Alumni

Former employees and students of the workgroup

Postdoctoral Researchers

Dr. Bashir Sajo Mienda

Lecturer in Systems Biology
Biotechnologist

b.miendaspam prevention@fud.edu.ng

​​​​​ Further information

Research Assistants

Mahdi Sadeghi

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

Thorsten Tiede

MSc in Bioinformatics
Sand 14 ⋅ Office C107

72076 Tübingen
Germany

 +49-7071-29-70452
 +49-7071-29-5152
tiedespam prevention@informatik.uni-tuebingen.de

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

 

 

Thomas M. Hamm

Biologist (t.o.)

Participation

November 2016 to November 2019

Further information

Personal website
GitHub profile

Student assistants

Oskar Wacker

Master in Bioinformatics

Participation: Since September 2020

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

Mentor:
Dr. Reihaneh Mostolizadeh

 

Constantin Holzapfel

Major: Bioinformatics

Thesis

Visual analysis of flux sampling simulations based on extracellular metabolomic measurements

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

Participation:
January and February 2021

Najia Ahmadi

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

 

Anastasiia Grekova

Major: Bioinformatics

Thesis

Reconstruction and Analysis of Staphylococcus epidermidis

Defense: 
June 16th 2020

Participation

March 2020 to September 2020

Further information

GitHub profile

Thomas J. Zajac

BSc in Bioinformatics

Participation:

  • May 2016 to February 2018
  • Since November 2019
Further information

GitHub profile

 

 

Onur Özel

Major: Computer Science

Participation:
November 2019 to May 2020

Further information

GitHub profile

 

David E. Vetter

BSc in Bioinformatics

Participation:
October 2019 to April 2020

Further information

GitHub profile

 

Antonia I. Schuster

MSc in Biology

Subject: Bioinformatics

Participation:
October 2019

Maria E. Heitmeier

Subject: Cognitive science

Participation:
April to August 2019

Further information

GitHub profile

Anton J. Rabe

Subject: Cognitive science

Participation:
November 2018 to April 2019

Further information

GitHub profile

Christoph Blessing

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

Veronika Kohler

Bachelor in media informatics

Assistance:
May to August 2016

Further information

LinkedIn profile

Master students

Tanja Urz

Subject: Molecular Medicine

Research Project

Reconstruction of Corynebacterium striatum

Defense:
June 2nd 2020

Marietta Hamberger

BSc in Computational Linguistics

Research Project

Graphical editor for systems biology models

Defense:
May 5th 2020

Further information

LinkedIn profile

Lina Widerspick

Subject: Molecular Medicine

Research Project

Reconstruction of Dolosigranulum pigrum

Defense:
March 16th 2020

Pia Rautenstrauch

Subject: Bioinformatics

Research Project

Reconstruction of Moraxella catarrhalis BBH18

Defense:
September 10th 2019 in C118a

Silvia Morini

Field of study: biology

Thesis

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

Graduation: September 2018

Further information

LinkedIn profile

Marc Alexander Voigt

Field of study: bioinformatics

Thesis

Representation of ME-models in SBML

Graduation: June 2018

Further information

GitHub profile

Bachelor students

Elisabeth Fritze

Major: Bioinformatics

Thesis

Automating the Assignment of SBO-Terms

Expected completion:
September 2020

Further information

Github profile

Manuel Dienert

Major: Bioinformatics

Thesis

Derivation of gene-protein reaction rules

Defense:
May 5th 2020

Further information

GitHub profile

Niklas Henle

Subject: Computer Science

Thesis

Expanded genome-scale model of Haemophilus influenzae

Graduation: September 2019

Further information

GitHub profile

Robert Deibel

Subject: Bioinformatics

Thesis

Development of an editor for large-scale biochemical models

Graduation: March 2019

Further information

GitHub profile

Lisa Falk

Field of study: bioinformatics

Thesis

Valiation and Simulation of Qualitative Models

Graduation: February 2018

Further information

GitHub profile

Lea F. Buchweitz

Field of study: cognitive science

Thesis

Dynamic visualization of metabolic networks

Graduation: September 2017

Further information

GitHub profile
LinkedIn profile
ResearchGate profile

External Students

Google Summer of Code and the NRNB Academy repeatedly fund several of the research group's software products. These programs allow international students to join the team and actively participate in the development of open source software.

Google Summer of Code 2020

Hemil Panchiwala

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

Hemant Yadav

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

Google Summer of Code 2019

Nikhil Ghodke

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

Kaustubh Trivedi

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

Project

Extending ModelPolisher to a universal model annotation tool
Source code on GitHub

Participation: April to September 2019

Mentors

Jun.-Prof. Andreas Dräger,
Thomas J. Zajac, and Dr. Matthias König

Further information

Project blog
GitHub profile
Twitter channel

Bhavye Jain

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

Google Summer of Code 2018

Shalin Shah

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

Google Summer of Code 2017

Takhiro G. Yamada

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

Google Summer of Code 2016

Roman Schulte

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 DrägerDr. Sarah M. KeatingDr. Michael Hucka, and Nicolas Rodriguez

Participation: May to August 2016

Further information

GitHub profile
Personal homepage

Tramy Nguyen

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 HuckaJun.-Prof. Dr. Andreas DrägerProf. Dr. Chris J. Myers, Prof. Dr. Akira Funahashi, and Nicolas Rodriguez

Further Information

Project blog
GitHub profile

Hovakim Grabski

Kaito Ii

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 FunahashiJun.-Prof. Dr. Andreas DrägerNicolas Rodriguez, and Dr. Michael Hucka

Further Information

Project blog
GitHub profile
LinkedIn profile

Devesh Khandelwal

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