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PUBLICATIONS

2017

Liu, R., M. D. M. AbdulHameed, K. Kumar, X. Yu, A. Wallqvist, and J. Reifman. Data-driven prediction of adverse drug reactions induced by drug-drug interactions. BMC Pharmacology and Toxicology. 2017 June 8; 18(1):44. [PDF]

Woo, H. J., C. Yu, K. Kumar, and J. Reifman. Large-scale interaction effects reveal missing heritability in schizophrenia, bipolar disorder and posttraumatic stress disorder. Translational Psychiatry. 2017 April 11; 7:e1089. [PDF]

Xu, C., A. Silder, J. Zhang, J. Reifman, and G. Unnikrishnan. A cross-sectional study of the effects of load carriage on running characteristics and tibial mechanical stress: implications for stress-fracture injuries in women. BMC Musculoskeletal Disorders. 2017 March 23; 18(1):125. [PDF]

Tewari, S. G., S. T. Prigge, J. Reifman, and A. Wallqvist. Using a genome-scale metabolic network model to elucidate the mechanism of chloroquine action in Plasmodium falciparum. International Journal for Parasitology: Drugs and Drug Resistance. 2017 March 22; 7(2):138-146. [PDF]

Chaudhury, S., G. D. Gromowski, D. R. Ripoll, I. V. Khavrutskii, V. Desai, and A. Wallqvist. Dengue virus antibody database: systematically linking serotype-specificity with epitope mapping in dengue virus. PLOS Neglected Tropical Diseases. 2017 February 21; 11(2):e0005395. [PDF]

Khavrutskii, I. V., and A. Wallqvist. Beta-aminoalcohols as potential reactivators of aged sarin-/soman-inhibited acetylcholinesterase. ChemistrySelect. 2017 February 13; 2(5):1885-1890. [PDF]

Blais, E. M., K. D. Rawls, B. V. Dougherty, Z. I. Li, G. L. Kolling, P. Ye, A. Wallqvist, and J. A. Papin. Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions. Nature Communications. 2017 February 8; 8:14250. [PDF]

Mitrophanov, A. Y., F. Szlam, R. M. Sniecinski, J. H. Levy, and J. Reifman. In reply to "Clinical and practical aspects of restoring thrombin generation in acute coagulopathic bleeding." Anesthesia & Analgesia. 2017 February; 124(2):702. [PDF]

Mitrophanov, A. Y., F. Szlam, R. M. Sniecinski, J. H. Levy, and J. Reifman. In reply to "If the goal is balance, why not fresh frozen plasma?" Anesthesia & Analgesia. 2017 February; 124(2):699-700. [PDF]

Lee, D. W., I. V. Khavrutskii, A. Wallqvist, S. Bavari, C. L. Cooper, and S. Chaudhury. BRILIA: integrated tool for high-throughput annotation and lineage tree assembly of B-cell repertoires. Frontiers in Immunology. 2017 January 17; 7:681. [PDF]

Nagaraja, S., L. Chen, J. Zhou, Y. Zhao, D. Fine, L. A. DiPietro, J. Reifman, and A. Y. Mitrophanov. Predictive analysis of mechanistic triggers and mitigation strategies for pathological scarring in skin wounds. Journal of Immunology. 2017 January 15; 198(2):832-841. [PDF]

Woo, H. J., C. Yu, and J. Reifman. Collective genetic interaction effects and the role of antigen-presenting cells in autoimmune diseases. PLOS ONE. 2017 January 12; 12(1):e0169918. [PDF]

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2016

Reifman, J., K. Kumar, N. J. Wesensten, N. A. Tountas, T. J. Balkin, and S. Ramakrishnan. 2B-Alert Web: an open-access tool for predicting the effects of sleep/wake schedules and caffeine consumption on neurobehavioral performance. Sleep. 2016 December 1; 39(12):2157-2159. [PDF]

Liu, R., X. Yu, and A. Wallqvist. Using chemical-induced gene expression in cultured human cells to predict chemical toxicity. Chem Res Toxicol. 2016 November 21; 29(11):1883-1893. [PDF]

Schyman, P., R. Liu, and A. Wallqvist. Using the variable-nearest neighbor method to identify P-glycoprotein substrates and inhibitors. ACS Omega. 2016 November 16; 1(5):923-929. [PDF]

Ripoll, D. R., I. Khavrutskii, A. Wallqvist, and S. Chaudhury. Modeling the role of epitope arrangement on antibody binding stoichiometry in flaviviruses. Biophysical Journal. 2016 October 18; 111(8):1641-1654. [PDF]

AbdulHameed, M. D., D. L. Ippolito, and A. Wallqvist. Predicting rat and human pregnane X receptor activators using Bayesian classification models. Chemical Research in Toxicology. 2016 October 17; 29(10):1729-1740. [PDF]

AbdulHameed, M. D., D. L. Ippolito, J. D. Stallings, and A. Wallqvist. Mining kidney toxicogenomics using gene co-expression modules. BMC Genomics. 2016 October 10; 17:790. [PDF]

Xu, C., A. Silder, J. Zhang, J. Hughes, G. Unnikrishnan, J. Reifman, and V. Rakesh. An integrated musculoskeletal-finite-element model to evaluate effects of load carriage on the tibia during walking. Journal of Biomechanical Engineering. 2016 October 1; 138(10). [PDF]

Ramakrishnan, S., N. J. Wesensten, G. H. Kamimori, J. E. Moon, T. J. Balkin, and J. Reifman. A unified model of performance for predicting the effects of sleep and caffeine. Sleep. 2016 October 1; 39(10):1827-1841. [PDF]

Memisevic, V., K. Kumar, N. Zavaljevski, D. DeShazer, A. Wallqvist, and J. Reifman. DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems. BMC Bioinformatics. 2016 September 20; 17:387. [PDF]

Te, J. A., M. D. AbdulHameed, and A. Wallqvist. Systems toxicology of chemically induced liver and kidney injuries: histopathology-associated gene co-expression modules. Journal of Applied Toxicology. 2016 September; 36(9):1137-1149. [PDF]

Mitrophanov, A. Y., F. Szlam, R. M. Sniecinski, J. H. Levy, and J. Reifman. A step toward balance: thrombin generation improvement via procoagulant factor and antithrombin supplementation. Anesth Analg. 2016 September; 123(3):535-546. [PDF]

