Dimitris Kalamatianos

Dr. Dimitris Kalamatianos

Principal Investigator/Lecturer

Hamilton Institute
Office 31
NUI Maynooth
Phone: +353 (0)1 708 6826
Fax: +353 (0)1 708 62 69
Email: dimitris.kalamatianos at nuim.ie

About me

I was born in Cholargos, Attika (Greece) and I grew up in Pyrgos, Elia. I attended the University of Patras (Greece) as an undergraduate in 1996, obtaining a first class honours degree in electrical and computer engineering and receiving the prestigious scholarship from the I. Latsis Foundation. In October 2001, I started my Ph.D. in Electrical and Electronic Engineering at the University of Manchester Institute of Science and Technology (UMIST), UK. My research involved the development of a novel near-infrared spectrometer for non-intrusive life-science measurements and it was supported by the Engineering and Physical Sciences Research Council (EPSRC). In October 2004, I joined the Systems Biology group at the Hamilton Institute, National University of Ireland, Maynooth as a postdoctoral researcher. Since January 2008 I have been the head of the Hamilton Institute's Image to Mathematical Model Transition (IMMT) group and adjunct Lecturer at the Department of Electronic Engineering.

Research Interests

Mathematical Modelling and analysis of signal transduction networks
Data Mining and Machine learning for biomedical data analysis
Biomedical image processing

Recent Publications

For a full list of publications click here

Kalamatianos, D. (2010), "Image analysis for automated live-cell imaging", In TOPIM 2010 - Imaging Systems Biology. Bardonecchia, Italy, Feb 8--12, 2010.

[BibTeX]

BibTeX:

@conference{Kalamatianos:10,
  author = {Kalamatianos, D.},
  title = {Image analysis for automated live-cell imaging},
  booktitle = {TOPIM 2010 - Imaging Systems Biology},
  year = {2010},
  note = {Invited talk}
}

López-Caamal, F., Oyarzún, D., Moreno, J.A. & Kalamatianos, D. (2010), "Control Structure and Limitations of Biochemical Networks", In American Control Conference. Baltimore, MD, USA. Jun 30 - Jul 2 2010., pp. 6668 - 6673.

[BibTeX]

BibTeX:

@inproceedings{Caamal:10,
  author = {López-Caamal, F. and Oyarzún, D. and Moreno, J. A. and Kalamatianos, D.},
  title = {Control Structure and Limitations of Biochemical Networks},
  booktitle = {American Control Conference},
  year = {2010},
  pages = {6668 - 6673}
}

Paul, P., Düssmann, H., Bernas, T., Huber, H. & Kalamatianos, D. (2010), "Automatic noise quantification for confocal fluorescence microscopy images", Computerized Medical Imaging and Graphics., September, 2010. Vol. 34(6), pp. 426-434.

[BibTeX] [DOI] [URL]

BibTeX:

@article{Paul:10a,
  author = {Paul, P. and Düssmann, H. and Bernas, T. and Huber, H. and Kalamatianos, D.},
  title = {Automatic noise quantification for confocal fluorescence microscopy images},
  journal = {Computerized Medical Imaging and Graphics},
  year = {2010},
  volume = {34},
  number = {6},
  pages = {426-434},
  note = {Accepted},
  url = {http://dx.doi.org/10.1016/j.compmedimag.2010.04.001},
  doi = {http://dx.doi.org/10.1016/j.compmedimag.2010.04.001}
}

Paul, P., Düssmann, H., Wenus, J., Huber, H. & Kalamatianos, D. (2010), "On-line Multiple cell tracking and feature extraction for multivariate time lapse single cell imaging", IEEE Transactions on Medical Imaging.

[BibTeX]

BibTeX:

@article{Paul:10b,
  author = {Paul, P. and Düssmann, H. and Wenus, J. and Huber, H. and Kalamatianos, D.},
  title = {On-line Multiple cell tracking and feature extraction for multivariate time lapse single cell imaging},
  journal = {IEEE Transactions on Medical Imaging},
  year = {2010},
  note = {In preparation}
}

Setty, Y., Chen, C.-C., Secrier, M., Kugler, H. & Kalamatianos, D. (2010), "How neurons migrate: an in silico approach for neuron migration study", Journal of the Royal Society.

[BibTeX]

BibTeX:

@article{Setty:10,
  author = {Setty, Y. and Chen, C.-C. and Secrier, M. and Kugler, H. and Kalamatianos, D.},
  title = {How neurons migrate: an in silico approach for neuron migration study},
  journal = {Journal of the Royal Society},
  year = {2010},
  note = {Submitted}
}

Düssmann, H., Wenus, J., Kalamatianos, D., Paul, P., Wellstead, P., Huber, H. & Prehn, J. (2009), "Real-Time automated live cell image acquisition and analysis using confocal laser scanning microscopy", In Neuroscience 2009. Chicago, ILL, Oct 17--21, 2009.

