| Schwab B, Yin J. | Computational multigene interactions in virus growth and infection spread. | Virus Evolution, Volume 10, Issue 1, 2024. |
| Trubl G, Stedman KM, Bywaters KF, Matula EE, Sommers P, Roux S, Merino N, Yin J, Kaelber JT, Avila-Herrera A, Johnson PA. | Astrovirology: how viruses enhance our understanding of life in the Universe. | International Journal of Astrobiology. 2023 Apr 5:1-25. |
| Boigenzahn, H. and Yin, J., | Glycine to oligoglycine via sequential trimetaphosphate activation steps in drying environments. | Origins of Life and Evolution of Biospheres, 52(4), pp.249-261. 2022. |
| Jaskowak, D., Nunez, R., Ramachandran, R., Alhajjar, E., Yin, J., Guidoboni, G., & Danziger, Z. C. | Mathematical modeling of the lower urinary tract: A review. | Neurourology and urodynamics, 41(6), 1305-1315.(2022). |
| Shi, H and Yin, J | Kinetics of Asian and African Zika virus lineages over single-cycle and multi-cycle growth in culture: Gene expression, cell killing, virus production, and mathematical modeling. | Biotechnology & Bioengineering 2021, |
| Crespi E, Burnap R, Chen J, Das M, Gassman N, Rosa E, Simmons R, Wada H, Wang ZQ, Xiao J et al: | Resolving the Rules of Robustness and Resilience in Biology Across Scales. | Integrative and Comparative Biology 2021. |
| Sibilska-Kaminski IK and Yin J: | Toward Molecular Cooperation by De Novo Peptides. | Origins of Life and Evolution of Biospheres 2021, 51(1), 71-82. |
| Jin T, Yin J: | Patterns of Virus Growth Across the Diversity of Life. | Integrative Biology 2021, 13(2), 44-59. |
| Sibilska IK, Feng Y, Li L, Yin J: | Trimetaphosphate Activates Prebiotic Peptide Synthesis across a Wide Range of Temperature and pH. | Origins of Life and Evolution of Biospheres 2018 Sep 29. |
| Yin J, Redovich J: | Kinetic Modeling of Virus Growth in Cells. | Microbiology and Molecular Biology Reviews 2018, 82:e0006617. |
| Sibilska IK, Chen B, Li L, Yin J: | Effects of Trimetaphosphate on Abiotic Formation and Hydrolysis of Peptides. | Life (Basel) 2017, 7(4). |
| Babatunde O, Baltes A, Yin J: | Image-Based Identification of Cell Cultures by Machine Learning. | Journal of Advances in Mathematics and Computer Science 2017, 23(1):1-25. |
| Timm AC, Warrick JW, Yin J: | Quantitative profiling of innate immune activation by viral infection in single cells. | Integrative Biology (Cambridge) 2017, 9(9): 782-791. |
| Baltes A, Akpinar F, Inankur B, Yin J: | Inhibition of infection spread by co-transmitted defective interfering particles. | PLoS One 2017, 12(9): e0184029. |
| Watters, K., Inankur, B., Gardiner, J.C., Warrick, J., Sherer, N.M., Yin, J., and Palmenberg, A.C. | Differential Disruption of Nucleocytoplasmic Trafficking Pathways by Rhinovirus 2A Proteases. | Journal of Virology. Feb 8. pii: JVI.02472-16, (2017). |
| Loewe, L., Scheuer, K.S., Keel, S.A., Vyas, V., Liblit, B., Hanlon, B., Ferris, M.C., Yin, J., Dutra, I., Pietsch, A., et al. | Evolvix BEST Names for semantic reproducibility across code2brain interfaces. | Annals of the New York Academy of Sciences 1387, 124-144 (2017). |
| Akpinar F, Inankur B, Yin J: | Spatial-temporal patterns of viral amplification and interference initiated by a single infected cell. | Journal of Virology, 10.1128/JVI.00807-16 (2016). |
| Voigt EA, Swick A, Yin J: | Rapid induction and persistence of paracrine-induced cellular antiviral states arrest viral infection spread in A549 cells. | Virology, 496:59-66 (2016). |
| Potts GK, Voigt EA, Bailey DJ, Rose CM, Westphall MS, Hebert AS, Yin J, Coon JJ. | Neucode labels for multiplexed, absolute protein quantification. | Analytical Chemistry, 88(6):3295-3303 (2016). |
| Fu Q, Inankur B, Yin J, Striker R, Lan Q. | Sterol Carrier Protein 2, a Critical Host Factor for Dengue Virus Infection, Alters the Cholesterol Distribution in Mosquito Aag2 Cells. | Journal of Medical Entomology; 55(5): 1124-1134 . First published online: 21 August 2015 tjv114. |
