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Welcome to our Forschungsseminar wiki


Prof. Dr. Alexander Bockmayr


The Forschungsseminar is a regular (weekly) meeting of the Mathematics in Life Sciences group.
As part of an active research climate, the seminar offers researchers and students affiliated
with the group the opportunity to present and discuss their own ongoing research and to stay
up to date with the overall research agenda of the work group. Primarily a platform for
theses status reports, paper presentation talks and conference trip reports,
the Forschungsseminar will also host invited talks and tutorials.

Time and Location

Summer Term 2021 | Webex |


Link to the Forschungsseminar of the Work Group Discrete Biomathematics

Additional Material

Schedule Summer Term 2021

Date Title presented by
08.07.21 PhD rehearsal talk Katinka Becker

Schedule Former Terms

Winter Term 2020/2021

Date Title presented by
12.10.20 Development of a Regulatory-Metabolic Network of E. coli and a Software Package to Solve Regulatory deFBA Models Hannes Baukmann

Summer Term 2020

No group meetings

Winter Term 2019/2020

Date Title presented by
15.10.19 Group meeting and planning for the new semester All
15.11.19 Logical data analysis of biological data sets using ASP Katinka Becker
18.12.19 Trap spaces in buffered logical networks Aurélien Naldi
07.01.20 Cellular trade-offs and resource allocation during photoautotrophic growth Marjan Faizi
23.01.20 CoLoMoTo notebook: current and future integration of complementary logical modelling tools Aurélien Naldi
04.02.20 Towards a deFBA Model of Escherichia coli Hannes Baukmann
12.03.20 PhD rehearsal talk Lin Liu
19.03.20 2nd PhD rehearsal talk Lin Liu

Summer Term 2019

No group meetings

Winter Term 2018/2019

Date Title presented by
29.10.18 Group meeting and planning for the new semester All
19.11.18 Analysing MycoDB - An Application of Deep Learning in Ecology Stefan Stiller
26.11.18 Formalizing metabolic-regulatory networks by hybrid automata Lin Liu
17.12.18 Logical Analysis of Cookies Katinka Becker and Alexander Bockmayr
07.01.19 dFBA Alexander Bockmayr
14.01.19 SR-FBA Alexander Bockmayr
21.01.19 iFBA Alexander Bockmayr
28.01.19 idFBA Alexander Bockmayr
19.02.19 Group meeting All
25.02.19 Group meeting All
25.03.19 Model reduction of a metabolic-genetic network
Formalizing metabolic-regulatory networks by hybrid automata
Neveen Eshtewy
Lin Liu
04.04.19 Formalizing metabolic-regulatory networks by hybrid automata Lin Liu

Summer Term 2018

Date Title presented by
17.04.18 Group meeting and planning for the new semester All
24.04.18 Mathematical Modeling of Cell Metabolism coupled to Enzyme Turnover Dana Wehner
25.05.18 Inferring regulatory rules Manon Bondouy
30.07.18 Bilevel optimisation in metabolic engineering
Reduction, Projection, and Simplification of Metabolic Networks
A. Röhl
07.08.18 A mathematical framework for yield (vs. rate) optimization Jürgen Zanghellini
07.08.18 PhD Defense A. Röhl
28.08.18 Gene regulation in FBA & comparing to the previous study
Logical modelling: inferring structure from dynamics
Hung-Ching Chang
Ling Sun
26.09.18 Comparing Answer Set Programming (ASP) and Mixed Integer Programming (MIP) in Logical Analysis of Data (LAD) Hafiz Muhammad Hamid
04.10.18 Model reduction of a small metabolic-genetic network Neveen Eshtewy
12.10.18 Model reduction of a small metabolic-genetic network Neveen Eshtewy

