Photo of Natasa Przulj

Natasa Przulj

 
I am an Assistant Professor in the Department of Computer Science, UC Irvine.  I am also a member of the UCI Cancer Center, the UCI Center for Complex Biological Systems (CCBS), the UCI's program in Mathematical, Computational and Systems Biology (MCSB), and the UCI’s Institute for Genomics and Bioinformatics (IGB). I received an NSF CAREER award for 2007-2011.

My research involves applications of graph theory, mathematical modeling, and computational techniques to solving large-scale problems in computational and systems biology. I am interested in computational and 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).

Software

            Visit our new network analysis and modeling software, GraphCrunch, published in BMC Bioinformatics and listed as Highly accessed.

Open Positions

There are several open Ph.D. student positions and one open post-doc position in my lab.

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

I have done various types of academic service including serving on NSF and other grant reviewing panels as well as on program committees of: (1) 16th International Symposium on Graph Drawing, Crete, Greece, September 21-24, 2008; (2) BIOKDD at ACM SIGKDD 2008, Las Vegas, NV, August 24-27, 2008; (3) ISMB/ECCB 2007, Vienna, Austria, July 21-25, 2007; and (4) BIOKDD at ACM SIGKDD 2007, San Jose, CA, USA, August 12,2007 (listed in my CV below).  I received various academic and industrial awards including an NSF CAREER award (see my CV below).

I was a postdoctoral fellow at Samuel Lunenfeld Research Institute, Mt. Sinai Hospital in Toronto from March to July 2005, working under the supervision of Prof. Jeff Wrana. I received my Ph.D. from the  University of Toronto, Department of Computer Science in April 2005.  My Ph.D. research focused on applications of graph theory in computational biology (proteomics) and software engineering. I was supervised by Prof. Derek Corneil and Prof. Igor Jurisica.  In my Ph.D. thesis, I analyzed large protein-protein interaction networks and proposed an improved, geometric random graph model, for these networks. 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.  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 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.

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

Refereed Journal Papers

1.      T. Milenkovic, I. Filippis, M. Lappe, and N. Przulj, Optimized Null Model for Protein Structure Networks, submitted, 2008.

2.      C. Guerrero, T. Milenkovic, N. Przulj, J. J. Jones, P. Kaiser, L. Huang, Characterization of the Yeast Proteasome Interaction Network by QTAX-Based Tag-Team Mass Spectrometry and Protein Interaction Network Analysis, PNAS, to appear.

3.      Tijana Milenkovic and N. Przulj, Uncovering Biological Network Function via Graphlet Degree Signatures, Cancer Informatics, 2008:4 257-273, 2008.

4.      D. J. Higham, M. Rasajskim, and N. Przulj, Fitting a Geometric Graph to a Protein-Protein Interaction Network, Bioinformatics, 24 (8):1093-1099, 2008.

5.      T. Milenkovic, J. Lai, and N. Przulj, GraphCrunch: A Tool for Large Network Analyses, BMC Bioinformatics, 9:70, January 30, 2008.  Highly accessed.

6.      F. Hormozdiari, P. Berenbrink, N. Przulj, and C. Sahinalp, Not All Scale Free Networks are Born Equal: the Role of the Seed Graph in PPI Netwok Emulation, PLoS Computational Biology, 3(7):e118, doi:10.1371/journal.pcbi.0030118, July 2007.

7.      N. Przulj, Biological Network Comparison Using Graphlet Degree Distribution, Proceedings of the 2006 European Conference on Computational Biology, ECCB '06, Eilat, Israel, January 21-24, 2007, acceptance rate 18%. Bioinformatics, volume 23, pages e177-e183, 2007.

8.      N. Przulj and Des Higham, Modelling Protein-Protein Interaction Networks via a Stickiness Index, Journal of the Royal Society Interface, volume 3, number 10, pages 711 - 716, 2006.

9.      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.

10.  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.

11.  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.

12.  N. Przulj, D. G. Corneil, and I. Jurisica, Modeling Interactome: Scale-Free or Geometric?, Bioinformatics, volume 20, number 18, pages 3508-3515, 2004.

