Publications...

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Peer-reviewed journal publications:

Research articles:

  1. V. Memišević, N. Zavaljevski, S.V. Rajagopala, K. Kwon, R. Pieper, D. DeShazer, J. Reifman, and A. Wallqvist, "Mining protein interaction data to characterize Burkholderia mallei pathogenicity mechanisms," PLOS Computational Biology, 11(3):e1004088, 2015. PMID: 25738731
  2. A. Wallqvist, V. Memišević, N. Zavaljevski, R. Pieper, S.V. Rajagopala, K. Kwon, C. Yu, T.A. Hoover, and J. Reifman, "Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors," BMC Genomics, 16:1106, 2015.PMID: 26714771
  3. C.Y. Chiang, I. Uzoma, D. J. Lane, V. Memišević, F. Alem, K. Yao, K.P. Kota, S. Bavari, A. Wallqvist, R. M. Hakami, and R. G. Panchal, "A reverse-phase protein array-based screen to identify host signaling dynamics upon Burkolderia spp. Infection," Frontiers in Microbiology, 6:683, 2015. PMID: 26284031
  4. V. Memišević, K. Kumar, L. Cheng, N. Zavaljevski, D. DeShazer, A. Wallqvist, and J. Reifman, "DBSecSys: A Database of Burkholderia mallei Secretion Systems," BMC Bioinformatics, 5:244-252, 2014. PMID: 25030112
  5. V. Memišević, N. Zavaljevski, R. Pieper, S.V. Rajagopala, K. Kwon, K. Townsend, C. Yu, X. Yu, D. DeShazer, J. Reifman, and A. Wallqvist, "Novel Burkholderia mallei Virulence Factors Linked to Specific Host-Pathogen Protein Interactions," Molecular & Cellular Proteomics, 12(11):3036-3051, 2013. PMID: 23800426
  6. V. Memišević, A. Wallqvist, and J. Reifman, "Reconstituting protein interaction networks using parameter-dependent domain-domain interactions," BMC Bioinformatics, 14(1):154, 2013. PMID: 23651452
  7. V.Memišević and N. Pržulj, “C–GRAAL: Common–Neighbors–Based Global GRAph ALignment of Biological Networks,” Integrative Biology, 4:734-743, 2012. PMID: 22234340
  8. X. Yu, J. Ivanic, V.Memišević, A. Wallqvist, and J. Reifman, “Categorizing biases in high-confidence high-throughput protein-protein interaction data sets,” Molecular & Cellular Proteomics, 10(12):M111.012500, 2011. PMID: 21876202
  9. T. Milenković, V. Memišević, A. Bonato and N. Pržulj, “Dominating Biological Networks,” PLOS ONE, 6(8): e23016, 2011. PMID: 21887225
  10. H. Ho, T. Milenković, V. Memišević, J. Aruri, N. Pržulj, and A.K. Ganesan, “Protein Interaction Network Topology Uncovers Melanogenesis Regulatory Network Components Within Functional Genomics Datasets,” BMC Systems Biology, 4:84, 2010. PMID: 20550706
  11. V. Memišević, T. Milenković, and N. Pržulj, “Complementarity of network and sequence information in homologous proteins,” Journal of Integrative Bioinformatics, 7(3): 135, 2010. PMID: 20375452
  12. V. Memišević, T. Milenković, and N. Pržulj, “An integrative approach to modeling biological networks,” Journal of Integrative Bioinformatics, 7(3):120, 2010. PMID: 20375453
  13. O. Kuchaiev, T. Milenković, V. Memišević, W. Hayes, and N. Pržulj, “Topological network alignment uncovers biological function and phylogeny,” Journal of the Royal Society Interface, doi:10.1098/rsif.2010.0063, 2010. PMID: 20236959
  14. T. Milenković, V. Memišević, A.K. Ganesan, and N. Pržulj, “Systems-level cancer gene identification from protein interaction network topology applied to melanogenesisrelated functional genomics data,” Journal of the Royal Society Interface, 7(44):353-350, (doi: 10.1098/rsif.2009.0192), 2010. PMID: 19625303

Review articles:

  1. F.G. Vital-Lopez, V. Memišević and B. Dutta, “Tutorial on biological networks,” Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 2(4): 298-325, 2012.


Conference presentations and publications:

Research articles:

  1. V. Memišević, T. Milenković, and N. Pržulj, “Complementarity of network and sequence information in homologous proteins,” Proceedings of the 6th International Symposium on Integrative Bioinformatics, 22-24 March 2010, Cambridge, United Kingdom. Journal version is listed above.
  2. V. Memišević, T. Milenković, and N. Pržulj, “An integrative approach to modeling biological networks,” Proceedings of the 6th International Symposium on Integrative Bioinformatics, 22-24 March 2010, Cambridge, United Kingdom. Journal version is listed above.

