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2021
Aghamiri S., Amin R.*, Helikar T*, Recent applications of quantitative systems pharmacology and machine learning models across diseases. Journal of Pharmacokinetics and Pharmacodynamics. https://doi.org/10.1007/s10928-021-09790-9
Wertheim K.Y., Puniya B.L., La Fleur A., Shah, A. R., Barberis M., Helikar T*. Multi-Approach and Multi-Scale Model of CD4+ T Cells Predicts Switch-Like and Oscillatory Emergent Behaviors in Inflammatory Response to Infection. PLoS Computational Biology. 17 (8), e1009209
Yook J.S., You M., Kim J., Toney A. M., Fan R., Lal Puniya B., Helikar T., Vaulont S., Deschemin J. C., Okla M., Xie L., Manik G., Rauault T. A., Lee J., Chung, S. Coordination of beige adipogenesis with IRP, hepcidin, and HIF2α-dependent iron mobilization. Proceedings of the National Academy of Sciences. 118 (40)
Ostaszewski, M., Niarakis, A., Mazein, A., …. Helikar, T., Puniya, B., …. Schneider, R. COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms. Molecular Systems Biology. 17:e10387
Booth C., Crowther A., Helikar R., Luong T., Howell M., Couch B., Roston R., Dijk K., Helikar T.* Teaching advanced concepts in regulation of the lac operon with modeling and simulation. CourseSource. Accepted/In Press
Moore, R., Puniya, B., Powers, R., Guda, C., Bayles, K.W., Berkowitz, D., Helikar, T.* Integrative network analyses of transcriptomics data reveal potential drug targets for acute radiation syndrome. Scientific Reports., 11, 5585
Lal Puniya B., Lichter B., Moore R., Townsend S., Ciuraj A., Shah A.R., Barberis M., Helikar T.* Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders. NPJ Systems Biology and Applications. 7:1. pp.1-18
Booth C. S., Song C., Howell M., Rasquinha A., Saska A., Helikar R., Sikich S., Couch B., Dijk K.van, Roston R.L., Helikar T.* Using computational modeling to teach metabolism as a dynamic system improves student performance. CBE-Life Sciences. 20 (1), ar13.
2020
Helikar T*. Research-grade systems modeling technologies for life science education. Trends in Molecular Medicine. 2020 Dec 15:S1471-4914(20)30292-6. doi: 10.1016/j.molmed.2020.11.005. Epub ahead of print. PMID: 33334676.
Larson, M.A, Abdalhamid, B., Puniya, B. L., Helikar, T., Kelley, D.W., Iwen, P. C. Differences in Blood-derived Francisella tularensis Type B Strains from Clinical Cases of Tularemia. Microorganisms. 8 (10), 1515. [IF: 4.152]
Johnson A., Grove R.A, Madhavan D., Boone C. H. T., Braga C., Kyllo H., Samson K., Simeone K., Simeone T., Helikar T., Hanson C. K., and Adamec J., Changes in lipid profiles of epileptic mouse model. Metabolomics. 16, 106.
*Niarakis A. and *Helikar T., A practical guide to mechanistic computational modeling of biochemical and biological networks, using logical models. Briefings in Bioinformatics. bbaa236.
Clark, C., Helikar, T., Dauer, J. Simulating a computational biological model, rather than reading, elicits changes in brain activity consistent with complex reasoning. CBE – Life Sciences Education, 19(3).
Saska, A., Tichy, D., Moore II, R., Rasquinha, A., Akdas, C., Zhao, X., Fabbri, R., Jelicic, A., Grover, G., Jotwani, H., Shadab, M., Helikar, R., Helikar, T.* ccNetViz: A WebGL based Javascript library for visualization of large networks. Bioinformatics. btaa559
Lampe AT, Hain JL, Puniya BL, Ballweg MD, Grint KJ, Helikar T, Brown DM. Combined TLR4 and TLR9 agonists induce distinct transcriptional changes in dendritic cells leading to enhanced anti-viral responses. Cellular Immunology. 104149
Aghamiri, S., Singh, V., Naldi, A., Helikar, T., Soliman, S., Niarakis, A. 2020. Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics. btaa484
Keating, S., Waltemath, D., Konig, M., Zhang, F., Drager, A., Chaouiya, C., Bergmann, F., Finney, A., Gillespie, C., Helikar, T., … [40 authors]… Doyle, J. SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Sys Bio. 16:e9110
Howell, M., Booth, C., Helikar, T., van Dijk, K., Couch, B., Roston, R. 2020. Interactive learning modules with 3D printed models improve student understanding of protein structure-function relationships. Biochem and Mol Biol Edu. 48(4).
