Publications

SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

published date:

2023/12/10

authors:

Chaouiya C., Berenguier D... Helikar T.

Immune Digital Twin Blueprint: A Comprehensive Simulatable Model of the Human Immune System

published date:

2023/05/16

authors:

Robert Moore, Rada Amin, Sara Aghamiri, Akram Mohammed, Alyssa La Fleur, Bhanwar Lal Puniya, Tomáš Helikar

COMO: A Pipeline for Multi-Omics Data Integration in Metabolic Modeling and Drug Discovery

published date:

2023/05/09

authors:

Brandt Bessell, Josh Loecker, Zhongyuan Zhao, Sara Sadat Aghamiri, Sabyasachi Mohanty, Rada Amin, Tomáš Helikar, Bhanwar Lal Puniya

A multiscale mechanistic model of human dendritic cells for in-silico investigation of immune responses and novel therapeutics discovery

published date:

2023/03/10

authors:

Aghamiri SS, Puniya BL, Amin R and Helikar T

Arginine Catabolism and Polyamine Biosynthesis Pathway Disparities Within Francisella tularensis Subpopulations

published date:

2022/06/20

authors:

Yue Y, Puniya BL, Helikar T, Girardo B, Hinrichs SH and Larson MA

A computational approach to investigate constitutive activation of NF-κB

published date:

2022/05/27

authors:

Ahmed Mobeen, Bhanwar Lal Puniya, Srinivasan Ramachandran

Recent applications of quantitative systems pharmacology and machine learning models across diseases.

published date:

2022/02

authors:

Aghamiri S., Amin R.*, Helikar T*

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

published date:

2021/10/19

authors:

Marek Ostaszewski et al.

An in silico, structural, and biological analysis of lactoferrin of different mammals

published date:

2021/09/30

authors:

Dielson da S. Vieira a, Richard C. Polveiro b, Thomas J. Butler c, Timothy A. Hackett d, Camila P. Braga d, Bhanwar Lal Puniya... Francisco L.F. Feitosa

Coordination of beige adipogenesis with IRP, hepcidin, and HIF2α-dependent iron mobilization.

published date:

2021/09/30

authors:

Yook J.S., You M., Kim J., Toney A. M., Fan R., Lal Puniya B., Helikar T., Vaulont S., Deschemin J. C., Okla M., Xie L., Manik G., Rauault T. A., Lee J., Chung, S.

A multi-approach and multi-scale platform to model CD4+ T cells responding to infections

published date:

2021/08/03

authors:

Wertheim K.Y., Puniya B.L., La Fleur A., Shah, A. R., Barberis M., Helikar T.

Integrative network analyses of transcriptomics data reveal potential drug targets for acute radiation syndrome.

published date:

2021/03/10

authors:

Moore, R., Puniya, B., Powers, R., Guda, C., Bayles, K.W., Berkowitz, D., Helikar, T.

Integrative network analyses of transcriptomics data reveal potential drug targets for acute radiation syndrome

published date:

2021/03/10

authors:

Moore, R., Puniya, B.L., Powers, R. et al.

TaBooN Boolean Network Synthesis Based on Tabu Search

published date:

2021/03/04

authors:

Sara Sadat Aghamiri, Franck Delaplace

Using computational modeling to teach metabolism as a dynamic system improves student performance.

published date:

2021/02/26

authors:

Booth C. S., Song C., Howell M., Rasquinha A., Saska A., Helikar R., Sikich S., Couch B., Dijk K.van, Roston R.L., Helikar T.

Research-grade systems modeling technologies for life science education.

published date:

2021/02

authors:

Helikar T.

Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders.

published date:

2021/01/22

authors:

Lal Puniya B., Lichter B., Moore R., Townsend S., Ciuraj A., Shah A.R., Barberis M., Helikar T.

Teaching advanced concepts in regulation of the lac operon with modeling and simulation.

published date:

2021

authors:

Booth C., Crowther A., Helikar R., Luong T., Howell M., Couch B., Roston R., Dijk K., Helikar T.

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms.

published date:

2021

authors:

Ostaszewski, M., Niarakis, A., Mazein, A., …. Helikar, T., Puniya, B., …. Schneider, R.

A practical guide to mechanistic computational modeling of biochemical and biological networks, using logical models.

published date:

2020/10/16

authors:

Niarakis A. and Helikar T.

Changes in lipid profiles of epileptic mouse model.

published date:

2020/10/06

authors:

Johnson A., Grove R.A, Madhavan D., Boone C. H. T., Braga C., Kyllo H., Samson K., Simeone K., Simeone T., Helikar T., Hanson C. K., and Adamec J.

Differences in Blood-derived Francisella tularensis Type B Strains from Clinical Cases of Tularemia.

published date:

2020/10/01

authors:

Larson, M.A, Abdalhamid, B., Puniya, B. L., Helikar, T., Kelley, D.W., Iwen, P. C.

Simulating a computational biological model, rather than reading, elicits changes in brain activity consistent with complex reasoning.

published date:

2020/09/01

authors:

Clark, C., Helikar, T., Dauer, J.

Combined TLR4 and TLR9 agonists induce distinct transcriptional changes in dendritic cells leading to enhanced anti-viral responses.

published date:

2020/09

authors:

Lampe AT, Hain JL, Puniya BL, Ballweg MD, Grint KJ, Helikar T, Brown DM.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

published date:

2020/08/26

authors:

Keating, S., Waltemath, D., Konig, M., Zhang, F., Drager, A., Chaouiya, C., Bergmann, F., Finney, A., Gillespie, C., Helikar, T., … [40 authors]… Doyle, J.

ccNetViz: a WebGL-based JavaScript library for visualization of large networks.

published date:

2020/08/15

authors:

Saska, A., Tichy, D., Moore II, R., Rasquinha, A., Akdas, C., Zhao, X., Fabbri, R., Jelicic, A., Grover, G., Jotwani, H., Shadab, M., Helikar, R., Helikar, T.

