Research Output per year
Research Output 2008 2019
Modelling activities integrating construction and simulation supported explanatory and evaluative reasoning
King, G. P., Bergan-Roller, H., Galt, N., Helikar, T. & Dauer, J. T., Jan 1 2019, In : International Journal of Science Education. 41, 13, p. 1764-1786 23 p.Research output: Contribution to journal › Article
Student Understanding of DNA Structure–Function Relationships Improves from Using 3D Learning Modules with Dynamic 3D Printed Models
Howell, M. E., Booth, C. S., Sikich, S. M., Helikar, T., Roston, R. L., Couch, B. A. & van Dijk, K., May 1 2019, In : Biochemistry and Molecular Biology Education. 47, 3, p. 303-317 15 p.Research output: Contribution to journal › Article
Visualizing the invisible: A guide to designing, printing, and incorporating dynamic 3D molecular models to teach structure–function relationships
Howell, M. E., Van Dijk, K., Booth, C. S., Helikar, T., Couch, B. A. & Roston, R. L., Jan 1 2019, In : Journal of Microbiology and Biology Education. 19, 3, 1663.Research output: Contribution to journal › Article
A mechanistic computational model reveals that plasticity of CD4+ T cell differentiation is a function of cytokine composition and dosage
Puniya, B. L., Todd, R. G., Mohammed, A., Brown, D. M., Barberis, M. & Helikar, T., Aug 2 2018, In : Frontiers in Physiology. 9, AUG, 878.Research output: Contribution to journal › Article
CancerDiscover: An integrative pipeline for cancer biomarker and cancer class prediction from high-throughput sequencing data
Mohammed, A., Biegert, G., Adamec, J. & Helikar, T., Jan 1 2018, In : Oncotarget. 9, 2, p. 2565-2573 9 p.Research output: Contribution to journal › Article
Identification of biologically essential nodes via determinative power in logical models of cellular processes
Pentzien, T., Puniya, B. L., Helikar, T. & Matache, M. T., Aug 31 2018, In : Frontiers in Physiology. 9, AUG, 1185.Research output: Contribution to journal › Article
Simulated computational model lesson improves foundational systems thinking skills and conceptual knowledge in biology students
Bergan-Roller, H. E., Galt, N. J., Chizinski, C. J., Helikar, T. & Dauer, J. T., Jan 1 2018, In : BioScience. 68, 8, p. 612-621 10 p.Research output: Contribution to journal › Article
Simulation of stimulation: Cytokine dosage and cell cycle crosstalk driving timing-dependent T cell differentiation
Barberis, M., Helikar, T. & Verbruggen, P., Aug 2 2018, In : Frontiers in Physiology. 9, AUG, 879.Research output: Contribution to journal › Article
The CoLoMoTo interactive notebook: Accessible and reproducible computational analyses for qualitative biological networks
Naldi, A., Hernandez, C., Levy, N., Stoll, G., Monteiro, P. T., Chaouiya, C., Helikar, T., Zinovyev, A., Calzone, L., Cohen-Boulakia, S., Thieffry, D. & Paulevé, L., Jun 19 2018, In : Frontiers in Physiology. 9, JUN, 680.Research output: Contribution to journal › Article
Using concept maps to characterise cellular respiration knowledge in undergraduate students
Bergan-Roller, H. E., Galt, N. J., Helikar, T. & Dauer, J. T., Jan 1 2018, (Accepted/In press) In : Journal of Biological Education.Research output: Contribution to journal › Article
Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers
Mohammed, A., Biegert, G., Adamec, J. & Helikar, T., Oct 17 2017, In : Oncotarget. 8, 49, p. 85692-85715 24 p.Research output: Contribution to journal › Article
Logical modeling and dynamical analysis of cellular networks
Abou-Jaoudé, W., Traynard, P., Monteiro, P. T., Saez-Rodriguez, J., Helikar, T., Thieffry, D. & Chaouiya, C., May 31 2016, In : Frontiers in Genetics. 7, MAY, 94.Research output: Contribution to journal › Review article
Programmatic access to logical models in the Cell Collective modeling environment via a REST API
Kowal, B. M., Schreier, T. R., Dauer, J. T. & Helikar, T., Jan 1 2016, In : BioSystems. 139, p. 12-16 5 p.Research output: Contribution to journal › Article
Systems perturbation analysis of a large-scale signal transduction model reveals potentially influential candidates for cancer therapeutics
Puniya, B. L., Allen, L., Hochfelder, C., Majumder, M. & Helikar, T., Feb 11 2016, In : Frontiers in Bioengineering and Biotechnology. 4, FEB, 10.Research output: Contribution to journal › Article
Cooperative development of logical modelling standards and tools with CoLoMoTo