Woo, H. J., C. Yu, K. Kumar, B. Gold, and J. Reifman. Genotype distribution-based inference of collective effects in genome-wide association studies: insights to age-related macular degeneration disease mechanism. BMC Genomics. 2016 August 30; 17:695. [PDF]

Wallqvist, A., X. Fang, S. G. Tewari, P. Ye, and J. Reifman. Metabolic host responses to malarial infection during the intraerythrocytic developmental cycle. BMC Systems Biology. 2016 August 8; 10:58. [PDF]

Chaudhury, S., C. F. Ockenhouse, J. A. Regules, S. Dutta, A. Wallqvist, E. Jongert, N. C. Waters, F. Lemiale, and E. Bergmann-Leitner. The biological function of antibodies induced by the RTS,S/AS01 malaria vaccine candidate is determined by their fine specificity. Malaria Journal. 2016 May 31; 15:301. [PDF]

Govindarajan, V., V. Rakesh, J. Reifman, and A. Y. Mitrophanov. Computational study of thrombus formation and clotting factor effects under venous flow conditions. Biophysical Journal. 2016 April 26; 110(8):1869-1885. [PDF]

Tomaiuolo, M., M. Kottke, R. W. Matheny, J. Reifman, and A. Y. Mitrophanov. Computational identification and analysis of signaling subnetworks with distinct functional roles in the regulation of TNF production. Molecular BioSystems. 2016 March 1; 12(3):826-838. [PDF]

Reisner, A. T., S. Edla, J. Liu, J. T. Rubin, J. E. Thorsen, E. Kittell, J. B. Smith, D. D. Yeh, and J. Reifman. Muscle oxygen saturation improves diagnostic association between initial vital signs and major hemorrhage: a prospective observational study. Academic Emergency Medicine. 2016 March; 23(3):353-357. [PDF]

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]

Schyman, P., R. Liu, and A. Wallqvist. General purpose 2D and 3D similarity approach to identify hERG blockers. Journal of Chemical Information and Modeling. 2016 January 25; 56(1):213-222. [PDF]

Ippolito, D. L., M. D. AbdulHameed, G. J. Tawa, C. E. Baer, M. G. Permenter, B. C. McDyre, W. E. Dennis, M. H. Boyle, C. A. Hobbs, M. A. Streicker, B. S. Snowden, J. A. Lewis, A. Wallqvist, and J. D. Stallings. Gene expression patterns associated with histopathology in toxic liver fibrosis. Toxicological Sciences. 2016 January; 149(1):67-88. [PDF]

Ramakrishnan, S., N. J. Wesensten, T. J. Balkin, and J. Reifman. A unified model of performance: validation of its predictions across different sleep/wake schedules. Sleep. 2016 January 1; 39(1):249-262. [PDF]

Loers, G., V. Saini, B. Mishra, S. Gul, S. Chaudhury, A. Wallqvist, G. Kaur, and M. Schachner. Vinorelbine and epirubicin share common features with polysialic acid and modulate neuronal and glial functions. Journal of Neurochemistry. 2016 January; 136(1):48-62. [PDF]

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2015

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]

Nagaraja, S., J. Reifman, and A. Y. Mitrophanov. Computational identification of mechanistic factors that determine the timing and intensity of the inflammatory response. PLOS Computational Biology. 2015 December 3; 11(12):e1004460. [PDF]

Mao, H., G. Unnikrishnan, V. Rakesh, and J. Reifman. Untangling the effect of head acceleration on brain responses to blast waves. Journal of Biomechanical Engineering. 2015 December 1; 137(12):124502. [PDF]

Laxminarayan, S., J. Reifman, S. S. Edwards, H. Wolpert, and G. M. Steil. Bolus estimation - rethinking the effect of meal fat content. Diabetes Technology and Therapeutics. 2015 December; 17(12):860-866. [PDF]

Stallings, J. D., D. L. Ippolito, A. Wallqvist, B. C. McDyre, and J. Reifman. Host response to environmental hazards: using literature, bioinformatics, and computation to derive candidate biomarkers of toxic industrial chemical exposure. Proceedings of the HFM-254 Symposium on Health Surveillance and Informatics in Missions: Multidisciplinary Approaches and Perspectives. Paris, France. 2015 October 12-14; 7:1-14. [PDF]

Ramakrishnan, S., S. Laxminarayan, N. J. Wesensten, T. J. Balkin, and J. Reifman. Can we predict cognitive performance decrements due to sleep loss and the recuperative effects of caffeine? Proceedings of the HFM-254 Symposium on Health Surveillance and Informatics in Missions: Multidisciplinary Approaches and Perspectives. Paris, France. 2015 October 12-14; 20:1-20. [PDF]

Reifman, J., J. Liu, M. Y. Khitrov, S. Edla, and A. T. Reisner. Automated analysis of vital signs identified patients with substantial bleeding prior to hospital arrival. Proceedings of the HFM-254 Symposium on Health Surveillance and Informatics in Missions: Multidisciplinary Approaches and Perspectives. Paris, France. 2015 October 12-14; 17:1-14. [PDF]

Laxminarayan, S., V. Rakesh, M. J. Buller, W. J. Tharion, and J. Reifman. Preventing heat injuries by predicting individualized human core temperature. Proceedings of the HFM-254 Symposium on Health Surveillance and Informatics in Missions: Multidisciplinary Approaches and Perspectives. Paris, France. 2015 October 12-14; 21:1-14. [PDF]

Vital-Lopez, F. G., J. Reifman, and A. Wallqvist. Biofilm formation mechanisms of Pseudomonas aeruginosa predicted via genome-scale kinetic models of bacterial metabolism. PLOS Computational Biology. 2015 October 2; 11(10):e1004452. [PDF]

Mitrophanov, A. Y., F. R. Rosendaal, and J. Reifman. Mechanistic modeling of the effects of acidosis on thrombin generation. Anesthesia & Analgesia. 2015 August; 121(2):278-288. [PDF]

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]

Scheff, J. D., J. D. Stallings, J. Reifman, and V. Rakesh. Mathematical modeling of the heat-shock response in HeLa cells. Biophysical Journal. 2015 July 12; 109(2):182-193. [PDF]