13.  A. D. King, N. Przulj, and I. Jurisica, Protein complex prediction via cost-based clustering, Bioinformatics, volume 20, number 17, pages 3013 - 3020, 2004.

14.  N. Przulj, D. Wigle, and I. Jurisica, Functional Topology in a Network of Protein Interactions, Bioinformatics, volume 20, number 3, pages 340-348, 2004.

15.  N. Przulj, D. G. Corneil, and E. Koehler, Hereditary Dominating Pair Graphs, Discrete Applied Mathematics, volume 134, pages 239-261, 2004.

16.  A. L. Liestman and N. Przulj, Minimum Average Time Broadcast Graphs, Par. Proc. Lett., volume 8, pages 139-147, 1998.

 

Refereed Conference Papers

 

17.  N. Przulj, Geometric local structure in biological networks, IEEE Xplore digital library, Invited Paper, Proceedings of the 2007 IEEE Information Theory Workshop (ITW 2007), Lake Tahoe, California, September 2-6, 2007.

18.  F. Hormozdiari, P. Berenbrink, N. Przulj, and C. Sahinalp, Not All Scale Free Networks are Born Equal: the Role of the Seed Graph in PPI Netwok Emulation, In  RECOMB Satellite Conferences on Systems Biology and Computational Proteomics, UC San Diego, December 1-3, 2006, acceptance rate 26%.  Lecture Notes in Computer Science, volume 4532/2007, pages 1-13, September 19, 2007. (Same as 5. above.)

19.  N. Przulj, Biological Network Comparison Using Graphlet Degree Distribution, Proceedings of the 2006 European Conference on Computational Biology, ECCB '06, Eilat, Israel, January 21-24, 2007, acceptance rate 18%. Bioinformatics, volume 23, pages e177-e183, 2006. (Same as 7. above.)

                                                                                                              

Refereed Book Chapters

 

20.  N. Przulj and T. Milenkovic, Computatioanl Methods for Analyzing and Modeling Biological Networks, a chapter in “Biological Data Mining”, edited by Jake Chen and Stefano Lonardi,, CRC Press, forthcoming.

21.  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.

 

Refereed Posters

 

22.  T. Milenkovic and N. Przulj, ``Uncovering Biological Network Function via Graphlet Degree Signatures,''  European Conference on Computational Biology (ECCB) 2008, Cagliari, Italy, September 22-26, 2008.

23.  T. Milenkovic, J. Lai, and N. Przulj, ``GraphCrunch: A Tool for Large Network Analyses,'' European Conference on Computational Biology (ECCB) 2008, Cagliari, Italy, September 22-26, 2008.

24.  D. J. Higham, M. Rasajski, and N. Przulj, ``Discovering Geometric Structure in Protein-Protein Interaction Networks: The Embedding Algorithm,'' European Conference on Computational Biology (ECCB) 2008, Cagliari, Italy, September 22-26, 2008.

25.  T. Milenkovic and N. Przulj, ``Uncovering disease genes and function via graphlet degree signatures,'' International Conference on Systems Biology (ICSB) 2008}, Gothenburg, Sweden, August 22-28, 2008.

26.  D. J. Higham, M. Rasajski, and N. Przulj, ``Discovering Geometric Structure in Protein-Protein Interaction Networks,'' Intelligent Systems for Molecular Biology (ISMB) 2008, Toronto, Canada, July 19-23, 2008.

27.  T. Milenkovic and N. Przulj, ``Uncovering Biological Network Function via Graphlet Degree Signatures,'' Intelligent Systems for Molecular Biology (ISMB) 2008, Toronto, Canada, July 19-23, 2008.

28.  T. Milenkovic, I. Filippis, M. Lappe, and N. Przulj, ``Optimized Null Model for Protein Structure Networks,''Intelligent Systems for Molecular Biology (ISMB) 2008, Toronto, Canada, July 19-23, 2008.

