From 417ba2e6760b9028d2fc4a5ed680b448b5836809 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Fri, 28 Jun 2024 08:28:45 +0200 Subject: [PATCH 1/4] Update reference list --- documentation/amici_refs.bib | 37 ++++++++++++++++++++++++------------ documentation/references.md | 8 +++++++- 2 files changed, 32 insertions(+), 13 deletions(-) diff --git a/documentation/amici_refs.bib b/documentation/amici_refs.bib index b14d0e18b0..5c7741f631 100644 --- a/documentation/amici_refs.bib +++ b/documentation/amici_refs.bib @@ -1069,18 +1069,19 @@ @Article{LakrisenkoSta2023 } @Article{ContentoCas2023, - author = {Lorenzo Contento and Noemi Castelletti and Elba Raimúndez and Ronan {Le Gleut} and Yannik Schälte and Paul Stapor and Ludwig Christian Hinske and Michael Hoelscher and Andreas Wieser and Katja Radon and Christiane Fuchs and Jan Hasenauer}, - journal = {Epidemics}, - title = {Integrative modelling of reported case numbers and seroprevalence reveals time-dependent test efficiency and infectious contacts}, - year = {2023}, - issn = {1755-4365}, - pages = {100681}, - volume = {43}, - abstract = {Mathematical models have been widely used during the ongoing SARS-CoV-2 pandemic for data interpretation, forecasting, and policy making. However, most models are based on officially reported case numbers, which depend on test availability and test strategies. The time dependence of these factors renders interpretation difficult and might even result in estimation biases. Here, we present a computational modelling framework that allows for the integration of reported case numbers with seroprevalence estimates obtained from representative population cohorts. To account for the time dependence of infection and testing rates, we embed flexible splines in an epidemiological model. The parameters of these splines are estimated, along with the other parameters, from the available data using a Bayesian approach. The application of this approach to the official case numbers reported for Munich (Germany) and the seroprevalence reported by the prospective COVID-19 Cohort Munich (KoCo19) provides first estimates for the time dependence of the under-reporting factor. Furthermore, we estimate how the effectiveness of non-pharmaceutical interventions and of the testing strategy evolves over time. Overall, our results show that the integration of temporally highly resolved and representative data is beneficial for accurate epidemiological analyses.}, - creationdate = {2023-04-15T07:59:57}, - doi = {10.1016/j.epidem.2023.100681}, - keywords = {Compartmental model, Parameter estimation, Uncertainty quantification, COVID-19}, - url = {https://www.sciencedirect.com/science/article/pii/S1755436523000178}, + author = {Lorenzo Contento and Noemi Castelletti and Elba Raimúndez and Ronan {Le Gleut} and Yannik Schälte and Paul Stapor and Ludwig Christian Hinske and Michael Hoelscher and Andreas Wieser and Katja Radon and Christiane Fuchs and Jan Hasenauer}, + journal = {Epidemics}, + title = {Integrative modelling of reported case numbers and seroprevalence reveals time-dependent test efficiency and infectious contacts}, + year = {2023}, + issn = {1755-4365}, + pages = {100681}, + volume = {43}, + abstract = {Mathematical models have been widely used during the ongoing SARS-CoV-2 pandemic for data interpretation, forecasting, and policy making. However, most models are based on officially reported case numbers, which depend on test availability and test strategies. The time dependence of these factors renders interpretation difficult and might even result in estimation biases. Here, we present a computational modelling framework that allows for the integration of reported case numbers with seroprevalence estimates obtained from representative population cohorts. To account for the time dependence of infection and testing rates, we embed flexible splines in an epidemiological model. The parameters of these splines are estimated, along with the other parameters, from the available data using a Bayesian approach. The application of this approach to the official case numbers reported for Munich (Germany) and the seroprevalence reported by the prospective COVID-19 Cohort Munich (KoCo19) provides first estimates for the time dependence of the under-reporting factor. Furthermore, we estimate how the effectiveness of non-pharmaceutical interventions and of the testing strategy evolves over time. Overall, our results show that the integration of temporally highly resolved and representative data is beneficial for accurate epidemiological analyses.}, + creationdate = {2023-04-15T07:59:57}, + doi = {10.1016/j.epidem.2023.100681}, + keywords = {Compartmental model, Parameter estimation, Uncertainty quantification, COVID-19}, + modificationdate = {2024-06-28T08:27:57}, + url = {https://www.sciencedirect.com/science/article/pii/S1755436523000178}, } @Article{FroehlichGer2023, @@ -1332,6 +1333,18 @@ @PhdThesis{Mutsuddy2024 url = {https://tigerprints.clemson.edu/all_dissertations/3572}, } +@Misc{PhilippsKoe2024, + author = {Maren Philipps and Antonia Körner and Jakob Vanhoefer and Dilan Pathirana and Jan Hasenauer}, + title = {Non-Negative Universal Differential Equations With Applications in Systems Biology}, + year = {2024}, + archiveprefix = {arXiv}, + creationdate = {2024-06-28T08:27:59}, + eprint = {2406.14246}, + modificationdate = {2024-06-28T08:27:59}, + primaryclass = {q-bio.QM}, + url = {https://arxiv.org/abs/2406.14246}, +} + @Comment{jabref-meta: databaseType:bibtex;} @Comment{jabref-meta: grouping: diff --git a/documentation/references.md b/documentation/references.md index f17da06c55..957ca1f8d9 100644 --- a/documentation/references.md +++ b/documentation/references.md @@ -1,6 +1,6 @@ # References -List of publications using AMICI. Total number is 87. +List of publications using AMICI. Total number is 88. If you applied AMICI in your work and your publication is missing, please let us know via a new GitHub issue. @@ -55,6 +55,12 @@ Mutsuddy, Arnab. 2024. “Single Cell Pharmacodynamic Modeling of Cancer Cell Lines.” PhD thesis, Clemson University. https://tigerprints.clemson.edu/all_dissertations/3572. +