Edla, S., A. T. Reisner, J. Liu, V. A. Convertino, R. Carter III, and J. Reifman. In reply to "Utility of shock index calculation in hemorrhagic trauma." American Journal of Emergency Medicine. 2015 July; 33(7):978-979. [PDF]

Te, J. A., K. D. Spradling-Reeves, J. F. Dillman III, and A. Wallqvist. Neuroprotective mechanisms activated in non-seizing rats exposed to sarin. Brain Research. 2015 June 4; 1618:136-148. [PDF]

Ramakrishnan, S., W. Lu, S. Laxminarayan, N. J. Wesensten, T. L. Rupp, T. J. Balkin, and J. Reifman. Can a mathematical model predict an individual's trait-like response to both total and partial sleep loss? Journal of Sleep Research. 2015 June; 24(3):262-269. [PDF]

Laxminarayan, S., M. Buller, W. Tharion, and J. Reifman. Human core temperature prediction for heat-injury prevention. IEEE Journal of Biomedical and Health Informatics. 2015 May 7; 19(3):883-891. [PDF]

Liu, J., M. Y. Khitrov, J. D. Gates, S. R. Odom, J. M. Havens, M. A. de Moya, K. Wilkins, S. K. Wedel, E. O. Kittell, J. Reifman, and A. T. Reisner. Automated analysis of vital signs to identify patients with substantial bleeding before hospital arrival: a feasibility study. Shock. 2015 May; 43(5):429-436. [PDF]

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]

Liu, R., X. Yu, and A. Wallqvist. Data-driven identification of structural alerts for mitigating the risk of drug-induced human liver injuries. Journal of Cheminformatics. 2015 February 11; 7:4. [PDF]

Yu, C., A. Boutte, X. Yu, B. Dutta, J. D. Feala, K. Schmid, J. Dave, G. J. Tawa, A. Wallqvist, and J. Reifman. A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury. Journal of Neuroscience Research. 2015 February; 93(2):199-214. [PDF]

Edla, S., A. T. Reisner, J. Liu, V. A. Convertino, R. Carter, III, and J. Reifman. Is heart rate variability better than routine vital signs for prehospital identification of major hemorrhage? American Journal of Emergency Medicine. 2015 February; 33(2):254-261. [PDF]

Liu, R., P. Schyman, and A. Wallqvist. Critically assessing the predictive power of QSAR models for human liver microsomal stability. Journal of Chemical Information and Modeling. 2015; 55(8):1566-1575. [PDF]

Chaudhury, S., D. R. Ripoll, and A. Wallqvist. Structure-based pKa prediction provides a thermodynamic basis for the role of histidines in pH-induced conformational transitions in dengue virus. Biochemistry and Biophysics Reports. 2015; 4:375-385. [PDF]

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2014

Ippolito, D. L., J. A. Lewis, C. Yu, L. R. Leon, and J. D. Stallings. Alteration in circulating metabolites during and after heat stress in the conscious rat: potential biomarkers of exposure and organ-specific injury. BMC Physiology. 2014 December 24; 14:14. [PDF]

Stallings, J. D., D. L. Ippolito, V. Rakesh, C. E. Baer, W. E. Dennis, B. G. Helwig, D. A. Jackson, L. R. Leon, J. A. Lewis, and J. Reifman. Patterns of gene expression associated with recovery and injury in heat-stressed rats. BMC Genomics. 2014 December 3; 15:1058. [PDF]

Rakesh, V., J. D. Stallings, and J. Reifman. A virtual rat for simulating environmental and exertional heat stress. Journal of Applied Physiology. 2014 December 1; 117(11):1278-1286. [PDF]

Song, H. S., J. Reifman, and A. Wallqvist. Prediction of metabolic flux distribution from gene expression data based on the flux minimization principle. PLOS ONE. 2014 November 14; 9(11):e112524. [PDF]

Khavrutskii, I. V., P. M. Legler, A. M. Friedlander, and A. Wallqvist. A reaction path study of the catalysis and inhibition of the Bacillus anthracis CapD gamma-glutamyl transpeptidase. Biochemistry. 2014 November 11; 53(44):6954-6967. [PDF]

AbdulHameed, M. D., G. J. Tawa, K. Kumar, D. L. Ippolito, J. A. Lewis, J. D. Stallings, and A. Wallqvist. Systems level analysis and identification of pathways and networks associated with liver fibrosis. PLOS ONE. 2014 November 8; 9(11):e112193. [PDF]

Ramakrishnan, S., S. Laxminarayan, N. J. Wesensten, G. H. Kamimori, T. J. Balkin, and J. Reifman. Dose-dependent model of caffeine effects on human vigilance during total sleep deprivation. Journal of Theoretical Biology. 2014 October 7; 358:11-24. [PDF]

Fang, X., J. Reifman, and A. Wallqvist. Modeling metabolism and stage-specific growth of Plasmodium falciparum HB3 during the intraerythrocytic developmental cycle. Molecular BioSystems. 2014 October 1; 10:2526-2537. [PDF]

Hang, J., V. Desai, N. Zavaljevski, Y. Yang, X. Lin, R. V. Satya, L. J. Martinez, J. M. Blaylock, R. G. Jarman, S. J. Thomas, and R. A. Kuschner. 16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles. Microbiome. 2014 September 16; 2:31. [PDF]

Chaudhury, S., J. Reifman, and A. Wallqvist. Simulation of B cell affinity maturation explains enhanced antibody cross-reactivity induced by the polyvalent malaria vaccine AMA1. Journal of Immunology. 2014 September 1; 193(5):2073-2086. [PDF]

Tawa, G. J., M. D. AbdulHameed, X. Yu, K. Kumar, D. L. Ippolito, J. A. Lewis, J. D. Stallings, and A. Wallqvist. Characterization of chemically induced liver injuries using gene co-expression modules. PLOS ONE. 2014 September; 9(9):e107230. [PDF]

Sul, B., A. Wallqvist, M. J. Morris, J. Reifman, and V. Rakesh. A computational study of the respiratory airflow characteristics in normal and obstructed human airways. Computers in Biology and Medicine. 2014 September 1; 52:130-143. [PDF]

Smith, J. B., A. T. Reisner, S. Edla, J. Liu, S. Liddle, and J. Reifman. A platform for real-time acquisition and analysis of physiological data in hospital emergency departments. Proceedings of the 36th IEEE EMBS Annual International Conference. Chicago, IL. 2014 August 26-30; 2678-2681. [PDF]