29.  C. Guerrero, T. Milenkovic, J. J. Jones, N. Przulj, P. Kaiser, and L. Huang, “Characterizing the 26S Proteasome Network in Yeast using a Quantitative In-Vivo Crosslinking Strategy and PPI Network Analysis,'” 56th ASMS Conference on Mass Spectrometry, Denver, Colorado, June 1 - 5, 2008.

30.  T. Milenkovic and N. Przulj, "Protein Signatures: Interplay of Topology and Biology," a poster at the RECOMB Satellite Conference on Systems Biology 2007, San Diego, California November 30 - December 1, 2007.

31.  T. Milenkovic, J. Lai, and N. Przulj, "GraphCrunch: A Tool for Large Network Analyses," a poster at the RECOMB Satellite Conference on Systems Biology 2007, San Diego, California November 30 - December 1, 2007.

32.  D. J. Higham, M. Rasajski, and N. Przulj, "Networks as Geometric Random Graphs: A Direct Approach," a poster at the RECOMB Satellite Conference on Systems Biology 2007, San Diego, California November 30 - December 1, 2007.

33.  T. Milenkovic, I. Filippis, M. Lappe, and N. Przulj, "Optimized Null Model for Residue Interaction Graphs," a poster at the RECOMB Satellite Conference on Systems Biology 2007, San Diego, California November 30 - December 1, 2007.

34.  Milenkovic, J. Lai, and N. Przulj, "GraphCrunch: A Tool for Large Network Analyses," a poster at the International Conference on Systems Biology (ICSB) 2007, Long Beach, California October 1-6, 2007.

35.  D. J. Higham, M. Rasajski, and N. Przulj, "Fitting a Geometric Graph to a Protein-Protein Interaction Network," a poster at the International Conference on Systems Biology (ICSB) 2007, Long Beach, California October 1-6, 2007.

36.  T. Milenkovic, I. Filippis, M. Lappe, and N. Przulj, "Geometricity of Residue Interaction Graphs," a poster at the International Conference on Systems Biology (ICSB) 2007, Long Beach, California October 1-6, 2007.

37.  T. Milenkovic, J. Lai, and N. Przulj, "GraphCrunch: A Tool for Large Network Analyses," a poster at the Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2007, Vienna, Austria, July 21-25, 2007.

38.  Y. Wang and N. Przulj, "Biological implications of anti-motifs in transcriptional regulation networks" a poster at the European Conference on Computational Biology (ECCB), Eilat, Israel, January 21-24, 2007.

39.  N. Przulj, "Biological Network Comparison Using Graphlet Degree Distributions," a poster at the Intelligent Systems for Molecular Biology (ISMB) 2006, Fortaleza, Brazil, August 6-10, 2006.

40.  S. Zhou and N. Przulj, "Do Protein-Protein Interaction Networks Look Like a Jelly- Fish?" a poster at Intelligent Systems for Molecular Biology (ISMB) 2006, Fortaleza, Brazil, August 6-10 2006.

41.  N. Przulj, D. G. Corneil, and I. Jurisica, "Geometric Properties of Protein-Protein Interaction Networks," a poster at Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2004, Glasgow, UK, July 31 - August 4, 2004.

42.  N. Przulj and I. Jurisica, "A Call Graph Analysis," a poster at CASCON 2003, Markham, Ontario, Canada, October 6-9, 2003.

43.  N. Przulj, D. Wigle, and I. Jurisica, "Functional Topology in a Network of Protein Interactions," poster at Intelligent Systems for Molecular Biology (ISMB) 2003, Brisbane, Australia, June 29 - July 3, 2003.

 

Press Coverage

 

44.  An TV interview about my scientific work was shown on "Enter TV", Belgrade, Serbia, on September 28, 2007.

45.  An interview about my scientific work was published in a daily newspaper "Borba", Belgrade, Serbia, on September 26, 2007.

Invited Talks

1.      N. Przulj, Examining Biological Networks via Graphlet Degree Signatures, a mini-symposium on “Networks: Biological, Social and Internet” at the SIAM Annual Meeting, San Diego, California, July 7-11, 2008.