+Philipps, Maren, Antonia Körner, Jakob Vanhoefer, Dilan Pathirana, and +Jan Hasenauer. 2024. “Non-Negative Universal Differential +Equations with Applications in Systems Biology.” https://arxiv.org/abs/2406.14246. +
Sluijs, Bob van, Tao Zhou, Britta Helwig, Mathieu G. Baltussen, Frank H. T. Nelissen, Hans A. Heus, and Wilhelm T. S. Huck. 2024. From a535a7750e6ec98ecb30d9ffa62270583386e7a7 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Sat, 29 Jun 2024 14:03:43 +0200 Subject: [PATCH 2/4] BaltussenJon2024 --- documentation/amici_refs.bib | 13 +++++++++++++ documentation/references.md | 9 ++++++++- 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/documentation/amici_refs.bib b/documentation/amici_refs.bib index 5c7741f631..7321d97194 100644 --- a/documentation/amici_refs.bib +++ b/documentation/amici_refs.bib @@ -1345,6 +1345,19 @@ @Misc{PhilippsKoe2024 url = {https://arxiv.org/abs/2406.14246}, } +@Article{BaltussenJon2024, + author = {Baltussen, Mathieu G. and de Jong, Thijs J. and Duez, Quentin and Robinson, William E. and Huck, Wilhelm T. S.}, + journal = {Nature}, + title = {Chemical reservoir computation in a self-organizing reaction network}, + year = {2024}, + issn = {1476-4687}, + month = jun, + creationdate = {2024-06-29T14:03:08}, + doi = {10.1038/s41586-024-07567-x}, + modificationdate = {2024-06-29T14:03:08}, + publisher = {Springer Science and Business Media LLC}, +} + @Comment{jabref-meta: databaseType:bibtex;} @Comment{jabref-meta: grouping: diff --git a/documentation/references.md b/documentation/references.md index 957ca1f8d9..cf91afaf17 100644 --- a/documentation/references.md +++ b/documentation/references.md @@ -1,6 +1,6 @@ # References -List of publications using AMICI. Total number is 88. +List of publications using AMICI. Total number is 89. If you applied AMICI in your work and your publication is missing, please let us know via a new GitHub issue. @@ -14,6 +14,13 @@ If you applied AMICI in your work and your publication is missing, please let us

2024

+
+Baltussen, Mathieu G., Thijs J. de Jong, Quentin Duez, William E. +Robinson, and Wilhelm T. S. Huck. 2024. “Chemical Reservoir +Computation in a Self-Organizing Reaction Network.” +Nature, June. https://doi.org/10.1038/s41586-024-07567-x. +
Dorešić, Domagoj, Stephan Grein, and Jan Hasenauer. 2024. “Efficient Parameter Estimation for ODE Models of Cellular From 4c8e038879852733bd053b1063f79bb9cfb20139 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 1 Jul 2024 10:06:27 +0200 Subject: [PATCH 3/4] issue link --- documentation/recreate_reference_list.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/documentation/recreate_reference_list.py b/documentation/recreate_reference_list.py index 7750173ce1..ea456d05b6 100755 --- a/documentation/recreate_reference_list.py +++ b/documentation/recreate_reference_list.py @@ -75,7 +75,9 @@ def main(): ) f.write( "If you applied AMICI in your work and your publication is " - "missing, please let us know via a new GitHub issue.\n\n" + "missing, please let us know via a new GitHub " + "[issue](https://github.com/AMICI-dev/AMICI/issues/new" + "?labels=documentation&title=Add+publication).\n\n" ) f.write( """ From ff9a0783019370dc66db79de099ec13d8d68f4a0 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 1 Jul 2024 10:20:36 +0200 Subject: [PATCH 4/4] .. --- documentation/recreate_reference_list.py | 7 ++++--- documentation/references.md | 3 ++- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/documentation/recreate_reference_list.py b/documentation/recreate_reference_list.py index ea456d05b6..a188f1daa0 100755 --- a/documentation/recreate_reference_list.py +++ b/documentation/recreate_reference_list.py @@ -75,9 +75,10 @@ def main(): ) f.write( "If you applied AMICI in your work and your publication is " - "missing, please let us know via a new GitHub " - "[issue](https://github.com/AMICI-dev/AMICI/issues/new" - "?labels=documentation&title=Add+publication).\n\n" + "missing, please let us know via a new\n" + "[GitHub issue](https://github.com/AMICI-dev/AMICI/issues/new" + "?labels=documentation&title=Add+publication" + "&body=AMICI+was+used+in+this+manuscript:+DOI).\n\n" ) f.write( """ diff --git a/documentation/references.md b/documentation/references.md index cf91afaf17..cd103843fa 100644 --- a/documentation/references.md +++ b/documentation/references.md @@ -2,7 +2,8 @@ List of publications using AMICI. Total number is 89. -If you applied AMICI in your work and your publication is missing, please let us know via a new GitHub issue. +If you applied AMICI in your work and your publication is missing, please let us know via a new +[GitHub issue](https://github.com/AMICI-dev/AMICI/issues/new?labels=documentation&title=Add+publication&body=AMICI+was+used+in+this+manuscript:+DOI).