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RESEARCH

PROTEIN-PROTEIN INTERACTIONS

Protein-Protein Interactions

We aim to 1) characterize large-scale protein-protein interaction (PPI) networks of specific organisms, 2) compare large-scale PPI networks of related organisms, 3) understand the key properties of protein and protein-complex interactions, and 4) understand how host-pathogen PPIs lead to infection. The resulting knowledge will illuminate how biological processes are organized as well as the mechanisms of various biological actions, and identify proteins and interactions responsible for disease.

Software

Publications

Bozue, J. A., S. Chaudhury, K. Amemiya, J. Chua, C. K. Cote, R. G. Toothman, J. L. Dankmeyer, C. P. Klimko, C. L. Wilhemsen, J. L. Raymond, N. Zavaljevski, J. Reifman, and A. Wallqvist. Phenotypic characterization of a novel virulence-factor deletion strain of Burkholderia mallei that protects against aerosolized glanders in mice. Frontiers in Cellular and Infection Microbiology. 2016 February 26; 6:21. [PDF, PubMed]

Wallqvist, A., V. Memisevic, 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. 2015 December 29; 16:1106. [PDF, PubMed]

Chiang, C. Y., I. Uzoma, D. J. Lane, V. Memisevic, F. Alem, K. Yao, S. Bavari, A. Wallqvist, R. M. Hakami, and R. G. Panchal. A reverse-phase protein microarray-based screen identifies host signaling dynamics upon Burkholderia spp. infection. Frontiers in Microbiology. 2015 July 27; 6:683. [PDF, PubMed]

Memisevic, V., N. Zavaljevski, S. V. Rajagopala, K. Kwon, R. Pieper, D. DeShazer, J. Reifman, and A. Wallqvist. Mining host-pathogen protein interactions to characterize Burkholderia mallei infectivity mechanisms. PLOS Computational Biology. 2015 March 4; 11(3):e1004088. [PDF, PubMed]

Memisevic, V., K. Kumar, L. Cheng, N. Zavaljevski, D. DeShazer, A. Wallqvist, and J. Reifman. DBSecSys: a database of Burkholderia mallei secretion systems. BMC Bioinformatics. 2014 July 16; 15:244. [PDF, PubMed]

Memisevic, V., 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. 2013 November 1; 12(11):3036-3051. [PDF, PubMed]

Memisevic, V., A. Wallqvist, and J. Reifman. Reconstituting protein interaction networks using parameter-dependent domain-domain interactions. BMC Bioinformatics. 2013 May 7; 14:154. [PDF, PubMed]

Dutta, B., A. Wallqvist, and J. Reifman. PathNet: a tool for pathway analysis using topological information. Source Code for Biology and Medicine. 2012 September 24; 7:10. [PDF, PubMed]

Yu, X., A. Wallqvist, and J. Reifman. Inferring high-confidence human protein-protein interactions. BMC Bioinformatics. 2012 May 4; 13:79. [PDF, PubMed]

Yu, X., J. Ivanic, V. Memisevic, A. Wallqvist, and J. Reifman. Categorizing biases in high-confidence high-throughput protein-protein interaction data sets. Molecular & Cellular Proteomics. 2011 December; 10(12):M111.012500. [PDF, PubMed]

Gupta, S., A. Wallqvist, R. Bondugula, J. Ivanic, and J. Reifman. Unraveling the conundrum of seemingly discordant protein-protein interaction datasets. Proceedings of the 32nd IEEE EMBS Annual International Conference. Buenos Aires, Argentina. 2010 August 31-September 4; 783-786. [PDF, PubMed]

Yu, X., J. Ivanic, A. Wallqvist, and J. Reifman. A novel scoring approach for protein co-purification data reveals high interaction specificity. PLOS Computational Biology. 2009 September 25; 5(9):e1000515. [PDF, PubMed]

Frazier, J. M., Y. Chushak, and B. Foy. Stochastic simulation and analysis of biomolecular reaction networks. BMC Systems Biology. 2009 June 17; 3:64. [PDF, PubMed]

Ivanic, J., X. Yu, A. Wallqvist, and J. Reifman. Influence of protein abundance on high-throughput protein-protein interaction detection. PLOS ONE. 2009 June 5; 4(6):e5815. [PDF, PubMed]

Ivanic, J., A. Wallqvist, and J. Reifman. Probing the extent of randomness in protein interaction networks. PLOS Computational Biology. 2008 June 11; 4(7):e1000114. [PDF, PubMed]

Lebeda, F. J., M. Adler, K. Erickson, and Y. Chushak. Onset dynamics of type A botulinum neurotoxin-induced paralysis. Journal of Pharmacokinetics and Pharmacodynamics. 2008 June; 35(3):251-267. [PDF, PubMed]

Ivanic, J., A. Wallqvist, and J. Reifman. Evidence of probabilistic behaviour in protein interaction networks. BMC Systems Biology. 2008 February 2; 2:11. [PDF, PubMed]

Chushak, Y., B. Foy, and J. Frazier. Stochastic simulations of cellular biological processes. Proceedings of the HPCMP Users Group Conference. Pittsburgh, PA. 2007 June 18-22: 425-429. [PDF, DTIC]

Chushak, Y., B. Foy, and J. Frazier. Biomolecular network simulator: software for stochastic simulation of cellular biological processes. Proceedings of the Spring Simulation Multi-Conference. Norfolk, VA. 2007 March 25-29; 345-349. [PDF, DTIC]