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

Selected peer-reviewed research supporting the foundations of our scientific work.

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

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

From FAIR to CURE: guidelines for computational models of biological systems

Journal
ArXiv, arXiv: 2502.15597 v1
Authors
Herbert M Sauro, Eran Agmon, Michael L Blinov, John H Gennari, Joe Hellerstein, Adel Heydarabadipour, Peter Hunter, Bartholomew E Jardine, Elebeoba May, David P Nickerson, Lucian P Smith, Gary D Bader, Frank Bergmann, Patrick M Boyle, Andreas Dräger, James R Faeder, Song Feng, Juliana Freire, Fabian Fröhlich, James A Glazier, Thomas E Gorochowski, Tomas Helikar, Stefan Hoops, Princess Imoukhuede, Sarah M Keating, Matthias Konig, Reinhard Laubenbacher, Leslie M Loew, Carlos F Lopez, William W Lytton, Andrew McCulloch, Pedro Mendes, Chris J Myers, Jerry G Myers, Lealem Mulugeta, Anna Niarakis, David D van Niekerk, Brett G Olivier, Alexander A Patrie, Ellen M Quardokus, Nicole Radde, Johann M Rohwer, Sven Sahle, James C Schaff, TJ Sego, Janis Shin, Jacky L Snoep, Rajanikanth Vadigepalli, H Steve Wiley, Dagmar Waltemath, Ion Moraru

Toward mechanistic medical digital twins: some use cases in immunology

Journal
Frontiers in Digital Health 6, 1349595
Authors
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

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

Journal
Journal of integrative bioinformatics 21 (1), 20240008
Authors
Lucian P Smith, Frank T Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König

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

Modeling and Remodeling the Cell: How Digital Twins and HCMV Can Elucidate the Complex Interactions of Viral Latency, Epigenetic Regulation, and Immune Responses

Journal
Current clinical microbiology reports 10 (3), 141-151
Authors
H McMahon-Cole, A Johnson, SS Aghamiri, T Helikar, LB Crawford

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

Journal
BMC systems biology 3 (1), 58
Authors
Tomáš Helikar, Jim A Rogers

The Cell Collective: Toward an open and collaborative approach to systems biology

Journal
BMC Systems Biology 6 (1), 96
Authors
Tomas Helikar, Bryan Kowal, Sean McClenathan, Mitchell Bruckner, Thaine Rowley, Ben Wicks, Manish Shrestha, Kahani Limbu, Jim A Rogers

Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle

Journal
Bulletin of Mathematical Biology
Authors
Alex Madrahimov, Tomas Helikar, Bryan Kowal, Guoqing Lu, Jim Rogers

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Journal
BMC systems biology 7 (1), 135
Authors
Claudine Chaouiya, Duncan Bérenguier, Sarah M Keating, Aurélien Naldi, Martijn P Van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomáš Helikar

Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions

Journal
BMC systems biology 8 (1), 92
Authors
Naomi Kochi, Tomáš Helikar, Laura Allen, Jim A Rogers, Zhenyuan Wang, Mihaela T Matache

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

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

Discovering Cellular Respiration with Computational Modeling and Simulations

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

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

The CoLoMoTo interactive notebook: accessible and reproducible computational analyses for qualitative biological networks

Journal
Frontiers in physiology 9, 680
Authors
Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé

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

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

Logical modeling of cellular processes: from software development to network dynamics

Journal
Frontiers media SA
Authors
Matteo Barberis, Tomáš Helikar

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

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

ccNetViz: a WebGL-based JavaScript library for visualization of large networks

Journal
Bioinformatics 36 (16), 4527-4529
Authors
Ales Saska, David Tichy, Robert Moore, Achilles Rasquinha, Caner Akdas, Xiaodong Zhao, Renato Fabbri, Ana Jeličić, Gaurav Grover, Himanshu Jotwani, Mohamed Shadab, Resa M Helikar, Tomáš Helikar

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

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

Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC] 2 2019 CoLoMoTo/SysMod Workshop

Journal
Briefings in bioinformatics 22 (2), 1848-1859
Authors
Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S Malik Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C Freeman, Paul Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomáš Helikar, Laurence Calzone

A practical guide to mechanistic systems modeling in biology using a logic-based approach

Journal
Briefings in bioinformatics 22 (4), bbaa236
Authors
Anna Niarakis, Tomáš Helikar

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Journal
Molecular systems biology 17 (10), e10387
Authors
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 Cristobal Monraz Gomez, 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 Groues, 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, Aurelien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Auge, 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, COVID‐19 Disease Map Community

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Journal
Bioinformatics 37 (21), 3702-3706
Authors
Andreas Dräger, Tomáš Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar

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

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

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

Discovering Signal Transduction by Building and Simulating a Bacterial Chemotaxis Model

Journal
CourseSource 12
Authors
Kayla Kester, Skylar Loecker, Tomáš Helikar
Year
2025

AI‐Driven Applications in Clinical Pharmacology and Translational Science: Insights From the ASCPT 2024 AI Preconference Copy

Journal
Clinical and Translational Science 18 (4), e70203
Authors
Mohamed H Shahin, Prashant Desai, Nadia Terranova, Yuanfang Guan, Tomáš Helikar, Sebastian Lobentanzer, Qi Liu, James Lu, Subha Madhavan, Gary Mo, Flora T Musuamba, Jagdeep T Podichetty, Jie Shen, Lei Xie, Mathew Wiens, Cynthia J Musante

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

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Journal
BRIEFINGS IN BIOINFORMATICS 25 (3)
Authors
Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M Keating, David Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noel, Henning Hermjakob, Tomas Helikar, Sylvain Soliman, Laurence Calzone

