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PUBLICATIONS

2014

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 723 KB]

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 8340 KB]

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 2476 KB]

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 774 KB]

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 2535 KB]

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 2454 KB]

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 4714 KB]

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 1775 KB]

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 1832 KB]

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 657 KB]

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 728 KB]

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 697 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; 15:244-252. [PDF 1341 KB]

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 1815 KB]

Liu, R., N. Singh, G. Tawa, A. Wallqvist, and J. Reifman. Exploiting large-scale drug-protein interaction information for computational drug repurposing. BMC Bioinformatics. 2014 June 20; 15:210-225. [PDF 1845 KB]

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 192 KB]

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 2364 KB]

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 751 KB]

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 480 KB]

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 1365 KB]

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 1086 KB]

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 1000 KB]

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 698 KB]

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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 1692 KB]

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 1515 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]

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 749 KB]

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 2822 KB]

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 1460 KB]

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 1191 KB]

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 1460 KB]

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 1236 KB]

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 4884 KB]

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 344 KB]

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 609 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]

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 1371 KB]

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 542 KB]

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 1213 KB]

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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 1012 KB]

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 696 KB]

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 2885 KB]

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 816 KB]

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 1917 KB]

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 449 KB]

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 442 KB]

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 1467 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]

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 1983 KB]

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 1116 KB]

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 2032 KB]

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 634 KB]

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 393 KB]

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 1448 KB]

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 873 KB]

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 2459 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]

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 1370 KB]

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 3092 KB]

Sun, H., G. Tawa, and A. Wallqvist. Classification of scaffold-hopping approaches. Drug Discovery Today. 2012 April; 17(7-8):310-324. [PDF 1623 KB]

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 5251 KB]

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 806 KB]

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(1):4. [PDF 1933 KB]

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 2887 KB]

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 4752 KB]

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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 1742 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]

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 679 KB]

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 919 KB]

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 315 KB]

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 2157 KB]

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 501 KB]

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 487 KB]

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 2559 KB]

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 3494 KB]

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 824 KB]

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 361 KB]

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 255 KB]

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 2554 KB]

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 439 KB]

Woo, H. J., and A. Wallqvist. Nonequilibrium phase transitions associated with DNA replication. Physical Review Letters. 2011 February 11; 106:060601. [PDF 283 KB]

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 1244 KB]

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 592 KB]

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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 1094 KB]

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 233 KB]

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 703 KB]

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 3314 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]

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 3326 KB]

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 622 KB]

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 527 KB]

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 262 KB]

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 170 KB]

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 297 KB]

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 256 KB]

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 363 KB]

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 566 KB]

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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 2347 KB]

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 151 KB]

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 319 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]

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 1152 KB]

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 3589 KB]

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 462 KB]

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 448 KB]

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 919 KB]

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 435 KB]

Chushak, Y., and M. O. Stone. In silico selection of RNA aptamers. Nucleic Acids Research. 2009 July; 37(12):e87. [PDF 2902 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]

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 358 KB]

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 572 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]

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 1477 KB]

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 1585 KB]

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 594 KB]

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 300 KB]

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 321 KB]

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 374 KB]

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 2111 KB]

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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 500 KB]

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 1928 KB]

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 298 KB]

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 627 KB]

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 289 KB]

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 586 KB]

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 370 KB]

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 1283 KB]

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 339 KB]

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 638 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]

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 367 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]

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 838 KB]

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 558 KB]

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 190 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]

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 664 KB]

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 240 KB]

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 545 KB]

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 333 KB]

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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 150 KB]

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 251 KB]

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 97 KB]

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 1122 KB]

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 799 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]

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 769 KB]

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 264 KB]

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 989 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]

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 241 KB]

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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 321 KB]

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 1232 KB]

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 165 KB]

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 319 KB]

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 101 KB]

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 915 KB]

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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 97 KB]

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 802 KB]

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 172 KB]

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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 582 KB]

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 620 KB]

Reifman, J., and T. McKenna. Research at the command's bioinformatics cell. U.S. Army Medical Department Journal. 2004 October-December; 17-21. [PDF 1119 KB]

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 290 KB]

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 414 KB]

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 1866 KB]

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 428 KB]

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 59 KB]

Reifman, J. Alternative methods for modeling fatigue and performance. Aviation, Space, and Environmental Medicine. 2004 March; 75(3):A173-180. [PDF 206 KB]

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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 994 KB]

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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 43 KB]

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 125 KB]

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 115 KB]

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 123 KB]

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