Computational Systems Biology

Nantia Leonidou

M.Sc. in Bioinformatics

Office

Department for Computer Science
Institute for Bioinformatics and Medical Informatics
Sand 14 ･ Main Floor ･ Office C107
+49-7071-29-70452
nantia.leonidou@uni-tuebingen.de

 

 

 

Bibliography

Google-Scholar-Profile
NCBI-Pubmed-Profile
​​​​​​​Web-of-Science-Profil​​​​​​​

Social Media

Twitter Account
LinkedIn Profile
ORCID Account
GitHub Profile

 

Academic Qualifications

Research Visits

  • Visiting researcher, Laboratory of Pharmaceutical Microbiology (LPM), Ghent University, Belgium
    (Duration: 29. May – 30. June 2023; Supervisor: Prof. Aurélie Crabbé)
  • Visiting researcher, Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karl University of Tübingen, Germany
    (Duration: 13. March – 26. May 2023; Supervisor: Prof. Simon Heilbronner)

 

Research Interests

  • Systems Biology and Metabolic Engineering:

    • Systems-level analysis of molecular, biochemical, and metabolic mechanisms in pro- and eukaryotes in health and disease.

    • Constraint-based in silico reconstruction and analysis of mathematical networks enabling the discovery of unknown phenotypes and the development of novel therapies:

      • Eukaryotic biochemical models to understand, predict, and manipulate bacterial metabolism.

      • Host-pathogen metabolic models; analysis of infection mechanisms between pathogens and their host.

      • Microbial metabolic reconstructions & interactions in microbial communities.

    • Integration of multi-omics data to gain a comprehensive understanding of biological processes.

  • Visualization:

    • Creation of pathway maps and interpretation of metabolic processes.

  • Software Development:

    • Development of computational tools to analyze complex biological data, build context-specific models, and automated model annotation.

 

Experimental Experience

  • Aseptic Techniques
  • Microbial culture handling (streak plate and inoculation methods) and sterile sampling
  • Serial dilution and plating
  • Formulation and quantification of culture media
  • Gram stain
  • Microscopy
  • Creation and analysis of kinetic growth curves to understand microbial growth dynamics and response to environmental conditions
  • Interpretation of experimental observations
  • Execution of microbiological protocols

 

Current Research Projects

Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens

Project TTU 08.703 is funded by the German Center for Infection Research (DZIF, doi:10.13039/100009139) within the Deutsche Zentren der Gesundheitsforschung (BMBF-DZG, German Centers for Health Research of the Federal Ministery of Education and Research), grant № 8020708703. The research group is part of the network for research on Healthcare-Associated and Antibiotic Resistant Bacterial Infections (HAARBI). Funding period: July 2018 to June 2022.

Completed Research Projects

Cluster of Excellence – Controlling Microbes to Fight Infections
Computer Modeling and Experimental Validation of Microbial Interactions
Collaborative Project

The project № EXC-2124/05.037_0 is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, doi:10.13039/501100001659) under Germanyʼs Excellence Strategy – EXC 2124 – 390838134 and supported by the Cluster of Excellence CMFI (Controling Microbes to Fight Infections) from May 2021 to April 2024 as a collaboration with the group of Dr. Simon Heilbronner.

International Networking Program for female researchers

This program supports female researchers who are part of the Control of Microorganisms to Fight Infection (CMFI) Cluster of Excellence by funding a one to six week visit to outstanding research laboratories. The aim of the program is to encourage young female scientists to build international collaborations and networks, preferably in a laboratory led by female scientists. Each visit should last at least a week. The guest laboratory should be located at an institution outside of Germany with an excellent international reputation.

Federal Ministry of Education and Research (BMBF)
Identification of robust antiviral drug targets against SARS-CoV-2

This start-up project supports the identification of robust targets for the treatment of COVID-19 to be experimentally verified in subsequent projects.

Funded by the Federal Ministry of Education and Research (BMBF) and the Baden-Württemberg Ministry of Science as part of the Excellence Strategy of the German Federal and State Governments.