FROG analysis ensures the reproducibility of genome scale metabolic models

Journal
bioRxiv, 2024.09. 24.614797
Authors
Karthik Raman, Miroslav Kratochvil, Brett G Olivier, Matthias König, Pratyay Sengupta, Dinesh Kumar Kuppa Baskaran, Tung VN Nguyen, Daniel Lobo, St Elmo Wilken, Krishna Kumar Tiwari, Aswathy K Raghu, Indumathi Palanikumar, Lavanya Raajaraam, Maziya Ibrahim, Sanjaay Balakrishnan, Shreyansh Umale, Frank Bergmann, Tanisha Malpani, Venkata P Satagopam, Reinhard Schneider, Moritz E Beber, Sarah Keating, Mihail Anton, Alina Renz, Meiyappan Lakshmanan, Dong-Yup Lee, Lokanand Koduru, Reihaneh Mostolizadeh, Oscar Dias, Emanuel Cunha, Alexandre Oliveira, Yi Qing Lee, Karsten Zengler, Rodrigo Santibanez-Palominos, Manish Kumar, Matteo Barberis, Bhanwar Lal Puniya, Tomáš Helikar, Hoang V Dinh, Patrick F Suthers, Costas D Maranas, Isabella Casini, Seyed Babak Loghmani, Nadine Veith, Nantia Leonidou, Feiran Li, Yu Chen, Jens Nielsen, GaRyoung Lee, Sang Mi Lee, Gi Bae Kim, Pedro T Monteiro, Miguel C Teixeira, Hyun Uk Kim, Sang Yup Lee, Ulf W Liebal, Lars M Blank, Christian Lieven, Chaimaa Tarzi, Claudio Angione, Manga Enuh Blaise, Çelik Pınar Aytar, Mikhail Kulyashov, llya Akberdin, Dohyeon Kim, Sung Ho Yoon, Zhaohui Xu, Jyotshana Gautam, William T Scott Jr, Peter J Schaap, Jasper J Koehorst, Cristal Zuñiga, Gabriela Canto-Encalada, Sara Benito-Vaquerizo, Ivette Parera Olm, Maria Suarez-Diez, Qianqian Yuan, Hongwu Ma, Mohammad Mazharul Islam, Jason A Papin, Francisco Zorrilla, Kiran Raosaheb Patil, Arianna Basile, Juan Nogales, Granado San León, Freddy Castillo-Alfonso, Roberto Olivares-Hernández, Gabriela Canto-Encalada, Gabriel Vigueras-Ramírez, Henning Hermjakob, Andreas Dräger, Rahuman S Malik-Sheriff

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

COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery

Journal
Briefings in Bioinformatics 24 (6), bbad387
Authors
Brandt Bessell, Josh Loecker, Zhongyuan Zhao, Sara Sadat Aghamiri, Sabyasachi Mohanty, Rada Amin, Tomáš Helikar, Bhanwar Lal Puniya

Decision making in cells

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

Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle

Journal
Plos One 7 (10), e45780
Authors
Robert Todd, Tomas Helikar

A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells

Journal
PloS one 8 (4), e61757
Authors
Tomáš Helikar, Naomi Kochi, Bryan Kowal, Manjari Dimri, Mayumi Naramura, Srikumar M Raja, Vimla Band, Hamid Band, Jim A Rogers

Molecular phylogeny and evolutionary dynamics of influenza A nonstructural (NS) gene

Journal
Infection, Genetics and Evolution 22, 192-200
Authors
Jianpeng Xu, Haizhen A Zhong, Alex Madrahimov, Tomáš Helikar, Guoqing Lu

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

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

Journal
Journal of Integrative Bioinformatics 12 (2)
Authors
Claudine Chaouiya, Sarah M. Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomáš Helikar

Logical modeling and dynamical analysis of cellular networks

Journal
Frontiers in genetics 7, 94
Authors
Wassim Abou-Jaoudé, Pauline Traynard, Pedro T Monteiro, Julio Saez-Rodriguez, Tomáš Helikar, Denis Thieffry, Claudine Chaouiya

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

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

Automated pipeline for the inference of Boolean models from molecular interaction maps

Journal
Logical modelling of cellular networks ECCB 2018 Workshop
Authors
S Pankaew, S Soliman, T Helikar, A Niarakis

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

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

Translating Disease Networks to Executable Boolean Models

Journal
Young Researchers in Life Sciences Federation
Authors
Ss Aghamiri, V Singh, S Soliman, T Helikar, A Niarakis

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

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

SBML Level 3: an extensible format for the exchange and reuse of biological models

Journal
Molecular systems biology 16 (8), e9110
Authors
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, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde de Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker

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

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

Journal
Cold Spring Harbor Laboratory
Authors
Inna Kuperstein, Charles Auffray, Rupert W Overall, Lisa Matthews, Daniela Börnigen, Julia Somers, Tomáš Helikar, Lars MT Eijssen, Anton Yuryev, Olaf Wolkenhauer, Angela Bauch, Silvia Marchesi, Anna Niarakis, Bertrand De Meulder, Alberto Valdeolivas, Maria Peña-Chilet, Alexander R Pico, Ralf Stephan, Robert Phair, Tom C Freeman, Stuart Owen, Anastasia P Nesterova, Piotr Gawron, Agatha Treveil, Jeremy Zucker, John A Bachman, Laurence Calzone, Marius Rameil, Hiroaki Kitano, Nhung Pham, Muying Wang, M Vazquez, Kristina Hanspers, Veronica Shamovsky, Enrico Glaab, Marta Iannuccelli, Vidisha Singh, Zsolt Bocskei, Takahiro G Yamada, Rudi Balling, Tamas Korcsmaros, Egon Willighagen, Martina Kutmon, Martin Golebiewski, Emily E Ackerman, Yusuke Hiki, Jan Hasenauer, Kristie L Oxford, Cristoffer Sevilla, Corinna Montrone, Karen Rothfels, Alina Renz, Valentin Grouès, DAB Rex, Emek Demir, Goar Frishman, Miguel Ponce de Leon, Marta Conti, Anders Riutta, Gisela Fobo, Barbara Brauner, Alexander Mazein, Vanessa Nakonecnij, Vera Ortseifen, Joaquín Dopazo, Gokce Yagmur Summak, Aurelio Orta-Resendiz, Aurelien Dugourd, Dezso Modos, Jakob Vanhoefer, Xiaoming Hu, Bhanwar Lal Puniya, Jason E Shoemaker, Marton Olbei, Andrea Senff-Ribeiro, Sara Sadat Aghamiri, Franck Augé, Özgün Babur, Marek Ostaszewski, Noriko Hiroi, Lincoln Stein, Hanna Borlinghaus, Andreas Ruepp, Julia Scheel, Denise Slenter, Marina Esteban-Medina, Falk Schreiber, Andreas Dräger, Marcio Luis Acencio, Susan L Coort, Anita de Waard, Muhammad Naveez, Robin Haw, Venkata P Satagopam, Luana Licata, Guanming Wu, Benjamin M Gyori, Chris T Evelo, M Orlic-Milacic, Henning Hermjakob, Jeremy Teuton, Laurent Heirendt, Matti Hoch, Tobias Czauderna, Akira Funahashi, Carole Goble, Reinhard Schneider, Carlos Vega, Dénes Türei, Bijay Jassal, Dieter Maier, Leonard Schmiester, Jean-Marie Ravel, Ewa Smula, Sylvain Soliman, Shailendra K Gupta, Alfonso Valencia, Chris Sander, Thawfeek M Varusai, Francesca Sacco, Julio Saez-Rodriguez, Augustin Luna, Ebru Kocakaya, Pablo Porras, Liam Fergusson, Emmanuel Barillot, Kinza Rian, Marvin Martens, Jacques S Beckmann, Friederike Ehrhart, Aurélien Naldi, Arnau Montagud

