publications

New Interdisciplinary Textbook

  1. Analyzing Network Data in Biology and Medicine: An Interdisciplinary Textbook for Biological, Medical and Computational Scientists, Authored and Edited by Nataša Pržulj (see Book Chapters section below)
    Publisher: Cambridge University Press
    Publication date: March 2019
    Print publication year: 2019
    Online ISBN: 9781108377706

Refereed Journal Publications

  1. S. Windels, N. Malod-Dognin and N. Pržulj, Graphlet Laplacians for topology-function and topology-disease relationships, Bioinformatics, pii: btz455, doi: 10.1093/bioinformatics/btz455, 13 June 2019
  2. N. Malod-Dognin, J. Petschnigg, S. F. L. Windels, J. Povh, H. Hemmingway, R. Ketteler and N. Pržulj, Towards a data-integrated cell, Nature Communications, 10:805, 2019
  3. N. Malod-Dognin and N. Pržulj, Functional geometry of protein interactomes, Bioinformatics, pii: btz146, doi: 10.1093/bioinformatics/btz146, 1 March 2019
  4. T. Gaudelet, N. Malod-Dognin and N. Przulj, Higher-order molecular organization as a source of biological information, Bioinformatics, 34, 2018, i944–i953, ECCB 2018
  5. S. Kraljević Pavelić, J. Simović Medica, D. Gumbarević, A. Filošević, N. Przulj, and Krešimir Pavelić, Critical review on clinoptilolite safety and medical applications in vivo, Frontiers in Pharmacology, 9:1350, doi: 10.3389/fphar.2018.01350, eCollection 2018
  6. N. Malod-Dognin, J. Petschnigg and N. Przulj, Precision medicine ― A promising, yet challenging road lies ahead, Current Opinion in Systems Biology, In Press, Available online October 28, 2017
  7. N. Malod-Dognin and N. Przulj, Omics data complementarity underlines functional cross-communication in yeast, Journal of Integrative Bioinformatics 14(3), 2017
  8. N. Malod-Dognin, K. Ban and N. Przulj, Unified Alignment of Protein-Protein Interaction Networks, Scientific Reports - Nature 7:953, 2017
  9. K. Sokolina, S. Kittanakom, J.Snider, M. Kotlyar, P. Maurice, J. Gandía, A. Benleulmi-Chaachoua, K. Tadagaki, V. Wong, R. H. Malty, V. Deineko, H. Aoki, S. Amin, L. Riley, Z. Yao, X. Morato, S. Rahmati, H. Kobayashi, J. Menendez, D. Auerbach, S. Angers, N. Przulj, M. Bouvier, M. Babu, F. Ciruela, R. Jockers, I. Jurisica, and I. Stagljar, Systematic protein-protein interaction mapping for clinically-relevant human GPCRs, Molecular Systems Biology, DOI: 10.15252/msb.20167430, 13:918, 2017
  10. O. Yaveroglu, N. Malod-Dognin, T. Milenkovic, and N. Przulj, Rebuttal to the Letter to the Editor in response to the paper: Proper evaluation of alignment-free network comparison methods, Bioinformatics, doi.org/10.1093/bioinformatics/btw388, 33 (7): 1107-1109, 2017
  11. M. Costanzo, B. VanderSluis, E. N. Koch, A. Baryshnikova, C. Pons, G. Tan, W. Wang, M. Usaj, J. Hanchard, S. D. Lee, V. Pelechano, E. B. Styles, M. Billmann, J. van Leeuwen, N. van Dyk, Z.-Y. Lin, E. Kuzmin1, J. Nelson, J. S. Piotrowski, T. Srikumar, S. Bahr, Y. Chen, R. Deshpande, C. F. Kurat, S. C. Li, Z. Li, M. Mattiazzi Usaj, H. Okada, N. Pascoe, B.-J. San Luis, S. Sharifpoor, E. Shuteriqi, S. W. Simpkins, J. Snider, H. G. Suresh, Y. Tan, H. Zhu, N. Malod-Dognin, V. Janjic, N. Przulj, O. G. Troyanskaya, I. Stagljar, T. Xia, Y. Ohya, A.-C. Gingras, B. Raught, M. Boutros, L. M. Steinmetz, C. L. Moore, A. P. Rosebrock, A. A. Caudy, C. L. Myers, B. Andrews, C. Boone, A global genetic interaction network maps a wiring diagram of cellular function, Science, Vol. 353, Issue 6306, DOI: 10.1126/science.aaf1420, September 23, 2016
