand training mainly on gel-based proteomics approach along with manual booklet and parallel lectures on this and associated topics. In house, as well as invited experts drawn from other Universities and Institutes (national and international), delivered talks on different aspects of gel-based and gel-free proteomics. Importance of gel-free proteomics approach, translational proteomics, and INPPO roles were presented and interactively discussed by a group of three invited speakers Drs. Ganesh Kumar Agrawal (Nepal), Randeep Rakwal (Japan), and Antonio Masi (Italy). Given the output of this systematic workshop, it was proposed and thereafter decided to be organized every alternate year; the next workshop will be held in 2015. Furthermore, possibilities on providing advanced training to those students / researchers / teachers with basic knowledge in proteomics theory and experiments at national and international levels were discussed. INPPO is committed to generating next-generation trained manpower in proteomics, and it would only happen by the firm determination of scientists to come forward and do it.
    Full-text · Article · Jul 2014 · Proteomics
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    ABSTRACT: Early embryonic loss accounts for over 70% of total embryonic and foetal loss in dairy cattle. Early embryonic development and survival is associated with the concentration of systemic progesterone. To determine if the uterine proteome is influenced by stage of cycle or systemic progesterone concentrations, uterine flushings (UF) were collected from the ipsi- and contralateral uterine horns of beef heifers on Days 7 (n = 10) and 15 (n = 10) of the oestrous cycle. Animals were separated into low or high progesterone groups based on plasma progesterone concentrations on Day 5 of the cycle. Samples were albumin depleted before iTRAQ® labelling and subsequent SCX-LC-MS/MS analyses. A total of 20 proteins were up to 5.9-fold higher (P < 0.05) and 20 were up to 2.3-fold lower on Day 15 compared to Day 7. In addition, the expression of a number of proteins on Day 7 and/or 15 of the cycle was correlated with progesterone concentrations during Days 3-7 or the rate of change in progesterone between Days 3 and 7. This study highlights the dynamic changes occurring in the microenvironment surrounding the embryo during this period. The findings here also support the hypothesis that progesterone supports embryonic development by altering the maternal uterine environment. This article is protected by copyright. All rights reserved.
    Full-text · Article · Nov 2013 · Proteomics
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    ABSTRACT: The International Plant Proteomics Organization (INPPO) is a non-profit organization whose members are scientists involved or interested in plant proteomics. Since the publication of the first INPPO highlights in 2012, continued progress on many of the organization's mandates/goals has been achieved. Two major events are emphasized in this second INPPO highlights. First, the change of guard at the top, passing of the baton from Dominique Job, INPPO founding President to Ganesh Kumar Agrawal as the incoming President. Ganesh K. Agrawal, along with Dominique Job and Randeep Rakwal initiated the INPPO. Second, the most recent INPPO achievements and future targets, mainly the organization of first the INPPO World Congress in 2014, tentatively planned for Hamburg (Germany), are mentioned.
    Full-text · Article · Nov 2013 · PROTEOMICS
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    ABSTRACT: Summary: We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available.Availability: http://iann.pro/iannviewerContact: manuel.corpas@tgac.ac.uk
    Full-text · Article · Jun 2013 · Bioinformatics
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    Fang-Xiang Wu · Habtom Ressom · Michael J Dunn