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

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

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

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

Recent applications of quantitative systems pharmacology and machine learning models across diseases

Journal
Journal of pharmacokinetics and pharmacodynamics 49 (1), 19-37
Authors
Sara Sadat Aghamiri, Rada Amin, Tomáš Helikar

Building digital twins of the human immune system: toward a roadmap

Journal
NPJ digital medicine 5 (1), 64
Authors
Reinhard Laubenbacher, Anna Niarakis, Tomáš Helikar, Gary An, Bruce Shapiro, Rahuman S Malik-Sheriff, TJ Sego, Adam Knapp, Paul Macklin, James A Glazier

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

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

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

Forum on immune digital twins: a meeting report

Journal
pj Systems Biology and Applications 10 (1), 19
Authors
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

Immune digital twin blueprint: A comprehensive mechanistic model of the human immune system

Journal
bioRxiv
Authors
Rada Amin, Sara Sadat Aghamiri, Bhanwar Lal Puniya, Lauren Mayo, Dennis Startsev, Kashish Poore, Resa Helikar, Tomáš Helikar

Augusta: From RNA‐Seq to gene regulatory networks and Boolean models

Journal
Computational and Structural Biotechnology Journal 23, 783-790
Authors
J Musilova, Z Vafek, BL Puniya, R Zimmer, T Helikar, K Sedlar

A multiscale mechanistic model of human dendritic cells for in-silico investigation of immune responses and novel therapeutics discovery

Journal
Frontiers in Immunology 14, 1112985
Authors
SS Aghamiri, BL Puniya, R Amin, T Helikar

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

Boolean modeling of biochemical networks

Journal
The Open Bioinformatics Journal
Authors
Tomas Helikar, Naomi Kochi, John Konvalina, Jim A Rogers

Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models

Journal
PLoS ONE 7 (10), e46417
Authors
Tomas Helikar, Bryan Kowal, Alex Madrahimov, Manish Shrestha, Jay Pedersen, Kahani Limbu, Ishwor Thapa, Thaine Rowley, Rahul Satalkar, Naomi Kochi, John Konvalina, Jim Rogers

A cell simulator platform: the cell collective

Journal
Clinical Pharmacology & Therapeutics 93 (5), 393-395
Authors
Tomáš Helikar, B Kowal, JA Rogers

Cancer Biology: An Inquiry-Based Approach

Journal
Kendall Hunt Publishing
Authors
Christine Cutucache, Tomas Helikar

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Journal
Bioinformatics 31 (7)
Authors
Aurelien Naldi, Pedro T Monteiro, Christopher Müssel, Hans A Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomas Helikar, Claudine Chaouiya

Programmatic access to logical models in the Cell Collective modeling environment via a REST API

Journal
Biosystems 139, 12-16
Authors
Bryan M Kowal, Travis R Schreier, Joseph T Dauer, Tomáš Helikar

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

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

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

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

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

Executable Disease Networks: Adding dynamics to molecular maps

Journal
ECCB 2018-17th European Conference on Computational Biology
Authors
Vidisha Singh, Saran Pankaew, Marek Ostaszewski, George D Kalliolias, Sylvain Soliman, Tomáš Helikar, Anna Niarakis

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

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

Automated inference of Boolean models from molecular interaction maps using CaSQ

Journal
Bioinformatics 36 (16), 4473-4482
Authors
Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomáš Helikar, Sylvain Soliman, Anna Niarakis

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

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

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

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

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

Journal
Journal of integrative bioinformatics 18 (3), 20210021
Authors
Lucian P Smith, Frank T Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König

Two heads are better than one: current landscape of integrating QSP and machine learning

Journal
Journal of Pharmacokinetics and Pharmacodynamics 49 (1), 5-18
Authors
Tongli Zhang, Ioannis P Androulakis, Peter Bonate, Limei Cheng, Tomáš Helikar, Jaimit Parikh, Christopher Rackauckas, Kalyanasundaram Subramanian, Carolyn R Cho

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

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

Computational modelling in health and disease: highlights of the 6th annual SysMod meeting

Journal
Bioinformatics 38 (21), 4990-4993
Authors
Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomáš Helikar, Marc Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger

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

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

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

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

Toward mechanistic medical digital twins: some use cases in immunology

Journal
Frontiers in Digital Health 6, 1349595
Authors
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

Immune digital twin blueprint: A comprehensive mechanistic model of the human immune system

Journal
bioRxiv
Authors
Rada Amin, Sara Sadat Aghamiri, Bhanwar Lal Puniya, Lauren Mayo, Dennis Startsev, Kashish Poore, Resa Helikar, Tomáš Helikar

FROG analysis ensures the reproducibility of genome scale metabolic models

Journal
bioRxiv, 2024.09. 24.614797
Authors
Karthik Raman, Miroslav Kratochvil, Brett G Olivier, Matthias König, Pratyay Sengupta, Dinesh Kumar Kuppa Baskaran, Tung VN Nguyen, Daniel Lobo, St Elmo Wilken, Krishna Kumar Tiwari, Aswathy K Raghu, Indumathi Palanikumar, Lavanya Raajaraam, Maziya Ibrahim, Sanjaay Balakrishnan, Shreyansh Umale, Frank Bergmann, Tanisha Malpani, Venkata P Satagopam, Reinhard Schneider, Moritz E Beber, Sarah Keating, Mihail Anton, Alina Renz, Meiyappan Lakshmanan, Dong-Yup Lee, Lokanand Koduru, Reihaneh Mostolizadeh, Oscar Dias, Emanuel Cunha, Alexandre Oliveira, Yi Qing Lee, Karsten Zengler, Rodrigo Santibanez-Palominos, Manish Kumar, Matteo Barberis, Bhanwar Lal Puniya, Tomáš Helikar, Hoang V Dinh, Patrick F Suthers, Costas D Maranas, Isabella Casini, Seyed Babak Loghmani, Nadine Veith, Nantia Leonidou, Feiran Li, Yu Chen, Jens Nielsen, GaRyoung Lee, Sang Mi Lee, Gi Bae Kim, Pedro T Monteiro, Miguel C Teixeira, Hyun Uk Kim, Sang Yup Lee, Ulf W Liebal, Lars M Blank, Christian Lieven, Chaimaa Tarzi, Claudio Angione, Manga Enuh Blaise, Çelik Pınar Aytar, Mikhail Kulyashov, llya Akberdin, Dohyeon Kim, Sung Ho Yoon, Zhaohui Xu, Jyotshana Gautam, William T Scott Jr, Peter J Schaap, Jasper J Koehorst, Cristal Zuñiga, Gabriela Canto-Encalada, Sara Benito-Vaquerizo, Ivette Parera Olm, Maria Suarez-Diez, Qianqian Yuan, Hongwu Ma, Mohammad Mazharul Islam, Jason A Papin, Francisco Zorrilla, Kiran Raosaheb Patil, Arianna Basile, Juan Nogales, Granado San León, Freddy Castillo-Alfonso, Roberto Olivares-Hernández, Gabriela Canto-Encalada, Gabriel Vigueras-Ramírez, Henning Hermjakob, Andreas Dräger, Rahuman S Malik-Sheriff

