biomedical sciences research institute - Research - University of Ulster

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11. SYSTEMS BIOLOGY RESEARCH GROUPThe strategy of the Systems Biology Research Group (SBRG) is focused on the bioinformatics and computationalelements of the now strongly growing interdisciplinary field of systems biology. Systems biology is defined as “thequantitative analysis of the dynamic interactions between several components of a biological system and aims to understand thebehaviour of the system as a whole. It applies the concepts and methodologies of systems theory and engineering to the studyof complex biological systems through iteration between computational and mathematical modelling and experimentation.Systems Biology is a tool to increase understanding of the system, to develop more directed experiments and finally allowpredictions”.This strategic view on the Group’s research aligns well with national and international priorities. Complementing thisresearch strategy, academic members of the Group are currently in the process to develop a basic teaching coursein systems biology. As personalized medicine seems to find its way into national and international research agendas,first steps have been taken to explore this dimension in the context of systems biology.The main research themes investigated by the SBRG, include modelling of interactions in kinase/phosphatase systems;modelling and simulation of gene regulatory networks; qualitative modelling of the bile acid and xenobiotic system;computational study of the genetic causes of LQT syndrome; and various aspects of management and analysis ofbiological information.In the reporting period, members of the Group published a considerable number of articles in high-calibre internationaljournals and conferences (some of which were included in the 2008 RAE submission) and was awarded considerablelevels of research grants. The Group has also consolidated its research partner network nationally and internationally,including renowned organizations such as the University of Queensland, Brisbane, Australia; the Haifa Institute ofTechnology, Israel; Korea Advanced Institute of Science and Technology (KAIST), Republic of Korea. Some membersof the Group have been members of international advisory boards and journal editorial boards.The Group has 5 dual processor servers that provide Web services and content-management software, groupware,file and database services (Oracle Enterprise server 10G) as well as Grid services (Globus and CONDOR). Forlarge-scale computing tasks, there is a 64-way Itanium Altix 3700 supercomputer with 128GB of addressable memoryand 8 TB of disk storage. Projects using this system range from protein-unfolding simulations to tracing of stainedstructures in large image stacks.98
MEMBERS OF THE GROUPProfessor Werner Dubitzky, Group LeaderProfessor of BioinformaticsContact details:T: +44 (0)28 70324478w.dubitzky@ulster.ac.ukProfessor Dubitzky’s main research activities in the reporting period included:• preparation of research papers for RAE 2008;• preparation of research grant applications;• research in modelling, analyzing and simulating biomedical systems;• working on new edited volumes (books and special issues in international journals and an encyclopedia);• management and research on ongoing research projects;• networking.The key themes of Werner’s research activities in this reporting period revolved around computational elementsof systems biology and e-science (which are both part of national and European research priorities). These themeswill continue to be his research focus into the future, perhaps with a stronger element of personalized medicine,dynamical modelling and integration of heterogeneous information for modelling and simulation of biological systemsand scientific knowledge discovery.Publications:Romberg M, Benfenati E & Dubitzky W; Open Computing Grid for Molecular Sciences in E-G. Talbi & A. Zomaya(editors), Grids for Bioinformatics and Computational Biology, Wiley Book Series on Parallel and Distributed Computing;John Wiley & Sons, New York, pp1-22. ISBN: 978-0-471-78409-8, 2007Cashman KD, Hill TR, Cotter AA, Boreham CA, Dubitzky W, Murray L, Strain J, Flynn A, Robson PJ, Wallace JM & KielyM; Low vitamin D status adversely affects bone health parameters in adolescents, American Journal of Clinical Nutrition,87: 1039-1044, 2008Fuß H, Dubitzky W, Downes CS & Kurth MJ; Src family kinases and receptors: analysis of three activation mechanismsby dynamic systems modelling; Biophysical Journal, 94, 1995-2006, 2008Hill TR, Cotter AA, Mitchell S, Boreham CA, Dubitzky W, Murray L, Strain JJ, Flynn A, Robson PJ, Wallace JM, Kiely M& Cashman KD; Vitamin D status and its determinants in adolescents from the Northern Ireland Young Hearts 2000cohort; British Journal of Nutrition, 99: 1061-1067, 2008Kravtsov V, Schuster A, Carmeli D, Kurowski K & Dubitzky W; Grid-enabling complex system applications withQosCosGrid: An architectural perspective, in Proceedings of the International Conference on Grid Computing andApplications (GCA'08), Las-Vegas, USA, 2008Kravtsov V, Carmeli D, Dubitzky W, Orda A, Schuster A, Silberstein M & Yoshpa B; Quasi-Opportunistic Supercomputingin Grid Environments, in Proceedings of the International Conference on Algorithms and Architectures, Cyprus, 233-244,2008Kravtsov V, Swain M, Dubin U, Dubitzky W & Schuster A; A Fast and Efficient Algorithm for Topology-AwareCoallocation, in Proceedings of the International Conference on Computational Science, Krakow, Poland, 274-283, 200899