[BibTeX]

BibTeX:

@conference{Duessman:09,
  author = {Düssmann, H. and Wenus, J. and Kalamatianos, D. and Paul, P. and Wellstead, P. and Huber, H. and Prehn, J.},
  title = {Real-Time automated live cell image acquisition and analysis using confocal laser scanning microscopy},
  booktitle = {Neuroscience 2009},
  year = {2009}
}

Huber, H., Düssmann, H., Paul, P., Wenus, J., Kalamatianos, D. & Wuerstle, M. (2009), "Microscopy control system and method" (S20090230)

[BibTeX]

BibTeX:

@patent{Huber:09,
  author = {Huber, H. and Düssmann, H. and Paul, P. and Wenus, J. and Kalamatianos, D. and Wuerstle, M.},
  title = {Microscopy control system and method},
  year = {2009},
  number = {S20090230}
}

Kalamatianos, D., Anastasiadis, A.D. & Liatsis, P. (2009), "A Nonextensive method for spectroscopic data analysis with Artificial Neural Networks", Brazilian Journal of Physics., August, 2009. Vol. 39(2A), pp. 488-494.

[BibTeX] [URL]

BibTeX:

@article{Kalamatianos:09a,
  author = {Kalamatianos, D. and Anastasiadis, A. D. and Liatsis, P.},
  title = {A Nonextensive method for spectroscopic data analysis with Artificial Neural Networks},
  journal = {Brazilian Journal of Physics},
  year = {2009},
  volume = {39},
  number = {2A},
  pages = {488-494},
  url = {http://www.sbfisica.org.br/bjp/files/v39_488.pdf}
}

López-Caamal, F., Readman, M.C., Moreno, J.A. & Kalamatianos, D. (2009), "Structure identification and control mechanisms in the Extrinsic Apoptosis Pathway", In Conference on Dynamics in Systems Biology. Aberdeen, Scotland, Sep 14-18, 2009.

[BibTeX]

BibTeX:

@conference{Caamal:09b,
  author = {López-Caamal, F. and Readman, M. C. and Moreno, J. A. and Kalamatianos, D.},
  title = {Structure identification and control mechanisms in the Extrinsic Apoptosis Pathway},
  booktitle = {Conference on Dynamics in Systems Biology},
  year = {2009}
}

Oyarzún, D., Ingalls, B., Middleton, R. & Kalamatianos, D. (2009), "Sequential Activation of Metabolic Pathways: a Dynamic Optimization Approach", Bulletin of Mathematical Biology., May, 2009. Vol. 71(8), pp. 1851-1872.

[BibTeX] [DOI] [URL]

BibTeX:

@article{Oyarzun:09,
  author = {Oyarzún, D. and Ingalls, B. and Middleton, R. and Kalamatianos, D.},
  title = {Sequential Activation of Metabolic Pathways: a Dynamic Optimization Approach},
  journal = {Bulletin of Mathematical Biology},
  year = {2009},
  volume = {71},
  number = {8},
  pages = {1851-1872},
  url = {http://www.springerlink.com/content/77357073836804t2/},
  doi = {http://dx.doi.org/10.1007/s11538-009-9427-5}
}

Paul, P., Kalamatianos, D., Huber, H., Wenus, J. & Düssmann, H. (2009), "Automatic Real-Time Detection of the Onset of Apoptosis in Confocal Fluorescence Microscopy", In Proceedings of the Focus on Microscopy Conference. Krakow, Poland. Apr 5--8 2009., pp. 240.

[BibTeX]

BibTeX:

@inproceedings{Paul:09a,
  author = {Paul, P. and Kalamatianos, D. and Huber, H. and Wenus, J. and Düssmann, H.},
  title = {Automatic Real-Time Detection of the Onset of Apoptosis in Confocal Fluorescence Microscopy},
  booktitle = {Proceedings of the Focus on Microscopy Conference},
  year = {2009},
  pages = {240}
}

Wenus, J., Düssmann, H., Paul, P., Kalamatianos, D., Rehm, M., Wellstead, P., Prehn, J. & Huber, H. (2009), "ALISSA - An Automated Live-Cell Imaging System for Signal-Transduction Analyses", Biotechniques., December, 2009. Vol. 47(6), pp. 1033-1040.

[BibTeX] [DOI] [URL]

BibTeX:

@article{Wenus:09,
  author = {Wenus, J. and Düssmann, H. and Paul, P. and Kalamatianos, D. and Rehm, M. and Wellstead, P. and Prehn, J. and Huber, H.},
  title = {ALISSA - An Automated Live-Cell Imaging System for Signal-Transduction Analyses},
  journal = {Biotechniques},
  year = {2009},
  volume = {47},
  number = {6},
  pages = {1033-1040},
  url = {http://www.biotechniques.com/BiotechniquesJournal/2009/December/ALISSA-an-automated-live-cell-imaging-system-for-signal-transduction-analyses/biotechniques-181023.html},
  doi = {http://dx.doi.org/10.2144/000113247}
}

Zebrowska, M., Readman, M.C., Cloutier, M. & Kalamatianos, D. (2009), "A systems study of the autophagic pathway", In The 17th ECDO Euroconference on Apoptosis. Paris, France, Sep 23-26, 2009.

