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Welcome to our Forschungsseminar wiki


Prof. Dr. Heike Siebert


The Forschungsseminar is a regular (weekly) meeting of the Discrete Biomathematics group.
Primarily a platform for theses and dissertation status reports, the program will be complemented
by paper presentation talks, conference trip reports and invited talks.

We will also integrate a series of "What is" talks with topics from math, computer science and the life sciences.

Time and Location

Summer term 2021 | Tuesday 15.30-16.30 | Webex |


Link to the Forschungsseminar of the Work Group Mathematics in Life Sciences

Schedule Summer Term 2021

Date Title presented by
27.05.21 Comparing different clustering methods for bioregion identification using simulated scenarios Andrea Briega Álvarez
17.06.21 The state transition graph analysis of simple and chorded circuits in the Boolean modeling framework Ole Hedemann
01.07.21 Boolean buffer networks Elisa Tonello
08.07.21 PhD rehearsal talk Katinka Becker
03.08.21 PyStableMotifs: Exploiting nested trap spaces in Boolean networks Jordan Rozum from Pennsylvania State University

Schedule Former Terms

Winter Term 2020/2021

Date Title presented by
10.11.20 Reconciling qualitative, abstract, and scalable modeling of biological networks All
17.11.20 Most Permissive Boolean Networks Loïc Paulevé from CNRS/LaBRI, Bordeaux, France
19.01.21 Algorithm complexity Alexander Bockmayr
26.01.21 Algorithm complexity Alexander Bockmayr
02.02.21 Control of Boolean networks Jakob Grünwald
16.02.21 Some benchmark results on the algebraic classifier software Hannes Klarner
02.03.21 Modeling project using logical modeling approaches Kirsten Thobe
09.03.21 Development of agent-based models of cellular signalling pathways for the prediction of the effect of targeted drugs Larissa Pusch
17.03.21 Claudine's carcinoma model, Hannes' classifier calculations for it and further aspects we want to investigate All
23.03.21 Qualitative Clonality Modelling from Multi-Sample Analysis of Colorectal Cancer Gracia Andriamiadana

Summer Term 2020

Date Title presented by
24.04.20 Group meeting All
30.04.20 Group meeting All
14.05.20 Investigating Pattern Robustness in Cellular Automata Elisa Tonello
11.06.20 Recent work on distributed classifiers Melania Nowicka
25.06.20 Group meeting All
02.07.20 Group meeting All
22.07.20 Predicting the Internal Circadian Time based on a Supervised Learning Approach Rukeia El-Athman
10.09.20 Boolean control strategies Laura Cifuentes Fontanals
17.09.20 Rehearsal talk for CMSB Robert Schwieger

Winter Term 2019/2020

Date Title presented by
15.01.20 Spaces of attraction and control strategies of boolean networks Laura Cifuentes Fontanals
18.02.20 Bioregionalization models: review and past dynamics Andrea Briega

Summer Term 2019

Date Title presented by
11.04.19 Controling boolean models Laura Cifuentes Fontanals
21.05.19 Linking attractor complexity to model structure all
23.05.19 PhD rehearsal talk on the topic of network reduction Robert Schwieger
27.05.19 Circuits and attractors all
06.06.19 PhD rehearsal talk Robert Schwieger
14.06.19 PhD Defense Robert Schwieger
24.07.19 Discrete models capable of generating Turing patterns Tom Leyshon
11.09.19 Distributed boolean classifiers Melania Nowicka

Winter Term 2018/2019

Date Title presented by
22.11.18 Distributed discrete classifiers Carola Bothe
Cancelled Analysis of model pools using information theory measures Felix Mattes
14.01.19 Some results on spatial models and pattern generation of delta-notch signaling Elisa Tonello
24.01.19 Extended interaction graphs of Boolean functions Maike Resing
31.01.19 Network inference algorithms for Boolean models Nina Kersten

Summer Term 2018

Date Title presented by
17.05.18 TAC meeting Melania Novicka
24.05.18 Cell classifier project Melania Novicka
08.06.18 PyBoolNet Tutorial Hannes Klarner
11.06.18 Approaches for distinguishing state transition graphs Robert Schwieger
19.06.18 Earlier work as well as current project on Turing patterns Elisa Tonello
26.06.18 Supporting Malaria Elimination in the Asia-Pacific through Mathematical Modelling Sheetal Silal
17.07.18 Current modeling work at MDC Kirsten Thobe
25.09.18 ASP cell classifiers
Circuit functionality in (bio)logical regulatory networks
Melania Nowicka
Adrien Fauré

Winter Term 2017/2018

Date Title presented by
Group meeting
Modeling the circadian clock
Rukeia El-Athman
18.10.17 PhD defense rehearsal Ling Sun
25.10.17 PhD defense Ling Sun
08.11.17 Reports on the summer conferences Melania Nowicka and Robert Schwieger
15.11.17 Report on the CMSB 2017 Robert Schwieger
22.11.17 IMPRS Colloquium All
13.12.17 Group status meeting All
10.01.18 Group status meeting All
17.01.18 Journal Club All
24.01.18 Cell classifiers Melania Nowicka
31.01.18 10.00
31.01.18 11.15
Recent research work
Recent research work
Robert Altwasser
Jacob de Zoete
07.02.18 10.00
07.02.18 11.15
Research work on Boolean networks
Research work on analysis of biochemical reaction networks
Elisa Tonello
Abhishek Deshpande

