Alumni

Participation: October 2020 to August 2022

Further information

Lecturer in Systems Biology
Biotechnologist

Participation: September 2020 to February 2021

Contact

b.miendaspam prevention@fud.edu.ng

Further information

Participation

January 2019 to March 2022

Further information

MSc in Computer Science
Sand 14 ⋅ Office C107
72076 Tübingen
Germany

 +49-7071-29-70452
 +49-7071-29-5152
mahdi.sadeghispam prevention@uni-tuebingen.de

Participation

December 2019 to May 2020

Project

Development of essential software and resources for the scientific community for systems biology modelling via Java™

Further information

MSc in Bioinformatics
Sand 14 ⋅ Office C107
72076 Tübingen
Germany

 +49-7071-29-70452
 +49-7071-29-5152
thorsten.tiedespam prevention@gmail.com

Participation

December 2019 to April 2020

Project

Development of essential software and resources for the scientific community for systems biology modelling via Java™

Further information

GitHub profile

Biologist (t.o.)

Participation

November 2016 to November 2019

Further information

Personal website
GitHub profile

Participation: November 2022 to December 2023

Contact

fatma-ece.altinisik-kayaspam prevention@student.uni-tuebingen.de
 Further information

Subject: Bioinformatics

Thesis

Analyzing the metabolic phenotypes of Staphylococcus capitis using constraint-based modeling

Participation: January to September 2023
Graduation: May 23^rd, 2023

Contact

anna.lefarovaspam prevention@student.uni-tuebingen.de

Participation: August to December 2022

Contact

catalina.schlottererspam prevention@student.uni-tuebingen.de

Participation: May 2022 to August 2022

More information

GitHub

Contact

dario.eltznerspam prevention@student.uni-tuebingen.de

Participation:
April 2020 to July 2022

Thesis

Modelling and Visualization of specific resistance mechanisms in Pseudomonas aeruginosa

Graduation: September 2019

Participation: August 2021 to February 2022

Working on genome-scale model of Corynebacterium tuberculostearicum

Mentor:
Dr. Reihaneh Mostolizadeh

Participation: September 2020 to February 2022

Working on community model of D. pigrum and S. aureus 

Mentor:
Dr. Reihaneh Mostolizadeh

Participation: September 2021 to January 2022

Working on genome-scale model of Corynebacterium accolens

Mentor:
Dr. Reihaneh Mostolizadeh

Participation: September 2021 to January 2022

Working on genome-scale model of Corynebacterium accolens

Mentor:
Dr. Reihaneh Mostolizadeh

Master in Bioinformatics

Participation: Since September 2020 to April 2021

Working on community model of H. influenzae and S. aureus 

Mentor:
Dr. Reihaneh Mostolizadeh

Major: Bioinformatics

Thesis

Visual analysis of flux sampling simulations based on extracellular metabolomic measurements

Defense:
September 15^th 2020 at 11:30 a.m. via Zoom

Participation:
January and February 2021

Master in Medical informatics

Participation: September 2020 to November 2020

Working on community model of S. epidermidis and S. aureus, M. catarrhalis and S. aureus

Mentor:
Dr. Reihaneh Mostolizadeh

Major: Bioinformatics

Thesis

Reconstruction and Analysis of Staphylococcus epidermidis

Defense: 
June 16^th 2020

Participation

March 2020 to September 2020

Further information

GitHub profile

BSc in Bioinformatics

Participation:

• May 2016 to February 2018
• Since November 2019

Further information

GitHub profile

Major: Computer Science

Participation:
November 2019 to May 2020

Further information

GitHub profile

BSc in Bioinformatics

Participation:
October 2019 to April 2020

Further information

GitHub profile

MSc in Biology

Subject: Bioinformatics

Participation:
October 2019

Subject: Cognitive science

Participation:
April to August 2019

Further information

GitHub profile

Subject: Cognitive science

Participation:
November 2018 to April 2019

Further information

GitHub profile

Bachelor in bioinformatics

Assistance:
November 2017 to
February 2018

Thesis

Development of an interactive graphical editor for systems biology models

Graduation: September 2017

Further information

GitHub profile
LinkedIn profile

Bachelor in media informatics

Assistance:
May to August 2016

Further information

LinkedIn profile

Subject: Bioinformatics
famke.baeuerlespam prevention@student.uni-tuebingen.de

Participation since: November 2020

Graduation: May 2023

Thesis

Reconstruction of Corynebacterium striatum KC-Na-01

Further information

GitHub
ORCID
Twitter
LinkedIn

Master in Bioinformatics

Participation: September 2020 to November 2020 and October 2021 to December 2021

Working on Dynamic model of the microbial community

Mentor:

Dr. Reihaneh Mostolizadeh

Theses

Visual analysis of clinical multi-omics data in biological networks
Co-mentor of the thesis: Jun.-Prof. Dr. Michael Krone
Defense: November 19^th 2019 at 10:15 a.m. in C109

Reconstruction of a metabolic model of Proteus vulgaris

Further information

GitHub profile

Thesis

Reconstruktion of a metabolic model of Staphylococcus lugdunensis

Mentor

Jun.-Prof. Dr. Andreas Dräger

Graduation: December 2021

Further information

LinkedIn

Subject: Molecular Medicine

Research Project

Reconstruction of Corynebacterium striatum

Defense:
June 2^nd 2020

BSc in Computational Linguistics

Research Project

Graphical editor for systems biology models

Defense:
May 5^th 2020

Further information

LinkedIn profile

Subject: Molecular Medicine

Research Project

Reconstruction of Dolosigranulum pigrum

Defense:
March 16^th 2020

Subject: Bioinformatics

Research Project

Reconstruction of Moraxella catarrhalis BBH18

Defense:
September 10^th 2019 in C118a

Field of study: biology

Thesis

Genome-scale metabolic network reconstruction of the pathogen Treponema pallidum ssp. pallidum

Graduation: September 2018

Further information

LinkedIn profile

Thesis

Investigation of Finegoldia magna ATCC 29328 in the nasal environment

Participation since: September 2021
Expected graduation: Feburary 2022

Mentor

Nantia Leonidou

Contact

josua.carlspam prevention@student.uni-tuebingen.de

Further information

GitHub

Field of study: bioinformatics

Thesis

Representation of ME-models in SBML

Graduation: June 2018

Further information

GitHub profile

Thesis

Unraveling metabolic insights of Staphylococcus warneri using systems biology

Participation: November 2023 - March 2024

Mentor

Nantia Leonidou

Contact

sophia.krappenspam prevention@student.uni-tuebingen.de

Further information

GitHub

Thesis

Reconstruction of a genome-scale metabolic network of Staphylococcus lugdunensis N920143

Participation: April to September 2022

Mentors

Nantia Leonidou, Jun.-Prof. Dr. Andreas Dräger

Contact

selin.sahinspam prevention@student.uni-tuebingen.de

Thesis

A genome-scale metabolic model of Klebsiella pneumoniae HS11286

Participation: May to August 2022
Graduation: August 22^nd 2022

Mentors

Nantia Leonidou, Jun.-Prof. Dr. Andreas Dräger

Contact

meike.lipsspam prevention@student.uni-tuebingen.de

Thesis

Genome-scale metabolic modelling of Acinetobacter baumannii ATCC 17978

Participation since: March 2022
Graduation: August 22^nd 2022

Mentors

Nantia Leonidou, Jun.-Prof. Dr. Andreas Dräger

Contact

yufan.xiaspam prevention@student.uni-tuebingen.de

Further information

LinkedIn

Subject: Bioinformatics
jan-philipp.leuschspam prevention@student.uni-tuebingen.de

Participation since: May 2021

Thesis

The first genome-scale reconstruction of Corynebacterium simulans PES1

Expected graduation: September 2021

Major: Bioinformatics

Thesis

Automating the Assignment of SBO-Terms

Expected completion:
September 2020

Further information

Github profile

Major: Medical informatics

Thesis

Optimized Layouting of Biological Networks for the Comparative Visual Analysis

Defense:
June 2^nd 2020

Contact

ebru.cobanogluspam prevention@student.uni-tuebingen.de

Major: Bioinformatics

Thesis

Derivation of gene-protein reaction rules

Defense:
May 5^th 2020

Further information

GitHub profile

Subject: Computer Science

Thesis

Expanded genome-scale model of Haemophilus influenzae

Graduation: September 2019

Further information

GitHub profile

Subject: Computer Science

Thesis

Development of a plugin for the Insilico framework for the visual analysis of simulations of biological systems
Graduation: June 2019

Research Project

What makes a review helpful or funny?

Mentors:
Markus Viggiato, Prof. Dr. Cor-Paul Bezemer, Jun.-Prof. Dr. Andreas Dräger
Graduation: November 2019

Further information

GitHub profile
LinkedIn profile

Subject: Bioinformatics

Thesis

Development of an editor for large-scale biochemical models

Graduation: March 2019

Further information

GitHub profile

Field of study: bioinformatics

Thesis

Valiation and Simulation of Qualitative Models

Graduation: February 2018

Further information

GitHub profile

Field of study: cognitive science

Thesis

Dynamic visualization of metabolic networks

Graduation: September 2017

Further information

GitHub profile
LinkedIn profile
ResearchGate profile

Subject: Computer Science and Engineering (B. Tech.)