Publications

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

Karthik Raman, Miroslav Kratochvíl, Brett G. Olivier, Matthias König, 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, Shreyanash Umale, Frank T. Bergmann, Tanisha Malpani, Venkata P. Satagopam, Reinhard Schneider, Moritz E. Beber, Sarah M. 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 Santibáñez-Palominos, Manish Kumar, Matteo Barberis, Bhanwar Lal Puniya, Tomáš 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, Çelık 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 Zuñiga, Gabriel Canto-Encalada, Sara Benito-Vaquerizo, Ivette Parera Olm, Maria Suarez-Diez, Qianquian Yuan, Hongwu Ma, Mohammad Mazharul Islam, Jason A. Papin, Francisco Zorrilla, Kiran Raosaheb Patil, Arianna Basile, Juan Nogales, Granado San León, Freddy Castillo-Alfonso, Roberto Olivares-Hernández, Gabriel Vigueras-Ramírez, Henning Hermjakob, Andreas Dräger, and Rahuman S. Malik-Sheriff
BioRxiv, September, 26th, 2024
[ Details | DOI | PDF | PubMed | BibTeX ]

Genome-scale metabolic model of Staphylococcus epidermidis ATCC 12228 matches in vitro conditions

Nantia Leonidou, Alina Renz, Benjamin Winnerling, Anastasiia Grekova, Fabian Grein, and Andreas Dräger
BioRxiv, December, 20th, 2023.
[ Details | DOI | Preprint | PDF | PubMed | BibTeX ]

Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs

Alina Renz, Mirjam Hohner, Maximilian Breitenbach, Jonathan Josephs-Spaulding, Johanna Dürrwald, Lena Best, Raphaël Jami, Georgios Marinos, Nantia Leonidou, Filipe Cabreiro, Andreas Dräger, Michael Schindler, and Christoph Kaleta
Preprints 2023, November, 30th 2023.
[ Details | DOI | PDF | PubMed | BibTeX ]

Media and Press Releases

Press releases

03/24/2023
Germany

DZIF – Press Release

Preparing for the next pandemic: Targeted computer modelling to accelerate antiviral drug development

https://www.dzif.de/en/preparing-next-pandemic-targeted-computer-modelling-accelerate-antiviral-drug-development

03/23/2023

Germany

Cluster of Excellence – Controlling Microbes to Fight Infections (CMFI)

Targeted computer modelling to accelerate antiviral drug development: Preparing for the next pandemic: Researchers from Tübingen use computer models to detect targets for infections

https://www.cmfi.uni-tuebingen.de/en/news-events/news/targeted-computer-modelling-to-accelerate-antiviral-drug-development

03/23/2023

Germany

University of Tübingen
Targeted computer modelling to accelerate antiviral drug development
Preparing for the next pandemic: Researchers from Tübingen use computer models to detect targets for infections

https://uni-tuebingen.de/en/university/news-and-publications/press-releases/press-releases/article/targeted-computer-modelling-to-accelerate-antiviral-drug-development/

Radio broadcasting and podcasts

03/27/2023

Germany

SWR4 Baden-Württemberg

News

From the Tübingen studio on by 11:30 a.m.

Researchers from Tübingen are creating a computer program to develop active substances against viral diseases.

https://www.swr.de/swr4/nachrichten/index.html

Online journals

03/25/2023

Germany

RTF1

Universität Tübingen: Forscher suchen im Computermodell nach Angriffspunkten gegen Infektionen

https://www.rtf1.de/news.php?id=35160
03/23/2023

Phys.org

Using targeted computer modeling to accelerate antiviral drug development

https://phys.org/news/2023-03-antiviral-drug.html

Print media

04/10/2023

India

India Education Diary

Experts Develop Computer Modeling To Speed-Up The Development Of Antiviral Drugs

https://indiaeducationdiary.in/experts-develop-computer-modeling-to-speed-up-the-development-of-antiviral-drugs/

04/07/2023

USA

GenomeWeb

Modernized Algorithm Predicts Drug Targets for SARS-CoV-2, Other RNA Viruses

https://www.genomeweb.com/informatics/modernized-algorithm-predicts-drug-targets-sars-cov-2-other-rna-viruses#.ZD5W2C9Bzwo

03/28/2023

Germany

Reutlinger General-Anzeiger
Tübinger Forscher bereiten sich auf nächste Pandemie vor
Entwicklung antiviraler Wirkstoffe soll beschleunigt werden: Tübinger Forscher suchen im Computermodell nach Angriffspunkten gegen Infektionen

https://www.gea.de/neckar-alb/kreis-tuebingen_artikel,-tübinger-forscher-bereiten-sich-auf-nächste-pandemie-vor-_arid,6736337.html

Teaching

Summer term 2023

Introduction to Bioinformatics (BIOINF1110) – in German

Lecture Series with Excercises

Ms. M.Sc. Nantia Leonidou leads the exercises for this course throughout the semester.