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

A multiscale mechanistic model of human dendritic cells for in-silico investigation of immune responses and novel therapeutics discovery

Journal
Frontiers in Immunology 14, 1112985
Authors
SS Aghamiri, BL Puniya, R Amin, T Helikar

COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery

Journal
Briefings in Bioinformatics 24 (6), bbad387
Authors
Brandt Bessell, Josh Loecker, Zhongyuan Zhao, Sara Sadat Aghamiri, Sabyasachi Mohanty, Rada Amin, Tomáš Helikar, Bhanwar Lal Puniya

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

Journal
BMC systems biology 3 (1), 58
Authors
Tomáš Helikar, Jim A Rogers

Boolean modeling of biochemical networks

Journal
The Open Bioinformatics Journal
Authors
Tomas Helikar, Naomi Kochi, John Konvalina, Jim A Rogers

Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle

Journal
Plos One 7 (10), e45780
Authors
Robert Todd, Tomas Helikar

Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle

Journal
Bulletin of Mathematical Biology
Authors
Alex Madrahimov, Tomas Helikar, Bryan Kowal, Guoqing Lu, Jim Rogers

A cell simulator platform: the cell collective

Journal
Clinical Pharmacology & Therapeutics 93 (5), 393-395
Authors
Tomáš Helikar, B Kowal, JA Rogers

Molecular phylogeny and evolutionary dynamics of influenza A nonstructural (NS) gene

Journal
Infection, Genetics and Evolution 22, 192-200
Authors
Jianpeng Xu, Haizhen A Zhong, Alex Madrahimov, Tomáš Helikar, Guoqing Lu

Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions

Journal
BMC systems biology 8 (1), 92
Authors
Naomi Kochi, Tomáš Helikar, Laura Allen, Jim A Rogers, Zhenyuan Wang, Mihaela T Matache

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Journal
Bioinformatics 31 (7)
Authors
Aurelien Naldi, Pedro T Monteiro, Christopher Müssel, Hans A Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomas Helikar, Claudine Chaouiya

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

Journal
Journal of Integrative Bioinformatics 12 (2)
Authors
Claudine Chaouiya, Sarah M. Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomáš Helikar

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 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

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

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

Automated pipeline for the inference of Boolean models from molecular interaction maps

Journal
Logical modelling of cellular networks ECCB 2018 Workshop
Authors
S Pankaew, S Soliman, T Helikar, A Niarakis

The CoLoMoTo interactive notebook: accessible and reproducible computational analyses for qualitative biological networks

Journal
Frontiers in physiology 9, 680
Authors
Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé

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

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

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

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

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

SBML Level 3: an extensible format for the exchange and reuse of biological models

Journal
Molecular systems biology 16 (8), e9110
Authors
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, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde de Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker

ccNetViz: a WebGL-based JavaScript library for visualization of large networks

Journal
Bioinformatics 36 (16), 4527-4529
Authors
Ales Saska, David Tichy, Robert Moore, Achilles Rasquinha, Caner Akdas, Xiaodong Zhao, Renato Fabbri, Ana Jeličić, Gaurav Grover, Himanshu Jotwani, Mohamed Shadab, Resa M Helikar, Tomáš Helikar

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

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

Journal
Cold Spring Harbor Laboratory
Authors
Inna Kuperstein, Charles Auffray, Rupert W Overall, Lisa Matthews, Daniela Börnigen, Julia Somers, Tomáš Helikar, Lars MT Eijssen, Anton Yuryev, Olaf Wolkenhauer, Angela Bauch, Silvia Marchesi, Anna Niarakis, Bertrand De Meulder, Alberto Valdeolivas, Maria Peña-Chilet, Alexander R Pico, Ralf Stephan, Robert Phair, Tom C Freeman, Stuart Owen, Anastasia P Nesterova, Piotr Gawron, Agatha Treveil, Jeremy Zucker, John A Bachman, Laurence Calzone, Marius Rameil, Hiroaki Kitano, Nhung Pham, Muying Wang, M Vazquez, Kristina Hanspers, Veronica Shamovsky, Enrico Glaab, Marta Iannuccelli, Vidisha Singh, Zsolt Bocskei, Takahiro G Yamada, Rudi Balling, Tamas Korcsmaros, Egon Willighagen, Martina Kutmon, Martin Golebiewski, Emily E Ackerman, Yusuke Hiki, Jan Hasenauer, Kristie L Oxford, Cristoffer Sevilla, Corinna Montrone, Karen Rothfels, Alina Renz, Valentin Grouès, DAB Rex, Emek Demir, Goar Frishman, Miguel Ponce de Leon, Marta Conti, Anders Riutta, Gisela Fobo, Barbara Brauner, Alexander Mazein, Vanessa Nakonecnij, Vera Ortseifen, Joaquín Dopazo, Gokce Yagmur Summak, Aurelio Orta-Resendiz, Aurelien Dugourd, Dezso Modos, Jakob Vanhoefer, Xiaoming Hu, Bhanwar Lal Puniya, Jason E Shoemaker, Marton Olbei, Andrea Senff-Ribeiro, Sara Sadat Aghamiri, Franck Augé, Özgün Babur, Marek Ostaszewski, Noriko Hiroi, Lincoln Stein, Hanna Borlinghaus, Andreas Ruepp, Julia Scheel, Denise Slenter, Marina Esteban-Medina, Falk Schreiber, Andreas Dräger, Marcio Luis Acencio, Susan L Coort, Anita de Waard, Muhammad Naveez, Robin Haw, Venkata P Satagopam, Luana Licata, Guanming Wu, Benjamin M Gyori, Chris T Evelo, M Orlic-Milacic, Henning Hermjakob, Jeremy Teuton, Laurent Heirendt, Matti Hoch, Tobias Czauderna, Akira Funahashi, Carole Goble, Reinhard Schneider, Carlos Vega, Dénes Türei, Bijay Jassal, Dieter Maier, Leonard Schmiester, Jean-Marie Ravel, Ewa Smula, Sylvain Soliman, Shailendra K Gupta, Alfonso Valencia, Chris Sander, Thawfeek M Varusai, Francesca Sacco, Julio Saez-Rodriguez, Augustin Luna, Ebru Kocakaya, Pablo Porras, Liam Fergusson, Emmanuel Barillot, Kinza Rian, Marvin Martens, Jacques S Beckmann, Friederike Ehrhart, Aurélien Naldi, Arnau Montagud

