Tomas Helikar

  • 584 Citations
  • 11 h-Index
20082020

Research output per year

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Research Output

  • 584 Citations
  • 11 h-Index
  • 31 Article
  • 2 Review article
2020

Aberrant energy metabolism and redox balance in seizure onset zones of epileptic patients

Grove, R. A., 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., Jul 15 2020, In : Journal of Proteomics. 223, 103812.

Research output: Contribution to journalArticle

Combined TLR4 and TLR9 agonists induce distinct phenotypic changes in innate immunity in vitro and in vivo

Lampe, A. T., Puniya, B. L., Pannier, A. K., Helikar, T. & Brown, D. M., Sep 2020, In : Cellular Immunology. 355, 104149.

Research output: Contribution to journalArticle

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 2020, In : Journal of Biological Education. 54, 1, p. 33-46 14 p.

Research output: Contribution to journalArticle

3 Scopus citations
2019

Changes in students’ mental models from computational modeling of gene regulatory networks

Dauer, J. T., Bergan-Roller, H. E., King, G. P., Kjose, M. K., Galt, N. J. & Helikar, T., Dec 1 2019, In : International Journal of STEM Education. 6, 1, 38.

Research output: Contribution to journalArticle

Open Access

Modelling activities integrating construction and simulation supported explanatory and evaluative reasoning

King, G. P., Bergan-Roller, H., Galt, N., Helikar, T. & Dauer, J. T., 2019, In : International Journal of Science Education. 41, 13, p. 1764-1786 23 p.

Research output: Contribution to journalArticle

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 journalArticle

2 Scopus citations

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., 2019, In : Journal of Microbiology and Biology Education. 19, 3, 1663.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations
2018

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 journalArticle

5 Scopus citations

CancerDiscover: An integrative pipeline for cancer biomarker and cancer class prediction from high-throughput sequencing data

Mohammed, A., Biegert, G., Adamec, J. & Helikar, T., 2018, In : Oncotarget. 9, 2, p. 2565-2573 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

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 journalArticle

1 Scopus citations

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., 2018, In : BioScience. 68, 8, p. 612-621 10 p.

Research output: Contribution to journalArticle

4 Scopus citations

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 journalArticle

4 Scopus citations

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 journalArticle

6 Scopus citations
2017

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 journalArticle

4 Scopus citations
2016

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 journalReview article

74 Scopus citations

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 journalArticle

7 Scopus citations
2015

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, Keating, S. M., Klamt, S., Klarner, H., Laubenbacher, R., Le Novère, N., Niknejad, A., Rodriguez, N., Siebert, H., Stoll, G. & Zañudo., J. G. T., Apr 1 2015, In : Bioinformatics. 31, 7, p. 1154-1159 6 p.

Research output: Contribution to journalArticle

33 Scopus citations

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 journalArticle

10 Scopus citations

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., 2015, In : Journal of integrative bioinformatics. 12, 2, 1 p.

Research output: Contribution to journalArticle

8 Scopus citations
2014

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., 2014, In : Frontiers in immunology. 5, DEC, 599.

Research output: Contribution to journalArticle

10 Scopus citations

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

Xu, J., Zhong, H. A., Madrahimov, A., Helikar, T. & Lu, G., Mar 2014, In : Infection, Genetics and Evolution. 22, p. 192-200 9 p.

Research output: Contribution to journalArticle

9 Scopus citations

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 journalArticle

4 Scopus citations
2013

A cell simulator platform: The cell collective

Helikar, T., Kowal, B. & Rogers, J. A., May 2013, In : Clinical Pharmacology and Therapeutics. 93, 5, p. 393-395 3 p.

Research output: Contribution to journalArticle

15 Scopus citations

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 journalArticle

27 Scopus citations

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

Madrahimov, A., Helikar, T., Kowal, B., Lu, G. & Rogers, J., Jun 2013, In : Bulletin of Mathematical Biology. 75, 6, p. 988-1011 24 p.

Research output: Contribution to journalArticle

15 Scopus citations

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, Thieffry, D., Le Novère, N., Saez-Rodriguez, J. & Helikar, T., Dec 10 2013, In : BMC systems biology. 7, 135.

Research output: Contribution to journalArticle

63 Scopus citations
2012

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 journalArticle

9 Scopus citations

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 journalArticle

14 Scopus citations

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 journalArticle

69 Scopus citations
2011

Boolean modeling of biochemical networks

Helikar, T., Kochi, N., Konvalina, J. & Rogers, J. A., 2011, In : Open Bioinformatics Journal. 5, p. 16-25 10 p.

Research output: Contribution to journalReview article

25 Scopus citations
2009
39 Scopus citations
2008

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 journalArticle

119 Scopus citations