Liu, J., A. T. Reisner, S. Edla, and J. Reifman. A comparison of alerting strategies for hemorrhage identification during prehospital emergency transport. Proceedings of the 36th IEEE EMBS Annual International Conference. Chicago, IL. 2014 August 26-30; 2670-2673. [PDF]

Chen, X., A. T. Reisner, L. Chen, S. Edla, and J. Reifman. The matching of sinus arrhythmia to respiration: are trauma patients without serious injury comparable to healthy laboratory subjects? Proceedings of the 36th IEEE EMBS Annual International Conference. Chicago, IL. 2014 August 26-30; 3398-3401. [PDF]

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]

Mitrophanov, A. Y., A. S. Wolberg, and J. Reifman. Kinetic model facilitates analysis of fibrin generation and its modulation by clotting factors: implications for hemostasis-enhancing therapies. Molecular BioSystems. 2014 June 24; 10:2347-2357. [PDF]

Liu, R., N. Singh, G. J. Tawa, A. Wallqvist, and J. Reifman. Exploiting large-scale drug-protein interaction information for computational drug repurposing. BMC Bioinformatics. 2014 June 20; 15:210. [PDF]

Reisner, A., X. Chen, K. Kumar, and J. Reifman. Prehospital heart rate and blood pressure increase the positive predictive value of the Glasgow Coma Scale for high-mortality traumatic brain injury. Journal of Neurotrauma. 2014 May 15; 31(10):906-913. [PDF]

Bushman, J., B. Mishra, M. Ezra, S. Gul, C. Schulze, S. Chaudhury, D. Ripoll, A. Wallqvist, J. Kohn, M. Schachner, and G. Loers. Tegaserod mimics the neurostimulatory glycan polysialic acid and promotes nervous system repair. Neuropharmacology. 2014 April; 79:456-466. [PDF]

Liu, R., and A. Wallqvist. Merging applicability domains for in silico assessment of chemical mutagenicity. Journal of Chemical Information and Modeling. 2014 March 24; 54(3):793-800. [PDF]

Khitrov, M. Y., S. Laxminarayan, D. Thorsley, S. Ramakrishnan, S. Rajaraman, N. J. Wesensten, and J. Reifman. PC-PVT: a platform for psychomotor vigilance task testing, analysis, and prediction. Behavior Research Methods. 2014 March; 46(1):140-147. [PDF]

Nagaraja, S., A. Wallqvist, J. Reifman, and A. Y. Mitrophanov. Computational approach to characterize causative factors and molecular indicators of chronic wound inflammation. Journal of Immunology. 2014 February 15; 192(4):1824-1834. [PDF]

Munagala, S., G. Sirasani, P. Kokkonda, M. Phadke, N. Krynetskaia, P. Lu, F. J. Sharom, S. Chaudhury, M. D. AbdulHameed, G. Tawa, A. Wallqvist, R. Martinez, W. Childers, M. Abou-Gharbia, E. Krynetskiy, and R. B. Andrade. Synthesis and evaluation of Strychnos alkaloids as MDR reversal agents for cancer cell eradication. Bioorganic & Medicinal Chemistry. 2014 February 1; 22(3):1148-1155. [PDF]

Woo, H. J., and J. Reifman. Quantitative modeling of virus evolutionary dynamics and adaptation in serial passages using empirically inferred fitness landscapes. Journal of Virology. 2014 January; 88(2):1039-1050. [PDF]

Loers, G., V. Saini, B. Mishra, F. Papastefanaki, D. Lutz, S. Chaudhury, D. R. Ripoll, A. Wallqvist, S. Gul, M. Schachner, and G. Kaur. Nonyloxytryptamine mimics polysialic acid and modulates neuronal and glial functions in cell culture. Journal of Neurochemistry. 2014 January; 128(1):88-100. [PDF]

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2013

Rakesh, V., J. D. Stallings, B. G. Helwig, L. R. Leon, D. A. Jackson, and J. Reifman. A 3-D mathematical model to identify organ-specific risks in rats during thermal stress. Journal of Applied Physiology. 2013 December 15; 115(12):1822-1837. [PDF]

Liu, J., G. J. Tawa, and A. Wallqvist. Identifying cytochrome P450 functional networks and their allosteric regulatory elements. PLOS ONE. 2013 December 3; 8(12):e81980. [PDF]

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]

Khavrutskii, I. V., J. B. Smith, and A. Wallqvist. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization. Journal of Chemical Physics. 2013 October 25; 139(16):165104. [PDF]

Koehler, J. W., J. M. Smith, D. R. Ripoll, K. W. Spik, S. L. Taylor, C. V. Badger, R. J. Grant, M. M. Ogg, A. Wallqvist, M. C. Guttieri, R. F. Garry, and C. S. Schmaljohn. A fusion-inhibiting peptide against Rift Valley fever virus inhibits multiple, diverse viruses. PLOS Neglected Tropical Diseases. 2013 September 12; 7(9):e2430. [PDF]

Mitrophanov, A. Y., F. R. Rosendaal, and J. Reifman. Computational analysis of the effects of reduced temperature on thrombin generation: the contributions of hypothermia to coagulopathy. Anesthesia & Analgesia. 2013 September; 117(3):565-574. [PDF]

Reisner, A. T., M. Y. Khitrov, L. Chen, A. Blood, K. Wilkins, W. Doyle, S. Wilcox, T. Denison, and J. Reifman. Development and validation of a portable platform for deploying decision-support algorithms in prehospital settings. Applied Clinical Informatics. 2013 August 21; 4:392-402. [PDF]

Bergmann-Leitner, E. S., S. Chaudhury, N. J. Steers, M. Sabato, V. Delvecchio, A. S. Wallqvist, C. F. Ockenhouse, and E. Angov. Computational and experimental validation of B and T-cell epitopes of the in vivo immune response to a novel malarial antigen. PLOS ONE. 2013 August 16; 8(8):e71610. [PDF]

Vital-Lopez, F. G., A. Wallqvist, and J. Reifman. Bridging the gap between gene expression and metabolic phenotype via kinetic models. BMC Systems Biology. 2013 July 22; 7:63. [PDF]

