Natasa Przulj

This page has not been maintained, so please go to my current web page for up to date information.

My research involves applications of graph theory, mathematical modeling, and computational techniques to solve large scale problems in computational and systems biology. I am interested in theoretical solutions to practical problems in many areas of systems biology, planar cell polarity, proteomics, cancer informatics, and chemo-informatics. For details about sample projects, please see the list of publications (below).

Open Positions

Interested prospective Ph.D. students should apply on-line at http://www.ics.uci.edu/grad/index.php.

Independent, motivated, and productive finishing Ph.D. students or post-docs in computer science, mathematics, or a related discipline with some biological or bioinformatics experience are welcome to apply for the post-doc position. To apply, please e-mail me your CV, research statement, and letters of reference.
 

Experience Summary

In my Ph.D. thesis, I analyzed large protein-protein interaction networks and proposed an improved, geometric random graph model, for these networks (see refereed journal paper 4. below). In addition, I proposed new heuristic approaches for uncovering local structural properties in these networks.

I received my M.Sc. from the Department of Computer Science, University of Toronto, in January 2000. In my M.Sc. thesis, I analyzed the structure of Hereditary Dominating Pair Graphs (see refereed journal paper 6. below).

I worked as a Smallworld  GIS developer at Westech Information Systems  from May 1997 to August 1998 providing programming services for AM/FM/GIS applications using Magik/Smallworld GIS and Visual Basic.  As a co-op student, I worked in the quality assurance department of Hughes Aircraft of Canada Ltd. in 1995.

I received my B.Sc. (First Class Honors) in Mathematics and Computing Science in April 1997 from Simon Fraser University, Vancouver, Canada.  I completed the first two years of my undergraduate studies in Mathematics and Computer Science at the University of Belgrade, Yugoslavia.

I received various academic and industrial awards (listed in my CV below).

I was the president of the Computer Science Graduate Student Benevolent Society at U of T from the fall of 2000 to the fall of 2002; I have done other types of academic service as well (listed in my CV).

For more details, please see my CV (ps / pdf).

Refereed Journal Papers

1. N. Przulj and Des Higham, A Stickiness Model for Protein-Protein Interaction Networks, Journal of the Royal Society Interface, in press, 2006.
2. N. Przulj, Biological Network Comparison Using Graphlet Degree Distribution, Proceedings of the 2006 European Conference on Computational Biology, ECCB '06, Eilat, Israel, September 10-13, 2006, acceptance rate 18%. Bioinformatics, in press, 2006.
3. N. Przulj, D. G. Corneil, and I. Jurisica, Efficient estimation of graphlet frequency distributions in protein-protein interaction networks, Bioinformatics, volume 22, number 8, pages 974-980, 2006.
4. M. Barrios-Rodiles, K. R. Brown, B. Ozdamar, Z. Liu, R. S. Donovan, F. Shinjo, Y. Liu, R. Bose, J. Dembowy, I. W. Taylor, V. Luga, N. Przulj, M. Robinson, H. Suzuki, Y. Hayashizaki, I. Jurisica, and J. L. Wrana, High-Throughput Mapping of a Dynamic Signaling Network in Mammalian Cells, Science, volume 307, number 5715, pages 1621-1625, 2005.
5. N. Przulj and D. G. Corneil, 2-tree Probe Interval Graphs Have a Large Obsturction Set, Discrete Applied Mathematics, volume 150, number 1-3, pages 216-231, 2005.
6. N. Przulj, D. G. Corneil, and I. Jurisica, Modeling Interactome: Scale-Free or Geometric?, Bioinformatics, volume 20, number 18, pages 3508-3515, 2004.
7. A. D. King, N. Przulj, and I. Jurisica, Protein complex prediction via cost-based clustering, Bioinformatics, volume 20, number 17, pages 3013 - 3020, 2004.
8. N. Przulj, D. Wigle, and I. Jurisica, Functional Topology in a Network of Protein Interactions, Bioinformatics, volume 20, number 3, pages 340-348, 2004.
9. N. Przulj, D. G. Corneil, and E. Koehler, Hereditary Dominating Pair Graphs, Discrete Applied Mathematics, volume 134, pages 239-261, 2004.
10. A. L. Liestman and N. Przulj, Minimum Average Time Broadcast Graphs, Par. Proc. Lett., volume 8, pages 139-147, 1998.

Refereed Book Chapter

11. N. Przulj, Graph Theory Analysis of Protein-Protein Interactions, a chapter in "Knowledge Discovery in Proteomics", edited by Igor Jurisica and Dennis Wigle, CRC Press, 2005.