| Akpinar F, Timm A, Yin J. | High-throughput single-cell kinetics of virus infections in the presence of defective interfering particles. | Journal of Virology, 90(3): 1599-1612 (2015). |
| Lindsay SM, Yin J. | Temperature gradients drive radial fluid flow in Petri dishes and multi-well plates. | AIChE Journal 17 FEB (2016). |
| Warrick JW, Timm A, Swick A, Yin J. | Tools for single-cell kinetic analysis of virus-host interactions. | PLoS One, 11(1): e0145081 (2016). |
| Voigt EA, Yin J, | Kinetic differences and synergistic antiviral effects between type I and type III interferon signaling indicate pathway independence. | Journal of Interferon and Cytokine Research, 35(9):734-47. Epub 2015 May 4. PMID: 25938799 (2015). |
| Pesko K, Voigt E, Swick A, Morley VJ, Timm C, Yin J, and Turner PE. | Genome rearrangement affects RNA virus adaptability on prostate cancer cells. | Frontiers in Genetics (2015). |
| Timm C, Gupta A, Yin J. | Robust kinetics of an RNA virus: Transcription rates are set by genome levels. | Biotechnology & Bioengineering (2015). |
| Akpinar F, Yin J. | Characterization of vesicular stomatitis virus populations by tunable resistive pulse sensing. | Journal of Virological Methods. Feb 16. pii: S0166-0934(15)00028-2 (2015). |
| Timm C, Akpinar F, Yin J. | Quantitative characterization of defective virus emergence by deep sequencing. | Journal of Virology, Mar;88(5):2623-32 (2014). |
| Swick A, Baltes A, Yin J., | Visualizing infection spread: Dual-color fluorescent reporting of virus-host interactions. | Biotechnology & Bioengineering, Dec 12. (2013). |
| Voigt E, Inankur B, Baltes A, Yin J. | A quantitative infection assay for human type I, II, and III interferon antiviral activities. | Virology Journal. Jul 6;10:224. PMID: 23829314, (2013). |
| Timm, A., and Yin, J. | Kinetics of virus production from single cells. | Virology 424, 11-17, (2012). |
| Lindsay, S. M., Timm, A., and Yin, J. | A quantitative comet infection assay for influenza virus. | Journal of Virological Methods 179, 351-358, (2012). |
| Stauffer Thompson KA, Yin J. | Population dynamics of an RNA virus and its defective interfering particles in passage cultures. | Virology Journal. Sep 29;7(1):257, (2010). |
| Abedon ST, Yin J. | Bacteriophage plaques: theory and analysis, | Methods in Molecular Biology, 501:161-74 (2009). |
| Anekal, SG, Zhu Y, Graham MD, and Yin J. | Dynamics of Virus Spread in the Presence of Fluid Flow, | Integrative Biology, 1, 664-671, (2009). |
| Hensel, SC, JB Rawlings, and Yin J. | Stochastic Kinetic Modeling of Vesicular Stomatitis Virus Intracellular Growth, | Bulletin of Mathematical Biology, 72(7): 1671-92, (2009). |
| Stauffer Thompson KA, Rempala GA, Yin J. | Multiple-hit inhibition of infection by defective interfering particles. | Journal of General Virology 90(4): 888-99, (2009). |
| Zhu Y, Yongky A, Yin J. | Growth of an RNA virus in single cells reveals a broad fitness distribution. | Virology 385(1):39-46, (2009). |
| Lim KI, Yin J. | Computational fitness landscape for all gene-order permutations of an RNA virus. | PLoS Computational Biology 5(2): e1000283, (2009). |
| Zhu Y, Warrick JW, Haubert K, Beebe DJ, Yin J, | Infection on a chip: a microscale platform for simple and sensitive cell-based virus assays. | Biomedical Microdevices 11(3):565-70, (2009). |
| Haseltine EL, Yin J, Rawlings JB, | Implications of Decoupling the Intracellular and Extracellular Levels in Multi-level Models of Virus Growth. | Biotechnology & Bioengineering, 101(4): 811-20, (2008). |
| Haseltine EL, Lam V, Yin J, Rawlings JB, | Image-Guided Modeling of Virus Growth and Spread. | Bulletin of Mathematical Biology, 70(6): 1730-48, (2008). |
