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Dirk Fey

Research Fellow

School Of Medicine
Systems Biology Ireland
Temple Street
Dublin 1

Tel: +353 1 7166310
Email: dirk.fey@ucd.ie

Biography

Personal web page: https://sites.google.com/site/feydirk/

I was born in Heidelberg (Germany) and studied Engineering Cybernetics at the University of Stuttgart, where I came in touch with the intriguing, exciting field of Systems Biology. Fascinated from the question 'What is life?' I stayed in the field and visited the Daniel Baugh Institute for functional genomics and computational biology in Philadelphia for preparing my master thesis. Later I started my PhD in Ireland with the Systems Biology group of the Hamilton Institute in Maynooth, before I followed my supervisor Eric Bullinger to the University of Strathclyde in Glasgow, Scotland and then to the University of Liege in Belgium, where I obtained my PhD entitled Parameter estimation for biological models. Now I am a research fellow with Systems Biology Ireland and the School of Medicine at the University College Dublin.

Curriculum Vitae

11/2015 - now Research Fellow (junior group leader), Systems Biology Ireland & School of Medicine, University College Dublin  

02/2011 - 11/2015 Postdoctoral Research Fellow, Systems Biology Ireland, University College Dublin

03/2009 - 02/2011 PhD student, Systems Biology, Groupe Interdisciplinaire de Génoprotéomique Appliquée and PhD student, Systems & Modeling, Institute Montefiore, University of Liege, Belgium

10/2007 - 02/2009 PhD student, Industrial Control Centre, Department of Electronic & Electrical Engineering, Univeristy of Strathclyde, Glasgow, UK

01/2007 - 09/2007 PhD student, Systems Biology group, Hamilton Insitute, Natioal University Ireland Maynooth

06/2006 - 10/2006 Internship BASF Chemical Company Ludwigshafen, Germany

09/2005 - 04/2006 Master thesis, Daniel Baugh Institute for functional genomics and computational biology, Thomas Jefferson University, Philadelphia, USA

10/2001 - 03/2007 Studies Engineering Cybernetics (Master), University of Stuttgart, Germany

Awards:

03/02/2017 1st prize World Cancer Day Flash Talks, University College Dublin (UCD Conway news

25/03/2015 Finalist NDRC FutureHealth pre-accelerator programme (Irish Medical TimesUCD Conway Institute news)

10/09/2014 1st prize Cell Biology (moderated poster), Conway Festival of Research and Innovation, University College Dublin 

31/03/2011 Awarded the "European" label for the PhD by the University of Liege

20/01/2009 1st prize Dynamic Systems and Applications (oral presentation), Research Presentation Day, University of Strathclyde

24/06/2008 International Travel Grant, Royal Academy of Engineering

05/09/2007 University Postgraduate Scholorship, University of Strathclyde

20/07/2005 Stipend of the German Academic Exchange Service for preparing master thesis abroad

26/04/2005 e-fellows.net Stipend

Professional

Honours and Awards

Year: 2014.
Title: 1st prize Cell Biology (moderated poster) at the Conway Festival of Research and Innovation
Year: 2011.
Title: Awarded the "European" label for the PhD by the University of Liege
Year: 2009.
Title: 1st prize Dynamic Systems and Applications (oral presentation), University of Strathclyde Research Presentation Day
Year: 2008.
Title: International Travel Grant, Royal Academy of Engineering
Year: 2007.
Title: University of Strathclyde Postgraduate Scholarship
Year: 2005.
Title: Stipend for preparing Master thesis in the USA, German Academic Exchange Service
                         

Publications

 

Book Chapters

Schliemann-Bullinger, M; Fey, D; Bastogne, T; Findeisen, R; Scheurich, P; Bullinger, E (2015) 'The Experimental Side of Parameter Estimation' In: Geris, Liesbet; Gomez-Cabrero, David (eds). Uncertainty in Biology. Heidelberg: Springer. , pp.127 [Details]
Fey, D; Croucher, DR; Kolch, W; Kholodenko, BN (2012) 'Understanding Cell Fate Decisions by Identifying Crucial System Dynamics' In: D'Onofrio, A; Cerrai, P; Gandolfi, A (eds). New Challenges for Cancer Systems Biomedicine, SIMAI Springer Series. Heidelberg: Springer. , pp.83-104 [Details]
Fey, D and Findeisen, R and Bulliner, E; (2009) 'Identification of biochemical reaction networks using a parameter-free coordinate system' In: Fey, D and Findeisen, R and Bulliner, E; (eds). Control Theory and Systems Biology. Cambridge: MIT press. [Details]
 