  12. N. Przulj and N. Malod-Dognin, Network analytics in the age of big data, Science, Vol. 353, Issue 6295, pp. 123-124, 2016
  13. A. Sarajlic, N. Malod-Dognin, O. N. Yaveroglu and N. Przulj, Graphlet-based Characterization of Directed Networks, Scientific Reports - Nature 6, Article number: 35098, doi:10.1038/srep35098, 2016
  14. V. Gligorijevic, N. Malod-Dognin and N. Przulj, Integrative Methods for Analysing Big Data in Precision Medicine, Proteomics, 16(5):741-58, doi: 10.1002/pmic.201500396, 2016
  15. V. Gligorijevic, N. Malod-Dognin and N. Przulj, Fuse: Multiple Network Alignment via Data Fusion, Bioinformatics, 32(8):1195-203, doi: 10.1093/bioinformatics/btv731, 2016
  16. V. Gligorijevic and N. Przulj, Methods for Biological Data Integration: Perspectives and Challenges, Journal of the Royal Society Interface, 12 (112): 20150571, 2015
  17. O. N. Yaveroglu, S. M. Fitzhugh, M. Kurant, A. Markopoulou, C. T. Butts and N. Przulj, ergm.graphlets: A Package for ERG Modeling Based on Graphlet Statistics, Journal of Statistical Software 65(12), June 2015
  18. O. N. Yaveroglu, T. Milenkovic and N. Przulj, Proper evaluation of alignment-free network comparison methods, Bioinformatics, 31(16):2697-2704, doi: 10.1093/bioinformatics/btv170, March 24, 2015
  19. N. Malod-Dognin and N. Przulj, L-GRAAL: Lagrangian Graphlet-based Network Aligner, Bioinformatics, 31(13): 2182-2189, doi:10.1093/bioinformatics/btv130, February 28, 2015
  20. D. Davis, O. N. Yaveroglu, N. Malod-Dognin, A. Stojmirovic and N. Przulj, Topology-Function Conservation in Protein-Protein Interaction Networks, Bioinformatics, 31(10):1632-1639, doi:10.1093/bioinformatics/btv026, January 20, 2015
  21. A. Filipovic, Y. Lombardo, M. Fronato, J. Abrahams, E. Aboagye, Q.-D. Nguyen, B. Borda d’Aqua, A. Ridley, A. Green, E. Rahka, I. Ellis, C. Recchi, N. Przulj, A. Sarajlic, J.-R. Alattia, P. Fraering, M. Deonarain and R. Charles Coombes, Anti-nicastrin monoclonal antibodies elicit pleiotropic anti-tumor pharmacological effects in invasive breast cancer cells, Breast Cancer Research and Treatment, 148(2):455-62, 2014
  22. V. Gligorijevic, V. Janjic and N. Przulj, Integration of molecular network data reconstructs Gene Ontology, Vol. 30 ECCB 2014, pages i594–i600 (14% acceptance rate), Bioinformatics, doi:10.1093/bioinformatics/btu470, 2014
  23. A. Sarajlic, V. Gligorijevic, D. Radak and N. Przulj, Network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm, Integrative Biology, DOI: 10.1039/C4IB00125G, 2014
  24. Kai Sun, Natalie Buchan, Chris Larminie and N. Przulj, The integrated disease network, Integrative Biology, DOI: 10.1039/C4IB00122B, 2014
  25. Kai Sun, JoanaP Goncalves, Chris Larminie and N. Przulj, Predicting disease associations via biological network analysis, BMC Bioinformatics, 15:304, 2014
  26. V. Janjic and N. Przulj, Evolution of the Topology of the Human Interactome, Journal of Integrative Bioinformatics, 11(2):238, 2014
  27. M. Cvijovic et al., Bridging the Gaps in Systems Biology, Molecular Genetics and Genomics, DOI 10.1007/s00438-014-0843-3, April 13, 2014
  28. O. N. Yaveroglu, N. Malod-Dognin, D. Davis, Z. Levnajic, V. Janjic, R. Karapandza, A. Stojmirovic, and N. Przulj, Revealing the Hidden Language of Complex Networks, Scientific Reports - Nature, 4:4547, 2014
  29. A. Sarajlic and N. Przulj, Survey of Network-Based Approaches to Research of Cardiovascular Diseases, BioMed Research International, doi:10.1155/2014/527029, 2014
