publications

Refereed Journal Publications

  1. V. Memisevic, and N. Przulj, C-GRAAL: Common-neighbors-based Global Graph Alignment of Biological Networks, Integrative Biology, DOI: 10.1039/c2ib00140c, January 10, 2012.
  2. T. Milenkovic, V. Memisevic and N. Przulj, Dominating Biological Networks, PLoS ONE, 6(8):e23016, 2011.
  3. Arabidopsis Interactome Mapping Consortium, Evidence for Network Evolution in an Arabidopsis Interactome Map, Science, 333:601-607, July 29, 2011.
  4. O. Kuchaiev and N. Przulj, Integrative Network Alignment Reveals Large Regions of Global Network Similarity in Yeast and Human, Bioinformatics, 27(10): 1390-1396, 2011.
  5. O. Kuchaiev, A. Stefanovic, W. Hayes, and N. Przulj, GraphCrunch 2: Software tool for network modeling, alignment and clustering, BMC Bioinformatics, 12(24):1-13, 2011.
  6. N. Przulj, Protein-protein interactions: making sense of networks via graph-theoretic modeling, Bioessays, 33(2), February, 2011.
  7. T. Milenkovic, W.L. Wong, W. Hayes, and N. Przulj, Optimal network alignment with graphlet degree vectors, Cancer Informatics, 9:121-37, June 30, 2010.
  8. H. Ho, T. Milenkovic, V. Memisevic, J. Aruri, N. Przulj, and A. K. Ganesan, Protein Interaction Network Uncovers Melanogenesis Regulatory Network Components within Functional Genomics Datasets, BMC Systems Biology, 4:84, June 15, 2010.
  9. O. Kuchaiev, T. Milenkovic, V. Memisevic, W. Hayes, and N. Przulj, Topological network alignment uncovers biological function and phylogeny, Journal of the Royal Society Interface, 7:1341-1354, 2010.
  10. R. Kaake, T. Milenkovic, N. Przulj, P. Kaiser, L. Huang, Characterization of Cell Cycle Specific Interaction Network of the Yeast 26S Proteasome Complex by QTAX Strategy, Journal of Proteome Research, DOI: 10.1021/pr1000175, February 20, 2010.
  11. V. Memisevic, T. Milenkovic, and N. Przulj, An integrative approach to modelling biological networks, Journal of Integrative Bioinformatics, 7(3):120, 2010.
  12. V. Memisevic, T. Milenkovic, and N. Przulj, Complementarity of network and sequence information in homologous proteins, Journal of Integrative Bioinformatics, 7(3):135, 2010.
  13. T. Milenkovic, V. Memisevic, A. K. Ganesan, and N. Przulj, Systems-level Cancer Gene Identification from Protein Interaction Network Topology Applied to Melanogenesis-related Interaction Networks, Journal of the Royal Society Interface, 7 (44), 423-437, March 6, 2010.
  14. N. Przulj, Erratum to Biological Network Comparison Using Graphlet Degree Distribution, Bioinformatics, 26 (6): 853-854, 2010.
  15. O. Kuchaiev, M. Rasajski, D. J. Higham, and N. Przulj, Geometric De-noising of Protein-Protein Interaction Networks, PLoS Computational Biology, volume 5, issue 8, e1000454, August 2009.
  16. T. Milenkovic, I. Filippis, M. Lappe, and N. Przulj, Optimized Null Model for Protein Structure Networks, PLoS ONE, 4 (6), e5967, June 2009.
  17. C. Guerrero, T. Milenkovic, N. Przulj, P. Kaiser, L. Huang, Characterization of the Proteasome Interaction Network Using a QTAX-based Tag-Team Strategy and Protein Interaction Network Analysis, PNAS, 105 (36), 13333-13338, 2008.
  18. Tijana Milenkovic and N. Przulj, Uncovering Biological Network Function via Graphlet Degree Signatures, Cancer Informatics, 2008:6 257-273, 2008.
  19. D. J. Higham, M. Rasajskim, and N. Przulj, Fitting a Geometric Graph to a Protein-Protein Interaction Network, Bioinformatics, 24 (8):1093-1099, 2008.
  20. T. Milenkovic, J. Lai, and N. Przulj, GraphCrunch: A Tool for Large Network Analyses, BMC Bioinformatics, 9:70, January 30, 2008. Highly accessed.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. N. Przulj, D. G. Corneil, and I. Jurisica, Modeling Interactome: Scale-Free or Geometric?, Bioinformatics, volume 20, number 18, pages 3508-3515, 2004.
  28. A. D. King, N. Przulj, and I. Jurisica, Protein complex prediction via cost-based clustering, Bioinformatics, volume 20, number 17, pages 3013 - 3020, 2004.
  29. N. Przulj, D. Wigle, and I. Jurisica, Functional Topology in a Network of Protein Interactions, Bioinformatics, volume 20, number 3, pages 340-348, 2004.
  30. N. Przulj, D. G. Corneil, and E. Koehler, Hereditary Dominating Pair Graphs, Discrete Applied Mathematics, volume 134, pages 239-261, 2004.
  31. A. L. Liestman and N. Przulj, Minimum Average Time Broadcast Graphs, Par. Proc. Lett., volume 8, pages 139-147, 1998.