Hu, X., J. R. Compton, M. D. AbdulHameed, C. L. Marchand, K. L. Robertson, D. H. Leary, A. Jadhav, J. R. Hershfield, A. Wallqvist, A. M. Friedlander, and P. M. Legler. 3-substituted indole inhibitors against Francisella tularensis FabI identified by structure-based virtual screening. Journal of Medicinal Chemistry. 2013 July 1; 56(13):5275-5287. [PDF]

Feala, J. D., M. D. AbdulHameed, C. Yu, B. Dutta, X. Yu, K. Schmid, J. Dave, F. Tortella, and J. Reifman. Systems biology approaches for discovering biomarkers for traumatic brain injury. Journal of Neurotrauma. 2013 July 1; 30(13):1101-1116. [PDF]

Chaudhury, S., M. D. AbdulHameed, N. Singh, G. Tawa, P. M. D'haeseleer, A. T. Zemla, A. Navid, C. E. Zhou, M. C. Franklin, J. Cheung, M. J. Rudolph, J. Love, J. F. Graf, D. A. Rozack, J. L. Dankmeyer, K. Amemiya, S. Daefler, and A. Wallqvist. Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PLOS ONE. 2013 May 21; 8(5):e63369. [PDF]

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]

Rajdev, P., D. Thorsley, S. Rajaraman, T. L. Rupp, N. J. Wesensten, T. J. Balkin, and J. Reifman. A unified mathematical model to quantify performance impairment for both chronic sleep restriction and total sleep deprivation. Journal of Theoretical Biology. 2013 April 24; 331:66-77. [PDF]

Ramakrishnan, S., S. Rajaraman, S. Laxminarayan, N. J. Wesensten, G. H. Kamimori, T. J. Balkin, and J. Reifman. A biomathematical model of the restoring effects of caffeine on cognitive performance during sleep deprivation. Journal of Theoretical Biology. 2013 February 21; 319:23-33. [PDF]

Chen, L., A. T. Reisner, X. Chen, A. Gribok, and J. Reifman. Are standard diagnostic test characteristics sufficient for the assessment of continual patient monitoring? Medical Decision Making. 2013 February; 33(2):225-234. [PDF]

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2012

Rajaraman, S., S. Ramakrishnan, D. Thorsley, N. Wesensten, T. Balkin, and J. Reifman. A new metric for quantifying performance impairment on the psychomotor vigilance test. Journal of Sleep Research. 2012 December; 21(6):659-674. [PDF]

Mitrophanov, A. Y., F. R. Rosendaal, and J. Reifman. Computational analysis of intersubject variability and thrombin generation in dilutional coagulopathy. Transfusion. 2012 November; 52(11):2475-2486. [PDF]

Laxminarayan, S., J. Reifman, and G. M. Steil. Use of a food and drug administration-approved type 1 diabetes mellitus simulator to evaluate and optimize a proportional-integral-derivative controller. Journal of Diabetes Science and Technology. 2012 November; 6(6):1401-1412. [PDF]

Thorsley, D., R. Leproult, K. Spiegel, and J. Reifman. A phenomenological model for circadian and sleep allostatic modulation of plasma cortisol concentration. American Journal of Physiology - Endocrinology and Metabolism. 2012 November; 303(10):E1190-1201. [PDF]

Singh, N., S. Chaudhury, R. Liu, M. D. AbdulHameed, G. Tawa, and A. Wallqvist. QSAR classification model for antibacterial compounds and its use in virtual screening. Journal of Chemical Information and Modeling. 2012 October 22; 52(10):2559-2569. [PDF]

Liu, R., G. Tawa, and A. Wallqvist. Locally weighted learning methods for predicting dose-dependent toxicity with application to the human maximum recommended daily dose. Chemical Research in Toxicology. 2012 October 15; 25(10):2216-2226. [PDF]

Peach, M. L., A. V. Zakharov, R. Liu, A. Pugliese, G. Tawa, A. Wallqvist, and M. C. Nicklaus. Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software. Future Medicinal Chemistry. 2012 October; 4(15):1907-1932. [PDF]

Reisner, A. T., L. Chen, and J. Reifman. The association between vital signs and major hemorrhagic injury is significantly improved after controlling for sources of measurement variability. Journal of Critical Care. 2012 October; 27(5):533.e1-10. [PDF]

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]

Vijaya Satya, R., N. Zavaljevski, and J. Reifman. A new strategy to reduce allelic bias in RNA-Seq readmapping. Nucleic Acids Research. 2012 September 1; 40(16):e127. [PDF]

Fang, X., A. Wallqvist, and J. Reifman. Modeling phenotypic metabolic adaptations of Mycobacterium tuberculosis H37Rv under hypoxia. PLOS Computational Biology. 2012 September; 8(9):e1002688. [PDF]

Ripoll, D. R., I. V. Khavrutskii, S. Chaudhury, J. Liu, R. A. Kuschner, A. Wallqvist, and J. Reifman. Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase. PLOS Computational Biology. 2012 August; 8(8):e1002665. [PDF]

Ramakrishnan, S., S. Laxminarayan, D. Thorsley, N. J. Wesensten, T. J. Balkin, and J. Reifman. Individualized performance prediction during total sleep deprivation: accounting for trait vulnerability to sleep loss. Proceedings of the 34th IEEE EMBS Annual International Conference. San Diego, CA. 2012 August 28-September 1; 5574-5577. [PDF]

Woo, H. J., and J. Reifman. A quantitative quasispecies theory-based model of virus escape mutation under immune selection. Proceedings of the National Academy of Sciences of the United States of America. 2012 August 7; 109(32):12980-12985. [PDF]

Mitrophanov, A. Y., F. R. Rosendaal, and J. Reifman. Therapeutic correction of thrombin generation in dilution-induced coagulopathy: computational analysis based on a data set of healthy subjects. The Journal of Trauma and Acute Care Surgery. 2012 August; 73(2 Suppl 1):S95-102. [PDF]

Liu, R., J. Liu, G. Tawa, and A. Wallqvist. 2D SMARTCyp reactivity-based site of metabolism prediction for major drug-metabolizing cytochrome P450 enzymes. Journal of Chemical Information and Modeling. 2012 June 25; 52(6):1698-1712. [PDF]