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BIOMEDICAL SCIENCESRESEARCH INSTITU
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1 Foreword by the Pro Vice-Chancell
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2 Foreword by the Research Institut
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The BMSRI Research StructureThe BMS
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BMSRI Core FacilitiesContact: Karen
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of Metabolomics, pharmacy, nutritio
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BMSRI Academic Heads new Regional N
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4. BIOMEDICAL GENOMICS RESEARCH GRO
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Recent Funding Initiatives:C-TRIC:
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Dr Mateus Webba da SilvaLecturer in
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5. BIOIMAGING RESEARCH GROUPResearc
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developmental alterations that mani
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Publications:Bigot S, Lucas L, Morr
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Publications:Barnes CA, O’Hagan B
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We also measure the genotoxic effec
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6. CANCER AND AGEING RESEARCH GROUP
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Professor Anthony P McHaleProfessor
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Professor Stephanie McKeownProfesso
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an Alzheimer Research Trust collabo
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JM, Waugh DJJ; Dexamethasone potent
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have wider applications in vivo, in
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Inter-relationships between diet an
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Flatt PR; Effective surgical treatm
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These areas are the subject of seve
Page 50 and 51: Dr YHA Abdel-WahabSenior Lecturer i
Page 52 and 53: Dr VA GaultLecturer in Molecular Bi
Page 54 and 55: McClean PL, Irwin N, Hunter K, Gaul
Page 56 and 57: Publications:Duffy NA, Green BD, Ir
Page 58 and 59: 8. MICROBIOLOGY AND BIOTECHNOLOGYRE
Page 60 and 61: Publications:Graham RJL, Graham C,
Page 62 and 63: analyses. However there is still a
Page 64 and 65: Plessas S, Bekatorou A, Koutinas AA
Page 66 and 67: Biochemical studies/ viral evasion
Page 68 and 69: Dr Stephen McCleanLecturer in Prote
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Page 72 and 73: 9. NORTHERN IRELAND CENTRE FOR FOOD
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Page 78 and 79: Dr Alison GallagherSenior Lecturer
Page 80 and 81: In addition, results of a pilot stu
Page 82 and 83: Dr Maeve KerrResearch AssociateCont
Page 84 and 85: Memberships of External Committees/
Page 86 and 87: Indicators of Esteem:Professor McNu
Page 88 and 89: were examined. The intervention and
Page 90 and 91: Within this work both short-term an
Page 92 and 93: micronutrient supplementation at a
Page 94 and 95: 10. STEM CELL & EPIGENETICS RESEARC
Page 96 and 97: Publications:Lees-Murdock DJ, Lau H
Page 98 and 99: Publications:Lees-Murdock DJ, Lau H
Page 102 and 103: Kravtsov V, Swain M, Schuster A, Du
Page 104 and 105: Dr Daniel BerrarLecturer in Biomedi
Page 106 and 107: Zhang et al; Incorporating Feature
Page 108 and 109: Bala P, Baldridge K, Benfenati E, C
Page 110 and 111: In addition there is a growing them
Page 112 and 113: Clinical work involves development
Page 114 and 115: In 2009 he was appointed Chairman o
Page 116 and 117: Stevenson TR, Goodall EA and Moore
Page 118 and 119: Dr Raymond BeirneLecturer in Optome
Page 120 and 121: Dr Julie McClellandLecturer in Opto
Page 122 and 123: Graham JE, Moore JE, Moore JE, McCl
Page 124 and 125: Research Staff:Dr David OrrSenior R
Page 126 and 127: Dr Victoria McGilliganResearch Asso
Page 128 and 129: 13. Externally Funded Projects duri
Page 130 and 131: Grant Holder Anderson, Prof RSFundi
Page 132 and 133: Funding Body Royal Irish AcademyAmo
Page 134 and 135: 14. BIOMEDICAL SCIENCES RESEARCH IN
Page 136 and 137: Student: Simon GenglerTitle: Effect
Page 138 and 139: Student: Anisha MazumdarTitle: Anal
Page 140 and 141: Student: Clare RyanTitle: How does
Page 142 and 143: CONGRATULATIONS TO THE FOLLOWING PO
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