Institutes | BHSAI | BIC
Biotechnology High Performance Computing Software Applications Institute
Khavrutskii, I., and A. Wallqvist. Improved Binding Free Energy Predictions from Single-reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. Journal of Chemical Theory and Computation. 2011; 7(9):3001-3011. [PDF]
Mitrophanov, A. Y., and J. Reifman. Kinetic Modeling Sheds Light on the Mode of Action of Recombinant Factor VIIa on Thrombin Generation. Thrombosis Research. 2011 Oct; 128(4):381-390. [PDF]
Vijaya Satya, R., N. Zavaljevski, and J. Reifman. SNIT: SNP Identification for Strain Typing. Source Code Biol Med. 2011 Sep 8; 6(1):14. [PDF]
Woo, H.-J., and A. Wallqvist. Spontaneous Buckling of Lipid Bilayer and Vesicle Budding Induced by Antimicrobial Peptide Magainin 2: A Coarse-Grained Simulation Study. Journal of Physical Chemistry B. 2011 June 30; 115(25):8122-8129. [PDF]
Fang, X., A. Wallqvist, and J. Reifman. Modeling Synergistic Drug Inhibition of Mycobacterium Tuberculosis Growth in Murine Macrophages. Molecular BioSystems. 2011 September 1; 7(9):2622-2636. [PDF]
Hu, X., M. S. Lee, K. Kumar, and A. Wallqvist. An Integrated Docking Pipeline for the Prediction of Large-scale Protein-protein Interactions. Proceedings of the HPCMP Users Group Conference. Schaumburg, IL. 2010 June 14-17:228-232. [PDF]
Yu, C., V. Desai, N. Zavaljevski, and J. Reifman. Large-scale Orthology Predictions for Inferring Gene Functions Across Multiple Species. Proceedings of the HPCMP Users Group Conference. Schaumburg, IL. 2010 June 14-17:228-232. [PDF]
Yu, C., N. Zavaljevski, V. Desai, and J. Reifman. QuartetS: A Fast and Accurate Algorithm for Large-scale Orthology Detection. Nucleic Acids Research. 2011 May 13; 39(13). [PDF]
Bondugula, R., A. Wallqvist, and M. S. Lee. Can Computationally Designed Protein Sequences Improve Secondary Structure Prediction? Protein Engineering Design & Selection. 2011 May; 24(5):455-461. [PDF]
Kumar, K., V. Desai, L. Cheng, M. Khitrov, D. Grover, R. Vijaya Satya, C. Yu, N. Zavaljevski, and J. Reifman. AGeS: A Software System for Microbial Genome Sequence Annotation. PLoS ONE. 2011; 6(3). [PDF]
Woo, H.-J., and A. Wallqvist. Nonequilibrium Phase Transitions Associated with DNA Replication. Physical Review Letters. 2011 February 11; 106(6):060601. [PDF]
Yeh, I. C., and A. Wallqvist. On the Proper Calculation of Electrostatic Interactions in Solid-Supported Bilayer systems. Journal of Chemical Physics. 2011 February 7; 134(5). [PDF]
Lee, M., and M. Olson. Protein Folding Simulations Combining Self-guided Langevin Dynamics and Temperature-based Replica Exchange. Journal Chemical Theory and Computation. 2010; 6(8):2477-2487. [PDF]
Fang, X., A. Wallqvist, and J. Reifman. Development and Analysis of an In Vivo-compatible Metabolic Network of Mycobacterium tuberculosis. BMC Systems Biology. 2010; 4(1):160. [PDF]
Khavrutskii, I., and A. Wallqvist. Computing Relative Free Energies of Solvation Using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. Journal of Chemical Theory and Computation. 2010; 6(11):3427-3441. [PDF]
Wallqvist, A., N. Zavaljevski, R. Vijaya Satya, R. Bondugula, V. Desai, X. Hu, K. Kumar, M. S. Lee, I.-C. Yeh, C. Yu, and J. Reifman. Accelerating Biomedical Research in Designing Diagnostic Assays, Drugs, and Vaccines. Computing in Science & Engineering. 2010 September; 12(5):46-55. [PDF]
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 Annual International Conference of the IEEE Engineering in Medicine and Biology Society Conference. Buenos Aires, Argentina. 2010 August 31-September 4. [PDF]
Vijaya Satya, R., K. Kumar, N. Zavaljevski, and J. Reifman. A High-throughput Pipeline for the Design of Real-time PCR Signatures. BMC Bioinformatics. 2010 June 23; 11:340. [PDF]
Hu, X., M. S. Lee, and A. Wallqvist. Interaction of the Disordered Yersinia Effector Protein YopE with its Cognate Chaperone SycE. Biochemistry. 2009 December 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 September 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 September 25; 5(9):e1000515. [PDF]
Fang, X., A. Wallqvist, and J. Reifman. A Systems Biology Framework for Modeling Metabolic Enzyme Inhibition of Mycobacterium tuberculosis. BMC Systems Biology. 2009 September 15; 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]
Lee, M. S., R. Bondugula, V. Desai, N. Zavaljevski, I.-C. Yeh, A. Wallqvist, and J. Reifman. A Web-accessible Protein Structure Prediction Pipeline. Proceedings of the HPCMP Users Group Conference. San Diego, CA. 2009 June 15-19:169-174. [PDF]
Vijaya Satya, R., K. Kumar, N. Zavaljevski, and J. Reifman. Parallel Implementation of a Bioinformatics Pipeline for the Design of Pathogen Diagnostic Assays. Proceedings of the HPCMP Users Group Conference. San Diego, CA. 2009 June 15-19:213-218. [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):1055-1060. [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(1):496. [PDF]
Harbaugh, S. V., M. E. Davidson, Y. G. Chushak, N. Kelley-Loughnane, and M. O. 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. A., 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]
Yeh, I.-C., M. Olson, M. S. Lee, and A. Wallqvist. Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations. Proceedings of the HPCMP Users Group Conference. Seattle, WA. 2008 July 14-17:208-213. [PDF]
Yu, C., V. Desai, N. Zavaljevski, and J. Reifman. PIPA: A High-throughput Pipeline for Protein Function Annotation. Proceedings of the HPCMP Users Group Conference. Seattle, WA. 2008 July 14-17:241-246. [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. A., I.-C. Yeh, and M. S. 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. A. Wilson. A Tool for Creating and Parallelizing Bioinformatics Pipelines. Proceedings of the 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. Proceedings of the 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. Proceedings of the 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. S., I.-C. Yeh, N. Zavaljevski, P. Wilson, and J. Reifman. A Software Pipeline for Protein Structure Prediction. Proceedings of the 25th Army Science Conference. Orlando, FL. 2006 November 17-21:423-430. [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]
Chen, D., D. Hua, X. Cheng, and J. Reifman. Gene Selection for Multiclass Prediction of Microarray Data. Proceedings of the IEEE Computer Society Bioinformatics Conference. Stanford, CA. 2003 August 11-14.
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.