Niarakis A., … [16 authors] … *Helikar T. and *Calzone L. 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. Briefings in Bioinformatics. bbaa046
Grove R, Madhavan D, Boone C.H.T., Braga C.P., Papackova Z., Kyllo H., Samson K., Simeone K., Simeone T., Helikar T., Hanson C.K., Adamec J. 2020. Aberrant energy metabolism and redox balance in seizure onset zones of epileptic patients. Journal of Proteomics, 223.
2019
*Dauer, J.T., H. Bergan-Roller, G. King, N. Galt, M. Kjose, and T. Helikar. Changes in students’ mental models from computational modeling of gene regulatory networks. International Journal of STEM Education. 6 (1), 38
King G, Bergan-Roller HE, Galt NJ, Helikar T, Dauer JT. Modelling activities integrating construction and simulation supported explanatory and evaluative reasoning. International Journal of Science Education. 41 (13), 1764-1786
Howell ME, Booth CS, Sikich SM, Helikar T, Roston RL, Couch BA, van Dijk K. Student Understanding of DNA Structure-Function Relationships Improves from Using 3D Learning Modules with Dynamic 3D Printed Models. Biochem Mol Biol Educ. doi: 10.1002/bnb.21234
King G, Helikar R, Briona L, Dauer JT, *Helikar T. Learning about Photosynthesis through Interactive Modeling and Simulations. Proceedings of the Association for Biology Laboratory Education 40 (10)
Crowther A., Bergan-Roller H., Galt N., Dauer J., *Helikar T. Learning about the Regulation of the lac Operon with Computational Modeling. CourseSource. https://doi.org/10.24918/cs.2019.4
2018
Puniya B., Todd R.G., Mohammed A., Brown D., Barberis M., *Helikar T. (2018) A mechanistic computational model reveals that plasticity of CD4+ T cell differentiation is a function of cytokine composition and dosage. Frontiers in Physiology 9, 462
Barberis M., Helikar T., Verbruggen P. (2018) Simulation of Stimulation: Cytokine Dosage and Cell Cycle Crosstalk Drive Timing-Dependent T Cell Differentiation. Frontiers in Physiology. 9:879
Singh V., Marek Ostaszewski M., Kalliolias G. D., Chiocchia G., Olaso R., Petit-Teixeira E., Helikar T., Niarakis A. (2018) Computational Systems Biology Approach for the Study of Rheumatoid Arthritis: From a Molecular Map to a Dynamical Model. Genomics and Computational Biology. 4:1
Naldi A, Hernandez C, Levy N, Stoll G, Monteiro P, Chaouiya C, Helikar T, Zinovyev A, Calzone L, Cohen-Boulakia S, Thieffry D, and Pauleve L, (2018) The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. Frontiers in Physiology 9, 680
Biegert G., Mohammed A., Adamec J., *Helikar T. (2018) CancerDiscover: An automated pipeline for cancer classification and biomarker discovery using machine learning. Oncotarget 9 (2), 2565
Pentzien T, Lal Puniya B, Helikar T, Matache MT. (2018) Identification of biologically essential nodes via determinative power in logical models of cellular processes. Frontiers in Physiology. 9: 1185
Howell ME, van Dijk K, Booth CS, Helikar T, Couch BA, Roston RL. Visualizing the Invisible: A Guide to Designing, Printing, and Incorporating Dynamic 3D Molecular Models to Teach Structure-Function Relationships. Journal of microbiology and biology education. 19 (3).
Crowther A, Bergan-Roller HE, Galt NJ, Dauer JT, *Helikar T. Learning about the Regulation of the lac Operon with Computational Modeling. CourseSource. In Press
Crowther A, Bergan-Roller HE, Galt NJ, Booth C, Dauer JT, *Helikar T. Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon. CourseSource. https://doi.org/10.24918/cs.2018.9
Appleby L, Bergan-Roller HE, Dauer JT, *Helikar T. Engaging Complexity: Learning about Biological Systems via Construction of and Interaction with Computational Models. Proceedings of the Association for Biology Laboratory Education. 39 (1).
Bergan-Roller HE, Galt NJ, Helikar T, Dauer JT. Using Concept Maps to Characterise Cellular Respiration Knowledge in Undergraduate Students. Journal of Biological Education. pp 1-14.
