About
team
publicatIONS
PARTNERS
Support
Science
Immune Digital Twin
education & workforce development
Research
Careers
Contact Us

Our Research

Our work spans systems immunology, multiscale modeling, host–pathogen dynamics, and educational innovation — forming the scientific foundation of the immune digital twin.

Immune Health

We use multi-scale mechanistic models to characterize markers predictive of immune system's propensity to respond to a threat.

See more

Immune Health

We use multi-scale mechanistic models to characterize markers predictive of immune system's propensity to respond to a threat.

See more

Immune Health

We use multi-scale mechanistic models to characterize markers predictive of immune system's propensity to respond to a threat.

See more

Drug Discovery and Development

We use our models to identify novel drug targets for diseases and new clinical applications for existing drugs.

See more

Drug Discovery and Development

We use our models to identify novel drug targets for diseases and new clinical applications for existing drugs.

See more

Drug Discovery and Development

We use our models to identify novel drug targets for diseases and new clinical applications for existing drugs.

See more

Host-Directed Antiviral Therapeutics

We are developing novel broad-spectrum antiviral therapeutics.

See more

Host-Directed Antiviral Therapeutics

We are developing novel broad-spectrum antiviral therapeutics.

See more

Host-Directed Antiviral Therapeutics

We are developing novel broad-spectrum antiviral therapeutics.

See more

Model-Based Immunology and Life Sciences Education

We advance research-driven education by enabling students to learn immunology and biology like scientists do—through building, simulating, and testing computational models of biological systems.

See more

Model-Based Immunology and Life Sciences Education

We advance research-driven education by enabling students to learn immunology and biology like scientists do—through building, simulating, and testing computational models of biological systems.

See more

Model-Based Immunology and Life Sciences Education

We advance research-driven education by enabling students to learn immunology and biology like scientists do—through building, simulating, and testing computational models of biological systems.

See more

Immune Health

We use multi-scale mechanistic models to characterize markers predictive of immune system's propensity to respond to a threat.

Emergent decision-making in biological signal transduction networks

Journal
Proceedings of the National Academy of Sciences 105 (6), 1913-1918
Authors
Tomáš Helikar, John Konvalina, Jack Heidel, Jim A Rogers

Design, Assessment, and in vivo Evaluation of a Computational Model Illustrating the Role of CAV1 in CD4+ T-lymphocytes

Journal
Frontiers in immunology 5, 599
Authors
Brittany D Conroy, Tyler A Herek, Timothy D Shew, Matthew Latner, Joshua J Larson, Laura Allen, Paul H Davis, Tomáš Helikar, Christine E Cutucache

A Mechanistic Computational Model Reveals That Plasticity of CD4+ T Cell Differentiation Is a Function of Cytokine Composition and Dosage

Journal
Frontiers in physiology 9, 878
Authors
Bhanwar Lal Puniya, Robert G Todd, Akram Mohammed, Deborah M Brown, Matteo Barberis, Tomáš Helikar

Combined TLR4 and TLR9 agonists induce distinct phenotypic changes in innate immunity in vitro and in vivo

Journal
Cellular immunology 355, 104149
Authors
Anna T Lampe, Bhanwar Lal Puniya, Angela K Pannier, Tomás Helikar, Deborah M Brown

Decision making in cells

Journal
Systems biology for signaling networks, 295-336
Authors
Tomáš Helikar, Naomi Kochi, John Konvalina, Jim A Rogers

Computational Modeling of Human Fatty Acid Transport Protein 2

Journal
The FASEB Journal 31, 630.20-630.20
Authors
Vincent Michael Perez, Bhanwar Lal Puniya, Tomáš Helikar, Concetta C DiRusso, Paul N Black

Simulation of stimulation: cytokine dosage and cell cycle crosstalk driving timing-dependent T cell differentiation

Journal
Frontiers in Physiology 9, 879
Authors
Matteo Barberis, Tomáš Helikar, Paul Verbruggen

A multi-approach and multi-scale platform to model CD4+ T cells responding to infections

Journal
PLoS computational biology 17 (8), e1009209
Authors
Kenneth Y Wertheim, Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomáš Helikar

Drug Discovery and Development

We use our models to identify novel drug targets for diseases and new clinical applications for existing drugs.

