Attila Csikasz-Nagy
Attila Csikasz-Nagy
e-mail:
affiliation: The Microsoft Research - University of Trento
research area(s): Computational Biology
Course: Biomolecular Sciences
University/Istitution: Università di Trento
Education:
Santa Fe Institute,Summer school, 2001,Mathematical Biology
Budapest University of Technology and Economics,PhD,2000,Chemistry (Summa cum laude)
Budapest University of Technology and Economics, MSc, 1998, Bioengineering

Professional Experience:
2011 Jan - Principal Investigator, The Microsoft Research - University of Trento Centre for Computational and Systems Biology
2007 Jun - 2011 Jan Researcher, The Microsoft Research - University of Trento Centre for Computational and Systems Biology
2007 Jan - 2007 May Main Research Fellow, Materials Structure and Modelling Research Group of the Hungarian Academy of Sciences
2004 May - 2007 May Assistant Professor, Molecular Network Dynamics Research Group, Budapest University of Technology and Economics
2000 Sep - 2005 Aug Postdoctoral fellow, Dept. of Agricultural Chemical Technology, Budapest University of Technology and Economics, Hungary (with Béla Novák).
2004 Jan - 2004 Dec Postdoctoral fellow, Virginia Tech, Blacksburg, VA, USA, (with John J. Tyson)
2003 Feb - 2003 July Junior fellow, Collegium Budapest, Hungary. Member of the Computational Molecular Biology focus group.
Research visits:
2010 Program of Evolutionary Dynamics, Harvard University, Cambridge, MA, USA, 1 week
2007 Kavli Institute for Theoretical Physics, Santa Barbara, CA, USA, 4 weeks
2002 Santa Fe Institute, Santa Fe, NM, USA. 3 weeks.
1997, 1999 Virginia Tech, Blacksburg, VA, USA. 3 months (1997), 4 months (1999).
1996 University of Edinburgh, UK, 2 weeks

Memberships: International Society for Computational Biology, European Society for Mathematical and Theoretical Biology, Hungarian Society for Bioinformatics, Hungarian Biochemical Society

Professional Affiliations:
2009- Advisory Board member of the Encyclopedia of Systems Biology by Springer
2009- Member of the International Doctoral School of Biomolecular Sciences (University of Trento)
2006-2007 Counselor to the Board of the European Society for Mathematical and Theoretical Biology
2005-2007 Member of the Scientific Board of the Bio- and Chemical Engineering Faculty of Budapest University of Technology and Economics


PhD committee member, external reviewer:
Stellenbosch University (Stellenbosch, South Africa), Technologies Avancées pour le Génome et la Clinique (Marseille, France), European School of Molecular Medicine (Milan, Italy)
The main research line focuses on the regulation of cell growth and proliferation, especially dealing with cell cycle regulation. Recently I extended this line towards spatial control of cell growth and investigate how various pathways affect the cell cycle. I also investigate some of these and other signaling pathways in more details.

Specific research interest:
-Cell cycle regulation—regulation of DNA replication and mitosis in space and time
-Effects of circadian clock - cell cycle coupling
-Spatial and temporal pattern of cell growth, polarity and morphology
-Molecular network dynamics
-Budding yeast, fission yeast
-Evolutionary game theory, cooperation-competition, network dynamics
-Multilevel tissue and tumor formation modeling
-Tools for network analysis: bifurcation analysis, phase plane techniques, coupled ODE systems, reaction-diffusion equations
2011

Csikász-Nagy A, Cardelli L, Soyer OS: Response dynamics of phosphorelays suggest their potential utility in cell signaling. J R Soc Interface 2011, 8(57):480-8.

2010

Conradie R, Bruggeman FJ, Ciliberto A, Csikász-Nagy A, Novák B, Westerhoff HV, Snoep JL.Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex. FEBS J. 2010 277(2):357-67

Csikász-Nagy A, Mura I.Role of mRNA gestation and senescence in noise reduction during the cell cycle. In Silico Biol. 2010 10:0006.