| Agosto MA, Middleton JK, Freimont EC, Yin J, Nibert ML, | Thermolabilizing Pseudoreversions in Reovirus Outer-Capsid Protein Mu1 Rescue the Entry Defect Conferred by a Thermostabilizing Mutation, | Journal of Virology, 81(14): 7400-9 (2007). |
| Suthers P, Gourse R, Yin J, | Rapid Responses of Ribosomal RNA Synthesis to Nutrient Shifts, | Biotechnology & Bioengineering, 97(5): 1230-45 (2007). |
| Middleton JK, Agosto MA, Severson TF, Yin J, Nibert ML, | Thermostabilizing mutations in reovirus outer-capsid protein m1 selected by heat inactivation of infectious subvirion particles, | Virology, 361(2): 412-25 (2007). |
| Zhu Y, Yin J, | A quantitative comet assay: imaging and analysis of virus plaques formed with a liquid overlay, | Journal of Virological Methods, 139, 100-102 (2007). |
| Lim KI, Lang T, Lam V, Yin J, | Model-based design of growth-attenuated viruses, | PLoS Computational Biology 2(9): e116 (2006). |
| You L, Yin J | Evolutionary Design on a Budget: Robustness and Optimality of Bacteriophage T7 | IEE Proceedings Systems Biology 153(2):46-52 (2006) |
| Lam V, Boehme KW, Compton T, Yin J | Spatial patterns of protein expression in focal infections of human cytomegalovirus | Biotechnology & Bioengineering, Apr 20; 93(6):1029-39, (2006). |
| Napier J, Yin J | Formation of peptides in the dry state | Peptides Apr;27(4):607-10, (2006). |
| Lim KI, Yin J | Dynamic tradeoffs in the raft-mediated entry of human immunodeficiency virus type 1 into cells | Biotechnology & Bioengineering Feb 5;93(2):246-57, (2006). |
| Kim H, Yin J | Effects of RNA Splicing and Posttranscriptional Regulation on HIV-1 Growth: a Quantitative and Integrated Perspective | IEE Proceedings Systems Biology, 152(3), 138-152 (2005). |
| Kim H, Yin J | Robust growth of human immunodeficiency virus type 1 (HIV-1) | Biophysical Journal, 89(4), 2210-2221, (2005). |
| Kim H, Yin J | In silico Mutagenesis of RNA Splicing in HIV-1 | Biotechnology & Bioengineering, 91(7): 877-93, (2005). |
| Endler E, Nealey P, Yin J | Fidelity of Micropatterned Cell Cultures | Journal of Biomedical Materials Research: Part A, 74(1): 92-103 (2005). |
| Lam V, Duca KA, Yin J | Arrested Spread of Vesicular Stomatitis Virus Infections In Vitro Depends on Interferon-Mediated Antiviral Activity | Biotechnology & Bioengineering, 90: 793-804, (2005). |
| Lim KI, Yin J | Localization of Receptors in Lipid Rafts Can Inhibit Signal Transduction | Biotechnology and Bioengineering, 90: 694-702, (2005). |
| Haseltine E, Rawlings JB, Yin J | Dynamics of Viral Infections: Incorporating both the Intracellular and Extracellular Levels | Computers and Chemical Engineering, 29(3): 675-686, (2005). |
| Yin J | Genome function—a virus-world view | Advances in Experimental Medicine and Biology, 547: 31-46 (2004). |
| Kim H, Yin J | Energy-efficient Growth of Phage Qb in Escherichia coli | Biotechnology and Bioengineering, 88(2): 148-156, (2004). |
| Lim KI, Narayan S, Young JAT, Yin J | Effects of Lipid Rafts on the Dynamics of Retroviral Entry and Trafficking: a Quantitative Analysis | Biotechnology and Bioengineering, 86(6): 650-660, (2004). |
| Kim H, Yin J | Quantitative Analysis of a Parasitic Antiviral Strategy | Antimicrobial Agents and Chemotherapy, 48(3): 1017-1020, (2004). |
| You L, Hoonlor A, Yin J | Modeling biological systems using Dynetica–a simulator of dynamic networks | Bioinformatics. 19(3), 435-436 (2003). |
| Endler EE, Duca KA, Nealey PF, Whitesides GM, Yin J | Propagation of Viruses on Micropatterned Host Cells | Biotechnology and Bioengineering, 81(6), 719-725 (2003). |
| Srivastava R, You L, Summers J, Yin J | Stochastic versus Deterministic Modeling of Intracellular Viral Kinetics | Journal of Theoretical Biology, 218, 309-321 (2002). |