Yu, C., V. Desai, L. Cheng, and J. Reifman. QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. BMC Bioinformatics. 2012 June 22; 13:143. [PDF]

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

Woo, H. J., R. Vijaya Satya, and J. Reifman. Thermodynamic basis for the emergence of genomes during prebiotic evolution. PLOS Computational Biology. 2012 May; 8(5):e1002534. [PDF]

Cardellina, J. H., V. Roxas-Duncan, V. Montgomery, V. Eccard, Y. Campbell, X. Hu, I. Khavrutskii, G. Tawa, A. Wallqvist, J. Gloer, N. Phatak, U. Hoeller, A. Soman, B. Joshi, S. Hein, D. Wicklow, and L. A. Smith. Fungal bis-naphthopyrones as inhibitors of botulinum neurotoxin serotype A. ACS Medicinal Chemistry Letters. 2012 April 2; 3(5):387-391. [PDF]

Sun, H., G. Tawa, and A. Wallqvist. Classification of scaffold-hopping approaches. Drug Discovery Today. 2012 April; 17(7-8):310-324. [PDF]

Yeh, I.-C., D. R. Ripoll, and A. Wallqvist. Free energy difference in indolicidin attraction to eukaryotic and prokaryotic model cell membranes. Journal of Physical Chemistry B. 2012 March 15; 116(10):3387-3396. [PDF]

AbdulHameed, M. D., S. Chaudhury, N. Singh, H. Sun, A. Wallqvist, and G. J. Tawa. Exploring polypharmacology using a ROCS-based target fishing approach. Journal of Chemical Information Model. 2012 February 27; 52(2):492-505. [PDF]

Singh, N., H. Sun, S. Chaudhury, M. D. AbdulHameed, A. Wallqvist, and G. Tawa. A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space. Journal of Cheminformatics. 2012 February 8; 4:4. [PDF]

Chaudhury, S., M. A. Olson, G. Tawa, A. Wallqvist, and M. S. Lee. Efficient conformational sampling in explicit solvent using a hybrid replica exchange molecular dynamics method. Journal of Chemical Theory and Computation. 2012 February; 8(2):677-687. [PDF]

Hu, X., P. M. Legler, I. Khavrutskii, A. Scorpio, J. R. Compton, K. L. Robertson, A. M. Friedlander, and A. Wallqvist. Probing the donor and acceptor substrate specificity of the y-glutamyl transpeptidase. Biochemistry. 2012 January 17; 51(6):1199-1212. [PDF]

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2011

Koehler, J. W., L. C. Dupuy, A. R. Garrison, B. F. Beitzel, M. J. Richards, D. R. Ripoll, A. Wallqvist, S. Y. Teh, A. A. Vaewhongs, F. S. Vojdani, H. S. Padgett, and C. S. Schmaljohn. Novel plant-derived recombinant human interferons with broad spectrum antiviral activity. Antiviral Research. 2011 December; 92(3):461-469. [PDF]

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]

Olson, M. A., S. Chaudhury, and M. S. Lee. Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations. Journal of Computational Chemistry. 2011 November 15; 32(14):3014-3022. [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 October; 128(4):381-390. [PDF]

Vijaya Satya, R., N. Zavaljevski, and J. Reifman. SNIT: SNP identification for strain typing. Source Code Biology and Medicine. 2011 September 8; 6:14. [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]

Chen, X., L. Chen, A. T. Reisner, and J. Reifman. Using confidence intervals to assess the reliability of instantaneous heart rate and respiratory rate. Proceedings of the 33rd IEEE EMBS Annual International Conference. Boston, MA. 2011 August 30-September 3; 6939-6942. [PDF]

Lu, Y., S. Rajaraman, W. K. Ward, R. A. Vigersky, and J. Reifman. Predicting human subcutaneous glucose concentration in real time: a universal data-driven approach. Proceedings of the 33rd IEEE EMBS Annual International Conference. Boston, MA. 2011 August 30-September 3; 7945-7948. [PDF]

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 August 15; 7(9):3001-3011. [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]

Kumar, K., V. Desai, L. Cheng, M. Khitrov, D. Grover, R. Vijaya Satya, C. Yu, N. Zavaljevski, and J. Reifman. A web-based high-throughput tool for next-generation sequence annotation. Proceedings of the HPCMP Users Group Conference. Portland, OR. 2011 June 20-24; 320-326. [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):e88. [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]

Cardellina, J. H., R. Vieira, V. Eccard, J. Skerry, V. Montgomery, Y. Campbell, V. Roxas-Duncan, W. Leister, C. A. LeClair, D. J. Maloney, D. Padula, G. Pescitelli, I. Khavrutskii, X. Hu, A. Wallqvist, and L. A. Smith. Separation of Betti reaction product enantiomers: absolute configuration and inhibition of botulinum neurotoxin A. ACS Medicinal Chemistry Letters. 2011 March; 2(5):396-401. [PDF]

Kumar, K., V. Desai, L. Cheng, M. Khitrov, D. Grover, R. V. Satya, C. Yu, N. Zavaljevski, and J. Reifman. AGeS: a software system for microbial genome sequence annotation. PLOS ONE. 2011 March; 6(3):e17469. [PDF]

Woo, H. J., and A. Wallqvist. Nonequilibrium phase transitions associated with DNA replication. Physical Review Letters. 2011 February 11; 106:060601. [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):055109. [PDF]

Gribok, A. V., X. Chen, and J. Reifman. A robust method to estimate instantaneous heart rate from noisy electrocardiogram waveforms. Annals of Biomedical Engineering. 2011 February; 39(2):824-834. [PDF]

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2010

Fang, X., A. Wallqvist, and J. Reifman. Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis. BMC Systems Biology. 2010 November 26; 4:160. [PDF]

Chen, L., A. T. Reisner, A. Gribok, and J. Reifman. Is respiration-induced variation in the photoplethysmogram associated with major hypovolemia in patients with acute traumatic injuries? Shock. 2010 November; 34(5):455-460. [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 October 21; 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 IEEE EMBS Annual International Conference. Buenos Aires, Argentina. 2010 August 31-September 4; 783-786. [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 July 26; 6(8):2477-2487. [PDF]

Gribok, A., M. Buller, R. Hoyt, and J. Reifman. A real-time algorithm for predicting core temperature in humans. IEEE Transactions on Information Technology in Biomedicine. 2010 July; 14(4):1039-1045. [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, 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; 269-272. [PDF]