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

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

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

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

A practical guide to mechanistic systems modeling in biology using a logic-based approach

Journal
Briefings in bioinformatics 22 (4), bbaa236
Authors
Anna Niarakis, 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

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

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Journal
Bioinformatics 37 (21), 3702-3706
Authors
Andreas Dräger, Tomáš Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar

Two heads are better than one: current landscape of integrating QSP and machine learning

Journal
Journal of Pharmacokinetics and Pharmacodynamics 49 (1), 5-18
Authors
Tongli Zhang, Ioannis P Androulakis, Peter Bonate, Limei Cheng, Tomáš Helikar, Jaimit Parikh, Christopher Rackauckas, Kalyanasundaram Subramanian, Carolyn R Cho

Building digital twins of the human immune system: toward a roadmap

Journal
NPJ digital medicine 5 (1), 64
Authors
Reinhard Laubenbacher, Anna Niarakis, Tomáš Helikar, Gary An, Bruce Shapiro, Rahuman S Malik-Sheriff, TJ Sego, Adam Knapp, Paul Macklin, James A Glazier

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

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

Discovering Signal Transduction by Building and Simulating a Bacterial Chemotaxis Model

Journal
CourseSource 12
Authors
Kayla Kester, Skylar Loecker, Tomáš Helikar
Year
2025

AI‐Driven Applications in Clinical Pharmacology and Translational Science: Insights From the ASCPT 2024 AI Preconference Copy

Journal
Clinical and Translational Science 18 (4), e70203
Authors
Mohamed H Shahin, Prashant Desai, Nadia Terranova, Yuanfang Guan, Tomáš Helikar, Sebastian Lobentanzer, Qi Liu, James Lu, Subha Madhavan, Gary Mo, Flora T Musuamba, Jagdeep T Podichetty, Jie Shen, Lei Xie, Mathew Wiens, Cynthia J Musante

From FAIR to CURE: guidelines for computational models of biological systems

Journal
ArXiv, arXiv: 2502.15597 v1
Authors
Herbert M Sauro, Eran Agmon, Michael L Blinov, John H Gennari, Joe Hellerstein, Adel Heydarabadipour, Peter Hunter, Bartholomew E Jardine, Elebeoba May, David P Nickerson, Lucian P Smith, Gary D Bader, Frank Bergmann, Patrick M Boyle, Andreas Dräger, James R Faeder, Song Feng, Juliana Freire, Fabian Fröhlich, James A Glazier, Thomas E Gorochowski, Tomas Helikar, Stefan Hoops, Princess Imoukhuede, Sarah M Keating, Matthias Konig, Reinhard Laubenbacher, Leslie M Loew, Carlos F Lopez, William W Lytton, Andrew McCulloch, Pedro Mendes, Chris J Myers, Jerry G Myers, Lealem Mulugeta, Anna Niarakis, David D van Niekerk, Brett G Olivier, Alexander A Patrie, Ellen M Quardokus, Nicole Radde, Johann M Rohwer, Sven Sahle, James C Schaff, TJ Sego, Janis Shin, Jacky L Snoep, Rajanikanth Vadigepalli, H Steve Wiley, Dagmar Waltemath, Ion Moraru

Forum on immune digital twins: a meeting report

Journal
pj Systems Biology and Applications 10 (1), 19
Authors
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

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Journal
BRIEFINGS IN BIOINFORMATICS 25 (3)
Authors
Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M Keating, David Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noel, Henning Hermjakob, Tomas Helikar, Sylvain Soliman, Laurence Calzone

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

Journal
Journal of integrative bioinformatics 21 (1), 20240008
Authors
Lucian P Smith, Frank T Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König

Augusta: From RNA‐Seq to gene regulatory networks and Boolean models

Journal
Computational and Structural Biotechnology Journal 23, 783-790
Authors
J Musilova, Z Vafek, BL Puniya, R Zimmer, T Helikar, K Sedlar

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

Modeling and Remodeling the Cell: How Digital Twins and HCMV Can Elucidate the Complex Interactions of Viral Latency, Epigenetic Regulation, and Immune Responses

Journal
Current clinical microbiology reports 10 (3), 141-151
Authors
H McMahon-Cole, A Johnson, SS Aghamiri, T Helikar, LB Crawford

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

Decision making in cells

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

The Cell Collective: Toward an open and collaborative approach to systems biology

Journal
BMC Systems Biology 6 (1), 96
Authors
Tomas Helikar, Bryan Kowal, Sean McClenathan, Mitchell Bruckner, Thaine Rowley, Ben Wicks, Manish Shrestha, Kahani Limbu, Jim A Rogers

Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models

Journal
PLoS ONE 7 (10), e46417
Authors
Tomas Helikar, Bryan Kowal, Alex Madrahimov, Manish Shrestha, Jay Pedersen, Kahani Limbu, Ishwor Thapa, Thaine Rowley, Rahul Satalkar, Naomi Kochi, John Konvalina, Jim Rogers

A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells

Journal
PloS one 8 (4), e61757
Authors
Tomáš Helikar, Naomi Kochi, Bryan Kowal, Manjari Dimri, Mayumi Naramura, Srikumar M Raja, Vimla Band, Hamid Band, Jim A Rogers

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Journal
BMC systems biology 7 (1), 135
Authors
Claudine Chaouiya, Duncan Bérenguier, Sarah M Keating, Aurélien Naldi, Martijn P Van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomáš Helikar

Cancer Biology: An Inquiry-Based Approach

Journal
Kendall Hunt Publishing
Authors
Christine Cutucache, Tomas Helikar

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

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

Programmatic access to logical models in the Cell Collective modeling environment via a REST API

Journal
Biosystems 139, 12-16
Authors
Bryan M Kowal, Travis R Schreier, Joseph T Dauer, Tomáš Helikar