| You L, Yin J | Dependence of Epistasis on Environment and Mutation Severity as Revealed by in silico Mutagenesis of Phage T7 | Genetics, 160, 1273-1281 (2002). |
| You L, Suthers PF, Yin J | Effects of Escherichia coli Physiology on the Growth of Phage T7 in vivo and in silico | Journal of Bacteriology, 184(7), 1888-1894 (2002). |
| Middleton JK, Severson TF, Chandran K, Gillian AL, Yin J, Nibert M | 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). |
| Duca KA, Lam V, Keren I, Endler EE, Letchworth GJ, Novella IS, Yin J | Quantifying Viral Propagation in vitro: Towards a Method for Characterization of Complex Phenotypes | Biotechnology Progress, 17(6), 1156-1165 (2001). |
| Endy D, You L, Yin J, Molineux IJ | Computation, Prediction, and Experimental Tests of Fitness for Bacteriophage T7 Mutants with Permuted Genomes | Proceedings of the National Academy of Sciences, 97(10), 5375-5380 (2000). |
| Endy D, Yin J | Toward Antiviral Strategies that Resist Viral Escape | Antimicrobial Agents and Chemotherapy, 44(4), 1097-1099 (2000). |
| You L, Yin J | Patterns of Regulation from mRNA and Protein Time-series | Metabolic Engineering, 2(3), 210-217, (2000). |
| You L, Yin J | Amplification and Spread of Viruses in a Growing Plaque | Journal of Theoretical Biology, 200(4), 365-73 (1999). |
| Reddy B, Yin J | Quantitative intracellular kinetics of HIV Type-1 | AIDS Research and Human Retroviruses, 15(3), 273-283, (1999). |
| Daly BM, Yin J | 3.0.CO;2-1>Subsurface oxidation of polyethylene | Journal of Biomedical Materials Research, 42, 523-529, (1998). |
| Lee Y, Eisner SD, Yin J | 3.0.CO;2-I>Antiserum Inhibition of Propagating Viruses | Biotechnology & Bioengineering, 55(3), 542-546, (1997). |
| Endy D, Kong D, Yin J | 3.0.CO;2-G>Intracellular Kinetics of a Growing Virus: A Genetically-Structured Simulation for Bacteriophage T7 | Biotechnology & Bioengineering, 55(2), 375-389, (1997). |
| Lee Y, Yin J | 3.0.CO;2-F>Imaging the Propagation of Viruses | Biotechnology & Bioengineering, 52, 438-442, (1996). |
| Lee Y, Yin J | Detection of Evolving Viruses | Nature Biotechnology,14: 491-493, (1996). |
| Whang T, Daly B, Yin J | Metal-Ion Discrimination by Phage T7 | Journal of Inorganic Biochemistry, 63, 1-7, (1996). |
| Gupta K, Lee Y, Yin J | Extremo-Phage: In Vitro Selection of Tolerance to a Hostile Environment | Journal of Molecular Evolution, 41: 113-114, (1995). |
| Kong D, Yin J | Whole-Virus Vaccine Development by Continuous Culture on a Complementing Host | Bio/Technology, 13(6), 583-586, (1995). |
| Gupta K, Yin J | Metal Recognition by In-Vitro Selection | Biotechnology & Bioengineering, 45(5), 458-462, (1995). |
| Yin J | Spatially-Resolved Evolution of Viruses | Annals of the New York Academy of Sciences, 745, 399-408, (1994). |
| Yin J | Evolution of Bacteriophage T7 in a Growing Plaque | Journal of Bacteriology, 175(5), 1272-1277, (1993). |
| Yin J, McCaskill JS | Replication of Viruses in a Growing Plaque: A Reaction-Diffusion Model | Biophysical Journal, 61, 1540-1549, (1992). |
| Yin J | A Quantifiable Phenotype of Viral Propagation | Biochemical and Biophysical Research Communications, 174(2), 1009-1014, (1991). |
| Yin J, Blanch HW | A Bio-Mimetic Cadmium Adsorbent: Design, Synthesis and Characterization | Biotechnology & Bioengineering, 34(2), 180-188, (1989). |
| Furlong CE, Sundstrom JA, Weiler EB, Cheung PW, Yin J, Blanch HW | Exploitation of the high affinity and specificity of proteins in waste stream treatment | Basic Life Sciences, 45: 271-80, (1988). |
| Filipski J, Yin J, Kohn KW | Reconstitution of Intercalator Induced DNA Scission by the Active Component from Nuclear Extracts | Biochimica et Biophysica Acta, 741, 116-122, (1983). |
| Filipski, Yin J, Kohn KW | Topoisomerase I Activities in L-1210 Cell Nuclei | Enzyme, 31, 89-94, (1983). |
