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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -9,7 +9,7 @@ MEmilio implements various models for infectious disease dynamics, from simple c

If you use MEmilio, please cite our work

- Bicker J, Kerkmann D, Korf S, Plötzke L, Schmieding R, Wendler A, Zunker H et al. (2025) *MEmilio - a High Performance Modular Epidemics Simulation Software*. Available at https://github.com/SciCompMod/memilio and https://elib.dlr.de/219141/ .
- Bicker J, Gerstein C, Kerkmann D, Korf S, Schmieding R, Wendler A, Zunker H et al. (2026) *MEmilio - A high performance Modular Epidemics Simulation software for multi-scale and comparative simulations of infectious disease dynamics*. Submitted for publication. https://doi.org/10.48550/arXiv.2602.11381

and, in particular, for

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14 changes: 6 additions & 8 deletions docs/source/literature.rst
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@@ -1,8 +1,6 @@
.. |MEmilio_citation| replace:: Bicker J, Kerkmann D, Korf S, Ploetzke L, Schmieding R, Wendler AC, Zunker H, Nguyen K, Abele D, Gerstein C, Lenz P, Betz M, Schmidt A, Hannemann-Tamas R, Volmer K, Waßmuth N, Tritzschak H, Richter D, Heger M, Basermann A, Meyer-Hermann M, Hasenauer J, Kühn MJ. (2025). *MEmilio - a High Performance Modular Epidemics Simulation Software*. Available at |MEmilio_github|_ and |MEmilio_elib|_.
.. |MEmilio_github| replace:: https://github.com/SciCompMod/memilio
.. _MEmilio_github: https://github.com/SciCompMod/memilio
.. |MEmilio_elib| replace:: https://elib.dlr.de/213614/
.. _MEmilio_elib: https://elib.dlr.de/213614/
.. |MEmilio_citation| replace:: Bicker J, Gerstein C, Kerkmann D, Korf S, Schmieding R, Wendler A, Zunker H, Abele D, Betz M, Nguyen K, Plötzke L, Volmer K, SchmidtA, Waßmuth N, Lenz P, Richter D, Tritzschak H, Hannemann-Tamas R, Litz J, Johannssen P, Borges M, Jungklaus A, Heger M, Lange A, Kluth E, Rack K, Wieland V, Arruda J, Binder S, Klitz M, Siggel M, Dahmen M, Basermann A, Meyer-Hermann M, Hasenauer J, Kühn MJ. (2026). *MEmilio -- A high performance Modular EpideMIcs simuLatIOn software for multi-scale and comparative simulations of infectious disease dynamics*. Submitted for publication. |MEmilio_DOI|_
.. |MEmilio_DOI| replace:: DOI:10.48550/arXiv.2602.11381
.. _MEmilio_DOI: https://doi.org/10.48550/arXiv.2602.11381

.. |Novel_travel_time_aware_metapopulation_models| replace:: Zunker H, Schmieding R, Kerkmann D, Schengen A, Diexer S, Mikolajczyk R, Meyer-Hermann M, Kühn MJ. (2024). *Novel travel time aware metapopulation models and multi-layer waning immunity for late-phase epidemic and endemic scenarios*. *PLOS Computational Biology* 20(12): e1012630. |Novel_travel_time_aware_metapopulation_models_DOI|_
.. |Novel_travel_time_aware_metapopulation_models_DOI| replace:: DOI:10.1371/journal.pcbi.1012630
Expand All @@ -20,9 +18,9 @@
.. |Hybrid_metapopulation_agent-based_DOI| replace:: DOI:10.1016/j.idm.2024.12.015
.. _Hybrid_metapopulation_agent-based_DOI: https://doi.org/10.1016/j.idm.2024.12.015

.. |Graph_Neural_Network_Surrogates| replace:: Schmidt A, Zunker H, Heinlein A, Kühn MJ. (2025). *Graph Neural Network Surrogates to leverage Mechanistic Expert Knowledge towards Reliable and Immediate Pandemic Response*. Submitted for publication. |Graph_Neural_Network_Surrogates_DOI|_
.. |Graph_Neural_Network_Surrogates_DOI| replace:: arXiv:2411.06500
.. _Graph_Neural_Network_Surrogates_DOI: https://arxiv.org/abs/2411.06500
.. |Graph_Neural_Network_Surrogates| replace:: Schmidt A, Zunker H, Heinlein A, Kühn MJ. (2026). *Graph neural network surrogates to leverage mechanistic expert knowledge towards reliable and immediate pandemic response*. *Scientific Reports*. |Graph_Neural_Network_Surrogates_DOI|_
.. |Graph_Neural_Network_Surrogates_DOI| replace:: DOI:10.1038/s41598-026-39431-5
.. _Graph_Neural_Network_Surrogates_DOI: https://doi.org/10.1038/s41598-026-39431-5

