Author (s)LinkedTitleJournal
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, JKinetics 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 JEvolutionary Design on a Budget: Robustness and Optimality of Bacteriophage T7IEE Proceedings Systems Biology 153(2):46-52 (2006)
Lam V, Boehme KW, Compton T, Yin JSpatial patterns of protein expression in focal infections of human cytomegalovirusBiotechnology & Bioengineering, Apr 20; 93(6):1029-39, (2006).
Napier J, Yin JFormation of peptides in the dry statePeptides  Apr;27(4):607-10, (2006).
Lim KI, Yin JDynamic tradeoffs in the raft-mediated entry of human immunodeficiency virus type 1 into cellsBiotechnology & Bioengineering Feb 5;93(2):246-57, (2006).
Kim H, Yin JEffects of RNA Splicing and Posttranscriptional Regulation on HIV-1 Growth: a Quantitative and Integrated PerspectiveIEE Proceedings Systems Biology, 152(3), 138-152 (2005).
Kim H, Yin JRobust growth of human immunodeficiency virus type 1 (HIV-1)Biophysical Journal, 89(4), 2210-2221, (2005).
Kim H, Yin JIn silico Mutagenesis of RNA Splicing in HIV-1Biotechnology & Bioengineering, 91(7): 877-93, (2005).
Endler E, Nealey P, Yin JFidelity of Micropatterned Cell CulturesJournal of Biomedical Materials Research: Part A, 74(1): 92-103 (2005).
Lam V, Duca KA, Yin JArrested Spread of Vesicular Stomatitis Virus Infections In Vitro Depends on Interferon-Mediated Antiviral Activity Biotechnology & Bioengineering, 90:  793-804, (2005).
Lim KI, Yin JLocalization of Receptors in Lipid Rafts Can Inhibit Signal TransductionBiotechnology and Bioengineering, 90:  694-702, (2005).
Haseltine E, Rawlings JB, Yin JDynamics of Viral Infections: Incorporating both the Intracellular and Extracellular LevelsComputers and Chemical Engineering, 29(3): 675-686, (2005).
Yin JGenome function—a virus-world viewAdvances in Experimental Medicine and Biology, 547: 31-46 (2004). 
Kim H, Yin JEnergy-efficient Growth of Phage Qb in Escherichia coliBiotechnology and Bioengineering, 88(2): 148-156, (2004).
Lim KI, Narayan S, Young JAT, Yin JEffects of Lipid Rafts on the Dynamics of Retroviral Entry and Trafficking: a Quantitative AnalysisBiotechnology and Bioengineering, 86(6): 650-660, (2004).
Kim H, Yin JQuantitative Analysis of a Parasitic Antiviral StrategyAntimicrobial Agents and Chemotherapy, 48(3): 1017-1020, (2004).
You L, Hoonlor A, Yin JModeling biological systems using Dynetica–a simulator of dynamic networksBioinformatics. 19(3), 435-436 (2003).
Endler EE, Duca KA, Nealey PF, Whitesides GM, Yin JPropagation of Viruses on Micropatterned Host CellsBiotechnology and Bioengineering, 81(6), 719-725 (2003).
Srivastava R, You L, Summers J, Yin JStochastic versus Deterministic Modeling of Intracellular Viral KineticsJournal of Theoretical Biology, 218, 309-321 (2002).
You L, Yin JDependence of Epistasis on Environment and Mutation Severity as Revealed by in silico Mutagenesis of Phage T7Genetics, 160, 1273-1281 (2002).
You L, Suthers PF, Yin JEffects of Escherichia coli Physiology on the Growth of Phage T7 in vivo and in silicoJournal of Bacteriology, 184(7), 1888-1894 (2002).
Middleton JK, Severson TF, Chandran K, Gillian AL, Yin J, Nibert MThermostability of reovirus disassembly intermediates, ISVPs, correlates with genetic, biochemical, and thermodynamic properties of major surface protein m1Journal of Virology, 76(3), 1051-1061 (2002).