Summer Term 2017

Date Title presented by
11.05.17 PhD rehearsal talk Kirsten Thobe
19.05.17 PhD defense Kirsten Thobe
12.06.17 Report on the research stay in Paris Hannes Klarner
06.07.17 miRNA classifier project Melania Nowicka

Winter Term 2016/17

Date Title presented by
26.10.16 Journal club Kirsten Thobe et al
09.11.16 Report about the iGEM meeting in Boston Melania Nowicka
16.11.16 BMS 10th Anniversary All
23.11.16 Model of Host-Pathogen Interaction Dynamics Links In Vivo Optical Imaging and Immune Responses Angelique Ale
14.12.16 Topological sensitivity analysis Ann Babtie
04.01.17 Enumerating minimal precursor sets in metabolic networks, report on research internship Irene Ziska
01.02.17 Development of a Matlab toolbox for automatic transformation of given ODE systems into Boolean networks Radostina Misirkova
08.02.17 Meeting of the group working on Angelique Ale's project Heike Siebert et al
28.02.17 Some results on dynamics of classes of boolean models Robert Schwieger

Summer Term 2016

Date Title presented by
20.04.16 Group meeting All
27.04.16 Software Discussion All
11.05.16 The Digital Future Conference  
18.05.16 An extension for NuSMV Softwarepraktikum group
01.06.16 Tremppi Softwarepraktikum group
15.06.16 Dynamical equivalence for multi-valued networks Felix Mattes
22.06.16 Modellierung und Simulation von pathologischen Veränderungen beim Cross-Talk von MAPK- und PIK3CA-Signalnetzen Alexander Lüttringhaus
29.06.16 Network-based identification of possible biomarkers using mass spectrometry data Marcel Flemming
08.07.16 Basins of attraction of Boolean networks Hannes Klarner
28.07.16 Cellular automata Sylvia Thieffry

Winter Term 2015/16

Date Title presented by
14.10.15 Group meeting All, Room 126, A6
21.10.15 Research Meeting with Anne Siegel  
04.11.15 Logical modeling of REDD1 regulation in oncogenic signaling Parnika Mukherjee
18.11.15 Random Walks in Protein Interaction Networks Lam-Ha Ly
25.11.15 Dynamic resource allocation within the metabolism of Synechococcus elongatus 7942 Alexandra Reimers
10.12.15 Implementing a method to translate an ODE model into a boolean model Radostina Misirkova
10.02.16 Conference planning All
02.03.16 Unraveling the regulation of mTORC2 using logical modeling Kirsten Thobe
09.03.16 Data discretization, results from PhD thesis Adam Streck

Summer Term 2015

Date Title presented by
22.04.15 Group meeting All
06.05.15 Hierarchical model checking Hannes Klarner
13.05.15 Combining formalisms for analysing HGF signaling Adam Streck
27.05.15 Profile likelihood shifted to July
03.06.15 DiBiMath group internal  
10.06.15 T-helper cell plasticity and reprogramming Hannes Klarner
15.06.15 Networks-of-Networks Peter Koltai
24.06.15 IMPRS colloquium start at 14:00 at MPI lecture hall
01.07.15 Modeling of mTor signaling Kirsten Thobe
08.07.15 Combining network-based method with statistical data analysis Marcel Flemming
15.07.15 ECMath project meeting and summer outing  
29.07.15 Software TREMPPI for generating and analyzing model pools Adam Streck

Winter Term 2014/15

Date Title presented by
15.10.14 Group meeting All
29.10.14 EGFR paper - data A. Streck
05.11.14 EGFR paper - analysis A. Streck
12.11.14 Model integration and crosstalk analysis of logical regulatory networks K. Thobe
26.11.14 Modular response analysis Torsten Gross
03.12.14 PhD rehearsal talk Hannes Klarner
10.12.14 PhD defense Hannes Klarner
17.12.14 PhD defense Laszlo David
14.01.15 Group meeting All
21.01.15 EGFR paper All
28.01.15 Computing trap spaces Hannes Klarner
04.02.15 Dynamics and control at feedback vertex sets Dominik Otto
18.02.15 EGFR paper etc. All
04.03.15 Construction of toy models All

Summer Term 2014

Date Title presented by
24.04.14 Group meeting All
08.05.14 Steady state assumption A. Grigore and A. Reimers
15.05.14 Crosstalk analysis (external talk at ITB) K. Thobe
22.05.14 EFM recorder A. Röhl / Y. Goldstein
12.06.14 Metabolic modeling of different degrees of steatohepatitis in mice Vikash Pandey
19.06.14 Master thesis defense
Bericht Forschungspraktikum
Alexandra Grigore
Janko Tackmann
26.06.14 Exploiting matroid theory for the analysis of metabolic networks
Report on the TED conference "Bits of Knowledge"
A. Reimers
03.07.14 PhD defense
Numerical and discrete modeling of reproductive endocrinological networks
Claudia Stötzel
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