    Preview · Article · Jan 2013 · Proteomics
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    ABSTRACT: In the current investigation, we aimed to characterize the differential protein expression in each of the hippocampal subregions in healthy control samples (n = 20). We used laser-assisted microdissection and difference in-gel electrophoresis to enrich for these tissues and to compare protein profiles. Image analysis was carried out using Progenesis SameSpots. Samples with a false discovery rate smaller than 5%, a p-value of < 0.01, and an expression of at least ± 1.2 were considered significant. Proteins were identified using LC-ESI-MS/MS. The raw mass spectral data were analyzed using DataAnalysis software. Data were searched against the Swissprot database using MASCOT. Samples were grouped according to the different subregions and we found 182 spots to be differentially expressed between the different hippocampal subregions. These have been made available as part of the UCD-2DPAGE database at http://proteomics-portal.ucd.ie:8082. The associated MS data have been submitted to PRIDE (Accession numbers 21593-21745). This baseline data will be helpful in helping us to understand the central role of the hippocampus in health and the evidence that particular hippocampal subregions are differentially affected in disease.
    No preview · Article · Aug 2012 · Proteomics
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    ABSTRACT: Neuroproteomics is a powerful platform for targeted and hypothesis driven research, providing comprehensive insights into cellular and sub-cellular disease states, Gene × Environmental effects, and cellular response to medication effects in human, animal, and cell culture models. Analysis of sub-proteomes is becoming increasingly important in clinical proteomics, enriching for otherwise undetectable proteins that are possible markers for disease. Membrane proteins are one such sub-proteome class that merit in-depth targeted analysis, particularly in psychiatric disorders. As membrane proteins are notoriously difficult to analyse using traditional proteomics methods, we evaluate a paradigm to enrich for and study membrane proteins from human post-mortem brain tissue. This is the first study to extensively characterise the integral trans-membrane spanning proteins present in human brain. Using Triton X-114 phase separation and LC-MS/MS analysis, we enriched for and identified 494 membrane proteins, with 194 trans-membrane helices present, ranging from 1 to 21 helices per protein. Isolated proteins included glutamate receptors, G proteins, voltage gated and calcium channels, synaptic proteins, and myelin proteins, all of which warrant quantitative proteomic investigation in psychiatric and neurological disorders. Overall, our sub-proteome analysis reduced sample complexity and enriched for integral membrane proteins by 2.3 fold, thus allowing for more manageable, reproducible, and targeted proteomics in case vs. control biomarker studies. This study provides a valuable reference for future neuroproteomic investigations of membrane proteins, and validates the use Triton X-114 detergent phase extraction on human post mortem brain.
    Full-text · Article · Jun 2012 · PLoS ONE
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    ABSTRACT: The eye lens remains transparent because of soluble lens proteins known as crystallins. For years γ-crystallins have been known as the main lens proteins in lower vertebrates such as fish and amphibians. The unique growth features of the lens render it an ideal structure to study ageing; few studies have examined such changes in anuran lenses. This study aimed to investigate protein distribution patterns in Litoria infrafrenata and Phyllomedusa sauvagei species. Lenses were fractionated into concentric layers by controlled dissolution. Water-soluble proteins were separated into high (HMW), middle (MMW) and low molecular weight (LMW) fractions by size-exclusion HPLC and constituents of each protein class revealed by 1DE and 2DE. Spots were selected from 2DE gels on the basis of known ranges of subunit molecular weights and pH ranges and were identified by MALDI-TOF/TOF MS following trypsin digestion. Comparable lens distribution patterns were found for each species studied. Common crystallins were detected in both species; the most prominent of these was γ-crystallin. Towards the lens centre, there was a decrease in α- and β-crystallin proportions and an increase in γ-crystallins. Subunits representing taxon-specific crystallins demonstrating strong sequence homology with ζ-crystallin/quinone oxidoreductase were found in both L. infrafrenata and P. sauvagei lenses. Further work is needed to determine which amphibians have taxon-specific crystallins, their evolutionary origins, and their function.
    Full-text · Article · Jun 2012 · Proteomics
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    ABSTRACT: Early embryo loss is a key factor affecting fertility in dairy and beef herds. Prior to implantation, the bovine embryo spends around 16 days free-floating in the uterine environment and is dependent on the composition of uterine fluid for normal growth and development. However, there is a lack of information regarding the protein composition of the bovine uterus and how it relates to plasma. In this study, uterine flushings (UF) (n = 6) and blood plasma (n = 4) were collected from beef heifers on day 7 of the oestrous cycle, albumin depleted and compared using iTRAQ proteomics. A total of 35 proteins were higher and 18 were lower in UF including metabolic enzymes, proteins with anti-oxidant activity and those involved in modulation of the immune response. This study confirms the dynamic nature of the bovine uterine proteome and that it differs from plasma. Factors affecting the uterine proteome and how it impacts on embryo survival warrant further study.
    Full-text · Article · Jun 2012 · Proteomics
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    ABSTRACT: The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO's official launch in 2011 via its website (www.inppo.com) and publication of the 'Viewpoint paper' in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) to achieve INPPO objectives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO's primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a section dedicated to plant proteomics has been introduced starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January and July) newsletter entitled 'INPPO Express: News & Views' with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, and Medicago truncatula. Altogether, the INPPO progress and upcoming activities are because of immense support, dedication, and hard work of all members of the INPPO community, and also due to the wide encouragement and support from the communities (scientific and non-scientific).
    Full-text · Article · Feb 2012 · Proteomics
  • Michael J Dunn