Duca KA, Lam V, Keren I, Endler EE, Letchworth GJ, Novella IS, Yin JQuantifying Viral Propagation in vitro: Towards a Method for Characterization of Complex PhenotypesBiotechnology Progress, 17(6), 1156-1165 (2001).
Endy D, You L, Yin J, Molineux IJComputation, Prediction, and Experimental Tests of Fitness for Bacteriophage T7 Mutants with Permuted GenomesProceedings of the National Academy of Sciences, 97(10), 5375-5380 (2000).
Endy D, Yin JToward Antiviral Strategies that Resist Viral EscapeAntimicrobial Agents and Chemotherapy, 44(4), 1097-1099 (2000).
You L, Yin JPatterns of Regulation from mRNA and Protein Time-seriesMetabolic Engineering, 2(3), 210-217, (2000).
You L, Yin JAmplification and Spread of Viruses in a Growing PlaqueJournal of Theoretical Biology, 200(4), 365-73 (1999). 
Reddy B, Yin JQuantitative intracellular kinetics of HIV Type-1AIDS Research and Human Retroviruses, 15(3), 273-283, (1999).
Daly BM, Yin J3.0.CO;2-1>Subsurface oxidation of polyethyleneJournal of Biomedical Materials Research, 42, 523-529, (1998).
Lee Y, Eisner SD, Yin J3.0.CO;2-I>Antiserum Inhibition of Propagating VirusesBiotechnology & Bioengineering, 55(3), 542-546, (1997).
Endy D, Kong D, Yin J3.0.CO;2-G>Intracellular Kinetics of a Growing Virus:  A Genetically-Structured Simulation for Bacteriophage T7Biotechnology & Bioengineering, 55(2), 375-389, (1997).
Lee Y, Yin J3.0.CO;2-F>Imaging the Propagation of VirusesBiotechnology & Bioengineering, 52, 438-442, (1996).
Lee Y, Yin JDetection of Evolving VirusesNature Biotechnology,14: 491-493, (1996).
Whang T, Daly B, Yin JMetal-Ion Discrimination by Phage T7Journal of Inorganic Biochemistry, 63, 1-7, (1996).
Gupta K, Lee Y, Yin JExtremo-Phage: In Vitro Selection of Tolerance to a Hostile EnvironmentJournal of Molecular Evolution, 41: 113-114, (1995).
Kong D, Yin JWhole-Virus Vaccine Development by Continuous Culture on a Complementing HostBio/Technology, 13(6), 583-586, (1995).
Gupta K, Yin JMetal Recognition by In-Vitro SelectionBiotechnology & Bioengineering, 45(5), 458-462, (1995).
Yin JSpatially-Resolved Evolution of VirusesAnnals of the New York Academy of Sciences, 745, 399-408, (1994).
Yin JEvolution of Bacteriophage T7 in a Growing PlaqueJournal of Bacteriology, 175(5), 1272-1277, (1993).
Yin J, McCaskill JSReplication of Viruses in a Growing Plaque: A Reaction-Diffusion ModelBiophysical Journal, 61, 1540-1549, (1992).
Yin JA Quantifiable Phenotype of Viral PropagationBiochemical and Biophysical Research Communications, 174(2), 1009-1014, (1991).
Yin J, Blanch HWA Bio-Mimetic Cadmium Adsorbent: Design, Synthesis and CharacterizationBiotechnology & Bioengineering, 34(2), 180-188, (1989).
Furlong CE, Sundstrom JA, Weiler EB, Cheung PW, Yin J, Blanch HWExploitation of the high affinity and specificity of proteins in waste stream treatmentBasic Life Sciences, 45: 271-80, (1988).
Filipski J, Yin J, Kohn KWReconstitution of Intercalator Induced DNA Scission by the Active Component from Nuclear ExtractsBiochimica et Biophysica Acta, 741, 116-122, (1983).
Filipski, Yin J, Kohn KWTopoisomerase I Activities in L-1210 Cell NucleiEnzyme, 31, 89-94, (1983).