2.      N. Przulj, ``Towards a Theory of Biological Networks,'' Imperial College London, June 30, 2008.

3.      N. Przulj, ``Towards a Theory of Biological Networks,'' University of Southampton, UK, June 27, 2008.

4.      N. Przulj, ``Towards a Theory of Biological Networks,'' University of Helsinki, Finland, June 24, 2008.

5.      N Przulj, From Structure to Function in Biological Networks, 2008 UCI Center for Complex Biological Systems Retreat, Pasadena, California, March 28-30, 2008.

6.      N. Przulj, From Structure to Function in Biological Networks, 2007 UCI Cancer Center Conference, Rancho Mirage, California, November 9-11, 2007.

7.      N. Przulj, Protein-Protein Interaction and Other Biological Networks, Biological Chemistry, UC Irvine, September 21, 2007.

8.      N. Przulj, Geometric Local Structure in Biological Networks, 2007 IEEE Information Theory Workshop (ITW 2007), Lake Tahoe, California, September 2-6, 2007.

9.      N. Przulj, Graphs, Proteins, and Simulations, Petnica Research Station, Valjevo, Serbia, August 11, 2007.

10.  N. Przulj, Geometric Local Structure in Biological Networks,"39th Symposium on the Interface: Computing Science and Statistic (Theme: Systems Biology), Philadelphia, Pennsylvania, May 23-26, 2007.

11.  N. Przulj, Geometric Local Structure in Biological Networks, Department of Defense Biotechnology HPC Software Applications Institute, Fort Detrick, Frederick, MD, May, 23, 2007.

12.  N. Przulj, Modeling Large Biological Networks, Center for Complex Biological Systems at UC Irvine, CCBS/MCB/MCSB Retreat, Redondo Beach, March 23-25, 2007.

13.  N. Przulj, Protein-Protein Interaction Networks: Issues, Models, and Comparisons, Institute for Mathematical Behavioral Sciences, UC Irvine, Human Complex Systems Conference, December 8, 2006.

14.  N. Przulj, Comparing and Modeling Protein-Protein Interaction Networks, University of Glasgow, Computing Science Seminar, Glasgow, UK, October 20, 2006.

15.  N. Przulj, Comparing and Modeling Protein-Protein Interaction Networks, University of Strathclyde, Mathematics Colloquium, Glasgow, UK, October 18, 2006.

16.  N. Przulj, Comparing and Modeling Protein-Protein Interaction Networks, Max Planck Institute for Molecular Genetics, Berlin, Germany, September 28, 2006.

17.  N. Przulj, Comparing and Modeling Protein-Protein Interaction Networks, University of Bremen, Germany, September 26, 2006.

18.  N. Przulj, Protein-Protein Interaction Networks: Issues, Models, and Comparisons, The Foundation for Research and Technology -- Hellas (FORTH) Research Center, Heraklion, Greece, September 14, 2006.

19.  N. Przulj, Protein-Protein Interaction Networks: Issues, Models, and Comparisons, International mathematical conference: Topics in Mathematical Analysis and Graph Theory (MAGT'06), Belgrade, Serbia, September 1-4, 2006.

20.  N. Przulj, Comparing and Modeling Protein-Protein Interaction Networks, The Institute of Physics, University of Belgrade, Belgrade, Serbia, August 29, 2006.

21.  N. Przulj, Comparing and Modeling Protein-Protein Interaction Networks, Petnica Research Station, Valjevo, Serbia, August 26, 2006.

22.  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

23.  N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, Simon Fraser University, Vancouver, Canada, December 14, 2005

24.  N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, University of Victoria, Victoria, Canada, December 13, 2005

25.  N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, University of British Columbia, Vancouver, Canada, December 12, 2005

26.  N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, Institute of Physics, University of Belgrade, Zemun, Serbia and Montenegro, September 14, 2005

27.  N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, BMC Research Center, RIKEN, Nagoya, Japan, May 24, 2005

28.  N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, UC Riverside, Riverside, CA, April 25, 2005

29.  N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interaction Example, UC Irvine, Irvine, CA, March 17, 2005

30.  N. Przulj, Analyzing Software Call Graphs, Microsoft Research, Redmond, WA, August 22, 2003

31.  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

Tutorial

32.  N. Przulj and T. Milenkovic, "Biological Networks: Analyses, Models, Functions, and Disease”, 9th Conference on Systems Biology (ICSB'08), Gothenburg, Sweden, August 22-28, 2008.

