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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. Forntiers 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 modelling 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