Bergan-Roller HE, Galt NJ, Chizinski C, Helikar T, Dauer JT. (2018) Simulated Computational Model Lesson Improves Foundational Systems Thinking Skills and Conceptual Knowledge in Biology Students. BioScience. 68:8, 612-621
2017
Biegert G., Mohammed A., Adamec J., *Helikar T. Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers Oncotarget 8, 85692-85715
Perez V.M., Puniya B., Helikar T., DiRusso C.C., Black P.N. (2017) Computational Modeling of Human Fatty Acid Transport Protein 2. The FASEB Journal. 630.20-630.20
Bergan-Roller H., Galt N., Dauer J., *Helikar T. (2017) Discovering Cellular Respiration with Computational Modeling and Simulations. CourseSource https://doi.org/10.24918/cs.2017.10
2016
Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C. (2016) Cellular Networks: Logics and Dynamics. Frontiers in Genetics.7:94
Puniya B., Allen L., Hochfelder C., Majumder M., Helikar T. (2016) Systems Perturbation Analysis of a Large Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics. Frontiers in Bioengineering and Biotechnology.4:10. doi: 10.3389/fbioe.2016.00010
Kowal B., Schreier T.R., Dauer T.J., Helikar T. (2015) Programmatic Access to Logical Models in the Cell Collective Modeling Environment via a REST API. BioSystems. 139:12-16
2015
Chaouiya C., Keating S.M., Berenguier D., Naldi A., Thieffry D., van Iersel M.P., le Novère N., Helikar T. (2015) The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. Journal of Integrative Bioinformatics. doi: 10.2390/biecoll-jib-2015-270
Naldi A., Monteiro P., Mussel C., Consortium for Logical Modelling and Tools, Kestler H.A., Thieffry D., Xenarios I., Saez-Rodriguez J., Helikar T., Chaouiya C. (2015) Cooperative development of logical modeling standards and tools with CoLoMoTo. Bioinformatics. doi: 10.1093/bioinformatics/btv013
Helikar T., Cutucache C. E., Herek T., Rogers J. (2015) Integrating interactive computational modeling in biology curricula. PLoS Computational Biology. 11(3): e1004131
2014
Conroy B. D., Herek T.A., Shew T. D., Latner M., Larson J. J., Allen L., Davis P. H., Helikar T., Cutucache C. E. (2014) Design, Assessment, and In Vivo Evaluation of a Computational Model Illustrating the Role of CAV1 in CD4+ T Lymphocytes. Frontiers in Immunology 5:599
Kochi N., Helikar T., Allen L., Rogers J.A., Wang Z., and Matache M.T. (2014) Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions. BMC Systems Biology 8(1):92
Xu J., Zhong A.H., Madrahimov A., Helikar T., Lu G. (2014) Molecular Phylogeny and Evolutionary Dynamics of Influenza A Nonstructural (NS) Gene Infection, Genetics and Evolution 192-200
Cutucache C. & Helikar T. (2014) Cancer Biology: An Inquiry-Based Approach. Kendall/Hunt. Dubuque, IA. Print [Sample Chapters].
2013
Chaouiya C., Berenguier D., Keating S.M., Naldi A., van Iersel M.P., Rodriguez N., Dräger A, Büchel F., Cokelaer T., Kowal B., Wicks B., Gonçalves E., Dorier J., Page M., Monteiro P.T., von Kamp A., Xenarios I., de Jong H., Hucka M., Klamt S., Thieffry D. le Novère N., Saez-Rodriguez J., Helikar T. (2013) SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology. 7:135
Helikar T., Kochi N., Dimri M., Naramura M., Raja S., Band V., Band H., Rogers J. A. (2013) A comprehensive dynamical model of signal transduction in a human mammary epithelial cell. PLoS ONE. DOI: 10.1371/journal.pone.0061757
Helikar T. Kowal B., Rogers J.A. (2013) A cell simulator platform: The Cell Collective. Clinical Pharmacology and Therapeutics. DOI:10.1038/clpt.2013.41
2012
Madrahimov A., Helikar T., Kowal B., Lu G., Rogers J. (2012) Dynamics of influenza-host interactions during infection and virus replication cycle. Bulletin of Mathematical Biology. DOI: 10.1007/s11538-012-9777-2
Helikar T., Kowal B., Madrahimov A., Shrestha M., Pedersen J., Konvalina J., and Rogers J.A. (2012) Bio-Logic Builder: A non-technical tool for building dynamical, qualitative models. PLoS ONE 7(10): e46417
Todd R., Helikar T. (2012) Ergodic sets as cell phenotype of budding yeast cell cycle. PLoS ONE 7(10): e45780
Helikar T., Kowal B., McClenathan S., Bruckner M., Rowley T., Madrahimov A., Wicks B., Shrestha M., Limbu K., and Rogers J.A. (2012) The Cell Collective: Toward an open and collaborative approach to systems biology. BMC Systems Biology. 6:96
-2011
Helikar T., Kochi N., Konvalina J., Rogers J.A. (2011) Boolean modeling of biochemical networks. The Open Bioinformatics Journal. 5. pp. 16-25
Helikar T., Kochi N., Konvalina J., Rogers J.A. (2010) Decision making in cells. In: Systems biology for signaling networks. Springer.
Helikar T., Rogers J.A. 2009. ChemChains: A Platform for Simulation and Analysis of Biochemical Networks Aimed to Laboratory Scientists. BMC Systems Biology. 3:58.
Helikar T., Konvalina J., Heidel J., Rogers J.A. (2008) Emergent Decision-making in Biological Signal Transduction Networks. Proc. Natl. Acad. Sci USA. 105(6). pp.1913-8