  30. V. Janjic, R. Sharan, and N. Przulj, Modelling the Yeast Interactome, Scientific Reports - Nature, 4:4273, doi:10.1038/srep04273, March 4, 2014
  31. N. Malod-Dognin and N. Przulj, GR-Align: Fast and Flexible Alignment of Protein 3D Structures Using Graphlet Degree Similarity, Bioinformatics, doi:10.1093/bioinformatics/btu020, January 17, 2014
  32. A. Sarajlic, A. Filipovic, V. Janjic, R.C. Coombes, and N. Przulj, The Role of Genes Co-Amplified with Nicastrin in Breast Invasive Carcinoma, Breast Cancer Research and Treatment, doi:10.1007/s10549-013-2805-6, 2013
  33. M. Zitnik, V. Janjic, C. Larminie , B. Zupan, and N. Przulj, Discovering disease-disease associations by fusing systems-level molecular data, Scientific Reports - Nature, 3:3202, 2013
  34. A. Sarajlic, V. Janjic, N. Stojkovic, D. Radak, and N. Przulj, Network Topology Reveals Key Cardiovascular Disease Genes, PLoS ONE, 8(8):e71537, 2013
  35. W. Hayes, K. Sun, and N. Przulj, Graphlet-based measures are suitable for biological network comparison, Bioinformatics, 29(4): 483-491, 2013
  36. V. Janjic, and N. Przulj, Biological function through network topology: a survey of the human diseasome, Briefings in Functional Genomics, 11(6):522-532, 2012
  37. V. Janjic, and N. Przulj, The Core Diseasome, a special issue on Emerging Investigators, Molecular BioSystems, 8:2614-2625, 2012
  38. V. Memisevic, and N. Przulj, C-GRAAL: Common-neighbors-based Global Graph Alignment of Biological Networks, Integrative Biology, 4:734-743, 2012
  39. T. Milenkovic, V. Memisevic and N. Przulj, Dominating Biological Networks, PLoS ONE, 6(8):e23016, 2011
  40. Arabidopsis Interactome Mapping Consortium, Evidence for Network Evolution in an Arabidopsis Interactome Map, Science, 333:601-607, July 29, 2011
  41. 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
  42. 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
  43. N. Przulj, Protein-protein interactions: making sense of networks via graph-theoretic modeling, Bioessays, 33(2), February, 2011
  44. 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
  45. 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
  46. 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
  47. 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
  48. V. Memisevic, T. Milenkovic, and N. Przulj, An integrative approach to modelling biological networks, Journal of Integrative Bioinformatics, 7(3):120, 2010
  49. V. Memisevic, T. Milenkovic, and N. Przulj, Complementarity of network and sequence information in homologous proteins, Journal of Integrative Bioinformatics, 7(3):135, 2010
  50. 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
  51. N. Przulj, Erratum to Biological Network Comparison Using Graphlet Degree Distribution, Bioinformatics, 26 (6): 853-854, 2010
  52. 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
  53. T. Milenkovic, I. Filippis, M. Lappe, and N. Przulj, Optimized Null Model for Protein Structure Networks, PLoS ONE, 4 (6), e5967, June 2009
  54. 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
  55. Tijana Milenkovic and N. Przulj, Uncovering Biological Network Function via Graphlet Degree Signatures, Cancer Informatics, 2008:6 257-273, 2008
  56. D. J. Higham, M. Rasajskim, and N. Przulj, Fitting a Geometric Graph to a Protein-Protein Interaction Network, Bioinformatics, 24 (8):1093-1099, 2008
  57. T. Milenkovic, J. Lai, and N. Przulj, GraphCrunch: A Tool for Large Network Analyses, BMC Bioinformatics, 9:70, January 30, 2008 Highly accessed.
