Welcome to our Forschungsseminar wiki

Organizer

Prof. Dr. Heike Siebert

Description

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 |

News

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
16.10.17 16.10.17	Group meeting Modeling the circadian clock	All 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

For materials see Research wiki (restricted)