Jun.-Prof. Dr. Dräger teaches the lecture on “Systems Biology: Using Computer Models to Simulate Metabolism” on Thursday, May 11th, 2023, at 1:15 p.m. (45 min) in lecture hall N02 at Morgenstelle, Tübingen. This lecture is taught in German.

On the website of this lecture, you can find further information.

Alma
ILIAS
Further information

Winter term 2022/2023

Mathematics of life: Modelling molecular mechanisms

Virtual lecture series in English

This lecture is virtually conducted by the European Bioinformatics Institute (EMBL-EBI) with contribution by Jun.-Prof. Dr. Andreas Dräger. For further information, see the website of the class.

Topic: “Introduction to Constraint-Based Reconstruction and Modeling”, September 14th, 2022 at 10:30 a.m. British Summer Time, i.e., 11:30 a.m. German time.

Fundametals of Systems Biology (BIOINF3372)

Introductory Seminar Course

Instructors: Jun. Prof. Dr. Andreas Dräger and M.Sc. Nantia Leonidou

Alma
 ILIAS Syllabus

MINT-Plus Biology (BIOINF3379)

This class is conducted in a collaboration with the high school “Otto Hahn” in Nagold and the Youth Research Center Schwarzwald-Schönbuch e.V.

Seminar Digi-MINT

This course takes place at the Otto-Hahn-Gymnasium Nagold in German language.

This class is conducted in a collaboration with the high school “Otto Hahn” in Nagold and the Youth Research Center Schwarzwald-Schönbuch e.V.

Summer term 2022

Systems Biology II: Simulation of Dynamic Network States (BIOINF4394)

Lecture with Excercises

In case of any questions regarding this class, please do not hesitate to contact your lecturer, Dr. Reihaneh Mostolizadeh, or your tutor, M.Sc. Nantia Leonidou.

Alma
ILIAS
Syllabus

Winter term 2021/2022

Bioinformatics Preparatory Course

The Bioinformatics Vorkurs aims at introducing students to the basic computational issues. It is not going to cover entire programming taught in the Bachelor Bioinformatics course, rather it is meant to provide a starting point for those who are planning a career in bioinformatics, but have no experience with Linux-like systems and programming. It is a Vorkurs, therefore no ECTS points are awarded.

Please see https://bioinfprep.github.io for further information about this course.

Systems Biology I: Constraint-Based Reconstruction and Analysis (BIOINF3371)

Lecture with Excercises

Lecturer: Jun.-Prof. Dr. Andreas Dräger
Tutor: M.Sc. Nantia Leonidou

The language of this lecture is English. For further information, please see the Syllabus document linked below and the entry in the Alma system.

Alma
ILIAS
Syllabus

Summer term 2021

Bioinformatics Preparatory Course

The Bioinformatics Vorkurs aims at introducing students to the basic computational issues. It is not going to cover entire programming taught in the Bachelor Bioinformatics course, rather it is meant to provide a starting point for those who are planning a career in bioinformatics, but have no experience with Linux-like systems and programming. It is a Vorkurs, therefore no ECTS points are awarded.

Please see https://bioinfprep.github.io for further information about this course.

Systems Biology II: Simulation of Dynamic Network States (BIOINF4394)

Lecture with Excercises

Because of the worldwide COVID-19 pandemic, this course will take place this semester as a flipped classroom course on tuesdays at 2 p.m. c.t. via ZOOM. The weekly tutorial session is taking place on thursdays at 2 p.m. c.t. via ZOOM. The corresponding Alma page provides more detailed information. If you encounter any difficulties to access the information, please contact Jun.-Prof. Dr. Andreas Dräger.