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. N. Przulj, D. G. Corneil, and I. Jurisica, Modeling Interactome: Scale-Free or Geometric?, Bioinformatics, volume 20, number 18, pages 3508-3515, 2004
  65. A. D. King, N. Przulj, and I. Jurisica, Protein complex prediction via cost-based clustering, Bioinformatics, volume 20, number 17, pages 3013 - 3020, 2004
  66. N. Przulj, D. Wigle, and I. Jurisica, Functional Topology in a Network of Protein Interactions, Bioinformatics, volume 20, number 3, pages 340-348, 2004
  67. N. Przulj, D. G. Corneil, and E. Koehler, Hereditary Dominating Pair Graphs, Discrete Applied Mathematics, volume 134, pages 239-261, 2004
  68. A. L. Liestman and N. Przulj, Minimum Average Time Broadcast Graphs, Par. Proc. Lett., volume 8, pages 139-147, 1998

Refereed Conference Papers

  1. T. Gaudelet, N. Malod-Dognin and N. Przulj, Higher-order molecular organization as a source of biological information, European Conference on Computational Biology (ECCB) 2018, 17% acceptance rate, Athens, Greece, September 8-12, 2018; also in Bioinformatics, 34, 2018, i944–i953, ECCB 2018
  2. V. Gligorijevic, N. Malod-Dognin and N. Przulj, Patient-Specific Data Fusion for Cancer Stratification and Personalized Treatment, Pacific Symposium on Biocomputing (PSB), 21:321-332(2016), Big Island, Hawaii, January 4-9, 2016
  3. V. Gligorijevic, V. Janjic and N. Przulj, Integration of molecular network data reconstructs Gene Ontology, European Conference on Computational Biology (ECCB) 2014 (14% acceptance rate), Strasburg, France, September 6-10, 2014
  4. A. Sarajlic, V. Gligorijevic, D. Radak and N. Przulj, Network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm, ECCB 2014 Worksong on Drug Development 2.0 -- Computational integrative biology methods for drug repurposing, target discovery and translational research, Strasbourg, France, September 7, 2014
  5. Kai Sun, Natalie Buchan, Chris Larminie and N. Przulj, The integrated disease network, ECCB 2014 Worksong on Drug Development 2.0 -- Computational integrative biology methods for drug repurposing, target discovery and translational research, Strasbourg, France, September 7, 2014
  6. V. Janjic and N. Przulj, Evolution of the Topology of the Human Interactome, International Symposium on Integrative Bioinformatics, Newcastle, UK, May 12-14, 2014
  7. S. Drezgic, I. Grudenic, A. Ionescu, and N. Przulj, A technical approach to local government amalgamation, Proceedings of 18th Dubrovnik Economic Conference, Croatian National Bank, Dubrovnik, Croatia, June 12-14, 2012
  8. 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
  9. 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.)
  10. 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.)
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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.)
  16. 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. N. Malod-Dognin, S. Windels and N. Przulj, “Machine Learning for Data Integration in Cancer Precision Medicine: Matrix Factorization Approaches,” a chapter in Analyzing Network Data in Biology and Medicine, edited by Natasa Przulj, Cambridge University Press, to appear, 2019
  2. L. Leal, R. Kosir and N. Przulj, “From Genetic Data to Medicine: from DNA samples to disease risk prediction in personalized genetic tests,” a chapter in Analyzing Network Data in Biology and Medicine, edited by Natasa Przulj, Cambridge University Press, to appear, 2019
  3. N. Malod-Dognin and N. Przulj, “Network Alignment,” a chapter in Analyzing Network Data in Biology and Medicine, edited by Natasa Przulj, Cambridge University Press, to appear, 2019
  4. T. Gaudelet and N. Przulj, “Introduction to graph and network theory,” a chapter in Analyzing Network Data in Biology and Medicine, edited by Natasa Przulj, Cambridge University Press, to appear, 2019
  5. K. Pavelic, M. Klobucar, D. Kuzelj, N. Przulj, and S. Kraljevic Pavelic, “Analysis of the signatures of cancer stem cells in malignant tumours using protein interactomes and STRING database,” a chapter in Analyzing Network Data in Biology and Medicine, edited by Natasa Przulj, Cambridge University Press, to appear, 2019
  6. V. Gligorijevic and N. Przulj, "Computational Methods for Integration of Biological Data," Personalised Medicine: A New Medical and Social Challenge, edited by N. Bodiroga-Vukobrat, K. Pavelic, D. Rukavina, and G. G. Sander, Springer International Publishing, ISBN 978-3-319-39349-0, 2016
  7. 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
  8. 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
  9. 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
  10. 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
  11. N. Przulj, “From Topology to Phenotype in Protein-Protein Interaction Networks,” a chapter in "Complex Networks across the Natural and Technological Sciences," edited by Des Higham, Ernesto Estrada, Maria Fox, and Gian-Luca Oppo, Springer, pp 31-49, DOI: 10.1007/978-1-84996-396-13, 2010
