Research Output per year
Research Output 2008 2019
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
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 journal › Article
Learning
Students
DNA
Biochemistry
Molecular Structure
2
Citations
(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 journal › Article
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 journal › Article
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 journal › Article
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 journal › Article
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 journal › Article
Systems Analysis
students
Students
Biological Sciences
Cell Respiration
4
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 journal › Article
Cell Differentiation
Cell Cycle
Cytokines
T-Lymphocytes
Interleukins
4
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 journal › Article
Workflow
Biological Models
Learning Curve
Software
Boidae
2
Citations
(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 journal › Article
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 journal › Article
Tumor Biomarkers
Neoplasms
Critical Pathways
Feasibility Studies
2016
63
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 journal › Review 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 journal › Article
Application programming interfaces (API)
Programming
Cell
Modeling
Model
7
Citations
(Scopus)
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
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, , Apr 1 2015, In : Bioinformatics. 31, 7, p. 1154-1159 6 p.Research output: Contribution to journal › Article
Computer Simulation
Software
Research Personnel
Modeling
Reusability
9
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 journal › Article
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 journal › Article
Systems Biology
Language
Gene Expression
2014
9
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 journal › Article
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 journal › Article
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 journal › Article
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 journal › Article
Drug Repositioning
Biological Models
Drug Design
Drug Discovery
Pharmaceutical Preparations
27
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 journal › Article
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 journal › Article
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, , Dec 10 2013, In : BMC systems biology. 7, 135.Research output: Contribution to journal › Article
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 journal › Article
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 journal › Article
Saccharomycetales
Yeast
cell cycle
Cell Cycle
Cyclins
61
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 journal › Article
Systems Biology
Cell
Model
Laboratory Personnel
Biological Phenomena
2011
24
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 journal › Review article
Systems Biology
Cells
Kinetics
2009
36
Citations
(Scopus)
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
Laboratory Personnel
Biochemical Networks
Computer Simulation
Software
Simulation
2008
113
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 journal › Article
Information Services
Automatic Data Processing
Cluster Analysis
Noise
Signal Transduction