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Update reference list #2414

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Update reference list #2414

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Update reference list
dweindl Apr 29, 2024
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LakrisenkoPat2024
dweindl May 30, 2024
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Mutsuddy2024
dweindl May 30, 2024
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46 changes: 36 additions & 10 deletions documentation/amici_refs.bib
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Original file line number Diff line number Diff line change
Expand Up @@ -1196,16 +1196,6 @@ @Article{TunedalVio2023
url = {https://physoc.onlinelibrary.wiley.com/doi/abs/10.1113/JP284652},
}

@Unknown{HasenauerMer2023,
author = {Hasenauer, Jan and Merkt, Simon and Ali, Solomon and Gudina, Esayas and Adissu, Wondimagegn and Münchhoff, Maximilian and Graf, Alexander and Krebs, Stefan and Elsbernd, Kira and Kisch, Rebecca and Sirgu, Sisay and Fantahun, Bereket and Bekele, Delayehu and Rubio-Acero, Raquel and Gashaw, Mulatu and Girma, Eyob and Yilma, Daniel and Zeynudin, Ahmed and Paunovic, Ivana and Wieser, Andreas},
creationdate = {2023-09-19T09:21:01},
doi = {10.21203/rs.3.rs-3307821/v1},
modificationdate = {2023-09-19T09:21:01},
month = {09},
title = {Long-term monitoring of SARS-CoV-2 seroprevalence and variants in Ethiopia provides prediction for immunity and cross-immunity},
year = {2023},
}

@Article{RaimundezFed2023,
author = {Elba Raim{\'{u}}ndez and Michael Fedders and Jan Hasenauer},
journal = {{iScience}},
Expand Down Expand Up @@ -1306,6 +1296,42 @@ @Article{DoresicGre2024
url = {https://www.biorxiv.org/content/early/2024/01/30/2024.01.26.577371},
}

@Article{MerktAli2024,
author = {Merkt, Simon and Ali, Solomon and Gudina, Esayas Kebede and Adissu, Wondimagegn and Gize, Addisu and Muenchhoff, Maximilian and Graf, Alexander and Krebs, Stefan and Elsbernd, Kira and Kisch, Rebecca and Betizazu, Sisay Sirgu and Fantahun, Bereket and Bekele, Delayehu and Rubio-Acero, Raquel and Gashaw, Mulatu and Girma, Eyob and Yilma, Daniel and Zeynudin, Ahmed and Paunovic, Ivana and Hoelscher, Michael and Blum, Helmut and Hasenauer, Jan and Kroidl, Arne and Wieser, Andreas},
journal = {Nature Communications},
title = {Long-term monitoring of SARS-CoV-2 seroprevalence and variants in Ethiopia provides prediction for immunity and cross-immunity},
year = {2024},
issn = {2041-1723},
month = apr,
number = {1},
volume = {15},
creationdate = {2024-04-29T08:30:06},
doi = {10.1038/s41467-024-47556-2},
modificationdate = {2024-04-29T08:30:06},
publisher = {Springer Science and Business Media LLC},
}

@Misc{LakrisenkoPat2024,
author = {Polina Lakrisenko and Dilan Pathirana and Daniel Weindl and Jan Hasenauer},
title = {Exploration of methods for computing sensitivities in ODE models at dynamic and steady states},
year = {2024},
archiveprefix = {arXiv},
creationdate = {2024-05-30T09:48:00},
eprint = {2405.16524},
modificationdate = {2024-05-30T09:48:00},
primaryclass = {q-bio.QM},
}

@PhdThesis{Mutsuddy2024,
author = {Mutsuddy, Arnab},
school = {Clemson University},
title = {Single cell pharmacodynamic modeling of cancer cell lines},
year = {2024},
creationdate = {2024-05-30T09:51:58},
modificationdate = {2024-05-30T09:53:40},
url = {https://tigerprints.clemson.edu/all_dissertations/3572},
}

@Comment{jabref-meta: databaseType:bibtex;}

@Comment{jabref-meta: grouping:
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28 changes: 20 additions & 8 deletions documentation/references.md
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@@ -1,6 +1,6 @@
# References

List of publications using AMICI. Total number is 85.
List of publications using AMICI. Total number is 87.

