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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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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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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Forum on immune digital twins: a meeting report by Reinhard Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, Tomas Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E. Yankeelov, Tjalf Ziemssen

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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks by Aurélien Naldi, Céline Hernandez, Nicolas Levy, Nicolas Levy, Gautier Stoll, Gautier Stoll, Gautier Stoll, Gautier Stoll, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Andrei Zinovyev, Andrei Zinovyev, Andrei Zinovyev, Laurence Calzone, Laurence Calzone, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé

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Toward mechanistic medical digital twins: some use cases in immunology by Reinhard Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, Tomas Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E. Yankeelov, Thomas E. Yankeelov, Thomas E. Yankeelov, Tjalf Ziemssen

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SBML Level 3: an extensible format for the exchange and reuse of biological models by Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, SBML Level 3 Community members

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Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches by Anna Niarakis, Anna Niarakis, Marek Ostaszewski, Alexander Mazein, Inna Kuperstein, Inna Kuperstein, Inna Kuperstein, Martina Kutmon, Marc E. Gillespie, Marc E. Gillespie, Akira Funahashi, Marcio Luis Acencio, Ahmed Hemedan, Michael Aichem, Karsten Klein, Tobias Czauderna, Felicia Burtscher, Takahiro G. Yamada, Yusuke Hiki, Noriko F. Hiroi, Noriko F. Hiroi, Finterly Hu, Finterly Hu, Nhung Pham, Nhung Pham, Friederike Ehrhart, Egon L. Willighagen, Alberto Valdeolivas, Aurelien Dugourd, Francesco Messina, Marina Esteban-Medina, Marina Esteban-Medina, Maria Peña-Chilet, Maria Peña-Chilet, Maria Peña-Chilet, Kinza Rian, Sylvain Soliman, Sara Sadat Aghamiri, Bhanwar Lal Puniya, Aurélien Naldi, Tomáš Helikar, Vidisha Singh, Marco Fariñas Fernández, Viviam Bermudez, Eirini Tsirvouli, Arnau Montagud, Vincent Noël, Vincent Noël, Vincent Noël, Miguel Ponce-de-Leon, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Augustin Luna, Augustin Luna, Janet Piñero, Janet Piñero, Laura I. Furlong, Laura I. Furlong, Irina Balaur, Adrien Rougny, Adrien Rougny, Yohan Jarosz, Rupert W. Overall, Robert Phair, Livia Perfetto, Lisa Matthews, Devasahayam Arokia Balaya Rex, Marija Orlic-Milacic, Luis Cristobal Monraz Gomez, Luis Cristobal Monraz Gomez, Luis Cristobal Monraz Gomez, Bertrand De Meulder, Jean Marie Ravel, Jean Marie Ravel, Jean Marie Ravel, Bijay Jassal, Venkata Satagopam, Venkata Satagopam, Guanming Wu, Martin Golebiewski, Piotr Gawron, Laurence Calzone, Laurence Calzone, Laurence Calzone, Jacques S. Beckmann, Chris T. Evelo, Peter D’Eustachio, Falk Schreiber, Falk Schreiber, Julio Saez-Rodriguez, Joaquin Dopazo, Joaquin Dopazo, Joaquin Dopazo, Joaquin Dopazo, Martin Kuiper, Alfonso Valencia, Alfonso Valencia, Olaf Wolkenhauer, Olaf Wolkenhauer, Hiroaki Kitano, Emmanuel Barillot, Emmanuel Barillot, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID-19 Disease Map Community

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COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms by Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta‐Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic‐Milacic, Andrea Senff-Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean‐Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban‐Medina, Maria Peña‐Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Willighagen, Alexander R Pico, Chris T Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez‐Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID‐19 Disease Map Community

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