Refereed Conference Papers

  1. B. Betkaoui, D. B. Thomas, W. Luk, and N. Przulj, A Framework for FPGA Acceleration of Large Graph Problems: Graphlet Counting Case Study, Proceedings of International Conference on Field Progammable Technology (FPT’11), New Delhi, India, December 12-14, 2011.
  2. V. Memisevic, T. Milenkovic, and N. Przulj, "An integrative approach to modelling biological networks", 6th Annual International Symposium on Integrative Bioinformatics, Cambridge, UK, March 22-24, 2010. (Journal version is listed above.)
  3. V. Memisevic, T. Milenkovic, and N. Przulj, "Complementarity of network and sequence information in homologous proteins", 6th Annual International Symposium on Integrative Bioinformatics, Cambridge, UK, March 22-24, 2010. (Journal version is listed above.)
  4. N. Przulj, O. Kuchaiev, A. Stevanovic, and W. Hayes, Geometric Evolutionary Dynamics of Protein Interaction Networks, Proceedings of the 2010 Pacific Symposium on Biocomputing (PSB), Big Island, Hawaii, January 4-8, 2010.
  5. O. Kuchaiev, P. T. Wang, Z. Nenadic, and N. Przulj, Structure of Brain Functional Networks, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'09), Minneapolis, Minnesota, USA, September 2-6, 2009.
  6. O. Kuchaiev and N. Przulj, Learning the structure of protein-protein interaction networks, Proceedings of the 2009 Pacific Symposium on Biocomputing (PSB), Big Island, Hawaii, January 5-9, 2009.
  7. 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.
  8. 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. (Journal version is listed above.)
  9. 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. (Journal version is listed above.)

Refereed Book Chapters

  1. T. Milenkovic and N. Przulj, "Topological Characteristics of Molecular Networks," a chapter in Functional Coherence of Molecular Networks in Bioinformatics, edited by M. Koyuturk, S. Subramaniam, and A. Grama, Springer, 2012.
  2. N. Przulj, "Biological networks uncover evolution, disease and gene functions," a chapter in "Bioinformatics for Biologists", edited by Pavel Pevzner and Ron Shamir, Cambridge University Press, 2011.
  3. D. J. Higham and N. Przulj, “Random graph models and their application to protein-protein interaction networks,” a chapter in Handbook of Statistical Systems Biology, edited by D. Balding, M. Girolami and M. Stumpf, Wiley, 2011.
  4. T. Milenkovic and N. Przulj, "Topological Characteristics of Molecular Networks," a chapter in "Functional Coherence of Molecular Networks", edited by Mehmet Koyuturk, Springer, 2011.
  5. A. D. King, N. Przulj, and I. Jurisica, "Protein Complex Prediction with RNSC," a chapter in the special volume of "Methods in Molecular Biology" dedicated to Bacterial Molecular Networks, Humana Press, USA (part of the Springer publishing group), 2011.
  6. 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, 2010.
  7. 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.

Theses

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

Press Coverage

  1. An TV interview about Dr. Przulj's scientific work was shown on "Enter TV", Belgrade, Serbia, on September 28, 2007.
  2. An interview about Dr. Przulj's scientific work was published in a daily newspaper "Borba", Belgrade, Serbia, on September 26, 2007.

