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2017

Bergan-Roller HE, Galt NJ, Helikar T, Dauer JT. Days of lecture instruction have limited impact on student-constructed models of cellular respiration. under review

Bergan-Roller HE, Galt NJ, Chizinski C, Helikar T, Dauer JT. Simulated computational model lesson on cellular respiration improves systems thinking in undergraduate biology students. under review

Biegert G., Mohammed A., Adamec J., *Helikar T. CancerDiscover: An automated pipeline for cancer classification and biomarker discovery using machine learning. under review

Pentzien T, Lal Puniya B, Helikar T, Matache MT. Identification of biologically essential nodes via determinative power in logical models of cellular processes. Bulletin of Mathematical Biology. under revision

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