[BibTeX]

BibTeX:

@conference{Zebrowska:09b,
  author = {Zebrowska, M. and Readman, M. C. and Cloutier, M. and Kalamatianos, D.},
  title = {A systems study of the autophagic pathway},
  booktitle = {The 17th ECDO Euroconference on Apoptosis},
  year = {2009}
}

Oyarzún, D., Ingalls, B., Middleton, R. & Kalamatianos, D. (2008), "Optimal Metabolic Pathway Activation", In Proceedings of the 17th IFAC World Congress. Seoul, Korea. Jul 6--11 2008.

[BibTeX] [URL]

BibTeX:

@inproceedings{Oyarzun:08,
  author = {Oyarzún, D. and Ingalls, B. and Middleton, R. and Kalamatianos,D.},
  title = {Optimal Metabolic Pathway Activation},
  booktitle = {Proceedings of the 17th IFAC World Congress},
  year = {2008},
  url = {http://dx.doi.org/10.3182/20080706-5-KR-1001.0690}
}

Paul, P., Kalamatianos, D., Düssmann, H. & Huber, H. (2008), "Automatic quality assessment for fluorescence microscopy images", In Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering. Athens, Greece. Oct 8--10 2008., pp. 1-6.

[BibTeX] [URL]

BibTeX:

@inproceedings{Paul:08b,
  author = {Paul, P. and Kalamatianos, D. and Düssmann, H. and Huber, H.},
  title = {Automatic quality assessment for fluorescence microscopy images},
  booktitle = {Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering},
  year = {2008},
  pages = {1--6},
  url = {http://dx.doi.org/10.1109/BIBE.2008.4696665}
}

Wellstead, P., Bullinger, E., Kalamatianos, D., Mason, O. & Verwoerd, M. (2008), "The rôle of control and system theory in systems biology", Annual Reviews in Control., April, 2008. Vol. 32(1), pp. 33-47.

[BibTeX] [DOI] [URL]

BibTeX:

@article{Wellstead:08,
  author = {Wellstead, P. and Bullinger, E. and Kalamatianos, D. and Mason, O. and Verwoerd, M.},
  title = {The rôle of control and system theory in systems biology},
  journal = {Annual Reviews in Control},
  year = {2008},
  volume = {32},
  number = {1},
  pages = {33--47},
  url = {http://www.sciencedirect.com/science/article/B6V0H-4SHFSTX-1/2/ad9687f1ea3e9d525c68c26d48b438ae},
  doi = {http://dx.doi.org/10.1016/j.arcontrol.2008.02.001}
}

Bullinger, E., Findeisen, R., Kalamatianos, D. & Wellstead, P. (2007), "System and control theory furthers the understanding of biologicalsignal transduction", In Biology and control theory: current challenges. Berlin, Germany, August, 2007. Vol. 357, pp. 123-135. Springer-Verlag.

[BibTeX] [DOI] [URL]

BibTeX:

@incollection{Bullinger:07,
  author = {Bullinger, E. and Findeisen, R. and Kalamatianos, D. and Wellstead, P.},
  title = {System and control theory furthers the understanding of biologicalsignal transduction},
  booktitle = {Biology and control theory: current challenges},
  publisher = {Springer-Verlag},
  year = {2007},
  volume = {357},
  pages = {123--135},
  url = {http://www.springerlink.com/content/hq77j5mvk0u67354/},
  doi = {http://dx.doi.org/10.1007/978-3-540-71988-5_6}
}

Oyarzún, D., Ingalls, B. & Kalamatianos, D. (2007), "Optimal metabolic regulation by time varying enzyme activities: a control theoretic approach", In Proceedings of the Foundations of Systems Biology in Engineering Conference 2007. Stuttgart, Germany. Sep 9--12 2007., pp. 491-496.

[BibTeX] [URL]

BibTeX:

@inproceedings{Oyarzun:07,
  author = {Oyarzún, D. and Ingalls, B. and Kalamatianos, D.},
  title = {Optimal metabolic regulation by time varying enzyme activities: a control theoretic approach},
  booktitle = {Proceedings of the Foundations of Systems Biology in Engineering Conference 2007},
  year = {2007},
  pages = {491--496},
  url = {http://www.hamilton.ie/d.o/docs/oyarzun_etal07c.pdf}
}

Created by JabRef on 23/11/2010.