Steil, G. M., B. Hipszer, and J. Reifman. Update on mathematical modeling research to support the development of automated insulin delivery systems. Journal of Diabetes Science and Technology. 2010 May; 4(3):759-769. [PDF]

Reifman, J., L. Chen, M. Y. Khitrov, and A. T. Reisner. Automated decision-support technologies for prehospital care of trauma casualties. Proceedings of the RTO HFM Symposium on NATO Human Use of Advanced Technologies and New Procedures in Medical Field Operations. Essen, Germany. 2010 April 19-21; 40:1-14. [PDF]

Lu, Y., A. V. Gribok, W. K. Ward, and J. Reifman. The importance of different frequency bands in predicting subcutaneous glucose concentration in type 1 diabetic patients. IEEE Transactions on Biomedical Engineering. 2010 April 15; 57(8):1839-1846. [PDF]

Gani, A., A. V. Gribok, Y. Lu, W. K. Ward, R. A. Vigersky, and J. Reifman. Universal glucose models for predicting subcutaneous glucose concentration in humans. IEEE Transactions on Information Technology in Biomedicine. 2010 January; 14(1):157-165. [PDF]

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2009

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]

Rajaraman, S., N. J. Wesensten, T. J. Balkin, and J. Reifman. Individualized management of fatigue and cognitive performance impairment through biomathematical modeling. Proceedings of the RTO HFM Symposium on Human Performance Enhancement for NATO Military Operations (Science, Technology, and Ethics). Sofia, Bulgaria. 2009 October 5-7; 28:1-11. [PDF]

Rajaraman, S., A. V. Gribok, N. J. Wesensten, T. J. Balkin, and J. Reifman. An improved methodology for individualized performance prediction of sleep-deprived individuals with the two-process model. Sleep. 2009 October 1; 32(10):1377-1392. [PDF]

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]

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]

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. Journal of Physical Chemistry B. 2009 September 10; 113(36):12382-12390. [PDF]

Chen, L., A. T. Reisner, and J. Reifman. Automated beat onset and peak detection algorithm for field-collected photoplethysmograms. Proceedings of the 31st IEEE EMBS Annual International Conference. Minneapolis, MN. 2009 September 2-6; 5689-5692. [PDF]

Khitrov, M. Y., M. Rutishauser, K. Montgomery, A. T. Reisner, and J. Reifman. A platform for testing and comparing of real-time decision-support algorithms in mobile environments. Proceedings of the 31st IEEE EMBS Annual International Conference. Minneapolis, MN. 2009 September 2-6; 3417-3420. [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]

Chen, L., A. T. Reisner, A. Gribok, and J. Reifman. Exploration of prehospital vital sign trends for the prediction of trauma outcomes. Prehospital Emergency Care. 2009 July-September; 13(3):286-294. [PDF]

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

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]

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]

Chen, L., A. T. Reisner, A. Gribok, T. M. McKenna, and J. Reifman. Can we improve the clinical utility of respiratory rate as a monitored vital sign? Shock. 2009 June; 31(6):574-580. [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]

Steil, G. M., and J. Reifman. Mathematical modeling research to support the development of automated insulin-delivery systems. Journal of Diabetes Science and Technology. 2009 March; 3(2):388-395. [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 Research. 2009 February; 37(2):452-462. [PDF]

Gani, A., A. V. Gribok, S. Rajaraman, W. K. Ward, and J. Reifman. Predicting subcutaneous glucose concentration in humans: data-driven glucose modeling. IEEE Transactions on Biomedical Engineering. 2009 February; 56(2):246-254. [PDF]

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2008

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. Biophysical Journal. 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. Journal of Physical Chemistry 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]

Reisner, A. T., L. Chen, T. M. McKenna, and J. Reifman. Automatically-computed prehospital severity scores are equivalent to scores based on medic documentation. Journal of Trauma-Injury, Infection, and Critical Care. 2008 October; 65(4):915-923. [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. Chemistry Central Journal. 2008 September 8; 2(1):18. [PDF]

Chen, L., A. Gribok, A. T. Reisner, and J. Reifman. Exploiting the existence of temporal heart-rate patterns for the detection of trauma-induced hemorrhage. Proceedings of the 30th IEEE EMBS Annual International Conference. Vancouver, Canada. 2008 August 20-24; 2865-2868. [PDF]

Harbaugh, S. V., M. E. Davidson, Y. G. Chushak, N. Kelley-Loughnane, and M. O. Stone. Riboswitch-based sensor in low optical background. Proceedings of the Nanobiosystems: Processing, Characterization, and Applications - International Society of Optical Engineering. San Diego, CA. 2008 August 12-14; 7040:1-9. [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]

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]

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; 660-665. [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. Journal of Pharmacokinetics and Pharmacodynamics. 2008 June; 35(3):251-267. [PDF]

Chen, L., T. M. McKenna, A. T. Reisner, A. Gribok, and J. Reifman. Decision tool for the early diagnosis of trauma patient hypovolemia. Journal of Biomedical Informatics. 2008 June; 41(3):469-478. [PDF]

Gribok, A. V., M. J. Buller, and J. Reifman. Individualized short-term core temperature prediction in humans using biomathematical models. IEEE Transactions on Biomedical Engineering. 2008 May; 55(5):1477-1487. [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 Systems Biology. 2008 February 2; 2:11. [PDF]

Rajaraman, S., A. V. Gribok, N. J. Wesensten, T. J. Balkin, and J. Reifman. Individualized performance prediction of sleep-deprived individuals with the two-process model. Journal of Applied Physiology. 2008 February; 104(2):459-468. [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]

Liu, J., T. M. McKenna, A. Gribok, B. A. Beidleman, W. J. Tharion, and J. Reifman. A fuzzy logic algorithm to assign confidence levels to heart and respiratory rate time series. Physiological Measurement. 2008 January; 29(1):81-94. [PDF]

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2007

Reifman, J., S. Rajaraman, and A. V. Gribok. Moving towards individualized performance models. Sleep. 2007 September 1; 30(9):1081-1082. [PDF]