Logical modeling and dynamical analysis of cellular networks

Journal
Frontiers in genetics 7, 94
Authors
Wassim Abou-Jaoudé, Pauline Traynard, Pedro T Monteiro, Julio Saez-Rodriguez, Tomáš Helikar, Denis Thieffry, Claudine Chaouiya

Discovering Cellular Respiration with Computational Modeling and Simulations

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

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

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

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

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

Executable Disease Networks: Adding dynamics to molecular maps

Journal
ECCB 2018-17th European Conference on Computational Biology
Authors
Vidisha Singh, Saran Pankaew, Marek Ostaszewski, George D Kalliolias, Sylvain Soliman, Tomáš Helikar, Anna Niarakis

Translating Disease Networks to Executable Boolean Models

Journal
Young Researchers in Life Sciences Federation
Authors
Ss Aghamiri, V Singh, S Soliman, T Helikar, A Niarakis

Logical modeling of cellular processes: from software development to network dynamics

Journal
Frontiers media SA
Authors
Matteo Barberis, Tomáš Helikar

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

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

Automated inference of Boolean models from molecular interaction maps using CaSQ

Journal
Bioinformatics 36 (16), 4473-4482
Authors
Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomáš Helikar, Sylvain Soliman, Anna Niarakis

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

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

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

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

Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC] 2 2019 CoLoMoTo/SysMod Workshop

Journal
Briefings in bioinformatics 22 (2), 1848-1859
Authors
Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S Malik Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C Freeman, Paul Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomáš Helikar, Laurence Calzone

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

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

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Journal
Molecular systems biology 17 (10), e10387
Authors
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 Cristobal Monraz Gomez, 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 Groues, 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, Aurelien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Auge, 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, COVID‐19 Disease Map Community

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

Journal
Journal of integrative bioinformatics 18 (3), 20210021
Authors
Lucian P Smith, Frank T Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König

Recent applications of quantitative systems pharmacology and machine learning models across diseases

Journal
Journal of pharmacokinetics and pharmacodynamics 49 (1), 19-37
Authors
Sara Sadat Aghamiri, Rada Amin, Tomáš Helikar

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

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

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

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

Computational modelling in health and disease: highlights of the 6th annual SysMod meeting

Journal
Bioinformatics 38 (21), 4990-4993
Authors
Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomáš Helikar, Marc Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger

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

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

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

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

Toward mechanistic medical digital twins: some use cases in immunology

Journal
Frontiers in Digital Health 6, 1349595
Authors
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

Immune digital twin blueprint: A comprehensive mechanistic model of the human immune system

Journal
bioRxiv
Authors
Rada Amin, Sara Sadat Aghamiri, Bhanwar Lal Puniya, Lauren Mayo, Dennis Startsev, Kashish Poore, Resa Helikar, Tomáš Helikar

FROG analysis ensures the reproducibility of genome scale metabolic models

Journal
bioRxiv, 2024.09. 24.614797
Authors
Karthik Raman, Miroslav Kratochvil, Brett G Olivier, Matthias König, Pratyay Sengupta, Dinesh Kumar Kuppa Baskaran, Tung VN Nguyen, Daniel Lobo, St Elmo Wilken, Krishna Kumar Tiwari, Aswathy K Raghu, Indumathi Palanikumar, Lavanya Raajaraam, Maziya Ibrahim, Sanjaay Balakrishnan, Shreyansh Umale, Frank Bergmann, Tanisha Malpani, Venkata P Satagopam, Reinhard Schneider, Moritz E Beber, Sarah Keating, Mihail Anton, Alina Renz, Meiyappan Lakshmanan, Dong-Yup Lee, Lokanand Koduru, Reihaneh Mostolizadeh, Oscar Dias, Emanuel Cunha, Alexandre Oliveira, Yi Qing Lee, Karsten Zengler, Rodrigo Santibanez-Palominos, Manish Kumar, Matteo Barberis, Bhanwar Lal Puniya, Tomáš Helikar, Hoang V Dinh, Patrick F Suthers, Costas D Maranas, Isabella Casini, Seyed Babak Loghmani, Nadine Veith, Nantia Leonidou, Feiran Li, Yu Chen, Jens Nielsen, GaRyoung Lee, Sang Mi Lee, Gi Bae Kim, Pedro T Monteiro, Miguel C Teixeira, Hyun Uk Kim, Sang Yup Lee, Ulf W Liebal, Lars M Blank, Christian Lieven, Chaimaa Tarzi, Claudio Angione, Manga Enuh Blaise, Çelik Pınar Aytar, Mikhail Kulyashov, llya Akberdin, Dohyeon Kim, Sung Ho Yoon, Zhaohui Xu, Jyotshana Gautam, William T Scott Jr, Peter J Schaap, Jasper J Koehorst, Cristal Zuñiga, Gabriela Canto-Encalada, Sara Benito-Vaquerizo, Ivette Parera Olm, Maria Suarez-Diez, Qianqian Yuan, Hongwu Ma, Mohammad Mazharul Islam, Jason A Papin, Francisco Zorrilla, Kiran Raosaheb Patil, Arianna Basile, Juan Nogales, Granado San León, Freddy Castillo-Alfonso, Roberto Olivares-Hernández, Gabriela Canto-Encalada, Gabriel Vigueras-Ramírez, Henning Hermjakob, Andreas Dräger, Rahuman S Malik-Sheriff

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

A multiscale mechanistic model of human dendritic cells for in-silico investigation of immune responses and novel therapeutics discovery

Journal
Frontiers in Immunology 14, 1112985
Authors
SS Aghamiri, BL Puniya, R Amin, T Helikar

COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery

Journal
Briefings in Bioinformatics 24 (6), bbad387
Authors
Brandt Bessell, Josh Loecker, Zhongyuan Zhao, Sara Sadat Aghamiri, Sabyasachi Mohanty, Rada Amin, Tomáš Helikar, Bhanwar Lal Puniya

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

Journal
BMC systems biology 3 (1), 58
Authors
Tomáš Helikar, Jim A Rogers

Boolean modeling of biochemical networks

Journal
The Open Bioinformatics Journal
Authors
Tomas Helikar, Naomi Kochi, John Konvalina, Jim A Rogers

Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle

Journal
Plos One 7 (10), e45780
Authors
Robert Todd, Tomas Helikar

Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle

Journal
Bulletin of Mathematical Biology
Authors
Alex Madrahimov, Tomas Helikar, Bryan Kowal, Guoqing Lu, Jim Rogers

A cell simulator platform: the cell collective

Journal
Clinical Pharmacology & Therapeutics 93 (5), 393-395
Authors
Tomáš Helikar, B Kowal, JA Rogers

Molecular phylogeny and evolutionary dynamics of influenza A nonstructural (NS) gene

