Publications

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60. Hensel, S., J.B. Rawlings, and Yin J. 2009. Stochastic Kinetic Modeling of Vesicular Stomatitis Virus Intracellular Growth, Bulletin of Mathematical Biology, in press.

59. Abedon ST, Yin J. 2009. Bacteriophage plaques: theory and analysis. Methods Mol Biol. 501:161-74.

58. Thompson KAS, Rempala GA, Yin J. 2009. Multiple-hit inhibition of infection by defective interfering particles. J Gen Virol 90(Pt 4): 888-99.

57. Zhu Y, Yongky A, Yin J. 2009. Growth of an RNA virus in single cells reveals a broad fitness distribution. Virology 385(1): 39-46.

56. Lim KI, Yin J. 2009. Computational fitness landscape for all gene-order permutations of an RNA virus. PLoS Comput Biol 5(2): e1000283.

55. Zhu Y, Warrick JW, Haubert K, Beebe DJ, Yin J. 2009. Infection on a chip: a microscale platform for simple and sensitive cell-based virus assays. Biomed Microdevices, in press.

54. Haseltine, E. L., J. Yin, and J. B. Rawlings. 2008. Implications of Decoupling the Intracellular and Extracellular Levels in Multi-level Models of Virus Growth. Biotech. Bioeng . 101(4) :811-20.

53. Abedon S.T., Yin J. (2008). Impact of Spatial Structure on Phage Population Growth, in Bacteriophage Ecology: Population Growth, Evolution, and Impact of Bacterial Viruses, Cambr idge Uni versity Press.

52. Haseltine, E. L., V. Lam, J. Yin, and J. B. Rawlings. 2008. Image-Guided Modeling of Virus Growth and Spread. Bulletin of Mathematical Biology, 70(6):1730-48.

51. John Yin, “Chemical Engineering and Virology: Challenges and Opportunities at the Interface,” AIChE Journal, Sept 2007.

50. Agosto M.A., Middleton J.K., Freimont E.C., Yin J., Nibert M.L. (2007). Thermolabilizing Pseudoreversions in Reovirus Outer-Capsid Protein Mu1 Rescue the Entry Defect Conferred by a Therm ostabilizing Mutation. J Virol. 81(14): 7400-9.

49. Suthers, P., Gourse, R., Yin, J. (2007), Rapid Responses of Ribosomal RNA Synthesis to Nutrient Shifts, Biotech. Bioeng, 97(5): 1230-45.

48. Middleton, J.K, Agostod, M.A., Severson, T.F., Yin, J, Nibert, M.L. (2007), Heat-Resistant Mutants Selected by Heat Inactivation of Infectious Subvirion Particles of Mammalian Reo virus, V irology, 361(2): 412-25.

47. Zhu Y, Yin J. 2007. A quantitative comet assay: imaging and analysis of virus plaques formed with a liquid overlay. Journal of Virological Methods, 139, 100-102.

46. Lim KI, Lang T, Lam V, Yin J. 2006. Model-based design of growth-attenuated viruses. PLoS Computational Biology 2(9): e116.

45. You, L. and Yin, J. (2006) Evolutionary Design on a Budget: Robustness and Optimality of Bacteriophage T7. IEE Proc. Systems Biology 153(2):46-52.

44. Lam V, Boehme KW, Compton T, Yin J. Spatial patterns of protein expression in focal infections of human cytomegalovirus, Biotechnol Bioeng. 2006 Apr 20;93(6):1029-39.

43. Napier, J. and Yin, J. Formation of peptides in the dry state, Peptides 2006 Apr;27(4):607-10.

42. Lim, K. and Yin, J. Dynamic tradeoffs in the raft-mediated entry of human immunodeficiency virus type 1 into cells, Biotechnol Bioeng (2006) Feb 5;93(2):246-57.

41. Kim, H., and Yin, J. Effects of RNA Splicing and Posttranscriptional Regulation on HIV-1 Growth: a Quantitative and Integrated Perspective. IEE Proc. Systems Biology, 152(3), 138- 152 (200 5).