Peer Reviewed Journals

Fey, D; Kuehn, A; Kholodenko, BN (2016) 'On the personalised modelling of cancer signalling'. IFAC Proceedings Volumes (IFAC-PapersOnline), 49 (26):312-317. [DOI] Link to full text [Details]
Fey, D; Matallanas, D; Rauch, J; Rukhlenko, OS; Kholodenko, BN (2016) 'The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells'. Seminars in Cell and Developmental Biology, 58 :96-107. [DOI] [Details]
Rogers S, Fey D;McCloy RA;Parker BL;Mitchell NJ;Payne RJ;Daly RJ;James DE;Caldon CE;Watkins DN;Croucher DR;Burgess A (2016) 'PP1 initiates the dephosphorylation of MASTL, triggering mitotic exit and bistability in human cells'. Journal of Cell Science, . [DOI] [Details]
Duffy DJ*, Krstic A*, Halasz M*, Schwarzl T*, Fey D, Iljin K, Mehta JP, Killick K, Whilde J, Turriziani B, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W. *Joint first authors. (2015) 'Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma'. Oncotarget, . [DOI] [Details]
Duffy, DJ; Krstic, A; Schwarzl, T; Halasz, M; Iljin, K; Fey, D; Haley, B; Whilde, J; Haapa-Paananen, S; Fey, V; Fischer, M; Westermann, F; Henrich, KO; Bannert, S; Higgins, DG; Kolch, W. (2016) 'Wnt signalling is a bi-directional vulnerability of cancer cells'. Oncotarget, . Available Online [DOI] [Details]
Fey D, Halasz M;Dreidax D;Kennedy SP;Hastings JF;Rauch N;Munoz AG;Pilkington R;Fischer M;Westermann F;Kolch W;Kholodenko BN;Croucher DR (2015) 'Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients'. Science signaling, 8 (408). [DOI] [Details]
Ryu, H; Chung, M; Dobrzynski, M; Fey, D; Blum, Y; Lee, SS; Peter, M; Kholodenko, BN; Jeon, NL; Pertz, O (2015) 'Frequency modulation of ERK activation dynamics rewires cell fate'. Molecular Systems Biology, 11 :838. [DOI] [Details]
Duffy DJ, Krstic A;Halasz M;Schwarzl T;Fey D;Iljin K;Mehta JP;Killick K;Whilde J;Turriziani B;Haapa-Paananen S;Fey V;Fischer M;Westermann F;Henrich KO;Bannert S;Higgins DG;Kolch W (2015) 'Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma'. Oncotarget, 6 (41):43182-43201. [DOI] [Details]
Makadia, HK; Anderson, WD; Fey, D; Sauter, T; Schwaber, JS; Vadigepalli, R (2015) 'Multiscale Model of Dynamic Neuromodulation Integrating Neuropeptide-Induced Signaling Pathway Activity with Membrane Electrophysiology'. Biophysical Journal, 108 (1):211-223. [DOI] Link to full text [Details]
Nguyen LK, Dobrzy¿¿ski M;Fey D;Kholodenko BN (2014) 'Polyubiquitin chain assembly and organization determine the dynamics of protein activation and degradation'. Frontiers in Physiology, 5 . [DOI] [Details]
Diviney, M; Fey, D; Commins, S (2013) 'Hippocampal contribution to vector model hypothesis during cue-dependent navigation'. Learning & memory (Cold Spring Harbor, N.Y.), 20 (7):367-378. [Details]
Reiterer V, Fey D, Kolch W, Kholodenko BN, Farhan H (2013) 'Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2'. Proceedings of the National Academy of Sciences of the United States of America, 110 (31):1-43. [DOI] Link to full text [Details]
Nikonova E, Tsyganov MA, Kolch W, Fey D, Kholodenko BN (2013) 'Control of the G-protein cascade dynamics by GDP dissociation inhibitors'. Molecular BioSystems, 9 (10):2454-2462. [DOI] Link to full text [Details]
Fey, D; Croucher, DR; Kolch, W; Kholodenko, BN (2012) 'Crosstalk and Signaling Switches in Mitogen-Activated Protein Kinase Cascades'. Frontiers in physiology, 3 :355. [Details]
Dobrzynski, M.*, Fey, D.*, Nguyen, L.K.*, Kholodenko, B.N. (*co-first author) (2012) 'Bimodal Protein Distribution in Heterogeneous Oscillating Systems'. Lecture Notes in Computer Science, (7605):17-28. Available Online [Details]
Fey D, Croucher DR, Kolch W, Kholodenko BN (2012) 'Crosstalk and signaling switches in mitogen-activated protein kinase cascades'. Frontiers in Physiology, 3 . [DOI] Link to full text [Details]
Fey, D and Commins, S and Bullinger, E; (2010) 'Feedback control strategies for spatial navigation revealed by dynamic modelling of learning in the Morris Water maze'. International Journal of Computational Neuroscience, 30 (2):447-454. [Details]
Conzelmann, H and Fey, D and Gilles ED; (2008) 'Exact model reduction of combinatorial reaction networks'. BMC systems biology, 2 :78. [Details]