Gribok, A. V., M. J. Buller, R. W. Hoyt, and J. Reifman. Providing statistical measures of reliability for body core temperature predictions. Proceedings of the 29th IEEE EMBS Annual International Conference. Lyon, France. 2007 August 23-26: 545-548. [PDF]

Chen, L., A. T. Reisner, T. M. McKenna, A. Gribok, and J. Reifman. Diagnosis of hemorrhage in a prehospital trauma population using linear and nonlinear multiparameter analysis of vital signs. Proceedings of the 29th IEEE EMBS Annual International Conference. Lyon, France. 2007 August 23-26; 3748-3751. [PDF]

Reifman, J., S. Rajaraman, A. Gribok, and W. K. Ward. Predictive Monitoring for improved management of glucose levels. Journal of Diabetes Science and Technology. 2007 July; 1(4):478-486. [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 18-22; 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 18-22: 425-429. [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 18-22; 417-420. [PDF]

Oleng', N. O., A. Gribok, and J. Reifman. Error bounds for data-driven models of dynamical systems. Computers in Biology and Medicine. 2007 May; 37(5):670-679. [PDF]

McKenna, T. M., G. Bawa, K. Kumar, and J. Reifman. The physiology analysis system: an integrated approach for warehousing, management and analysis of time-series physiology data. Computer Methods and Programs in Biomedicine. 2007 April; 86(1):62-72. [PDF]

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]

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]

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2006

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]

Chen, L., T. McKenna, A. Reisner, and J. Reifman. Algorithms to qualify respiratory data collected during the transport of trauma patients. Physiological Measurement. 2006 September; 27(9):797-816. [PDF]

Gribok, A., T. McKenna, and J. Reifman. Regularization of body core temperature prediction during physical activity. Proceedings of the 28th IEEE EMBS Annual International Conference. New York, NY. 2006 August 30-September 3; 459-463. [PDF]

Yu, C., Z. Liu, T. McKenna, A. T. Reisner, and J. Reifman. A method for automatic identification of reliable heart rates calculated from ECG and PPG waveforms. Journal of the American Medical Informatics Association. 2006 May-June; 13(3):309-320. [PDF]

Liu, J., T. M. McKenna, A. Gribok, B. A. Beidleman, W. T. Tharion, and J. Reifman. Estimation of confidence levels for physiology variables measured by a vital signs detection system. Proceedings of the Chemical and Biological Sensing VIII - The International Society for Optical Engineering. Orlando, FL. 2006 April 17-21; 6218:18-26. [PDF]

Chen, L., T. McKenna, A. Gribok, and J. Reifman. LAM: a landscape matching algorithm for respiratory data alignment. Proceedings of the Signal Processing, Sensor Fusion, and Target Recognition XV - The International Society for Optical Engineering. Orlando, FL. 2006 April 17-21; 6235:1-10. [PDF]

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2005

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(1):i495-501. [PDF]

Oleng', N. O., and J. Reifman. Hybrid approaches to physiologic modeling and prediction. Proceedings of the Biomonitoring for Physiological and Cognitive Performance during Military Operations - International Society for Optical Engineering. Orlando, FL. 2005 March 31-April 1; 5797:193-203. [PDF]

Draghici, S., P. Khatri, Y. Liu, K. J. Chase, E. A. Bode, D. A. Kulesh, L. P. Wasieloski, D. A. Norwood, and J. Reifman. Identification of genomic signatures for the design of assays for the detection and monitoring of anthrax threats. Proceedings of the Pacific Symposium on Biocomputing. Maui, HI. 2005 January 4-8; 10:248-259. [PDF]

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2004

Reifman, J., J. Gunawardena, and Z. Liu. Physiology analysis system. Proceedings of the 4th IEEE International Symposium on Signal Processing and Information Technology. Rome, Italy. 2004 December 18-21; 521-525. [PDF]

Oleng', N., J. Reifman, L. Berglund, and R. Hoyt. Alternative approaches to improve physiological predictions. Proceedings of the 24th Army Science Conference. Orlando, FL. 2004 November 29-December 2; 415-422. [PDF]

Reifman, J., and T. McKenna. Research at the command's bioinformatics cell. U.S. Army Medical Department Journal. 2004 October-December; 17-21. [PDF]

Savell, C. T., M. Borsotto, J. Reifman, and R. W. Hoyt. Life sign decision support algorithms. Proceedings of the 11th World Congress on Medical Informatics. San Francisco, CA. 2004 September 7-11; 107(Pt 2):1453-1457. [PDF]

Borsotto, M., C. T. Savell, J. Reifman, R. W. Hoyt, G. Nunns, and C. J. Crick. Life-signs determination model for warfighter physiological status monitoring. Proceedings of the RTO HFM Symposium on Combat Casualty Care in Ground-Based Tactical Situations: Trauma Technology and Emergency Medical Procedures. St. Pete Beach, FL. 2004 August 16-18; 28:1-10. [PDF]

Draghici, S., D. Chen, and J. Reifman. Applications and challenges of DNA microarray technology in military medical research. Military Medicine. 2004 August; 169(8):654-659. [PDF]

Reifman, J., G. Gilbert, M. Parker, and D. Lam. Challenges of electronic medical surveillance systems. Proceedings of the RTO HFM Symposium on NATO Medical Surveillance and Response, Research and Technology Opportunity and Options. Budapest, Hungary. 2004 April 19-21; 12:1-17. [PDF]

Reifman, J. Alternative methods for modeling fatigue and performance. Aviation, Space, and Environmental Medicine. 2004 March; 75(3):A173-180. [PDF]

Reifman, J., and P. Gander. Commentary on the three-process model of alertness and broader modeling issues. Aviation, Space, and Environmental Medicine. 2004 March; 75(3):A84-88. [PDF]

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2003

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; 492-495. [PDF]

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2002

Hoyt, R. W., J. Reifman, T. S. Coster, and M. J. Buller. Combat medical informatics: present and future. Proceedings of the AMIA Annual Symposium. San Antonio, TX. 2002 November 9-13; 335-339. [PDF]

Reifman, J., G. R. Gilbert, L. Fagan, and R. Satava. Military research needs in biomedical informatics. Journal of the American Medical Informatics Association. 2002 September-October; 9(5):509-519. [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 functional classification. Proceedings of the International Conference on Bioinformatics. Bangkok, Thailand. 2002 February 6-8; O-BH-02. [PDF]

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