40. Kim, H., and Yin, J. (2005). Robust growth of human immunodeficiency virus type 1 (HIV-1). Biophysical Journal, 89(4), 2210-2221.

39. Kim H., and Yin, J. In silico Mutagenesis of RNA Splicing in HIV-1. Biotechnol Bioeng. 91(7): 877-93, (2005).

38. Endler, E., Nealey, P., and Yin, J. Fidelity of Micropatterned Cell Cultures. J. Biomed. Mater. Res.: Part A, 74(1): 92-103 (2005).

37. Lam, V., Duca, K.A., and Yin, J. Arrested Spread of Vesicular Stomatitis Virus Infections In Vitro Depends on Interferon-Mediated Antiviral Activity. Biotechnol. Bioeng., 90: 7 93-804, 2005

36. Lim, K., and Yin, J. Localization of Receptors in Lipid Rafts Can Inhibit Signal Transduction. Biotechnol. Bioeng., 90: 694-702, 2005.

35. Haseltine, E., Rawlings, J.B., and Yin, J. Dynamics of Viral Infections: Incorporating both the Intracellular and Extracellular Levels. Comput. Chem. Eng., 29(3): 675-686, 2005

34. Yin, J. Genome Function---A Virus World View. In: L.K. Opresko, J.M. Gephart, and M.B. Mann (Eds.), Advances in Systems Biology, Advances in Experimental Medicine and Biology, Vol. 547 , pp. 31-46. Kluwer Academic/Plenum Publishers, 2004.

33. Kim, H., and Yin, J. Energy-efficient Growth of Phage Qb in Escherichia coli. Biotechnol. Bioeng., 88(2): 148-156, 2004.

32. Lim, K., Narayan, S., Young, J.A.T., and Yin, J. Effects of Lipid Rafts on the Dynamics of Retroviral Entry and Trafficking: a Quantitative Analysis. Biotechnol. Bioeng., 86(6): 650-660

31. Kim, H., and Yin, J. Quantitative Analysis of a Parasitic Antiviral Strategy. Antimicrob. Agents Chemother., 48(3): 1017-1020, 2004.

30. Lingchong You, Apirak Hoonlor, and John Yin, “Modeling biological systems using Dynetica–a simulator of dynamic networks,” Bioinformatics. 19(3), 435-436 (2003).

29. Endler, Elizabeth E., Karen A. Duca, Paul F. Nealey, George M. Whitesides, and John Yin, “Propagation of Viruses on Micropatterned Host Cells,” Biotechnology and Bioengineering, 8 1(6), 71 9-725 (2003).

28. Srivastava, R., L. You, J. Summers and J. Yin, "Stochastic versus Deterministic Modeling of Intracellular Viral Kinetics," J. Theoretical Biology, 218, 309-321 (2002).

27. Lingchong You and John Yin, “Dependence of Epistasis on Environment and Mutation Severity as Revealed by in silico Mutagenesis of Phage T7," Genetics, 160, 1273-1281 (2002).

26. Lingchong You, Patrick F. Suthers and John Yin, “Effects of Escherichia coli Physiology on the Growth of Phage T7 in vivo and in silico," Journal of Bacteriology, 184(7), 1888-18 94 (2002 ).

25. Jason K. Middleton, Tonya F. Severson, Kartik Chandran, Anne Lynn Gillian, John Yin, and Max Nibert, "Thermostability of Reovirus Disassembly Intermediates, ISVPs, Correlates with Genetic , Biochemical, and Thermodynamic Properties of Major Surface Protein m1," Journal of Virology, 76(3), 1051-1061 (2002).

24. K.A. Duca, V. Lam, I. Keren, E.E. Endler, G.J. Letchworth, I.S. Novella and J. Yin, "Quantifying Viral Propagation in vitro: Towards a Method for Characterization of Complex Pheno types," Biotechnology Progress, 17(6), 1156-1165 (2001).

23. Lingchong You and John Yin, “Simulating the Growth of Viruses,” Pacific Symposium on Biocomputing 2001, R.B. Altman, A.K. Kunker, L. Hunter, K. Lauderdale, T.E. Klein, Eds., World Scienti fic, Singapore, 532-543, (2001).