Other Journals

Fey, D and Findeisen, R and Bullinger, E; (2008) 'Identifikation Biochemischer Reaktionsnetzwerke: Ein beobachterbasierter Ansatz' AT-Automatisierungstechnik 56 (5) :269-279. [Details]

Conference Publications

Kuehn, A; Kholodenko BN; Fey, D (2014) A dynamic model of the MYCN regulated DNA damage response in Neuroblastoma IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014) Workshop ¿Empowering Systems Medicine through optimal design of experimentation and computational modeling¿, Belfast Belfast, , 02-NOV-14 - 05-DEC-14 , pp.S3203 Link to full text [Details]
Dobrzynski, M; Fey, D; Nguyen, LK; Kholodenko, BN (2012) Bimodal Protein Distributions in Heterogeneous Oscillating Systems Proceedings of the 10th International Conference on Computational Methods in Systems Biology (CMSB), London, UK , pp.17-28 Available Online [Details]
Dobrzyński, M; Fey, D; Nguyen, LK; Kholodenko, BN (2012) Bimodal Protein Distributions in Heterogeneous Oscillating Systems . In: Gilbert, David and Heiner, Monika eds. 10th International Conference, CMSB 2012, London, UK Available Online [Details]
Fey, D and Bullinger, E; (2010) Limiting the parameter search space for dynamic models with rational kinetics using semi-definite programming Proceedings of the 11th Symposium on Computer Applications in Biotechnology (CAB), Leuven [Details]
Fey, D and Bullinger, E; (2009) A dissipative approach to the identification of kinetic reaction networks Proceedings of the 15th IFAC Symposium on Systems Identification (SYSID), Saint-Malo , pp.1259-1264 [Details]
Fey, D and Findeisen, R and Bullinger, E; (2008) Parameter estimation in kinetic reaction models using nonlinear observers is facilitated by model extensions Proceedings of the 17th International Federation of Automatic Control World Congress (IFAC WC), Seoul , pp.313-318 [Details]
                                                                                                                 

Research

Research Interests

My goal is a holistic, quantitative understanding of cancer related signalling networks across the scales ranging from the intracellular to the organism level. For example, how does variability on the cellular level affect cell fate? How do patient-to-patient differences affect clinical outcomes?
 
Current projects:
  • Development of theoretical frameworks relating signalling dynamics and cancer progression/prognosis
  • Modelling TrkA/B induced cell fate in neuroblastoma
  • Modelling and analysis of MAPK/JNK signalling
  • Development of identification methods for biochemical reaction systems
Former projects:
  • Modelling learning & memory: Modelling rat swimming behaviour in Morris water maze experiments. Aim: Better understanding of learning & memory by revealing contribution/trade offs between randomness & different search strategies & leaning protocols.
  • Parameter Estimation: Observer based approaches for parameter estimation of kinetic reaction models. Aim: Exploit biology specific properties (form of reaction kinetics) to develop accurate estimation methods (by mathematical proof).
  • Integrated modelling of signal transduction & electro-physiology 
  • Model reduction of signal transduction systems exhibiting combinatorial complexity
     

Teaching

 

Modules Coordinated

201600   MEIN40240     Medical Informatics: Systems Biology