Winter Term 2017/2018

Date Title presented by
04.10.17 Inference of logical rules for metabolic pathway activation
Understanding metabolic regulation and cellular resource allocation through optimization
A.-M. Reimers
12.10.17 PhD Defense A.-M. Reimers
16.10.17 Modeling the circadian clock R. El-Athman
18.10.17 Logical modelling and Drosophila embryo development
Relating the structure and dynamics of gene regulatory networks
L. Sun
25.10.17 PhD Defense L. Sun
06.11.17 Numerical solution of dynamic metabolic resource allocation problems M. Köbis
20.11.17 Predicting dynamic resource allocation with regulation L. Liu
27.11.17 Reduction of networks: Optimization and projection A. Röhl
05.12.17 Machine learning for aeronautical applications M. Bondouy
11.12.17 Kinetic modeling of a core metabolic network including enzyme resources N. Eshtewy
08.01.18 Deducing core models from sets of destination values T. Lorenz
17.01.18 The regulatory network of E. coli metabolism All
22.01.18 Continuation: The regulatory network of E. coli metabolism All
29.01.18 Continuation: The regulatory network of E. coli metabolism All
06.02.18 Intermediate results: The regulatory network of E. coli metabolism All
12.02.18 Curation, validation, and extension of a comprehensive metabolic human kidney model T. Marschall
20.02.18 Continuation: The regulatory network of E. coli metabolism All
14.03.18 Exploring the optimal solution space in regulatory flux balance analysis L. Liu
05.04.18 Rehearsal talks for the CBS retreat in Hiddensee N. Eshtewy and L. Liu

Summer Term 2017

Date Title presented by
25.04.17 Group meeting All
03.05.17 A minimal model for cyanobacterial resource allocation M. Faizi
16.05.17 IMPRS Colloquium  
23.05.17 Regulatory resource balance analysis L.Liu
31.05.17 Berechnung von elementaren Flussmodi durch Graphensuche M. Sarfert
13.06.17 Computation of minimal metabolic behaviors T. Riou
14.06.17 Aufbereitung der Darstellung von Zustandsmengen Boolescher biologischer Netzwerke S. Nee
27.06.17 Kinetic modeling of a small metabolic-genetic network N. Eshtewy
04.07.17 Enzyme cost and metabolic flux cost functions W. Liebermeister
11.07.17 Irreversible minimal cut sets A. Röhl
18.07.17 Multi-objective metabolic optimization for single organisms and for communities I. Ziska

Winter Term 2016/2017

Date Title presented by
17.10.16 Using optimization to predict activation in metabolic pathways F. Dick
24.10.16 Designing a small model of zinc homeostasis in human liver cells T. Marschall
14.11.16 Group meeting All
21.11.16 ODE-Models of the Cytokinin Signaling Pathway R. Schwieger
28.11.16 Exploring the optimal flux space in the growth of E.coli through regulatory FBA L. Liu
05.12.16 Analysis of dihedral angles of protein subsequences H. M. Hamid
12.12.16 Toolbox for modeling uncertain systems using logical models K. Thobe
09.01.17 Inferring a network through a matroid determined from perturbation data T. Gross
16.01.17 TREMPPI: What does it do? How does it do it? A. Streck
25.01.17 Group meeting All
06.02.17 BIMoS Day "Mixture Models as Tools for Complex Classification Problems" TU Berlin
13.02.17 Metabolic regulation All
07.03.17 Minimum sets of elementary flux modes A. Röhl
20.03.17 Translation of CellDesigner SBML to the rxncon language: turning large network maps into executable models
Petri Net Modelling of Regulatory Network Data Using the rxncon Framework
R. Henning

