Helikar Tomáš

基本信息

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Bio

My research expertise is in computational systems biology, technology development, and STEM education. I’ve built a unique technology, Cell Collective, online modeling, and simulation platform, which integrates life sciences research with education. On the research side, it enables expert scientists to study diseases and identify new drug targets, and on the education side, students learn about biology by building, simulation, and breaking computer models.

Research Interests

Papers共 110 篇Author StatisticsCo-AuthorSimilar Experts

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Forum on immune digital twins: a meeting report

Reinhard Laubenbacher,Fred Adler,Gary An,Filippo Castiglione,Stephen Eubank,Luis L. Fonseca,James Glazier,Tomas Helikar, Marti Jett-Tilton,Denise Kirschner,Paul Macklin,Borna Mehrad,Beth Moore, Virginia Pasour,Ilya Shmulevich,Amber Smith,Isabel Voigt,Thomas E. Yankeelov,Tjalf Ziemssen

npj Systems Biology and Applicationsno. 1 (2024): 1-8

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The Simulation Experiment Description Markup Language (SED-ML): Language Specification for Level 1 Version 5

Lucian P. Smith,Frank T. Bergmann,Alan Garny,Tomas Helikar,Jonathan Karr,David Nickerson,Herbert Sauro,Dagmar Waltemath,Matthias Koenig

JOURNAL OF INTEGRATIVE BIOINFORMATICSno. 1 (2024)

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Toward mechanistic medical digital twins: some use cases in immunology

FRONTIERS IN DIGITAL HEALTH (2024): 1349595-1349595

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Augusta: from RNA‐Seq to Gene Regulatory Networks and Boolean Models

Jana Musilova, Zdenek Vafek,Bhanwar Lal Puniya,Ralf Zimmer,Tomas Helikar,Karel Sedlar

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL（2024）

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FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

Karthik Raman,Miroslav Kratochvil,Brett G. Olivier,Matthias Konig,Pratyay Sengupta, Dinesh Kumar Kuppa Baskaran,Tung V N Nguyen,Daniel Lobo,St Elmo Wilken,Krishna Kumar Tiwari, Aswathy K. Raghu,Indumathi Palanikumar,Lavanya Raajaraam,Maziya Ibrahim, Sanjaay Balakrishnan,Shreyansh Umale, Frank Bergmann, Tanisha Malpani,Venkata P Satagopam,Reinhard Schneider,Moritz E. Beber, Sarah Keating,Mihail Anton,Alina Renz,Meiyappan Lakshmanan,Dong-Yup Lee,Lokanand Koduru,Reihaneh Mostolizadeh,Oscar Dias,Emanuel Cunha,Alexandre Oliveira,Yi Qing Lee,Karsten Zengler, Rodrigo Santibanez-Palominos, Manish Kumar,Matteo Barberis,Bhanwar Lal Puniya,Tomas Helikar,Hoang V. Dinh,Patrick F. Suthers,Costas D. Maranas,Isabella Casini,Seyed Babak Loghmani,Nadine Veith,Nantia Leonidou,Feiran Li,Yu Chen,Jens Nielsen,GaRyoung Lee,Sang Mi Lee,Gi Bae Kim,Pedro T. Monteiro,Miguel C. Teixeira,Hyun Uk Kim,Sang Yup Lee,Ulf W. Liebal,Lars M. Blank,Christian Lieven,Chaimaa Tarzi,Claudio Angione,Manga Enuh Blaise,Celik Pinar Aytar, Mikhail Kulyashov, llya Akberdin,Dohyeon Kim,Sung Ho Yoon, Zhaohui Xu,Jyotshana Gautam,William T. Scott,Peter J. Schaap,Jasper J. Koehorst,Cristal Zuniga, Gabriela Canto-Encalada,Sara Benito-Vaquerizo,Ivette Parera Olm, Maria Suarez-Diez,Qianqian Yuan,Hongwu Ma,Mohammad Mazharul Islam,Jason A. Papin,Francisco Zorrilla,Kiran Raosaheb Patil,Arianna Basile,Juan Nogales, Granado San Leon,Freddy Castillo-Alfonso,Roberto Olivares-Hernandez,Gabriel Vigueras-Ramirez,Henning Hermjakob, Andreas Drager,Rahuman S Malik-Sheriff

biorxiv（2024）

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Forum on Immune Digital Twins: a Meeting Report

Reinhard Laubenbacher, Frederick R. Adler,Gary An,Filippo Castiglione,Stephen Eubank,Luís L. Fonseca,James A. Glazier,Tomáš Helikar, Marti Jett‐Tilton,Denise E. Kirschner,Paul Macklin,Borna Mehrad,Bethany B. Moore, Virginia Pasour,Ilya Shmulevich, Amber M. Smith,Isabel Voigt,Thomas E. Yankeelov,Tjalf Ziemssen

npj systems biology and applicationsno. 1 (2024)

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Drug-target Identification in COVID-19 Disease Mechanisms Using Computational Systems Biology Approaches

Anna Niarakis,Marek Ostaszewski,Alexander Mazein,Inna Kuperstein,Martina Kutmon,Marc E. Gillespie,Akira Funahashi,Marcio Luis Acencio,Ahmed Hemedan,Michael Aichem,Karsten Klein,Tobias Czauderna,Felicia Burtscher,Takahiro G. Yamada,Yusuke Hiki,Noriko F. Hiroi,Finterly Hu,Nhung Pham,Friederike Ehrhart,Egon L. Willighagen,Alberto Valdeolivas,Aurelien Dugourd,Francesco Messina,Marina Esteban-Medina,Maria Pena-Chilet,Kinza Rian,Sylvain Soliman,Sara Sadat Aghamiri,Bhanwar Lal Puniya,Aurelien Naldi,Tomas Helikar,Vidisha Singh, Marco Farinas Fernandez, Viviam Bermudez,Eirini Tsirvouli,Arnau Montagud,Vincent Noel,Miguel Ponce-de-Leon,Dieter Maier,Angela Bauch,Benjamin M. Gyori,John A. Bachman,Augustin Luna,Janet Pinero,Laura I. Furlong,Irina Balaur,Adrien Rougny,Yohan Jarosz,Rupert W. Overall,Robert Phair,Livia Perfetto,Lisa Matthews,Devasahayam Arokia Balaya Rex,Marija Orlic-Milacic,Luis Cristobal Monraz Gomez,Bertrand De Meulder,Jean Marie Ravel,Bijay Jassal,Venkata Satagopam,Guanming Wu,Martin Golebiewski,Piotr Gawron,Laurence Calzone,Jacques S. Beckmann,Chris T. Evelo,Peter D'Eustachio,Falk Schreiber,Julio Saez-Rodriguez,Joaquin Dopazo,Martin Kuiper,Alfonso Valencia,Olaf Wolkenhauer,Hiroaki Kitano,Emmanuel Barillot,Charles Auffray,Rudi Balling,Reinhard Schneider

FRONTIERS IN IMMUNOLOGY (2024)

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

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

BRIEFINGS IN BIOINFORMATICSno. 6 (2023)

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

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

Current clinical microbiology reportsno. 3 (2023): 141-151

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A computational pipeline for drug discovery in immunometabolism against autoimmune diseases

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

JOURNAL OF IMMUNOLOGYno. 1 (2023): 85.15-85.15

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Associate Professor

Papers共 110 篇Author StatisticsCo-AuthorSimilar Experts