Refereed Posters

  1. T. Milenkovic, O. Kuchaiev, W. Hayes, and N. Przulj, “GraphCrunch 2 Network Analysis Tool and MI-GRAAL Network Aligner,” Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2011, Vienna, Austria, July 17-20, 2011.
  2. N. Przulj, “Topological network alignment uncovers biological function and phylogeny,” Highlights poster at Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2011, Vienna, Austria, July 17-20, 2011.
  3. T. Milenkovic, V. Memisevic, and N. Przulj, “Network topology complements sequence as a source of biological information,” Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2011, Vienna, Austria, July 17-20, 2011.
  4. T. Milenkovic and N. Przulj, “Network analysis uncovers key biological processes and pathways in molecular networks,” NetBio-SIG at Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2011, Vienna, Austria, July 15, 2011.
  5. N. Przulj, “Network topology complements sequence as a source of biological information,” Cold Spring Harbor Laboratory Meeting on Systems Biology: Networks, Cold Spring Harbor Laboratory, USA, March 22-26, 2011.
  6. N. Przulj, O. Kuchaiev, A. Stevanovic, M. Rasajski, W. Hayes, and D. Higham, "Geometric evolutionary dynamics and de-noising of protein-protein interaction networks" RECOMB 2010, Lisbon, Portugal, August 12-15, 2010.
  7. V. Memisevic, T. Milenkovic, and N. Przulj, "Complementarity of network and sequence information in homologous proteins", RECOMB 2010, Lisbon, Portugal, August 12-15, 2010.
  8. O. Kuchaiev, T. Milenkovic, V. Memisevic, W. Hayes, and N. Przulj, "Topological network alignment uncovers biological function and phylogeny", RECOMB 2010, Lisbon, Portugal, August 12-15, 2010.
  9. O. Kuchaiev, T. Milenkovic, V. Memisevic, W. L. Ng, W. Hayes, and N. Przulj, "Topological network alignment uncovers biological function, evolution, and disease", Intelligent Systems for Molecular Biology (ISMB) 2010, Boston, USA, July 11-13, 2010.
  10. N. Przulj, T. Milenkovic, O. Kuchaiev, V. Memisevic, W. L. Ng, W. Hayes, and A. Ganesan, "From biological networks to cancer and phylogeny", RECOMB Computational Cancer Biology 2010, Oslo, Norway, June 24-25, 2010.
  11. 45. O. Kuchaiev and N. Przulj, "Learning the Structure of Protein-Protein Interaction Networks", The 10th International Conference on Systems Biology (ICSB 2009), Stanford, CA, August 30 – September 4, 2009.
  12. T. Milenkovic, V. Memisevic, O. Kuchaiev, A. K. Ganesan, and N. Przulj, "Systems-level Cancer Gene Identification from Protein Interaction Network Topology Applied to Melanogenesis-Related Functional Genomics Data", The 10th International Conference on Systems Biology (ICSB 2009), Stanford, CA, August 30 – September 4, 2009.
  13. V. Memisevic, T. Milenkovic, O. Kuchaiev, and N. Przulj, "An Integrative Approach to Modelling Biological Networks", The 10th International Conference on Systems Biology (ICSB 2009), Stanford, CA, August 30 – September 4, 2009.
  14. O. Kuchaiev, T. Milenkovic, V. Memisevic, W. Hayes, and N. Przulj, "Topological Network Alignment Uncovers Biological Function and Phylogeny", The 10th International Conference on Systems Biology (ICSB 2009), Stanford, CA, August 30 – September 4, 2009.
  15. T. Milenkovic, V. Memisevic, A. K. Ganesan, and N. Przulj, "Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data", Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009, Stockholm, Sweden, June 27 - July 2, 2009.
  16. R. Kaake, T. Milenkovic, C. M. Guerrero, N. Przulj, P. Kaiser, L. Huang, "Quantifying Cell Cycle-dependent Changes in Posttranslational Modifications and Interacting Network of the Yeast 26S Proteasome", 57th ASMS Conference on Mass Spectrometry, Philadelphia, Pennsylvania, USA, May 31 - June 4, 2009.
  17. 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.
  18. 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.
  19. 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.
  20. T. Milenkovic, I. Filippis, M. Lappe, and N. Przulj, ``Optimized Null Model for Protein Structure Networks,'' European Conference on Computational Biology (ECCB) 2008, Cagliari, Italy, September 22-26, 2008.
  21. 55. 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.
  22. T. Milenkovic, J. Lai, and N. Przulj, ``GraphCrunch: A Tool for Large Network Analyses,'' (ICSB) 2008, Gothenburg, Sweden, August 22-28, 2008.
  23. T. Milenkovic, I. Filippis, M. Lappe, and N. Przulj, ``Optimized Null Model for Protein Structure Networks,'' (ICSB) 2008, Gothenburg, Sweden, August 22-28, 2008.
  24. D. J. Higham, M. Rasajski, and N. Przulj, ``Discovering Geometric Structure in Protein-Protein Interaction Networks: The Embedding Algorithm,'' (ICSB) 2008, Gothenburg, Sweden, August 22-28, 2008.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. N. Przulj and I. Jurisica, "A Call Graph Analysis", a poster at CASCON 2003, Markham, Ontario, Canada, October 6-9, 2003.
  42. 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.
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