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Nadia Ugel
NYU Bioinformatics Group,
715 Broadway, Rm 1011
New York, NY 10003
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Phone: 212 998 3112
Fax: 212 998 3484
e-mail:nadia [at] bioinformatics.nyu.edu
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Research Interest
My background is in Computer Science, but when I was introduced to the challenges posed by biology, I saw the possibility to integrate the various computational, mathematical and biological skills. My personal interest lies precisely at the border of the three disciplines: where I need to gain a lot of biological training and not only that which is strictly necessary to build a model. I like to work and discuss with biologists and mathematicians in an iterative process where together we build the model and together we proceed to further analysis.
Current Projects
The main project, in which I am involved at the NYU Bioinformatics Group, is
- Simpathica
I have been working on the front-end of the system trying to devise a standard model to describe metabolic pathways that allows to generate a system of differential equations to simulate them.
Additional tasks include integrating Simpathica with BioSpice technology and our own Bionformatics tool VALIS.
Two challenging topics provide me the test and application cases for Simpathica:
- Quantitative analysis of germline mitosis in adult C. elegans
- APAF-1 Apoptosis Pathway
Publications
Papers:
- John Maciejowski, Nadia Ugel, Bud Mishra, Marco Isopi and E. Jane Albert Hubbard
Quantitative analysis of germline mitosis in adult C. elegans,
Developmental Biology, Volume 292, Issue 1, 1 April 2006, Pages 142-151
(url)
- M. Antoniotti, S. Paxia, N. Ugel, B. Mishra
Simpathica: A Computational System Biology Tool within the Valis Bioinformatics Environment,
Computational Systems Biology, Ed. E. Eiles and A. Kriete eds., Elsevier, 2005
(doc)
- M. Antoniotti, A. Policriti, N. Ugel, B. Mishra
Model Building and Model Checking for Biochemical Processes,
Cell Biochemistry and Biophysics (CBB), 38(3): 271-286, Humana Press, June, 2003
(pdf)
- B. Mishra, et al.
A Sense of Life: Computational & Experimental Investigations with Models of Biochemical
& Evolutionary Processes,
OMICS - A Journal of Integrative Biology, (Special Issue on BioCOMP, S. Kumar, ed.), 7(3), 2003
(pdf)
- M. Antoniotti, F. Park, A. Policriti, N. Ugel, B. Mishra
Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes,
The Pacific Symposium on Biocomputing: PSB 2003, (Eds. R.B. Altman, A.K. Dunker, L. Hunter, T.A. Jung & T.E.Klein), pp 116-127, World Scientific, January, 2003
(pdf)
- M. Antoniotti, A. Policriti, N. Ugel, B. Mishra
xS-systems: eXtended S-systems and Algebraic Differential Automata for Modeling Cell Behavior,
High Performance Computing (HiPC 2002), S. Sahni, V. K. Prasanna e U. Shukla eds., LNCS 2552:431-442, Springer-Verlag, December 2002
(pdf)
Presentations and Abstracts
- J. Maciejowski, N. Ugel, M. Isopi, B. Mishra, E.J.A. Hubbard
Computational Approaches to Understand Germline Stem Cell Behavior in C. elegans,
Germ Cells Meeting, Cold Spring Harbor Lab, October, 2004
(url)
- N. Ugel, S.C. Lin, Y. Lazebnik, B. Mishra
Mathematical Models and Experimental Verification of a Cell-Death Process,
Invited speaker at the International Conference for Mathematics in Biology and Medicine (SMB - 2004), University of Michigan, July 25-28 2004
(abs, ppt)
- M. Antoniotti, F. Park, A. Policriti, N. Ugel, B. Mishra
Simulating Large Biochemical and Biological Processes and Reasoning about their Behaviour,
3rd International Conference on Systems Biology, ICSB 2002, Karolinska Institutet, Stockholm, Sweden, 2002
(pdf)
Poster at ICSB 2002, Stokholm, Sweden, December 2002
(pdf)
- M. Antoniotti, M. Isopi, V. Mittal, N. Ugel, B. Mishra
Mathematically Modeling Stem Cells Populations,
Poster at 2002 Meeting on Genome Sequencing and Biology, CSHL, Cold Spring
Harbor, NY, U.S.A., May 2002
Useful Links
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