Tomas Helikar

  • 514 Citations
  • 11 h-Index
20082019
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Research Output 2008 2019

  • 514 Citations
  • 11 h-Index
  • 28 Article
  • 2 Review article
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 journalArticle

simulation
student
group discussion
small group
biology

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

Learning
Students
DNA
Biochemistry
Molecular Structure
1 Citation (Scopus)

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 journalArticle

Open Access
molecular models
Printing
Molecular Models
structure-activity relationships
dynamic models
2018
4 Citations (Scopus)

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

Cell Differentiation
Cytokines
T-Lymphocytes
Phenotype
Transcription Factors

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 journalArticle

Tumor Biomarkers
Neoplasms
Software
Licensure
Quality Control

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

Information Theory
Entropy
Signal Transduction
Databases
2 Citations (Scopus)

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 journalArticle

Systems Analysis
students
Students
Biological Sciences
Cell Respiration
3 Citations (Scopus)

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

Cell Differentiation
Cell Cycle
Cytokines
T-Lymphocytes
Interleukins
3 Citations (Scopus)

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

Workflow
Biological Models
Learning Curve
Software
Boidae
1 Citation (Scopus)

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 journalArticle

Cell Respiration
college students
cell respiration
students
Students
2017
2 Citations (Scopus)

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

Tumor Biomarkers
Neoplasms
Critical Pathways
Feasibility Studies
2016
60 Citations (Scopus)

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

Biological Phenomena
Helper-Inducer T-Lymphocytes
Cell Cycle Checkpoints
Surveys and Questionnaires

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

Application programming interfaces (API)
Programming
Cell
Modeling
Model
7 Citations (Scopus)
Signal transduction
Essential Genes
Signal Transduction
Cell death
Genes
2015
30 Citations (Scopus)

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

Computer Simulation
Software
Research Personnel
Modeling
Reusability
8 Citations (Scopus)

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

Computational Modeling
curriculum
Curriculum
Curricula
Biology
6 Citations (Scopus)

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 journalArticle

Systems Biology
Language
Gene Expression
2014
8 Citations (Scopus)

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 journalArticle

Caveolin 1
T-Lymphocytes
Synapses
Cell Proliferation
T-Cell Leukemia
9 Citations (Scopus)

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 journalArticle

influenza
Phylogeny
Human Influenza
phylogeny
Swine
4 Citations (Scopus)

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

Boolean Networks
Information Services
Information fusion
Information Fusion
Biological Networks
2013
13 Citations (Scopus)

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 journalArticle

Drug Repositioning
Biological Models
Drug Design
Drug Discovery
Pharmaceutical Preparations
26 Citations (Scopus)

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

Signal transduction
Epidermal Growth Factor
Computer Simulation
breasts
signal transduction
15 Citations (Scopus)

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 journalArticle

influenza
Influenza
Orthomyxoviridae
Viruses
Replication
60 Citations (Scopus)

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

Markup languages
Systems Biology
Language
Infrastructure
Interaction
2012
9 Citations (Scopus)

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

Biological Phenomena
Laboratory Personnel
Saccharomycetales
Mathematics
Signal transduction
12 Citations (Scopus)

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

Saccharomycetales
Yeast
cell cycle
Cell Cycle
Cyclins
60 Citations (Scopus)

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

Systems Biology
Cell
Model
Laboratory Personnel
Biological Phenomena
2011
23 Citations (Scopus)

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 journalReview article

Systems Biology
Cells
Kinetics
2009
36 Citations (Scopus)
Laboratory Personnel
Biochemical Networks
Computer Simulation
Software
Simulation
2008
112 Citations (Scopus)

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

Information Services
Automatic Data Processing
Cluster Analysis
Noise
Signal Transduction