Identification of Potential Prophylactic Medical Countermeasures Against Acute Radiation Syndrome (ARS)

Journal
International journal of molecular sciences 26 (9), 4055
Authors
Kia T Liermann-Wooldrik, Arpita Chatterjee, Elizabeth A Kosmacek, Molly S Myers, Oluwaseun Adebisi, Louise Monga-Wells, Liu Mei, Michelle P Takacs, Patrick H Dussault, Daniel R Draney, Robert Powers, James W Checco, Chittibabu Guda, Tomáš Helikar, David B Berkowitz, Kenneth W Bayles, Alan H Epstein, Lynnette Cary, Daryl J Murry, Rebecca E Oberley-Deegan

A review of radiation-induced alterations of multi-omic profiles, radiation injury biomarkers, and countermeasures

Journal
Radiation research 199 (1), 89-111
Authors
Sushil K Shakyawar, Nitish K Mishra, Neetha N Vellichirammal, Lynnette Cary, Tomáš Helikar, Robert Powers, Rebecca E Oberley-Deegan, David B Berkowitz, Kenneth W Bayles, Vijay K Singh, Chittibabu Guda

Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers

Journal
Oncotarget 8, 85692-85715
Authors
Akram Mohammed, Greyson Biegert, Jiri Adamec, Tomas Helikar

CancerDiscover: an integrative pipeline for cancer biomarker and cancer class prediction from high-throughput sequencing data

Journal
Oncotarget 9 (2), 2565
Authors
Akram Mohammed, Greyson Biegert, Jiri Adamec, Tomáš Helikar

Identification of biologically essential nodes via determinative power in logical models of cellular processes

Journal
Frontiers in Physiology 9, 1185
Authors
Trevor Pentzien, Bhanwar L Puniya, Tomáš Helikar, Mihaela T Matache

Differences in Blood-Derived Francisella tularensis Type B Strains from Clinical Cases of Tularemia

Journal
Microorganisms 8 (10), 1515
Authors
Marilynn A Larson, Baha Abdalhamid, Bhanwar Lal Puniya, Tomáš Helikar, David W Kelley, Peter C Iwen

Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders

Journal
NPJ systems biology and applications 7 (1), 4
Authors
Bhanwar Lal Puniya, Rada Amin, Bailee Lichter, Robert Moore, Alex Ciurej, Sydney J Bennett, Ab Rauf Shah, Matteo Barberis, Tomáš Helikar

Essential role of systemic iron mobilization and redistribution for adaptive thermogenesis through HIF2-α/hepcidin axis

Journal
Proceedings of the National Academy of Sciences 118 (40), e2109186118
Authors
Jin-Seon Yook, Mikyoung You, Jiyoung Kim, Ashley M Toney, Rong Fan, Bhanwar Lal Puniya, Tomáš Helikar, Sophie Vaulont, Jean-Christophe Deschemin, Meshail Okla, Liwei Xie, Manik C Ghosh, Tracey A Rouault, Jaekwon Lee, Soonkyu Chung

Arginine Catabolism and Polyamine Biosynthesis Pathway Disparities Within Francisella tularensis Subpopulations

Journal
Frontiers in Microbiology 13, 890856
Authors
Yinshi Yue, Bhanwar Lal Puniya, Tomáš Helikar, Benjamin Girardo, Steven H Hinrichs, Marilynn A Larson

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Journal
Frontiers in immunology 14, 1282859
Authors
Anna Niarakis, Marek Ostaszewski, Alexander Mazein, Inna Kuperstein, Martina Kutmon, 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, Finterly Hu, Nhung Pham, Friederike Ehrhart, Egon L Willighagen, Alberto Valdeolivas, Aurelien Dugourd, Francesco Messina, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Sylvain Soliman, Sara Sadat Aghamiri, Bhanwar Lal Puniya, Aurelien Naldi, Tomáš Helikar, Vidisha Singh, Marco Fariñas Fernández, Viviam Bermudez, Eirini Tsirvouli, Arnau Montagud, Vincent Noël, Miguel Ponce-de-Leon, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Augustin Luna, Janet Piñero, Laura I Furlong, Irina Balaur, Adrien Rougny, Yohan Jarosz, Rupert W Overall, Robert Phair, Livia Perfetto, Lisa Matthews, Devasahayam Arokia Balaya Rex, Marija Orlic-Milacic, Luis Cristobal Monraz Gomez, Bertrand De Meulder, Jean Marie Ravel, Bijay Jassal, Venkata Satagopam, Guanming Wu, Martin Golebiewski, Piotr Gawron, Laurence Calzone, Jacques S Beckmann, Chris T Evelo, Peter D’Eustachio, Falk Schreiber, Julio Saez-Rodriguez, Joaquin Dopazo, Martin Kuiper, Alfonso Valencia, Olaf Wolkenhauer, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, COVID-19 Disease Map Community

Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics

Journal
Frontiers in Bioengineering and Biotechnology 4 (10)
Authors
Bhanwar Lal Puniya, Laura Allen, Colleen Hochfelder, Mahbubul Majumder, Tomáš Helikar

Computational systems biology approach for the study of rheumatoid arthritis: from a molecular map to a dynamical model

Journal
Genomics and computational biology 4 (1), e100050
Authors
Vidisha Singh, Marek Ostaszewski, George D Kalliolias, Gilles Chiocchia, Robert Olaso, Elisabeth Petit-Teixeira, Tomáš Helikar, Anna Niarakis