Naldi, A., Monteiro, P. T., Müssel, C., Kestler, H. A., Thieffry, D., Xenarios, I., Saez-Rodriguez, J., Helikar, T., Chaouiya, C., Albert, R., Barberis, M., Calzone, L., Chasapi, A., Cokelaer, T., Crespo, I., Dorier, J., Dräger, A., Hernandez, C., Hucka, M., De Jong, H. & 10 others, , Apr 1 2015, In : Bioinformatics. 31, 7, p. 1154-1159 6 p.Research output: Contribution to journal › Article
Integrating Interactive Computational Modeling in Biology Curricula
Helikar, T., Cutucache, C. E., Dahlquist, L. M., Herek, T. A., Larson, J. J. & Rogers, J. A., Mar 19 2015, In : PLoS computational biology. 11, 3, e1004131.Research output: Contribution to journal › Article
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1
Chaouiya, C., Keating, S. M., Berenguier, D., Naldi, A., Thieffry, D., van Iersel, M. P., Le Novère, N. & Helikar, T., Jan 1 2015, In : Journal of integrative bioinformatics. 12, 2, 1 p.Research output: Contribution to journal › Article
Design, assessment, and in vivo evaluation of a computational model illustrating the role of CAV1 in CD4+ T-lymphocytes
Conroy, B. D., Herek, T. A., Shew, T. D., Latner, M., Larson, J. J., Allen, L., Davis, P. H., Helikar, T. & Cutucache, C. E., Jan 1 2014, In : Frontiers in immunology. 5, DEC, 599.Research output: Contribution to journal › Article
Molecular phylogeny and evolutionary dynamics of influenza A nonstructural (NS) gene
Xu, J., Zhong, H. A., Madrahimov, A., Helikar, T. & Lu, G., Mar 1 2014, In : Infection, Genetics and Evolution. 22, p. 192-200 9 p.Research output: Contribution to journal › Article
Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions
Kochi, N., Helikar, T., Allen, L., Rogers, J. A., Wang, Z. & Matache, M. T., Sep 5 2014, In : BMC systems biology. 8, 1, 92.Research output: Contribution to journal › Article
A cell simulator platform: The cell collective
Helikar, T., Kowal, B. & Rogers, J. A., May 1 2013, In : Clinical Pharmacology and Therapeutics. 93, 5, p. 393-395 3 p.Research output: Contribution to journal › Article
A Comprehensive, Multi-Scale Dynamical Model of ErbB Receptor Signal Transduction in Human Mammary Epithelial Cells
Helikar, T., Kochi, N., Kowal, B., Dimri, M., Naramura, M., Raja, S. M., Band, V., Band, H. & Rogers, J. A., Apr 18 2013, In : PloS one. 8, 4, e61757.Research output: Contribution to journal › Article
Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle
Madrahimov, A., Helikar, T., Kowal, B., Lu, G. & Rogers, J. A., Jun 1 2013, In : Bulletin of Mathematical Biology. 75, 6, p. 988-1011 24 p.Research output: Contribution to journal › Article
SBML qualitative models: A model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Chaouiya, C., Bérenguier, 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. & 4 others, , Dec 10 2013, In : BMC systems biology. 7, 135.Research output: Contribution to journal › Article
Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models
Helikar, T., Kowal, B., Madrahimov, A., Shrestha, M., Pedersen, J., Limbu, K., Thapa, I., Rowley, T., Satalkar, R., Kochi, N., Konvalina, J. & Rogers, J. A., Oct 17 2012, In : PloS one. 7, 10, e46417.Research output: Contribution to journal › Article
Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle
Todd, R. G. & Helikar, T., Oct 1 2012, In : PloS one. 7, 10, e45780.Research output: Contribution to journal › Article
The Cell Collective: Toward an open and collaborative approach to systems biology
Helikar, T., Kowal, B., McClenathan, S., Bruckner, M., Rowley, T., Madrahimov, A., Wicks, B., Shrestha, M., Limbu, K. & Rogers, J. A., Aug 7 2012, In : BMC systems biology. 6, 96.Research output: Contribution to journal › Article
Boolean modeling of biochemical networks
Helikar, T., Kochi, N., Konvalina, J. & Rogers, J. A., Jul 11 2011, In : Open Bioinformatics Journal. 5, p. 16-25 10 p.Research output: Contribution to journal › Review article
ChemChains: A platform for simulation and analysis of biochemical networks aimed to laboratory scientists
Helikar, T. & Rogers, J. A., Jul 20 2009, In : BMC systems biology. 3, 58.Research output: Contribution to journal › Article
Emergent decision-making in biological signal transduction networks
Helikar, T., Konvalina, J., Heidel, J. & Rogers, J. A., Feb 12 2008, In : Proceedings of the National Academy of Sciences of the United States of America. 105, 6, p. 1913-1918 6 p.Research output: Contribution to journal › Article