Simulation of Stimulation: Cytokine Dosage and Cell Cycle Crosstalk Driving Timing-Dependent T Cell Differentiation by Matteo Barberis, Matteo Barberis, Tomáš Helikar, Paul Verbruggen

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Identification of Biologically Essential Nodes via Determinative Power in Logical Models of Cellular Processes by Trevor Pentzien, Bhanwar L. Puniya, Tomáš Helikar, Mihaela T. Matache

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A multiscale mechanistic model of human dendritic cells for in-silico investigation of immune responses and novel therapeutics discovery by Sara Sadat Aghamiri, Bhanwar Lal Puniya, Rada Amin, Tomáš Helikar

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The Effects of a Modeling and Computational Thinking Professional Development Program on STEM Educators’ Perceptions toward Teaching Science and Engineering Practices by Blake C. Colclasure, Tessa Durham Brooks, Tomáš Helikar, Scott J. King, Audrey Webb

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Augusta: From RNA‐Seq to gene regulatory networks and Boolean models by Jana Musilova, Zdenek Vafek, Bhanwar Lal Puniya, Ralf Zimmer, Tomas Helikar, Karel Sedlar

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Arginine Catabolism and Polyamine Biosynthesis Pathway Disparities Within Francisella tularensis Subpopulations by Yinshi Yue, Bhanwar Lal Puniya, Tomáš Helikar, Benjamin Girardo, Steven H. Hinrichs, Marilynn A. Larson

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Visualizing the Invisible: A Guide to Designing, Printing, and Incorporating Dynamic 3D Molecular Models to Teach Structure–Function Relationships by Michelle E. Howell, Karin van Dijk, Christine S. Booth, Tomáš Helikar, Brian A. Couch, Rebecca L. Roston

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Differences in Blood-Derived <i>Francisella tularensis</i> Type B Strains from Clinical Cases of Tularemia by Marilynn A. Larson, Baha Abdalhamid, Bhanwar Lal Puniya, Tomáš Helikar, David W. Kelley, Peter C. Iwen

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Author Correction: Integrative network analyses of transcriptomics data reveal potential drug targets for acute radiation syndrome by Robert Moore, Bhanwar Lal Puniya, Robert Powers, Chittibabu Guda, Kenneth W. Bayles, David B. Berkowitz, Tomáš Helikar

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Changes in students’ mental models from computational modeling of gene regulatory networks by Joseph T. Dauer, Heather E. Bergan-Roller, Gretchen P. King, McKenzie Kjose, Nicholas J. Galt, Tomáš Helikar

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Integrating interactive computational modeling in biology curricula. by Tomáš Helikar, Christine E Cutucache, Lauren M Dahlquist, Tyler A Herek, Joshua J Larson, Jim A Rogers

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The simulation experiment description markup language (SED-ML): language specification for level 1 version 4 by Smith Lucian P., Bergmann Frank T., Garny Alan, Helikar Tomáš, Karr Jonathan, Nickerson David, Sauro Herbert, Waltemath Dagmar, König Matthias

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A Mechanistic Computational Model Reveals That Plasticity of CD4+ T Cell Differentiation Is a Function of Cytokine Composition and Dosage by Bhanwar Lal Puniya, Robert G. Todd, Akram Mohammed, Deborah M. Brown, Deborah M. Brown, Matteo Barberis, Matteo Barberis, Tomáš Helikar

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A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells. by Tomáš Helikar, Naomi Kochi, Bryan Kowal, Manjari Dimri, Mayumi Naramura, Srikumar M Raja, Vimla Band, Hamid Band, Jim A Rogers

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SBML Level 3 package: Qualitative Models, Version 1, Release 1 by Chaouiya Claudine, Keating Sarah M., Berenguier Duncan, Naldi Aurélien, Thieffry Denis, Iersel Martijn P. van, Le Novère Nicolas, Helikar Tomáš

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Building digital twins of the human immune system: toward a roadmap by R. Laubenbacher, A. Niarakis, T. Helikar, G. An, B. Shapiro, R. S. Malik-Sheriff, T. J. Sego, A. Knapp, P. Macklin, J. A. Glazier

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Two heads are better than one: current landscape of integrating QSP and machine learning by Zhang, Tongli, Androulakis, Ioannis P., Bonate, Peter, Cheng, Limei, Helikar, Tomáš, Parikh, Jaimit, Rackauckas, Christopher, Subramanian, Kalyanasundaram, Cho, Carolyn R.

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Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders by Bhanwar Lal Puniya, Rada Amin, Bailee Lichter, Robert Moore, Alex Ciurej, Sydney J. Bennett, Ab Rauf Shah, Matteo Barberis, Tomáš Helikar

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Logical modeling and dynamical analysis of cellular networks by Wassim eAbou-Jaoudé, Pauline eTraynard, Pedro Tiago Monteiro, Julio eSaez Rodriguez, Tomáš eHelikar, Denis eThieffry, Claudine eChaouiya

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Design, Assessment, and In Vivo Evaluation of a Computational Model Illustrating the Role of CAV1 in CD4+ T Lymphocytes by Brittany D Conroy, Tyler A Herek, Timothy D Shew, Matthew eLatner, Joshua J Larson, Laura eAllen, Paul H Davis, Tomas eHelikar, Christine E Cutucache

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