Integrative Analysis and Dynamical Modelling of Signalling Pathways Involved in Rheumatoid Arthritis

Journal
Discrete models and formal verification in biology, Murray Edwards College
Authors
V Singh, M Ostaszewski, S Pankaew, G Kalliolias, G Chiocchia, R Olaso, E Petit-Teixeira, S Soliman, T Helikar, A Niarakis

Aberrant energy metabolism and redox balance in seizure onset zones of epileptic patients

Journal
Journal of proteomics 223, 103812
Authors
Ryan A Grove, Deepak Madhavan, Cory HT Boone, Camila Pereira Braga, Zuzana Papackova, Hannah Kyllo, Kaeli Samson, Kristina Simeone, Timothy Simeone, Tomas Helikar, Corrine K Hanson, Jiri Adamec

Changes in lipid profiles of epileptic mouse model

Journal
Metabolomics 16 (10), 106
Authors
Alicia Johnson, Ryan A Grove, Deepak Madhavan, Cory HT Boone, Camila Braga, Hannah Kyllo, Kaeli Samson, Kristina Simeone, Timothy Simeone, Tomas Helikar, Corrine K Hanson, Jiri Adamec

Integrative network analyses of transcriptomics data reveal potential drug targets for acute radiation syndrome

Journal
Scientific reports 11 (1), 5585
Authors
Robert Moore, Bhanwar Lal Puniya, Robert Powers, Chittibabu Guda, Kenneth W Bayles, David B Berkowitz, Tomáš Helikar

Fish Oil Intake During Gestation and Lactation Attenuated STZ-Induced Diabetes in Male Offspring via Activation of Brown Fat and Modulating Oxylipin Profile

Journal
Current Developments in Nutrition 6, 640
Authors
Rong Fan, Shalom Thomas, Mikyoung You, Zhuoheng Li, Brandt Bessell, Bhanwar Lal Puniya, Tomás Helikar, Zhenhua Liu, Soonkyu Chung

Model-Based Immunology and Life Sciences Education

We advance research-driven education by enabling students to learn immunology and biology like scientists do—through building, simulating, and testing computational models of biological systems.

Discovering Signal Transduction by Building and Simulating a Bacterial Chemotaxis Model Copy

Journal
CourseSource 12
Authors
Kayla Kester, Skylar Loecker, Tomáš Helikar

Cancer Biology: An Inquiry-Based Approach

Journal
Kendall Hunt Publishing
Authors
Christine Cutucache, Tomas Helikar

Discovering Cellular Respiration with Computational Modeling and Simulations

Journal
CourseSource
Authors
Heather E Bergan-Roller, Nicholas J Galt, Joseph T Dauer, Tomáš Helikar

Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon

Journal
CourseSource
Authors
Audrey Crowther, Heather E Bergan-Roller, Nicholas J Galt, Christine S Booth, Joseph T Dauer, Tomáš Helikar

Simulated computational model lesson improves foundational systems thinking skills and conceptual knowledge in biology students

Journal
BioScience 68 (8), 612-621
Authors
Heather E Bergan-Roller, Nicholas J Galt, Christopher J Chizinski, Tomáš Helikar, Joseph T Dauer

Student understanding of DNA structure–function relationships improves from using 3D learning modules with dynamic 3D printed models

Journal
Biochemistry and Molecular Biology Education 47 (3), 303-317
Authors
Michelle E Howell, Christine S Booth, Sharmin M Sikich, Tomáš Helikar, Rebecca L Roston, Brian A Couch, Karin van Dijk

Changes in students’ mental models from computational modeling of gene regulatory networks

Journal
International Journal of STEM Education 6 (1), 1-12
Authors
Joseph T Dauer, Heather E Bergan-Roller, Gretchen P King, McKenzie Kjose, Nicholas J Galt, Tomáš Helikar

Active learning about the dynamic and complex nature of CD4+ T cell differentiation with computer network modeling and simulations

Journal
The Journal of Immunology 204 (1_Supplement), 222.11-222.11
Authors
Tomas Helikar, Resa M Helikar, Deborah M Brown

Teaching metabolism in upper-division undergraduate biochemistry courses using online computational systems and dynamical models improves student performance

Journal
CBE—Life Sciences Education 20 (1), ar13
Authors
Christine S Booth, Changsoo Song, Michelle E Howell, Achilles Rasquinha, Aleš Saska, Resa Helikar, Sharmin M Sikich, Brian A Couch, Karin van Dijk, Rebecca L Roston, Tomáš Helikar

The need for research-grade systems modeling technologies for life science education

Journal
Trends in molecular medicine 27 (2), 100-103
Authors
Tomáš Helikar

Discovering prokaryotic gene regulation by building and investigating a computational model of the lac operon