Contributed Talks

33.  T. Milenkovic and N. Przulj, "From network structure to biological function in protein-protein interaction networks”, BioPathways '08 pre-conference of ISMB'08, Toronto, Canada, July 18-19, 2008.

34.  T. Milenkovic and N. Przulj, Uncovering Biological Network Function via Graphlet Degree Signatures, BioPathways '07 pre-conference of ISMB/ECCB'07, Vienna, Austria, July 19-20, 2007.

35.  N. Przulj, Biological Network Comparison Using Graphlet Degree Distributions, European Conference on Computational Biology (ECCB'06), acceptance rate 18%, Eilat, Israel, January 21-24, 2007.

36.  Fereydoun Hormozdiari, Petra Berenbrink, N. Przulj, and Cenk Sahinalp, Not All Scale Free Networks are Born Equal: the Role of the Seed Graph in PPI Netwok Emulation, Research in Computational Molecular Biology (RECOMB'06) Satellite Conferences on Systems Biology and Computational Proteomics, UC San Diego, December 1-3, 2006.

37.  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

38.  N. Przulj, Uncovering Structure in Protein-Protein Interaction Networks, BioPathways, a Satellite Conference of ISMB'05, Detroit, Michigan, June 23 - 24, 2005

39.  N. Przulj, Geometric Model of Protein Interaction Networks, CNET 2004, University of Aveiro, Portugal, August 29 - September 2, 2004

40.  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

41.  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

42.  N. Przulj, Minimal Hereditary Dominating Pair Graphs, Workshop on Structured Families of Graphs, The Fields Institute, May 8-13, 2000

43.  N. Przulj, Minimal Hereditary Dominating Pair Graphs, Special Year on Graph Theory and Combinatorial Optimization Program Seminar Series, The Fields Institute, March 22, 2000

44.  A. L. Liestman and N. Przulj, Minimum Average Time Broadcast Graphs, 27th SE International Conference on Combinatorics, Graph Theory, and Computing: March, 1997

Theses

o       N. Przulj, Analyzing Large Biological Networks: Protein-Protein Interactions Example, Ph.D. Thesis, Graduate Department of Computer Science, University of Toronto, April 2005.

o       N. Przulj, Minimal Hereditary Dominating Pair Graphs, M.Sc. Thesis, Graduate Department of Computer Science, University of Toronto, January 2000.

Teaching

Current:

o       CS 163 Graph Algorithms, undergraduate course, UC Irvine, Spring 2008

o       ICS 288A Biological Networks, graduate course, UC Irvine, Winter 2007

o       ICS 139W Technical Writing, undergraduate course, UC Irvine, Winter 2007

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

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

Past:

First year courses:

o       Teaching Assistant and Substitute Instructor:   CSC 199 Beautiful Algorithms, U of T, Fall 2001 and Spring 2002

o       Teaching Assistant:    MAT 154, 155, 157, 158 Applied Calculus Courses, SFU, Spring 1996

Second year course:

o       Teaching Assistant:   CSC 238 Discrete Mathematics, U of T, Summer 1999 and Summer 2001

Third year course:

o       Teaching Assistant:   MATC32 Graph Theory and Algorithms, U of T at Scarborough, Fall 2000

Graduate courses:

o       Teaching Assistant:   CSC 2414 Topics in ADM: Analysis of Algorithms, U of T, Spring 2002

Favorite Places

·        City of Belgrade

·        Motovun, Istria

·        Oprtalj, Istria

·        Le Chazelet, France

·       Glamoc, Bosnia

 

Contact Information

 

E-mail:  natasha [at] ics [dot] uci [dot] edu
Office:  Department of Computer Science, University of California
            Irvine, CA
            92697-3435
            USA
Phone: +1-949-824-7312
Fax:      +1-949-824-4056

Last updated July 6, 2008