.. |Revisiting_the_Linear_Chain| replace:: Plötzke L, Wendler A, Schmieding R, Kühn MJ. (2024). *Revisiting the Linear Chain Trick in epidemiological models: Implications of underlying assumptions for numerical solutions*. Mathematics and Computers in Simulation 239, pp. 823-844 (2026). |Revisiting_the_Linear_Chain_DOI|_
.. |Revisiting_the_Linear_Chain_DOI| replace:: DOI:10.1016/j.matcom.2025.07.045
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6 changes: 4 additions & 2 deletions docs/source/references.rst
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Expand Up @@ -8,14 +8,14 @@ The following gives an overview on (peer-reviewed) publications extending or usi
Recently submitted publications
--------------------------------------

- |MEmilio_citation|

- |Missing_Transmission_Chains|

- |Coupled_Epidemiological_and_Wastewater|

- |Differentially_private_federated_learning|

- |Graph_Neural_Network_Surrogates|



Peer-reviewed publications
Expand All @@ -27,6 +27,8 @@ Peer-reviewed publications

- |A_nonstandard_numerical_scheme|

- |Graph_Neural_Network_Surrogates|

**2025**

- |Risk-mediated_dynamic_regulation|
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24 changes: 24 additions & 0 deletions docs/source/team.rst
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Expand Up @@ -29,6 +29,7 @@ Martin Kühn studied at University of Cologne, Germany, and Université de Montr
.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|
* |Graph_Neural_Network_Surrogates|
* |A_nonstandard_numerical_scheme|
* |Revisiting_the_Linear_Chain|
Expand Down Expand Up @@ -64,6 +65,7 @@ Henrik Zunker is a PhD student at the Institute of Software Technology at the Ge
.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|
* |Risk-mediated_dynamic_regulation|
* |Graph_Neural_Network_Surrogates|
* |Novel_travel_time_aware_metapopulation_models|
Expand Down Expand Up @@ -94,6 +96,7 @@ His background is in numerical mathematics, where he studied at the University o
.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|
* |Agent-based_modeling_for|
* |Integrating_Human_Mobility_Models|
* |Missing_Transmission_Chains|
Expand All @@ -120,6 +123,7 @@ Julia Bicker is a PhD student at the Institute of Software Technology at the Ger
.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|
* |Hybrid_metapopulation_agent-based|
* |Integrative_Modeling_of_the|

Expand All @@ -145,6 +149,7 @@ Anna Wendler is a PhD student at the Institute of Software Technology at the Ger
.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|
* |A_nonstandard_numerical_scheme|
* |Revisiting_the_Linear_Chain|

Expand Down Expand Up @@ -172,6 +177,7 @@ Carlotta Gerstein completed her Bachelor's degree in Mathematics at the Universi
.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|
* |Agent-based_modeling_for|

.. dropdown:: Links
Expand All @@ -196,7 +202,15 @@ assistant in the group of Prof. Kevin Thurley and wrote his thesis on modeling i
2024 he joined the group of Prof. Jan Hasenauer at the Life and Medical Sciences Institute and the Bonn Center
for Mathematical Life Sciences as a PhD student to work on infectious disease modeling.

.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|

.. dropdown:: Links
:animate: fade-in-slide-down

* `ORCID Profile: 0009-0008-9861-0216 <https://orcid.org/0009-0008-9861-0216>`__

Maximilian Betz
^^^^^^^^^^^^^^^
Expand All @@ -211,6 +225,12 @@ Maximilian Betz

Maximilian Betz completed his Bachelor's degree in Computer Science at the DHBW Mannheim as an integrated degree program with the Department of High-Performance Computing at the German Aerospace Center (DLR). Afterwards, he continued with a Master's in Computer Science at the University of Cologne, where he focused on Machine Learning and High Performance Computing. During the Master's, he kept working at the DLR as a student assistant with a focus on automatic generation of Python bindings, metapopulation models to simulate the spatial spread of infectious diseases and Machine Learning based parameter inference.

.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|


René Schmieding
^^^^^^^^^^^^^^^

Expand All @@ -230,6 +250,7 @@ equation-based models.
.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|
* |Novel_travel_time_aware_metapopulation_models|
* |Hybrid_metapopulation_agent-based|
* |Integrating_Human_Mobility_Models|
Expand Down Expand Up @@ -258,6 +279,7 @@ He is interested in the development of agent-based models for infectious disease
.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|
* |Agent-based_modeling_for|
* |Novel_travel_time_aware_metapopulation_models|
* |Integrative_Modeling_of_the|
Expand All @@ -283,6 +305,7 @@ Daniel Abele is a research software engineer at the Institute of Software Techno
.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|
* |Assessment_of_effective_mitigation|

.. dropdown:: Links
Expand Down Expand Up @@ -344,6 +367,7 @@ Agatha Schmidt completed her Master's degree at the University of Cologne in col
.. dropdown:: Selected Publications
:animate: fade-in-slide-down

* |MEmilio_citation|
* |Graph_Neural_Network_Surrogates|

.. dropdown:: Links
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