Journal
CourseSource
Authors
Audrey Crowther, Heather E Bergan-Roller, Nicholas J Galt, Lara Appleby, Joseph T Dauer, Tomáš Helikar

Supporting university student learning of complex systems: an example of teaching the interactive processes that constitute photosynthesis

Journal
Springer International Publishing, 63-82
Authors
Joseph Dauer, Jenny Dauer, Lyrica Lucas, Tomáš Helikar, Tammy Long

DBERlibR: Automated data analysis for discipline-based education research

Journal
bioRxiv, 2022.08. 24.504993
Authors
Changsoo Song, Resa Helikar, Wendy M Smith, Tomáš Helikar

Factors Influencing Instructors’ Adoption and Continued Use of Computing Science Technologies: A Case Study in the Context of Cell Collective

Journal
CBE—Life Sciences Education 22 (3), ar29
Authors
C Song, R Helikar, WM Smith, T Helikar

Integrating Interactive Computational Modeling in Biology Curricula

Journal
PLoS Computational Biology
Authors
Tomáš Helikar, Christine E. Cutucache, Lauren A. Dahlquist, Tyler A. Herek, Joshua J. Larson, Jim A Rogers

Visualizing the invisible: a guide to designing, printing, and incorporating dynamic 3D molecular models to teach structure–function relationships

Journal
Journal of microbiology & biology education 19 (3), 10.1128/jmbe. v19i3. 1663
Authors
Michelle E Howell, Karin Van Dijk, Christine S Booth, Tomáš Helikar, Brian A Couch, Rebecca L Roston

Engaging Complexity: Learning about Biological Systems via Construction of and Interaction with Computational Models

Journal
Proceedings of the Association for Biology Laboratory Education 39 (1)
Authors
Lara Appleby, Heather Bergan-Roller, Audrey Crowther, Joseph Dauer, Tomas Helikar

Using concept maps to characterise cellular respiration knowledge in undergraduate students

Journal
Journal of Biological Education 54 (1), 33-46
Authors
Heather E Bergan-Roller, Nicholas J Galt, Tomáš Helikar, Joseph T Dauer

Modelling activities integrating construction and simulation supported explanatory and evaluative reasoning

Journal
International Journal of Science Education 41 (13), 1764-1786
Authors
Gretchen P King, Heather Bergan-Roller, Nicholas Galt, Tomáš Helikar, Joseph T Dauer

Simulating a computational biological model, rather than reading, elicits changes in brain activity during biological reasoning

Journal
CBE—Life Sciences Education 19 (3), ar45
Authors
Caron AC Clark, Tomáš Helikar, Joseph Dauer

Interactive learning modules with 3D printed models improve student understanding of protein structure–function relationships

Journal
Biochemistry and Molecular Biology Education 48 (4), 356-368
Authors
Michelle E Howell, Christine S Booth, Sharmin M Sikich, Tomáš Helikar, Karin van Dijk, Rebecca L Roston, Brian A Couch

Teaching advanced concepts in regulation of the lac operon with modeling and simulation.

Journal
CourseSource
Authors
CS Booth, A Crowther, R Helikar, T Luong, ME Howell, BA Couch, RL Roston, K van Dijk, T Helikar

Less (Learning How to Learn) & More (Learning): Teaching structure‐function with 3D‐printed models in large, undergraduate biochemistry classes

Journal
The FASEB Journal 35
Authors
Rebecca Roston, Michelle Howell, Christine Booth, Tomáš Helikar, Brian Couch, Karin Dijk

Teaching Advanced Concepts in Regulation of the Lac Operon With Modeling and Simulation

Journal
CourseSource
Authors
Christine S Booth, Audrey Crowther, Resa Helikar, Thuan Luong, Michelle E Howell, Brian A Couch, Rebecca L Roston, Karin van Dijk, Tomáš Helikar

The effects of a modeling and computational thinking professional development program on STEM educators’ perceptions toward teaching science and engineering practices

Journal
Education Sciences 12 (8), 570
Authors
Blake C Colclasure, Tessa Durham Brooks, Tomáš Helikar, Scott J King, Audrey Webb

Revision as an essential step in modeling to support predicting, observing, and explaining cellular respiration system dynamics

Journal
International Journal of Science Education 44 (13), 2152-2179
Authors
Lyrica Lucas, Tomáš Helikar, Joseph Dauer

We’re growing our team.

We’re looking for scientists, engineers, designers, and students interested in building the future of immune simulation and personalised immune health. Join us as we shape a new generation of computational immunology tools.

See our team
View open roles

We’re growing our team.

We’re looking for scientists, engineers, designers, and students interested in building the future of immune simulation and personalised immune health. Join us as we shape a new generation of computational immunology tools.

See our team
View open roles