2009

Soyer OS, Kuwahara H, Csikász-Nagy A.Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses. FEBS J. 2009 276(12):3290-8.

Hong CI, Zámborszky J, Csikász-Nagy A.Minimum criteria for DNA damage-induced phase advances in circadian rhythms. PLoS Comput Biol. 2009 5(5):e1000384.

Csikász-Nagy A.Computational systems biology of the cell cycle. Brief Bioinform. 2009 10(4):424-34

Csikász-Nagy A, Kapuy O, Tóth A, Pál C, Jensen LJ, Uhlmann F, Tyson JJ, Novák B.Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Mol Syst Biol. 2009;5:236.

Ballarini P, Mazza T, Palmisano A, Csikász-Nagy A.Studying irreversible transitions in a model of cell cycle regulation. ENTCS. 2009 232:39-53.

2008

Csikász-Nagy A, Novák B, Tyson JJ.Reverse engineering models of cell cycle regulation. Adv Exp Med Biol. 2008;641:88-97.

Mura I, Csikász-Nagy A.Stochastic Petri Net extension of a yeast cell cycle model. J Theor Biol. 2008 254(4):850-60.

Csikász-Nagy A, Soyer OS.Adaptive dynamics with a single two-state protein. J R Soc Interface. 2008 5 Suppl 1:S41-7.

Lovrics A, Csikász-Nagy A, Zsély IG, Zádor J, Turányi T, Novák B.Analysis of a budding yeast cell cycle model using the shapes of local sensitivity functions. Int J Chem Kinet. 2008 40(11):710-20.

2007

Zámborszky J, Hong CI, Csikász Nagy A.Computational analysis of mammalian cell division gated by a circadian clock: quantized cell cycles and cell size control. J Biol Rhythms. 2007 22(6):542-53.

Csikász-Nagy A, Gyorffy B, Alt W, Tyson JJ, Novák B.Spatial controls for growth zone formation during the fission yeast cell cycle.Yeast. 2008 25(1):59-69.

Novak B, Tyson JJ, Gyorffy B, Csikasz-Nagy A.Irreversible cell-cycle transitions are due to systems-level feedback.Nat Cell Biol. 2007 9(7):724-8.

Csikász-Nagy A, Kapuy O, Gyorffy B, Tyson JJ, Novák B.Modeling the septation initiation network (SIN) in fission yeast cells.Curr Genet. 2007 51(4):245-55.

2006

Lovrics A, Csikász-Nagy A, Zsély IG, Zádor J, Turányi T, Novák B. Time scale and dimension analysis of a budding yeast cell cycle model.BMC Bioinformatics. 2006 7:494.

Csikász-Nagy A, Battogtokh D, Chen KC, Novák B, Tyson JJ.Analysis of a generic model of eukaryotic cell-cycle regulation.Biophys J. 2006 90(12):4361-79.
Project Title:
“Mechanistic modeling of genetic and signaling networks connecting diet and diseases relying on mouse models of human disease.”
The candidate is expected to build an algorithmic model (see http://www.cosbi.eu/index.php/research/alg-sys-bio) of the folate cycle or other mechanisms that are related to obesity, relying on experimental data. The design and realization of the model will be done at COSBI within the molecular nutrition activities (see http://www.cosbi.eu/index.php/research/molecular-nutrition). The candidate is expected to perform his/her experimental work at ISB (Institute for Systems Biology) - Seattle in Nadeau's Lab (see http://www.systemsbiology.org/scientists_and_research/faculty_groups/Nadeau_Group).


Project Title:
“Modeling of human disease from multi-source data for supporting P4 medicine”.
The candidate is expected to build an algorithmic model (see http://www.cosbi.eu/index.php/research/alg-sys-bio) of a human disease (it could be either heart disease or a neuro-degenerative disease), relying on experimental data. The design and realization of the model will be done at COSBI (see http://www.cosbi.eu). The candidate is expected to perform his/her experimental work at ISB (Institute for Systems Biology) - Seattle in Hood's Lab (see http://www.systemsbiology.org/scientists_and_research/faculty_groups/Hood_Group/Profile).