M. Wajnberg

Summer Term 2016

Date Title presented by
19.04.16 Group meeting All
26.04.16 Internal group meeting AG MathLife
03.05.16 Relating trap spaces in different models of regulatory networks R. Schwieger
10.05.16 Talk on research internship in the group of Edda Klipp
Cancer classification based on miRNA profiles using ASP
S. Forgo
K. Becker and H. Klarner
17.05.16 Exploring the optimal polyhedron in dynamic rFBA L. Liu
24.05.16 From biological functions to underlying regulatory structure patterns L. Sun
30.05.16 Using optimization to predict activation in metabolic pathways F. Dick
14.06.16 Minimal Extreme Pathways and Minimal Metabolic Behaviours A. Röhl
21.06.16 Tutorial on MILP A. Bockmayr
28.06.16 Internal group meeting AG MathLife
12.07.16 Internal group meeting AG MathLife
19.07.16 Sign consistency in regulatory networks M. Liedtke
12.09.16 Evaluating the stoichiometric and energetic constraints of cyanobacterial diurnal growth A.-M. Reimers

Winter Term 2015/16

Date Title presented by
12.10.15 Two approaches for relating dynamics in discrete models to dynamics in continuous models of regulatory networks R. Schwieger
19.10.15 Confronting knowledge networks on signaling networks with phosphoproteomics datasets using combinatorial optimization approaches A. Siegel
02.11.15 Software tutorial for PyBoolNet H. Klarner
09.11.15 BIMoS Day Combinatorial Optimization  
23.11.15 Software tutorial for PyBoolNet H. Klarner
01.12.15 Software tutorial for TREMPPI A. Streck
14.12.15 Minimal cut sets M. Litz
04.01.16 Group meeting All
11.01.16 Mathematical modeling of medial calcification M. Faizi
18.01.16 Detecting patterns in biological datasets using answer set programming K. Becker
25.01.16 ECMath Workshop  
01.02.16 Reduction of metabolic network models A. Röhl
08.02.16 Sign consistency in interaction graphs M. Liedtke

Summer Term 2015

Date Title presented by
13.04.15 Group meeting All
20.04.15 Matheon Center Days  
27.04.15 Group meeting All
04.05.15 BIMoS Day Compressed Sensing  
11.05.15 PhD defense A. Palinkas
18.05.15 IMPRS  
01.06.15 BIMoS Day Machine Learning  
08.06.15 A discrete stochastic model of protein translation M. Seeger
15.06.15 Networks of networks P. Koltai
22.06.15 Rational Design of Antibiotic Treatment Plans Bernd Sturmfels
29.06.15 A delayed Boolean model of the mammalian core clock P. Pett
06.07.15 Overview diploma thesis R. Schwieger
13.07.15 Logical Analysis of Perturbation Data K. Becker
14.09.15 Integrated model of regulation and metabolism Prof. Zhuo Wang

Winter Term 2014/15

Date Title presented by
13.10.14 Group meeting All
20.10.14 Conference reports All
27.10.14 PhD defense V. Pandey
12.11.14 Model integration and crosstalk analysis of logical regulatory networks K. Thobe
17.11.14 Group meeting All
24.11.14 Logical Analysis of Data (LAD) A. Bockmayr
01.12.14 Discussion on logical data analysis All
08.12.14 Parameter estimation S. Röblitz
15.12.14 PhD rehearsal talk L. David
05.01.15 Group meeting All
12.01.15 Preparation of CSB Review A. Bockmayr
19.01.15 Metabolic regulation A. Bockmayr
26.01.15 Exploring interaction graphs producing a given set of fixpoints L. Sun
02.02.15 ASP K. Becker / A. Röhl
09.02.15 Dynamic flux balance analysis including enzyme costs A.-M. Reimers
02.03.15 Mathematical modeling of Mönckeberg's disease M. Faizi
09.03.15 Dynamic constraint-based modeling of the metabolism of photosynthetic organisms A.-M. Reimers
16.03.15 A Systems Biology Approach to Herbicide Resistance in Alopecurus myosuroides N. J. Wendel
19.03.15 Extensions for LTL model checking of Thomas networks
EFM-Recorder – Faster Elementary Mode Enumeration via Reaction Coupling Order
A. Streck
A. Röhl
23.03.15 Logical Analysis of Biological Data
Feedback loops and dynamical properties in discrete models of gene regulation
K. Becker
T. Lorenz