Automated inference of Boolean models from molecular interaction maps using CaSQ.

published date:

2020/08/15

authors:

Aghamiri, S., Singh, V., Naldi, A., Helikar, T., Soliman, S., Niarakis, A. 2020.

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

published date:

2020/07/15

authors:

Grove R, 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.

Interactive learning modules with 3D printed models improve student understanding of protein structure-function relationships.

published date:

2020/06/26

authors:

Howell, M., Booth, C., Helikar, T., van Dijk, K., Couch, B., Roston, R. 2020.

Automated inference of Boolean models from molecular interaction maps using CaSQ

published date:

2020/05/13

authors:

Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomáš Helikar, Sylvain Soliman, Anna Niarakis

Setting the basis of best practices and standards for curation and annotation of logical models in biology

published date:

2020/04/21

authors:

Niarakis A., … [16 authors] … *Helikar T. and *Calzone L.

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

published date:

2019/11/19

authors:

Dauer, J.T., H. Bergan-Roller, G. King, N. Galt, M. Kjose, and T. Helikar.

Modelling activities integrating construction and simulation supported explanatory and evaluative reasoning.

published date:

2019/07/22

authors:

King G, Bergan-Roller HE, Galt NJ, Helikar T, Dauer JT.

Student Understanding of DNA Structure-Function Relationships Improves from Using 3D Learning Modules with Dynamic 3D Printed Models.

published date:

2019/03/21

authors:

Howell ME, Booth CS, Sikich SM, Helikar T, Roston RL, Couch BA, van Dijk K.

Learning about Photosynthesis through Interactive Modeling and Simulations.

published date:

2019

authors:

King G, Helikar R, Briona L, Dauer JT, Helikar T.

Using Concept Maps to Characterise Cellular Respiration Knowledge in Undergraduate Students.

published date:

2018/11/08

authors:

Bergan-Roller HE, Galt NJ, Helikar T, Dauer JT.

Visualizing the Invisible: A Guide to Designing, Printing, and Incorporating Dynamic 3D Molecular Models to Teach Structure-Function Relationships.

published date:

2018/10/31

authors:

Howell ME, van Dijk K, Booth CS, Helikar T, Couch BA, Roston RL.

Computational Modeling of Human Fatty Acid Transport Protein 2.

published date:

2018/10/03

authors:

Perez V.M., Puniya B., Helikar T., DiRusso C.C., Black P.N.

Identification of biologically essential nodes via determinative power in logical models of cellular processes.

published date:

2018/08/31

authors:

Pentzien T, Lal Puniya B, Helikar T, Matache MT.

A mechanistic computational model reveals that plasticity of CD4+ T cell differentiation is a function of cytokine composition and dosage.

published date:

2018/08/02

authors:

Puniya B., Todd R.G., Mohammed A., Brown D., Barberis M., Helikar T.

Simulation of Stimulation: Cytokine Dosage and Cell Cycle Crosstalk Drive Timing-Dependent T Cell Differentiation.

published date:

2018/08/02

authors:

Barberis M., Helikar T., Verbruggen P.

Simulated Computational Model Lesson Improves Foundational Systems Thinking Skills and Conceptual Knowledge in Biology Students.

published date:

2018/06/20

authors:

Bergan-Roller HE, Galt NJ, Chizinski C, Helikar T, Dauer JT.

Computational Systems Biology Approach for the Study of Rheumatoid Arthritis: From a Molecular Map to a Dynamical Model.

published date:

2018

authors:

Singh V., Marek Ostaszewski M., Kalliolias G. D., Chiocchia G., Olaso R., Petit-Teixeira E., Helikar T., Niarakis A.

Engaging Complexity: Learning about Biological Systems via Construction of and Interaction with Computational Models.

published date:

2018

authors:

Appleby L, Bergan-Roller HE, Dauer JT, Helikar T.

CancerDiscover: An automated pipeline for cancer classification and biomarker discovery using machine learning.

published date:

2017/12/20

authors:

Biegert G., Mohammed A., Adamec J., Helikar T.

Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers.

published date:

2017/09/21

authors:

Biegert G., Mohammed A., Adamec J., Helikar T.

Discovering Cellular Respiration with Computational Modeling and Simulations.

published date:

2017

authors:

Bergan-Roller H., Galt N., Dauer J., Helikar T.

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

published date:

2016/10/18

authors:

Chaouiya C., Keating S.M., Berenguier D., Naldi A., Thieffry D., van Iersel M.P., le Novère N., Helikar T.

Cellular Networks: Logics and Dynamics.

published date:

2016/04/31

authors:

Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C.

Systems Perturbation Analysis of a Large Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics.

published date:

2016/02/11

authors:

Puniya B., Allen L., Hochfelder C., Majumder M., Helikar T.

Programmatic Access to Logical Models in the Cell Collective Modeling Environment via a REST API.

published date:

2016/01

authors:

Kowal B., Schreier T.R., Dauer T.J., Helikar T.

Integrating interactive computational modeling in biology curricula.

published date:

2015/03/19

authors:

Helikar T., Cutucache C. E., Herek T., Rogers J.

Cooperative development of logical modeling standards and tools with CoLoMoTo.

published date:

2015/01/25

authors:

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.