Affiliation: Indian Institute of Technology, Roorkee, India

Project

Simulation of systems biology models in Java: support for new features

Participation: May to September 2020

Mentors

Jun.-Prof. Dr. Andreas Dräger, Dr. Matthias König, Mykola Zakharchuk, and Shalin Shah

Further information

Projekt blog
GitHub profile
LinkedIn profile
Twitter channel
Medium link

Major: Computer Science and Technology (B. Tech)

Affiliation: Indian Institute of Technology, Roorkee, India

Project

Implementation of SBML-JSON converter and SBML-JSON scheme

Contact: hemantspam prevention@cs.iitr.ac.in

Participation: May to September 2020

Mentors

Jun.-Prof. Dr. Andreas Dräger, Dr. Matthias König, Lucian P. Smith, and Sarah M. Keating

Further Information

Project blog
GitHub profile
LinkedIn profile
Twitter channel
Medium link

Subject: Computer Engineering (B.Sc.)
Affiliation: Vishwakarma Institute of Technology, Pune

Project

Erstellsystem für das Plugin-Framework “InSilico”
Quellcode auf GitHub

Participation: April to September 2019

Mentors

Roman Schulte and Jun.-Prof. Andreas Dräger

Further information

Project blog
PivotalTracker
GitHub profile
Twitter channel

Subject: Computer Science and Engineering (B. Tech.)
Affiliation: Indian Institute of Technology, Roorkee

Project

Validierung räumlicher Modelle der Systembiologie in Java™
Quellcode auf GitHub

Participation: April to September 2019

Mentors

Nicolas Rodriguez, Thomas M. Hamm, and Lucian P. Smith, Ph.D.

Further information

Project blog
GitHub profile
Twitter channel

Target degree: Ph.D.

Affiliation: Duke University, Department for Electrical and Computer Engineering, NC, USA

Project

Simulating systems biology models in Java™

Participation: April to August 2018

Mentors

Jun.-Prof. Dr. Andreas Dräger and Dr. Matthias König

Further information

Project blog
GitHub profile

Current position: Research associate

Affiliation: Keio University, Institute for Biosciences and Informatics

Project

Develop a web service which provides simulation / steady state analysis / parameter estimation with SBML models

Participation: April to August 2017

Mentors

Jun.-Prof. Dr. Andreas Dräger, Kaito Ii, and Dr. Matthias König

Further Information

Project blog
GitHub profile
ResearchGate
ORCID

Field of study: computer science

Thesis

InSilico - Concept of a Modular Research Environment
Graduation: August 2018

Project within the Google Summer of Code 2016

JSBML Validation System

Mentors:
Jun.-Prof. Dr. Andreas Dräger, Dr. Sarah M. Keating, Dr. Michael Hucka, and Nicolas Rodriguez

Participation: May to August 2016

Further information

GitHub profile
Personal homepage

Position: Ph.D. student

Affiliation: University of Utah at Salt Lake City, UT, USA

Project

Interconversion between the systems biology modeling formats SBML and BioPAX

Participation: May to August 2016

Mentors

Dr. Michael Hucka, Jun.-Prof. Dr. Andreas Dräger, Prof. Dr. Chris J. Myers, Prof. Dr. Akira Funahashi, and Nicolas Rodriguez

Further Information

Project blog
GitHub profile

Position: Ph.D. student

Affiliation: Russian-Armenian University at Yeveran, Armenia

Project

Interconversion between the systems biology modeling formats SBML and BioPAX
Participation: May to August 2016

Mentors

Dr. Frank T. Bergmann, Dr. Sarah M. Keating, Jun.-Prof. Dr. Andreas Dräger, and Nicolas Rodriguez

Further Information

Projekt blog
GitHub profile
Twitter channel
ORCID

Position: Ph.D. student

Affiliation: Keio University, Institute for Biosciences and Informatics, Japan

Project

Interconvertible Layout software for CellDesigner

Participation: May to August 2016

Mentors

Prof. Dr. Akira Funahashi, Jun.-Prof. Dr. Andreas Dräger, Nicolas Rodriguez, and Dr. Michael Hucka

Further Information

Project blog
GitHub profile
LinkedIn profile

Subject: Information technology and mathematics

Affiliation: University of Delhi, Delhi, India

Project

Visual Biology with Escher

Participation: May to August 2016

Mentors

Zachary A. King and Jun.-Prof. Dr. Andreas Dräger

Further Information

Projekt blog
Projekt wiki
GitHub profile