Summer Term 2014

Date Title presented by
14.04.14 Group meeting All
22.04.14 Enzyme allocation problems in kinetic metabolic networks S. Müller
28.04.14 Answer Set Programming AG Schaub, Uni Potsdam
05.05.14 E. coli, Hinxton and Lausanne reports A. Streck, H. Klarner
12.05.14 Crosstalk analysis K. Thobe
19.05.14 A decomposition theory for vertex enumeration of polyhedra A.C. Reimers
26.05.14 IMPRS  
02.06.14 Selecting the optimal stimulus set for functional identification of glomeruli in the olfactory bulb
Analysis of a circadian clock DDE model
M. Schroeder

P. Pett
11.06.14 MAPK Case Study and ASP/ILP Benchmarks H. Klarner
23.06.14 On the relation between interaction and state transition graphs (Slides) L. Sun
14.07.14 Logical modelling of T-helper cell specification D. Thieffry

Winter Term 2013/14

Date Title presented by
14.10.13 Group meeting, conference reports All
22.10.13 Space-efficient reachability algorithm with applications in computational systems biology A. Streck
05.11.13 k-modules in metabolic networks A. Müller
12.11.13 Measuring techniques K. Thobe
26.11.13 Using linear programming solvers for flux coupling analysis T. Marschall
03.12.13 The IRMA article "A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches" All
06.12.13 Fixed point reachability in monotone Boolean networks A. Richard
17.12.13 Introduction into the topic of complexity Y. Goldstein
07.01.14 Predicting the Asymptotic Behaviors of Boolean Networks H. Klarner
21.01.14 The article "Network quantification of EGFR signaling unveils potential for targeted combination therapy" All
28.01.14 Mass spectrometry Tim Conrad
04.02.14 Further discussion of the article "Network quantification of EGFR signaling unveils potential for targeted combination therapy" All
11.02.14 Approaches to Modelling the Regulation of a Metabolic Network A. Palinkas

Summer Term 2013

Date Title presented by
08.04.13 Group meeting
15.04.13 Robustness of Circadian Rhythms S. Jamshidi
22.04.13 Using models to interprete signalling perturbation data N. Blüthgen
29.04.13 Gaussian Model for Transcriptional Regulatory Elements using ENCODE ChIP-seq Data
Discrete Modeling of the MAPK-mTor Pathway Connection in Cancer
M. Rauer
K. Thobe
06.05.13 Internship at Alacris Theranostics
Structural Control of Metabolic Flux
N. C. Wendel
M. Sajitz-Hermstein
13.05.13 Dynamical systems and NSA: A different approach to attractors J. Slavik
27.05.13 Inferring interaction graphs from state transition graphs L. Sun
03.06.13 Esther: Introducing an on-line platform for parameter identification A. Streck
10.06.13 Minimal representations of logical functions A. Palinkas
17.06.13 IMPRS Colloquium  
24.06.13 Steps to tFBA on E.coli iAF1260 - Propagation of Chemical Potentials A. Müller
01.07.13 Modeling and simulation of a mouse model in NASH
(Nonalcoholic Steatohepatitis)
V. Pandey
14.08.13 A dynamical neural network model for the competitive integration of bottom-up and top-down attention signals in superior colliculus J. Hesse
10.9.13 Flux modules in metabolic networks A. Müller
14.9.13 A lattice-theoretic framework for metabolic pathway analysis
Constrained flux coupling analysis
Y. Goldstein
L. David