Invited Talks

1. N. Przulj, Comparing and Modeling Protein-Protein Interaction Networks, A Workshop on Algorithms in Bioinformatics, French-Russian J.-V. Poncelet laboratory, Moscow, Russia, July 11-13, 2006
2. N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, Simon Fraser University, Vancouver, Canada, December 14, 2005
3. N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, University of Victoria, Victoria, Canada, December 13, 2005
4. N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, University of British Columbia, Vancouver, Canada, December 12, 2005
5. N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, Institute of Physics, University of Belgrade, Zemun, Serbia and Montenegro, September 14, 2005
6. N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, BMC Research Center, RIKEN, Nagoya, Japan, May 24, 2005
7. N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, UC Riverside, Riverside, CA, April 25, 2005
8. N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, UC Irvine, Irvine, CA, March 17, 2005
9. N. Przulj, Analyzing Software Call Graphs, Microsoft Research, Redmond, WA, August 22, 2003
10. N. Przulj, D. Wigle, and I. Jurisica, Functional Topology in a Network of Protein Interactions, a plenary talk at BioPathways, a Satellite Conference of ISMB'03, Brisbane, Australia, June 27 - 28, 2003

Contributed Talks

11. N. Przulj and Wayne Hayes, Biological network comparison using graphlet degree distributions, 3rd International Symposium on Networks in Bioinformatics (ISNB'06), acceptance rate 20%, Amsterdam, the Netherlands, May 29-31, 2006
12. N. Przulj, Uncovering Structure in Protein-Protein Interaction Networks, BioPathways, a Satellite Conference of ISMB'05, Detroit, Michigan, June 23 - 24, 2005
13. N. Przulj, Geometric Model of Protein Interaction Networks,CNET 2004, University of Aveiro, Portugal, August 29 - September 2, 2004
14. N. Przulj and D. G. Corneil, 2-tree Probe Interval Graphs Have a Large Obstruction Set, 12th Ontario Combinatorics Workshop, University of Ottawa, May 1-2, 2003
15. N. Przulj, G. Lee, and I. Jurisica, Functional Analysis of Large Software Networks, IBM Academy Conference on Proactive Problem Prediction, Avoidance and Diagnosis, IBM T.J. Watson Research Center, Yorktown, NY, April 28-29, 2003
16. N. Przulj, Minimal Hereditary Dominating Pair Graphs, Workshop on Structured Families of Graphs, The Fields Institute, May 8-13, 2000
17. N. Przulj, Minimal Hereditary Dominating Pair Graphs, Special Year on Graph Theory and Combinatorial Optimization Program Seminar Series, The Fields Institute, March 22, 2000
18. A. L. Liestman and N. Przulj, Minimum Average Time Broadcast Graphs, 27th SE International Conference on Combinatorics, Graph Theory, and Computing: March, 1997

Exhibits

19. N. Przulj, D. G. Corneil, and I. Jurisica, Geometric Properties of Protein-Protein Interaction Networks, a poster at ISMB/ECCB 2004, Glasgow, UK, July 31 - August 4, 2004
20. N. Przulj and I. Jurisica, A Call Graph Analysis, a poster at CASCON 2003, Markham, Ontario, Canada, October 6-9, 2003
21. N. Przulj, D. Wigle, and I. Jurisica, Functional Topology in a Network of Protein Interactions, a poster at ISMB 2003, Brisbane, Australia, June 29 - July 3, 2003

Theses

• N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interactions Example, Ph.D. Thesis, Graduate Department of Computer Science, University of Toronto, April 2005.
• N. Przulj, Minimal Hereditary Dominating Pair Graphs, M.Sc. Thesis, Graduate Department of Computer Science, University of Toronto, January 2000.

Teaching

Current:

• ICS 280 Biological Networks, graduate course, UC Irvine, Winter 2006

• ICS 265 Graph Algorithms, graduate course, UC Irvine, Winter 2006

Past:

• First year courses:
• Teaching Assistant and Substitute Instructor:   CSC 199 Beautiful Algorithms, U of T, Fall 2001 and Spring 2002
• Teaching Assistant:    MAT 154, 155, 157, 158 Applied Calculus Courses, SFU, Spring 1996
• Second year course:
• Teaching Assistant:   CSC 238 Discrete Mathematics, U of T, Summer 1999 and Summer 2001
• Third year course:
• Teaching Assistant:   MATC32 Graph Theory and Algorithms, U of T at Scarborough, Fall 2000
• Graduate courses:
• Teaching Assistant:   CSC 2414 Topics in ADM: Analysis of Algorithms, U of T, Spring 2002
• Instructor:   ICS 280: Biological Networks, UC Irvine, Winter 2006
• Instructor:   ICS 265: Graph Algorithms, UC Irvine, Winter 2006

Other Pages

• Information for new theory and combinatorics graduate students, U of Toronto
• CSC 199Y 2001/2002, U of Toronto
• MBP 1022, U of Toronto

Favorite Places

• City of Belgrade
• Motovun, Istria
• Oprtalj, Istria
• Le Chazelet, France
• Glamoc, Bosnia

Contact Information

Last updated July 26, 2006