Alma
ILIAS
Syllabus

Winter term 2016 until summer term 2021

Mathematics

Talks and Posters

Posters

  1. New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
    • 9th Conference on Systems Biology of Mammalian Cells (SBMC) 2024, Leipzig, Germany, 13-15 May, 2024
  2. Genome-scale metabolic modeling of Rothia mucilaginosa reveals insights into metabolic capabilities and antimicrobial strategies for cystic fibrosis
    • 3rd International Controlling Microbes to Fight Infections (CMFI) Conference 2023 (Link), Tübingen, Germany, 11-13 October, 2023
  3. Analyzing the metabolic phenotypes of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae using systems biology
    • DZIF-Jahrestagung 2023 (Link), Hannover, Germany, 25-26 September, 2023
    Manually Curated Genome-Scale Metabolic Reconstructions of the Multi-Drug Resistant Gram-Negative Pathogens A. Baumannii and K. Pneumoniae
    • 21st International Conference on Systems Biology (ICSB), Berlin, Germany, 8-12 October, 2022
    New Workflow Predicts Drug Targets Against Sars-Cov-2 Via Metabolic Changes in Infected Cells
    • 8th Conference on Constraint-Based Reconstruction and Analysis (COBRA), Galway, Ireland, 28-30 September, 2022
  6. Manually Curated Genome-Scale Metabolic Reconstructions of the Multi-Drug Resistant Gram-Negative Pathogens A. Baumannii and K. Pneumoniae
    • 8th Conference on Constraint-Based Reconstruction and Analysis (COBRA), Galway, Ireland, 28-30 September, 2022
  7. New Workflow Predicts Drug Targets Against Sars-Cov-2 Via Metabolic Changes in Infected Cells
    • 30th Conference on Intelligent Systems for Molecular Biology (SysMod@ISMB), Madison, United States, 10-14 June, 2022
  8. New Workflow Predicts Drug Targets Against Sars-Cov-2 Via Metabolic Changes in Infected Cells
    • DGI-DZIF Joint Annual Meeting (Link), Stuttgart, 1-3 June, 2022
    Tissue-specific reconstruction of constraint-based metabolic models based on ReconX 
    • 7th Conference on Constraint-Based Reconstruction and Analysis (COBRA), virtual, 1-2 March, 2021

Talks

    Manually Curated Genome-Scale Metabolic Reconstructions of the Multi-Drug Resistant Gram-Negative Pathogens A. Baumannii and K. Pneumoniae
    • 21st International Conference on Systems Biology (ICSB), Berlin, Germany, 8-12 October, 2022
  2. New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells
    • 21st International Conference on Systems Biology (ICSB), Berlin, Germany, 8-12 October, 2022
  3. Computational Systems Biology of Infection and Antimicrobial Resistance
  4. New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells
    • HARMONY, hybrid, 26-30 April 2022
  5. Tissue-specific reconstruction of constraint-based metabolic models based on ReconX
    • GCB 2021, virtuell, 6-8 September, 2021
  6. Tissue-specific reconstruction of constraint-based metabolic models based on ReconX

 

Awards and Honors

  1. ILW Recognition Award 2020/21
  2. Apolytirion with distinction from the 5th Lyceum in Kavala, Greece

 

Mentor in Final Theses

  1. Sophia Krappen Unraveling metabolic insights of Staphylococcus warneri using systems biology (2023)​​​​​​
  2. Carolin Brune Workflow Toward a Consensus Metabolic Network Model of Klebsiella Species (2023)
  3. Anna Lefarova Analyzing the metabolic phenotypes of Staphylococcus capitis using contraint-based modeling (2023)
  4. Selin Sahin Reconstruction of a genome-scale metabolic network of Staphylococcus lugdunensis N920143 (2022)
  5. Meike Lips A genome-scale metabolic model of Klebsiella pneumoniae HS11286 (2022)
  6. Yufan Xia: Genome-scale metabolic modelling of Acinetobacter baumannii ATCC 17978 (2022)
  7. Josua Carl: Investigation of Finegoldia magna ATCC 29328 in the nasal environment (2022)

Further Training

  • Tools for Systems Biology Modeling and Data Exchange - von de.NBI (April 2021)
  • Poster Presentation workshop (October 2021)
  • Scientific Writing workshop (November 2021)
  • BioCyC Webinar (November 2021)
  • Good Scientific Practice in the Life Sciences (October-November 2021)
  • Medical training on the decolonization of Staphylococcus aureus (colloquium on infectiology, May 2022)
  • Colloqium of microbiology and infections (October 2022)
  • Academic Writing for Doctoral Candidates (February 2022)
  • Practical course on Molecular Biology and Microbiology (Februar 2023)
  • Excellence in International S.T.E.M. Communication, Productivity & Career Skills – Masterclass by Dr. Paul Charlton (2023)

  • NFDI4Microbiota DZIF: Basic statistics with R (2024)