Winter Term 2012/13

Date Title presented by
08.10.12 Modeling and analysis of the cytokinin signaling pathway's regulatory mechanisms F. Topcu-Alici
15.10.12 Group meeting, conference reports All
22.10.12 Finding modules of alternative pathways A. Müller
29.10.12 Basics of omega-regular languages and model checking theory A. Streck
31.10.12 Intelligent LTL model checking in the framework of Thomas A. Streck
19.11.12 Morphogen interpretation in Boolean regulatory networks M. Seeger
26.11.12 Network-level dynamics of diffusively coupled cells. S. Waldherr
03.12.12 A primer on optimal control with applications to metabolic networks S. Waldherr
10.12.12 Was ist eine blockierte Reaktion im Zellstoffwechsel?
Ein Vergleich zweier diskreter Modellierungsansätze
Y. Goldstein
19.12.12 Untersuchung metabolischer Netzwerke mit Verbandstheorie (PhD Defense) Y. Goldstein
07.01.13 Gene network reconstruction A. Bockmayr
14.01.13 Gene regulation mediated by metabolism A. Palinkas
21.01.13 Updating Boolean automata networks M. Noual
28.01.13 Minimal paths in metabolic networks A. Kraft
04.02.13 Automated model generation with COPASI I. Parchao
B. Hillmer
11.02.13 Thesis progress report H. Klarner
18.03.13 Analysing a piecewise affine model using the Thomas formalism S. Jamshidi

Summer Term 2012

Date Title presented by
10.04.12 Group meeting All
24.04.12 Searching for synergetic regulations in gene and protein networks J. Bethune
26.04.12 Preparation TdM All
03.05.12 Preparation TdM All
22.05.12 Final presentations: Software project
05.06.12 Modeling and analysis of the cytokinin signaling pathway's regulatory mechanisms F. Topcu-Alici
12.06.12 Progress Report 1: A constraint language for parametrizations H. Klarner
18.06.12 Oscillations and variability in the p53-Mdm2 network W. Abou-Jaoudé
28.06.12 Optimising metabolic production with several steady-states A. Palinkas
03.07.12 Abstract Thermo Flows - Inferring Blocked Reactions from Metabolite Potentials A. Müller
10.07.12 Three approaches for finding internal components in metabolic networks. L. David
17.07.12 The Starbucks Lemma: Metabolic models blended to your personal flavor Y. Goldstein
14.08.12 Robustness analysis and adaptation in biochemical networks S. Waldherr

Winter Term 2011/12

Date Title presented by
11.10.11 Group meeting All
17.10.11 Group meeting All
24.10.11 Ordinary and piecewise linear differential equation models of regulatory networks S. Jamshidi
02.11.11 An S-System Parameter Estimation Method for Biological Networks - SPEM X. Yang
07.11.11 Lattice Theory for Metabolic Networks - About Applications for the Lattice’s Maximum Y. Goldstein
14.11.11 Thermodynamic Constraints in Metabolic Networks A. Müller
28.11.11 Tailoring the search for elementary modes L. David
05.12.11 Analysis and characterization of asynchronous state transition graphs using extremal states T. Lorenz
12.12.11 Group meeting All
02.01.12 2012 A. Bockmayr
09.01.12 Constructing logical models of gene regulatory networks: an entropy based approach G. Karlebach
16.01.12 Thermodynamic flux coupling analysis Y. Goldstein
A. Müller
23.01.12 Refined analysis of the structure and dynamics of Thomas models J. Hesse
S. Meiers
J. Tackmann
30.01.12 On the mathematical theory of Ganti's chemoton A. Rettig
06.02.12 Eine kurze Geschichte der Kauffman-Vermutung H. Siebert
13.02.12 Vorbereitung "Tag der Mathematik" All
20.02.12 Modeling of hepatic glucose metabolism in Humans M. König
29.02.12 Reverse engineering with trap sets H. Klarner
05.03.12 Modelling and simulation studies of biological systems related to steatohepatitis V. Pandey
15.03.12 Comparing Discrete and Piecewise-Affine Differential Equation Models of Gene Regulatory Networks S. Jamshidi
21.03.12 tba All
04.04.12 Regulation of metabolic networks in stoichiometric models A. Palinkas

