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Protein-Protein Interactions

Protein-Protein Interactions

This project aims 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 fundamental properties of protein and protein-complex interactions, and 4) understand how host-pathogen PPIs lead to host infection. This knowledge will aid our understanding of how biological processes are organized, give insights into the mechanisms of various biological actions, and identify the proteins and interactions that are 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 5825 KB]

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 5386 KB]

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 1613 KB]

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 1341 KB]

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 2010 KB]

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 2353 KB]

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 1457 KB]

Yu, X., A. Wallqvist, and J. Reifman. Inferring high-confidence human protein-protein interactions. BMC Bioinformatics. 2012 May 4; 13:79. [PDF 1796 KB]

Yu, X., J. Ivanic, V. Memisevic, A. Wallqvist, and J. Reifman. Categorizing biases in high-confidence high-throughput protein-protein interaction data sets. Molecular and Cellular Proteomics. 2011 December; 10(12):M111.012500. [PDF 3508 KB]

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 433 KB]

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 1747 KB]

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 972 KB]

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 639 KB]

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 452 KB]

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 315 KB]

Ivanic, J., A. Wallqvist, and J. Reifman. Evidence of probabilistic behaviour in protein interaction networks. BMC Systems Biology. 2008 February 2; 2:11. [PDF 855 KB]

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 865 KB]

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 723 KB]