    No preview · Article · Jan 2012 · Proteomics
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    ABSTRACT: Information storage in the brain depends on the ability of neurons to alter synaptic connectivity within key circuitries such as the hippocampus. Memory-associated synaptic plasticity is mediated by a temporal cascade of de novo protein synthesis and altered protein processing. Here, we have used two-dimensional difference in gel electrophoresis (2-D DIGE) to investigate memory-specific protein changes in the hippocampal dentate gyrus at increasing times following spatial learning. We identified 42 proteins that were significantly regulated in the first 24 h of spatial memory consolidation. Two distinct waves of protein expression regulation were evident, at 3 and 12 h post-learning and this is in agreement with studies employing inhibitors of global translation. Functional classification of the memory-associated proteins revealed that the majority of regulated proteins contributed either to cellular structure or cellular metabolism. For example, actins, tubulins and intermediate filament proteins, core proteins of the three major cytoskeletal components, were dynamically regulated at times that suggest a role in memory-associated synaptic reorganization. Increased proteasome-mediated protein degradation was evident in the early post-training period including the down-regulation of phosphoprotein enriched in astrocytes 15 kDa, a key inhibitor of extracellular signal-regulated kinase signaling. Some of the most substantial protein expression changes were observed for secreted carrier proteins including transthyretin and serum albumin at 6-12 h post-learning, regulations that could serve an important role in increasing the supply of retinoic acid and thyroid hormone, key synaptic plasticity-promoting signals in the adult brain. Together these observations provide further insight into protein level regulations occurring in the hippocampus during spatial memory consolidation.
    Full-text · Article · Nov 2011 · Proteomics

Publication Stats

18k Citations
2,078.82 Total Impact Points


  • 2005-2015
    • University College Dublin
      • School of Medicine & Medical Science
      Dublin, Leinster, Ireland
    • London Research Institute
      Londinium, England, United Kingdom
  • 2014
    • Beaumont Hospital
      Dublin, Leinster, Ireland
  • 2011
    • St. Vincents University Hospital
      Dublin, Leinster, Ireland
    • Royal College of Surgeons in Ireland
      • Department of Psychiatry
      Dublin, L, Ireland
  • 2003-2011
    • Imperial College London
      • Department of Medicine
      Londinium, England, United Kingdom
    • University of London
      Londinium, England, United Kingdom
    • Royal Brompton and Harefield NHS Foundation Trust
      • Cardiothoracic Surgery & Transplantation Unit
      Harefield, England, United Kingdom
  • 2009
    • TobaccoFree Research Institute Ireland
      Dublin, Leinster, Ireland
    • Wellcome Trust
      Londinium, England, United Kingdom
  • 2008
    • Mater Misericordiae University Hospital
      Dublin, Leinster, Ireland
  • 2003-2008
    • King's College London
      • • Institute of Psychiatry
      • • Department of Neuroscience (IoP)
      London, ENG, United Kingdom
  • 1997-2008
    • Medical College of Wisconsin
      • • Division of Cardiovascular Medicine
      • • Department of Medicine
      Milwaukee, Wisconsin, United States
    • Imperial Valley College
      Middlesex, New Jersey, United States
  • 1981-2006
    • Case Western Reserve University School of Medicine
      • Department of Medicine
      Cleveland, Ohio, United States
    • Harvard Medical School
      Boston, Massachusetts, United States
  • 2004-2005
    • UK Department of Health
      Londinium, England, United Kingdom
    • ICL
      Londinium, England, United Kingdom
  • 1989-2003
    • National Heart, Lung, and Blood Institute
      Maryland, United States
  • 2001
    • University of Sussex
      Brighton, England, United Kingdom
    • University of Florence
      Florens, Tuscany, Italy
    • The Scripps Research Institute
      La Jolla, California, United States
  • 1998
    • Policlinico San Matteo Pavia Fondazione IRCCS
      Ticinum, Lombardy, Italy
  • 1996
    • Gloucestershire Hospitals NHS Foundation Trust
      Gloucester, England, United Kingdom
  • 1995-1996
    • The Peninsula College of Medicine and Dentistry
      Plymouth, England, United Kingdom
  • 1979-1996
    • Case Western Reserve University
      • • School of Medicine
      • • Department of Physiology and Biophysics
      Cleveland, Ohio, United States
  • 1991-1995
    • The Heart Lung Center
      Londinium, England, United Kingdom
  • 1985-1992
    • Cleveland State University
      Cleveland, Ohio, United States
  • 1988
    • Loyola University Medical Center
      • Department of Medicine
      مايوود، إلينوي, Illinois, United States
  • 1982-1987
    • Ealing, Hammersmith & West London College
      Londinium, England, United Kingdom
  • 1984
    • Universität Heidelberg
      Heidelburg, Baden-Württemberg, Germany
  • 1979-1984
    • Rutgers, The State University of New Jersey
      Нью-Брансуик, New Jersey, United States