Summer Term 2011

Date Title presented by
12.04.11 Group meeting All
19.04.11 tba H. Klarner
26.04.11 Mapping Protein Patterns to Genome H. Aarabi
10.05.11 Discrete Dynamical Systems H. Siebert
11.05.11 PhD defense talk A. Marashi
17.05.11 Flux Coupling Analysis L. David
24.05.11 PhD students meeting A. Bockmayr
31.05.11 Advantages of the refined PADE S. Jamshidi
09.06.11 Regulatory Flux Balance Analysis (rFBA) A. Palinkas
14.06.11 Verbände in metabolischen Systemen --
Flusskopplungsanalyse durch Verbandstheorie vereinfachen
Y. Goldstein
21.06.11 Topological analysis and hybrid-based simulation studies of large cellular systems V. Pandey
28.06.11 How to find logical parameters of gene regulatory networks? CP vs. SAT J. Denissen
29.06.11 Ein Populationsmodell zur Produktion rekombinanter Antikörper N. Schöne
12.07.11 Detection of Structural Sources of Robustness in Biochemical
Reaction Networks Using a Simplified Analytical Method
J. Neigenfind
Reverse Engineering a Regulatory Network in Yeast
and Hybrid Methods for Parameter Estimation
B. Stigler
06.09.11 Parameter inference for asynchronous logical networks using discrete time series H. Klarner
27.09.11 Conference reports (ICSB, WCB, CMSB, Metabolic Pathways) All

Winter Term 2010/2011

Date Title presented by
09.09.10 Group meeting All
21.09.10 Stochasticity in reactions: a probabilistic Boolean modeling approach S. Twardziok
27.09.10 Algebraische Eigenschaften von Flussmustern Y. Goldstein
18.10.10 Group Meeting: Semesterplanung All
27.10.10 Projekt AG Holzhütter  
01.11.10 Model checking and parameter inference in the Thomas calculus J. Denißen
04.11.10 Using symbolic constraints in metabolic network modeling L. Jeschio
08.11.10 Identification of Potential Drug Targets in Kinetic Models:
From Experimental Data to Drug Candidates
M. Schulz
15.11.10 A new probabilistic approach in predictive microbiology N. Schöne
22.11.10 TBA meeting A. Bockmayr
29.11.10 Metabolome analysis in cancer S. Kempa (BIMSB)
02.12.10 Discrete tomography C. Heldt
06.12.10 TIGERNET  
13.12.10 Petri nets for integrated models of metabolism and its regulation A. Palinkas
14.12.10 PhD defense C. Heldt
10.01.11 Consistency of discrete formalisms S. Jamshidi
17.01.11 Thesis report S. Farke
24.01.11 Comparing multivalued regulatory networks with their Boolean counterpart T. Lorenz
31.01.11 PREDICT: Datenintegration J. Erehman
07.02.11 Journey to NY Y. Goldstein
14.02.11 The second Thomas conjecture H. Klarner

Summer Term 2010

Date Title presented by
13.04.10 Group meeting All
27.04.10 Extensions of ConsensusPathDB H. Galicka
04.05.10 Comparison of qualitative models of gene regulatory networks S. Jamshidi
20.05.10 Model selection with discretized protein expression data H. Klarner
27.05.10 Analysis of metabolic subnetworks by flux cone projection I L. David
S..A. Marashi
01.06.10 Analysis of metabolic subnetworks by flux cone projection II L. David
S.A. Marashi
03.06.10 Visualization of metabolic systems Y. Goldstein
22.06.10 Mechanisms of post-transctiptional regulation M. Jens (BIMSB)
23.06.10 Metabolism of C. reinhardtii M. Rügen
08.07.10 Projekt AG Holzhütter  
13.07.10 Ongoing diploma and master theses L. Jeschio
J. Denißen
A. Palinkas
T. Lorenz
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