BHSAI

Hu, X., M. S. Lee, and A. Wallqvist. Interaction of the disordered Yersinia effector protein YopE with its cognate chaperone SycE. Biochemistry. 2009 Dec 1; 48(47):11158-11160. [PDF]

Yeh, I. C., and A. Wallqvist. Structure and Dynamics of End-to-End Loop Formation of the Penta-Peptide Cys-Ala-Gly-Gln-Trp in Implicit Solvents. J Phys Chem B. 2009 Sep 10; 113(36):12382-12390. [PDF]

Yu, X., J. Ivanic, A. Wallqvist, and J. Reifman. A novel scoring approach for protein co-purification data reveals high interaction specificity. PLoS Comput Biol. 2009 Sep; 5(9):e1000515. [PDF]

Fang, X., A. Wallqvist, and J. Reifman. A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis. BMC Syst Biol. 2009; 3:92. [PDF]

Lee, M. S., R. Bondugula, V. Desai, N. Zavaljevski, I. C. Yeh, A. Wallqvist, and J. Reifman. PSPP: a protein structure prediction pipeline for computing clusters. PLoS One. 2009 July 16; 4(7):e6254. [PDF]

Chushak, Y., and M. O. Stone. In silico selection of RNA aptamers. Nucleic Acids Res. 2009 July; 37(12):e87. [URL]

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

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]

Harbaugh, S., N. Kelley-Loughnane, M. Davidson, L. Narayanan, S. Trott, Y. G. Chushak, and M. O. Stone. FRET-based optical assay for monitoring riboswitch activation. Biomacromolecules. 2009 May 11; 10(5):105. [PDF]

Hu, X., X. Jiang, D. E. Lenz, D. M. Cerasoli, and A. Wallqvist. In silico analyses of substrate interactions with human serum paraoxonase 1. Proteins. 2009 May 1; 75(2):486-498. [PDF]

Yu, C., N. Zavaljevski, V. Desai, and J. Reifman. Genome-wide enzyme annotation with precision control: Catalytic families (CatFam) databases. Proteins. 2009 February 1; 74:449-460. [PDF]

Bondugula, R., M. S. Lee, and A. Wallqvist. FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator. Nucleic Acids Res. 2009 February; 37(2):452-462. [PDF]

Yeh, I. C., M. A. Olson, M. S. Lee, and A. Wallqvist. Free-energy profiles of membrane insertion of the M2 transmembrane peptide from Influenza A virus. Biophys J. 2008 December; 95(11):5021-5029. [PDF]

Yeh, I. C., M. S. Lee, and M. A. Olson. Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models. J Phys Chem B. 2008 November 27; 112(47):15064-15073. [PDF]

Vijaya Satya, R., N. Zavaljevski, K. Kumar, E. Bode, S. Padilla, L. Wasieloski, J. Geyer, and J. Reifman. In silico microarray probe design for diagnosis of multiple pathogens. BMC Genomics. 2008 October 21; 9:496. [PDF]

Harbaugh, S., M. Davidson, Y. Chushak, N. Kelley-Loughnane, and M. Stone. Riboswitch-based sensor in low optical background. Nanobiosystems: Processing, Characterization and Applications. 2008 September 25; 70400C:1-9. [PDF]

Jiang, X., K. Kumar, X. Hu, A. Wallqvist, and J. Reifman. DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0. Chem Cent J. 2008 September 8; 2(1):18. [PDF]

Olson, M., I.-C. Yeh, and M. S. Lee. Molecular dynamics simulations of folding and insertion of the ebola virus fusion peptide into a membrane bilayer. Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology. Las Vegas, NV. 2008 July 14-17. [PDF]

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]

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

Vijaya Satya, R., N. Zavaljevski, K. Kumar, and J. Reifman. A high-throughput pipeline for designing microarray-based pathogen diagnostic assays. BMC Bioinformatics. 2008 April 12; 9:185. [PDF]

Zhang, S., K. Kumar, X. Jiang, A. Wallqvist, and J. Reifman. DOVIS: An implementation for high-throughput virtual screening using AutoDock. BMC Bioinformatics. 2008 February 29; 9:126. [PDF]

Ivanic, J., A. Wallqvist, and J. Reifman. Evidence of probabilistic behaviour in protein interaction networks. BMC Syst Biol. 2008 February 2; 2:11-19. [PDF]

Olson, M., I.-C. Yeh, and M. Lee. Coarse-grained lattice model simulations of sequence-structure fitness of a ribosome-inactivating protein. Biopolymers. 2008 February; 89(2):153-159. [PDF]

Yu, C., N. Zavaljevski, V. Desai, S. Johnson, F. J. Stevens, and J. Reifman. The development of PIPA: An integrated and automated pipeline for genome-wide protein function annotation. BMC Bioinformatics. 2008 January 29; 9:52. [PDF]

Yu, C., and P. Wilson. A tool for creating and parallelizing bioinformatics pipelines. Paper presented at HPCMP Users Group Conference. Pittsburgh, PA. 2007 June 18-21:417-420. [PDF]

Jiang, X., K. Kumar, A. Wallqvist, and J. Reifman. DOVIS: A tool for high-throughput virtual screening. Paper presented at HPCMP Users Group Conference Pittsburgh, PA. 2007 June 18-21:421-424. [PDF]

Chushak, Y., B. Foy, and J. Frazier. Stochastic simulations of cellular biological processes. Paper presented at HPCMP Users Group Conference Pittsburgh, PA. 2007 June 18-21:425-429. [PDF]

Tembe, W., N. Zavaljevski, E. Bode, C. Chase, J. Geyer, L. Wasieloski, G. Benson, and J. Reifman. Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics. 2007 January 1; 23(1):5-13. [PDF]

Chushak, Y., B. Foy, and J. Frazier. Biomolecular network simulator: Software for stochastic simulation of cellular biological processes. SpringSim. 2007; 1:345. [PDF]

Lee, M., I.-C. Yeh, N. Zavaljevski, P. Wilson, and J. Reifman. A software pipeline for protein structure prediction. Paper presented at 25th Army Science Conference. Orlando, FL. 2006 November 17-21:1-8. [PDF]

Yu, C., N. Zavaljevski, F. J. Stevens, K. Yackovich, and J. Reifman. Classifying noisy protein sequence data: A case study of immunoglobulin light chains. Bioinformatics. 2005 June; 21 Suppl 1:i495-501. [PDF]

Zavaljevski, N., F. J. Stevens, and J. Reifman. Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions. Bioinformatics. 2002 May; 18(5):689-696. [PDF]

Reifman, J., N. Zavaljevski, and F. J. Stevens. Support vector machines for protein function classification. Proceedings of the International Conference on Bioinformatics. Bangkok, Thailand. 2002 February 6-8.