22. Drew Endy, Lingchong You, John Yin and Ian J. Molineux, “Computation, Prediction, and Experimental Tests of Fitness for Bacteriophage T7 Mutants with Permuted Genomes,” Proceeding s of the National Academy of Sciences, 97(10), 5375-5380 (2000).

21. Drew Endy and John Yin, ”Toward Antiviral Strategies that Resist Viral Escape,” Antimicrobial Agents and Chemotherapy, 44(4), 1097-1099 (2000).

20. Lingchong You and John Yin, ”Patterns of Regulation from mRNA and Protein Time-series,” Metabolic Engineering, 2(3), 210-217, (2000).

19. John Yin, “Bio-Informatics---a chemical engineering frontier?,” Chem. Eng. Progress, 95(11), 65-74 (1999).

18. Lingchong You and John Yin, “Amplification and Spread of Viruses in a Growing Plaque,” J. Theoretical Biology, 200(4), 365-73 (1999).

17. Bindu Reddy and John Yin, “Quantitative intracellular kinetics of HIV Type-1,” AIDS Research and Human Retroviruses, 15(3), 273-283, (1999).

16. Brendan M. Daly and John Yin, “Sub-surface oxidation of polyethylene,” J. Biomedical Materials Research, 42, 523-529, (1998).

15. Yih Lee, Symma D. Eisner, and John Yin, “Antiserum Inhibition of Propagating Viruses,” Biotechnology & Bioengineering, 55(3), 542-546, (1997).

14. Drew Endy, Deyu Kong, and John Yin, "Intracellular Kinetics of a Growing Virus: A Genetically-Structured Simulation for Bacteriophage T7," Biotechnology & Bioengineering, 55(2), 375-389, (1997).

13. Yih Lee and John Yin, “Imaging the Propagation of Viruses,” Biotechnology & Bioengineering, 52, 438-442, (1996).

12. Yih Lee and John Yin, “Detection of Evolving Viruses,” Nature Biotechnology, 14 : 491-493, (1996). Commentary by John J. Holland, “Visualizing virus fitness gains,” presented in the same issue, 431-432.

11. Tom Whang, Brendan Daly, and John Yin, “Metal-Ion Discrimination by Phage T7,” J. Inorganic Biochemistry, 63, 1-7, (1996).

10. Kanika Gupta, Yih Lee, and John Yin, "Extremo-Phage: In Vitro Selection of Tolerance to a Hostile Environment," J. Molecular Evolution, 41: 113-114, (1995).

9. Deyu Kong and John Yin, "Whole-Virus Vaccine Development by Continuous Culture on a Complementing Host," Bio/Technology, 13(6), 583-586, (1995).

8. Kanika Gupta and John Yin, "Metal Recognition by In-Vitro Selection," Biotechnology & Bioengineering, 45(5), 458-462, (1995).

7. John Yin, "Spatially-Resolved Evolution of Viruses," Annals of the New York Academy of Sciences, 745, 399-408, (1994).

6. John Yin, "Evolution of Bacteriophage T7 in a Growing Plaque," Journal of Bacteriology, 175(5), 1272-1277, (1993).

5. John Yin and J.S. McCaskill, "Replication of Viruses in a Growing Plaque: A Reaction-Diffusion Model," Biophysical Journal, 61, 1540-1549, (1992).

4. John Yin, "A Quantifiable Phenotype of Viral Propagation," Biochemical and Biophysical Research Communications, 174(2), 1009-1014, (1991).

3. John Yin and Harvey W. Blanch, "A Bio-Mimetic Cadmium Adsorbent: Design, Synthesis and Characterization," Biotechnology & Bioengineering, 34(2), 180-188, (1989).

2. Jan Filipski, John Yin and Kurt W. Kohn, "Reconstitution of Intercalator Induced DNA Scission by the Active Component From Nuclear Extracts," Biochimica et Biophysica Acta, 741, 11 6-122, ( 1983).

1. Jan Filipski, John Yin and Kurt W. Kohn, "Topoisomerase I Activities in L-1210 Cell Nuclei," Enzyme, 31, 89-94, (1983).

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