If you applied AMICI in your work and your publication is missing, please let us know via a new GitHub issue.

Expand Down Expand Up @@ -29,13 +29,32 @@ complex</span>.”</span> <em>Nucleic Acids Research</em>, February,
gkae123. <a
href="https://doi.org/10.1093/nar/gkae123">https://doi.org/10.1093/nar/gkae123</a>.
</div>
<div id="ref-LakrisenkoPat2024" class="csl-entry" role="listitem">
Lakrisenko, Polina, Dilan Pathirana, Daniel Weindl, and Jan Hasenauer.
2024. <span>“Exploration of Methods for Computing Sensitivities in ODE
Models at Dynamic and Steady States.”</span> <a
href="https://arxiv.org/abs/2405.16524">https://arxiv.org/abs/2405.16524</a>.
</div>
<div id="ref-LangPen2024" class="csl-entry" role="listitem">
Lang, Paul F., David R. Penas, Julio R. Banga, Daniel Weindl, and Bela
Novak. 2024. <span>“Reusable Rule-Based Cell Cycle Model Explains
Compartment-Resolved Dynamics of 16 Observables in RPE-1 Cells.”</span>
<em>PLOS Computational Biology</em> 20 (1): 1–24. <a
href="https://doi.org/10.1371/journal.pcbi.1011151">https://doi.org/10.1371/journal.pcbi.1011151</a>.
</div>
<div id="ref-MerktAli2024" class="csl-entry" role="listitem">
Merkt, Simon, Solomon Ali, Esayas Kebede Gudina, Wondimagegn Adissu,
Addisu Gize, Maximilian Muenchhoff, Alexander Graf, et al. 2024.
<span>“Long-Term Monitoring of SARS-CoV-2 Seroprevalence and Variants in
Ethiopia Provides Prediction for Immunity and Cross-Immunity.”</span>
<em>Nature Communications</em> 15 (1). <a
href="https://doi.org/10.1038/s41467-024-47556-2">https://doi.org/10.1038/s41467-024-47556-2</a>.
</div>
<div id="ref-Mutsuddy2024" class="csl-entry" role="listitem">
Mutsuddy, Arnab. 2024. <span>“Single Cell Pharmacodynamic Modeling of
Cancer Cell Lines.”</span> PhD thesis, Clemson University. <a
href="https://tigerprints.clemson.edu/all_dissertations/3572">https://tigerprints.clemson.edu/all_dissertations/3572</a>.
</div>
<div id="ref-SluijsZho2024" class="csl-entry" role="listitem">
Sluijs, Bob van, Tao Zhou, Britta Helwig, Mathieu G. Baltussen, Frank H.
T. Nelissen, Hans A. Heus, and Wilhelm T. S. Huck. 2024.
Expand Down Expand Up @@ -84,13 +103,6 @@ Rewiring Contribute to Drug Resistance.”</span> <em>Molecular Systems
Biology</em> 19 (2): e10988. <a
href="https://doi.org/10.15252/msb.202210988">https://doi.org/10.15252/msb.202210988</a>.
</div>
<div id="ref-HasenauerMer2023" class="csl-entry" role="listitem">
Hasenauer, Jan, Simon Merkt, Solomon Ali, Esayas Gudina, Wondimagegn
Adissu, Maximilian Münchhoff, Alexander Graf, et al. 2023.
<span>“Long-Term Monitoring of SARS-CoV-2 Seroprevalence and Variants in
Ethiopia Provides Prediction for Immunity and Cross-Immunity.”</span> <a
href="https://doi.org/10.21203/rs.3.rs-3307821/v1">https://doi.org/10.21203/rs.3.rs-3307821/v1</a>.
</div>
<div id="ref-HuckBal2023" class="csl-entry" role="listitem">
Huck, Wilhelm, Mathieu Baltussen, Thijs de Jong, Quentin Duez, and
William Robinson. 2023. <span>“Chemical Reservoir Computation in a
Expand Down