  12. 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
  13. 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. Health: Learning from big data how life works, Interview ERC grantee Natasa Przulj, Professor of Biomedical Data Science at UCL, The European Research Council Magazine, September 20, 2018
  2. Mining Big Data for precious medical insight, The European Research Council, Projects & Figures, September 10, 2018
  3. Computer Science News: ERC Consolidator Grant for Nataša Pržulj, UCL Computer Science Department, December 12, 2017
  4. UCL-based researcher wins ERC Consolidator Grant, Scitech Europa, December 12, 2017
  5. Conquering Cancer, by Mike Hall, ITNOW (Autumn 2016) 58 (3): 40-41 doi:10.1093/itnow/bww076 (Oxford Journals; The British Computer Society), September 2016
  6. Computing Versus Prostate Cancer, by Mike Hall, MBCS CITP, who explains how Natasaa Przulj's BCS Needham Lecture on data mining has led to a potentially ground-breaking research project that could transform prostate cancer diagnosis and treatment. ITNOW (Autumn 2015) 57 (3): 54-55 doi:10.1093/itnow/bwv080 (Oxford Journals; The British Computer Society), September 2015
  7. A video interview for BCS regarding winning the 2014 Roger Needham Award, March, 2014
  8. Vecernje Novosti, Belgrade, Serbia: Srpkinja najbolji računarski istraživač u Britaniji. March 24, 2014
  9. BCS Academy of Computing press release Nataša Pržulj announced as BCS Roger Needham Award 2014 Award, March 7, 2014
  10. An interview for European Commission Community Research and Development Information Service (CORDIS) News titled "Beyond genetics: mining biological networks for new treatments for disease", October, 2013
  11. An interview for BioTechniques Journal of Life Sciences Methods titled "Finding Connections Between Genes and Diseases", December 12, 2013
  12. An interview for European Commission Community Research and Development Information Service (CORDIS) News titled "Beyond genetics: mining biological networks for new treatments for disease", October, 2013
  13. An TV interview about Dr. Przulj's scientific work was shown on "Enter TV", Belgrade, Serbia, on September 28, 2007
  14. An interview about Dr. Przulj's scientific work was published in a daily newspaper "Borba", Belgrade, Serbia, on September 26, 2007

Refereed Posters (not updated since 2014)

  1. N. Malod-Dognin and N. Przulj, L-GRAAL: Lagrangian Graphlet-based Network Aligner, ECCB 2014, Strasbourg, France, September 8-10, 2014
  2. D. Davis, O. N. Yaveroglu, N. Malod-Dognin, A. Stojmirovic and N. Przulj, Topology-Function Conservation in Protein-Protein Interaction Networks, ECCB 2014, Strasbourg, France, September 8-10, 2014
  3. V. Gligorijevic, V. Janjic and N. Przulj, Integration of molecular network data reconstructs Gene Ontology, ECCB 2014, Strasbourg, France, September 8-10, 2014
  4. A. Sarajlic, V. Gligorijevic, D. Radak and N. Przulj, Network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm, European Conference on Computational Biology (ECCB) 2014, Strasbourg, France, September 8-10, 2014
  5. A. Sarajlic, V. Janjic, Neda Stojkovic, Djordje Radak, and N. Przulj, "Key Cardiovascular Disease Genes," Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB'13), Berlin, Germany, 21-23 July 2013
  6. V. Janjic and N. Przulj, "The Core Diseasome," Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB'13), Berlin, Germaly, 21-23 July 2013
  7. W. Hayes, K. Sun, and N. Przulj, "On the suitability of graphlet-based measures for biological network comparison," Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB'13), Berlin, Germaly, 21-23 July 2013
  8. W. Hayes, K. Sun and N. Przulj, “On the Suitability of Graphlet-based Measures for Biological Network Comparison,” European Conference on Computational Biology (ECCB) 2012, Basel, Switzerland, September 8-12, 2012.
  9. N. Przulj, “Topology of signaling proteins in interaction networks reveals new biology,” EMBO conference ’Cellular Signaling and Molecular Medicine’, Dubrovnik, Croatia, May 25-29, 2012.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. V. Memisevic, T. Milenkovic, and N. Przulj, "Complementarity of network and sequence information in homologous proteins", RECOMB 2010, Lisbon, Portugal, August 12-15, 2010.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. T. Milenkovic, J. Lai, and N. Przulj, ``GraphCrunch: A Tool for Large Network Analyses,'' (ICSB) 2008, Gothenburg, Sweden, August 22-28, 2008.
  32. T. Milenkovic, I. Filippis, M. Lappe, and N. Przulj, ``Optimized Null Model for Protein Structure Networks,'' (ICSB) 2008, Gothenburg, Sweden, August 22-28, 2008.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. N. Przulj and I. Jurisica, "A Call Graph Analysis", a poster at CASCON 2003, Markham, Ontario, Canada, October 6-9, 2003.
  51. 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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