Journal
Infection, Genetics and Evolution 22, 192-200
Authors
Jianpeng Xu, Haizhen A Zhong, Alex Madrahimov, Tomáš Helikar, Guoqing Lu

Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions

Journal
BMC systems biology 8 (1), 92
Authors
Naomi Kochi, Tomáš Helikar, Laura Allen, Jim A Rogers, Zhenyuan Wang, Mihaela T Matache

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Journal
Bioinformatics 31 (7)
Authors
Aurelien Naldi, Pedro T Monteiro, Christopher Müssel, Hans A Kestler, Denis Thieffry, Ioannis Xenarios, Julio Saez-Rodriguez, Tomas Helikar, Claudine Chaouiya

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

Journal
Journal of Integrative Bioinformatics 12 (2)
Authors
Claudine Chaouiya, Sarah M. Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomáš Helikar

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 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

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

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

Automated pipeline for the inference of Boolean models from molecular interaction maps

Journal
Logical modelling of cellular networks ECCB 2018 Workshop
Authors
S Pankaew, S Soliman, T Helikar, A Niarakis

The CoLoMoTo interactive notebook: accessible and reproducible computational analyses for qualitative biological networks

Journal
Frontiers in physiology 9, 680
Authors
Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé

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

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

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

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

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

SBML Level 3: an extensible format for the exchange and reuse of biological models

Journal
Molecular systems biology 16 (8), e9110
Authors
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, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde de Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker

ccNetViz: a WebGL-based JavaScript library for visualization of large networks

Journal
Bioinformatics 36 (16), 4527-4529
Authors
Ales Saska, David Tichy, Robert Moore, Achilles Rasquinha, Caner Akdas, Xiaodong Zhao, Renato Fabbri, Ana Jeličić, Gaurav Grover, Himanshu Jotwani, Mohamed Shadab, Resa M Helikar, Tomáš Helikar

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

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

Journal
Cold Spring Harbor Laboratory
Authors
Inna Kuperstein, Charles Auffray, Rupert W Overall, Lisa Matthews, Daniela Börnigen, Julia Somers, Tomáš Helikar, Lars MT Eijssen, Anton Yuryev, Olaf Wolkenhauer, Angela Bauch, Silvia Marchesi, Anna Niarakis, Bertrand De Meulder, Alberto Valdeolivas, Maria Peña-Chilet, Alexander R Pico, Ralf Stephan, Robert Phair, Tom C Freeman, Stuart Owen, Anastasia P Nesterova, Piotr Gawron, Agatha Treveil, Jeremy Zucker, John A Bachman, Laurence Calzone, Marius Rameil, Hiroaki Kitano, Nhung Pham, Muying Wang, M Vazquez, Kristina Hanspers, Veronica Shamovsky, Enrico Glaab, Marta Iannuccelli, Vidisha Singh, Zsolt Bocskei, Takahiro G Yamada, Rudi Balling, Tamas Korcsmaros, Egon Willighagen, Martina Kutmon, Martin Golebiewski, Emily E Ackerman, Yusuke Hiki, Jan Hasenauer, Kristie L Oxford, Cristoffer Sevilla, Corinna Montrone, Karen Rothfels, Alina Renz, Valentin Grouès, DAB Rex, Emek Demir, Goar Frishman, Miguel Ponce de Leon, Marta Conti, Anders Riutta, Gisela Fobo, Barbara Brauner, Alexander Mazein, Vanessa Nakonecnij, Vera Ortseifen, Joaquín Dopazo, Gokce Yagmur Summak, Aurelio Orta-Resendiz, Aurelien Dugourd, Dezso Modos, Jakob Vanhoefer, Xiaoming Hu, Bhanwar Lal Puniya, Jason E Shoemaker, Marton Olbei, Andrea Senff-Ribeiro, Sara Sadat Aghamiri, Franck Augé, Özgün Babur, Marek Ostaszewski, Noriko Hiroi, Lincoln Stein, Hanna Borlinghaus, Andreas Ruepp, Julia Scheel, Denise Slenter, Marina Esteban-Medina, Falk Schreiber, Andreas Dräger, Marcio Luis Acencio, Susan L Coort, Anita de Waard, Muhammad Naveez, Robin Haw, Venkata P Satagopam, Luana Licata, Guanming Wu, Benjamin M Gyori, Chris T Evelo, M Orlic-Milacic, Henning Hermjakob, Jeremy Teuton, Laurent Heirendt, Matti Hoch, Tobias Czauderna, Akira Funahashi, Carole Goble, Reinhard Schneider, Carlos Vega, Dénes Türei, Bijay Jassal, Dieter Maier, Leonard Schmiester, Jean-Marie Ravel, Ewa Smula, Sylvain Soliman, Shailendra K Gupta, Alfonso Valencia, Chris Sander, Thawfeek M Varusai, Francesca Sacco, Julio Saez-Rodriguez, Augustin Luna, Ebru Kocakaya, Pablo Porras, Liam Fergusson, Emmanuel Barillot, Kinza Rian, Marvin Martens, Jacques S Beckmann, Friederike Ehrhart, Aurélien Naldi, Arnau Montagud

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

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

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

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

A practical guide to mechanistic systems modeling in biology using a logic-based approach

Journal
Briefings in bioinformatics 22 (4), bbaa236
Authors
Anna Niarakis, 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

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

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Journal
Bioinformatics 37 (21), 3702-3706
Authors
Andreas Dräger, Tomáš Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar

Two heads are better than one: current landscape of integrating QSP and machine learning

Journal
Journal of Pharmacokinetics and Pharmacodynamics 49 (1), 5-18
Authors
Tongli Zhang, Ioannis P Androulakis, Peter Bonate, Limei Cheng, Tomáš Helikar, Jaimit Parikh, Christopher Rackauckas, Kalyanasundaram Subramanian, Carolyn R Cho

Building digital twins of the human immune system: toward a roadmap

Journal
NPJ digital medicine 5 (1), 64
Authors
Reinhard Laubenbacher, Anna Niarakis, Tomáš Helikar, Gary An, Bruce Shapiro, Rahuman S Malik-Sheriff, TJ Sego, Adam Knapp, Paul Macklin, James A Glazier

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

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

Discovering Signal Transduction by Building and Simulating a Bacterial Chemotaxis Model

Journal
CourseSource 12
Authors
Kayla Kester, Skylar Loecker, Tomáš Helikar
Year
2025

AI‐Driven Applications in Clinical Pharmacology and Translational Science: Insights From the ASCPT 2024 AI Preconference Copy