Contributed talks:

  1. V. Memišević, N. Zavaljevski, R. Pieper, S.V. Rajagopala, K. Kwon, K. Townsend, C. Yu, X. Yu, D. DeShazer, J. Reifman, and A. Wallqvist, "Novel Burkholderia mallei Virulence Factors Linked to Specific Host-Pathogen Protein Interactions," Intelligent Systems for Molecular Biology (ISMB) 2014 Highlights, 12-15 July 2014, Boston, MA.
  2. V. Memišević, T. Milenković, and N. Pržulj, “Complementarity of network and sequence information in homologous proteins,” Proceedings of the 6th International Symposium on Integrative Bioinformatics, 22-24 March 2010, Cambridge, United Kingdom.
  3. V. Memišević, T. Milenković, and N. Pržulj, “An integrative approach to modeling biological networks,” Proceedings of the 6th International Symposium on Integrative Bioinformatics, 22-24 March 2010, Cambridge, United Kingdom.
  4. V. Memišević, A.K. Ganesan, and N. Pržulj, “Utilizing Systems-Level PPI Network Analysis to Visualize the Spatial Dynamics That Control Melanin Pigmentation in Human Cells,” Student Opportunity Award presentation, Center for Complex Biological Systems at University of California, Irvine, Santa Monica, California, March 2009.
  5. O. Kuchaiev, T. Milenković, V. Memišević, W. Hayes, N. Pržulj, “Topological network alignment uncovers biological function and phylogeny,” BioPathways meeting at ISMB/ECCB’09, Stockholm, Sweden, June 2009.

Poster presentations:

  1. V. Memišević, N. Zavaljevski, R. Pieper, S.V. Rajagopala, K. Kwon, K. Townsend, C. Yu, X. Yu, D. DeShazer, J. Reifman, and A. Wallqvist, "Novel Burkholderia mallei Virulence Factors Linked to Specific Host-Pathogen Protein Interactions," ISMB 2014, Boston, MA, 2014.
  2. V. Memišević, A. Wallqvist, and J. Reifman, “Extracting high-specificity domain-domain interactions from multi-domain proteins,” EECB2012, Basel, Switzerland, 2012.
  3. R. Pieper, S.V. Rajagopala, K. Kwon, K. Townsend, N. Zavaljevski, V. Memišević, C. Yu, X. Yu, A. Wallqvist, D. DeShazer, and J. Reifman, “Burkholderia mallei secretion system effectors interacting with mammalian host pathways,” Keystone conference for Proteomes and Interactomes, Sweden, 2012.
  4. T. Milenković, V. Memišević, and N. Pržulj, “Network topology complements sequence as a source of biological information,” ISMB/ECCB 2011, Vienna, Austria, 2011.
  5. T. Milenković, O. Kuchaiev, V. Memišević, W.L. Ng, W. Hayes, and N. Pržulj, “Topological network alignment uncovers biological function, evolution, and disease,” ISMB2010, Boston, USA, 2010.
  6. V. Memišević, T. Milenković, and N. Pržulj, “Complementarity of network and sequence information in homologous proteins,” RECOMB 2010, Lisbon, Portugal, 2010.
  7. O. Kuchaiev, T. Milenković, V. Memišević, W. Hayes, and N. Pržulj, “Topological network alignment uncovers biological function and phylogeny,” RECOMB 2010, Lisbon, Portugal, 2010.
  8. V. Memišević, T. Milenković, and N. Pržulj, “An integrative approach to modeling biological networks,” ICSB 2009, Stanford, California, 2009.
  9. O. Kuchaiev, T. Milenković, V. Memišević, W. Hayes, and N. Pržulj, “Topological network alignment uncovers biological function and phylogeny,” ICSB 2009, Stanford, California, 2009.
  10. T. Milenković, V. Memišević, A.K. Ganesan, and N. Pržulj, “Systems-level Cancer Gene Identification from Protein Interaction Network Topology Applied to Melanogenesis related Interaction Networks,” ICSB 2009, Stanford, California, 2009.
  11. O. Kuchaiev, T. Milenković, V. Memišević, W. Hayes, and N. Pržulj, “Topological network alignment uncovers biological function and phylogeny,” ISMB/ECCB 2009, Stockholm, Sweden, 2009.
  12. T. Milenković, V. Memišević, A.K. Ganesan, and N. Pržulj, “Systems-level Cancer Gene Identification from Protein Interaction Network Topology Applied to Melanogenesis related Interaction Networks,” ISMB/ECCB’09, Stockholm, Sweden, 2009.