Tomáš Helikar

ORCID: 0000-0003-3653-1906

Biochemistry, Genetics and Molecular BiologyComputer Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 29 papers. Top paper: “SBML Level 3: an extensible format for the exchange and reuse of biological models”.

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

Molecular Systems Biology(2020)10.15252/msb.20199110

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0.861DataRank · unranked

311 citations

Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya +95 more

Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

Briefings in Bioinformatics(2020)10.1093/bib/bbaa046

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0.757DataRank · unranked

38 citations

Martin Kuiper, Marek Ostaszewski, Rahuman S. Malik‐Sheriff, Cristina Casals‐Casas, Denis Thieffry +14 more

Changes in lipid profiles of epileptic mouse model

Metabolomics(2020)10.1007/s11306-020-01729-4

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0DataRank · unranked

16 citations

Ryan Grove, Deepak Madhavan, Cory H. T. Boone, Camila Pereira Braga, Hannah Kyllo +7 more

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

Cellular Immunology(2020)10.1016/j.cellimm.2020.104149

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0DataRank · unranked

15 citations

Bhanwar Lal Puniya, Angela K. Pannier, Tomáš Helikar, Deborah M. Brown, Anna T. Lampe

A practical guide to mechanistic systems modeling in biology using a logic-based approach

Briefings in Bioinformatics(2020)10.1093/bib/bbaa236

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0DataRank · unranked

36 citations

Tomáš Helikar, Anna Niarakis

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

Microorganisms(2020)10.3390/microorganisms8101515

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0DataRank · unranked

5 citations

Baha Abdalhamid, Bhanwar Lal Puniya, Tomáš Helikar, David W. Kelley, Peter C. Iwen +1 more

The Need for Research-Grade Systems Modeling Technologies for Life Science Education

Trends in Molecular Medicine(2020)10.1016/j.molmed.2020.11.005

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0DataRank · unranked

3 citations

Tomáš Helikar

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

Bioinformatics(2020)10.1093/bioinformatics/btaa559

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0DataRank · unranked

6 citations

David Tichy, Robert Moore, Achilles Rasquinha, Caner Akdas, Xiaodong Zhao +8 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.02.893164

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0DataRank · unranked

3 citations

Rada Amin, Bailee Lichter, Robert Moore, Alex Ciurej, Sydney Townsend +4 more

Multi-Approach and Multi-Scale Model of CD4+ T Cells Predicts Switch-Like and Oscillatory Emergent Behaviors in Inflammatory Response to Infection

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.26.964502

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0DataRank · unranked

3 citations

Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomáš Helikar +1 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.11.988238

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0DataRank · unranked

3 citations

Sara Sadat Aghamiri, Bhanwar Lal Puniya, Lauren Mayo, Dennis Startsev, Kashish Poore +3 more

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

INRIA a CCSD electronic archive server(2020)10.5281/zenodo.4245269

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0DataRank · unranked

0 citations

Tomáš Helikar, Matteo Barberis, Marc R. Birtwistle, Laurence Calzone, Claudine Chaouiya +7 more

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

Journal of Pharmacokinetics and Pharmacodynamics(2021)10.1007/s10928-021-09790-9

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0DataRank · unranked

62 citations

Rada Amin, Tomáš Helikar, Sara Sadat Aghamiri

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

npj Systems Biology and Applications(2021)10.1038/s41540-020-00165-3

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0DataRank · unranked

36 citations

Rada Amin, Bailee Lichter, Robert Moore, Alex Ciurej, Sydney J. Bennett +4 more

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

PLoS Computational Biology(2021)10.1371/journal.pcbi.1009209

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0DataRank · unranked

22 citations

Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomáš Helikar +1 more

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Bioinformatics(2021)10.1093/bioinformatics/btab229

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0DataRank · unranked

13 citations

Tomáš Helikar, Matteo Barberis, Marc R. Birtwistle, Laurence Calzone, Claudine Chaouiya +7 more

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

Scientific Reports(2021)10.1038/s41598-021-85044-5

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0DataRank · unranked

8 citations

Bhanwar Lal Puniya, Robert Powers, Chittibabu Guda, Kenneth W. Bayles, David B. Berkowitz +2 more

Building digital twins of the human immune system: toward a roadmap

npj Digital Medicine(2022)10.1038/s41746-022-00610-z

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0DataRank · unranked

160 citations

Anna Niarakis, Tomáš Helikar, Gary An, Bruce E. Shapiro, Rahuman S. Malik‐Sheriff +5 more

Two heads are better than one: current landscape of integrating QSP and machine learning

Journal of Pharmacokinetics and Pharmacodynamics(2022)10.1007/s10928-022-09805-z

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0DataRank · unranked

63 citations

Ioannis P. Androulakis, Peter L. Bonate, Limei Cheng, Tomáš Helikar, Jaimit Parikh +17 more

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Briefings in Bioinformatics(2022)10.1093/bib/bbac212

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0DataRank · unranked

30 citations

Dagmar Waltemath, James A. Glazier, Falk Schreiber, Sarah Keating, David P Nickerson +8 more

Arginine Catabolism and Polyamine Biosynthesis Pathway Disparities Within Francisella tularensis Subpopulations

Frontiers in Microbiology(2022)10.3389/fmicb.2022.890856

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0DataRank · unranked

4 citations

Bhanwar Lal Puniya, Tomáš Helikar, Benjamin Girardo, Steven H. Hinrichs, Marilynn A. Larson +1 more

Computational modelling in health and disease: highlights of the 6th annual SysMod meeting

Bioinformatics(2022)10.1093/bioinformatics/btac609

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0DataRank · unranked

3 citations

Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomáš Helikar, Marc R. Birtwistle +4 more

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

Frontiers in Immunology(2023)10.3389/fimmu.2023.1112985

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0DataRank · unranked

13 citations

Bhanwar Lal Puniya, Rada Amin, Tomáš Helikar, Sara Sadat Aghamiri

COMO: a pipeline for multi-omics data integration in metabolic modeling and drug discovery

Briefings in Bioinformatics(2023)10.1093/bib/bbad387

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0DataRank · unranked

10 citations

Josh Loecker, Zhongyuan Zhao, Sara Sadat Aghamiri, Sabyasachi Mohanty, Rada Amin +3 more

Modeling and Remodeling the Cell: How Digital Twins and HCMV Can Elucidate the Complex Interactions of Viral Latency, Epigenetic Regulation, and Immune Responses

Current Clinical Microbiology Reports(2023)10.1007/s40588-023-00201-w

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0DataRank · unranked

1 citations

Alicia Johnson, Sara Sadat Aghamiri, Tomáš Helikar, Lindsey B. Crawford, Hana McMahon-Cole

Forum on immune digital twins: a meeting report

arXiv (Cornell University)(2023)10.48550/arxiv.2310.18374

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0DataRank · unranked

1 citations

Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luís L. Fonseca +14 more

Forum on immune digital twins: a meeting report

npj Systems Biology and Applications(2024)10.1038/s41540-024-00345-5

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0DataRank · unranked

24 citations

Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luís L. Fonseca +14 more

Augusta: From RNA‐Seq to gene regulatory networks and Boolean models

Computational and Structural Biotechnology Journal(2024)10.1016/j.csbj.2024.01.013

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0DataRank · unranked

7 citations

Zdenek Vafek, Bhanwar Lal Puniya, Ralf Zimmer, Tomáš Helikar, Karel Sedlář +1 more

Automated inference of Boolean models from molecular interaction maps using CaSQ

Bioinformatics(2020)10.1093/bioinformatics/btaa484

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0DataRank · unranked

81 citations

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