Journal
Clinical and Translational Science 18 (4), e70203
Authors
Mohamed H Shahin, Prashant Desai, Nadia Terranova, Yuanfang Guan, Tomáš Helikar, Sebastian Lobentanzer, Qi Liu, James Lu, Subha Madhavan, Gary Mo, Flora T Musuamba, Jagdeep T Podichetty, Jie Shen, Lei Xie, Mathew Wiens, Cynthia J Musante

From FAIR to CURE: guidelines for computational models of biological systems

Journal
ArXiv, arXiv: 2502.15597 v1
Authors
Herbert M Sauro, Eran Agmon, Michael L Blinov, John H Gennari, Joe Hellerstein, Adel Heydarabadipour, Peter Hunter, Bartholomew E Jardine, Elebeoba May, David P Nickerson, Lucian P Smith, Gary D Bader, Frank Bergmann, Patrick M Boyle, Andreas Dräger, James R Faeder, Song Feng, Juliana Freire, Fabian Fröhlich, James A Glazier, Thomas E Gorochowski, Tomas Helikar, Stefan Hoops, Princess Imoukhuede, Sarah M Keating, Matthias Konig, Reinhard Laubenbacher, Leslie M Loew, Carlos F Lopez, William W Lytton, Andrew McCulloch, Pedro Mendes, Chris J Myers, Jerry G Myers, Lealem Mulugeta, Anna Niarakis, David D van Niekerk, Brett G Olivier, Alexander A Patrie, Ellen M Quardokus, Nicole Radde, Johann M Rohwer, Sven Sahle, James C Schaff, TJ Sego, Janis Shin, Jacky L Snoep, Rajanikanth Vadigepalli, H Steve Wiley, Dagmar Waltemath, Ion Moraru

Forum on immune digital twins: a meeting report

Journal
pj Systems Biology and Applications 10 (1), 19
Authors
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

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Journal
BRIEFINGS IN BIOINFORMATICS 25 (3)
Authors
Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M Keating, David Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noel, Henning Hermjakob, Tomas Helikar, Sylvain Soliman, Laurence Calzone

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

Journal
Journal of integrative bioinformatics 21 (1), 20240008
Authors
Lucian P Smith, Frank T Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König

Augusta: From RNA‐Seq to gene regulatory networks and Boolean models

Journal
Computational and Structural Biotechnology Journal 23, 783-790
Authors
J Musilova, Z Vafek, BL Puniya, R Zimmer, T Helikar, K Sedlar

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

Modeling and Remodeling the Cell: How Digital Twins and HCMV Can Elucidate the Complex Interactions of Viral Latency, Epigenetic Regulation, and Immune Responses

Journal
Current clinical microbiology reports 10 (3), 141-151
Authors
H McMahon-Cole, A Johnson, SS Aghamiri, T Helikar, LB Crawford

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

Decision making in cells

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

The Cell Collective: Toward an open and collaborative approach to systems biology

Journal
BMC Systems Biology 6 (1), 96
Authors
Tomas Helikar, Bryan Kowal, Sean McClenathan, Mitchell Bruckner, Thaine Rowley, Ben Wicks, Manish Shrestha, Kahani Limbu, Jim A Rogers

Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models

Journal
PLoS ONE 7 (10), e46417
Authors
Tomas Helikar, Bryan Kowal, Alex Madrahimov, Manish Shrestha, Jay Pedersen, Kahani Limbu, Ishwor Thapa, Thaine Rowley, Rahul Satalkar, Naomi Kochi, John Konvalina, Jim Rogers

A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells

Journal
PloS one 8 (4), e61757
Authors
Tomáš Helikar, Naomi Kochi, Bryan Kowal, Manjari Dimri, Mayumi Naramura, Srikumar M Raja, Vimla Band, Hamid Band, Jim A Rogers

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Journal
BMC systems biology 7 (1), 135
Authors
Claudine Chaouiya, Duncan Bérenguier, Sarah M Keating, Aurélien Naldi, Martijn P Van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomáš Helikar

Cancer Biology: An Inquiry-Based Approach

Journal
Kendall Hunt Publishing
Authors
Christine Cutucache, Tomas Helikar

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

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

Programmatic access to logical models in the Cell Collective modeling environment via a REST API

Journal
Biosystems 139, 12-16
Authors
Bryan M Kowal, Travis R Schreier, Joseph T Dauer, Tomáš Helikar

Logical modeling and dynamical analysis of cellular networks

Journal
Frontiers in genetics 7, 94
Authors
Wassim Abou-Jaoudé, Pauline Traynard, Pedro T Monteiro, Julio Saez-Rodriguez, Tomáš Helikar, Denis Thieffry, Claudine Chaouiya

Discovering Cellular Respiration with Computational Modeling and Simulations

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

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

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

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

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

Executable Disease Networks: Adding dynamics to molecular maps

Journal
ECCB 2018-17th European Conference on Computational Biology
Authors
Vidisha Singh, Saran Pankaew, Marek Ostaszewski, George D Kalliolias, Sylvain Soliman, Tomáš Helikar, Anna Niarakis

Translating Disease Networks to Executable Boolean Models

Journal
Young Researchers in Life Sciences Federation
Authors
Ss Aghamiri, V Singh, S Soliman, T Helikar, A Niarakis

Logical modeling of cellular processes: from software development to network dynamics

Journal
Frontiers media SA
Authors
Matteo Barberis, Tomáš Helikar

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

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

Automated inference of Boolean models from molecular interaction maps using CaSQ

Journal
Bioinformatics 36 (16), 4473-4482
Authors
Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomáš Helikar, Sylvain Soliman, Anna Niarakis

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

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

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

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

Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC] 2 2019 CoLoMoTo/SysMod Workshop

Journal
Briefings in bioinformatics 22 (2), 1848-1859
Authors
Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S Malik Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C Freeman, Paul Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomáš Helikar, Laurence Calzone

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

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

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Journal
Molecular systems biology 17 (10), e10387
Authors
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 Cristobal Monraz Gomez, 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 Groues, 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, Aurelien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Auge, 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, COVID‐19 Disease Map Community

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

Journal
Journal of integrative bioinformatics 18 (3), 20210021
Authors
Lucian P Smith, Frank T Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König

Recent applications of quantitative systems pharmacology and machine learning models across diseases

Journal
Journal of pharmacokinetics and pharmacodynamics 49 (1), 19-37
Authors
Sara Sadat Aghamiri, Rada Amin, Tomáš Helikar

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

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

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

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

Computational modelling in health and disease: highlights of the 6th annual SysMod meeting

Journal
Bioinformatics 38 (21), 4990-4993
Authors
Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomáš Helikar, Marc Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger

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

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