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Update list of papers using AMICI #1509

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Update list of papers using AMICI
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Update documentation/amici_refs.bib
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63 changes: 58 additions & 5 deletions documentation/amici_refs.bib
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Original file line number Diff line number Diff line change
Expand Up @@ -549,7 +549,7 @@ @Article{LinesPas2019
@Article{VillaverdeRai2019,
author = {Alejandro F. Villaverde and Elba Raimúndez and Jan Hasenauer and Julio R. Banga},
journal = {IFAC-PapersOnLine},
title = {A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology⁎⁎This research has received funding from the European Unions Horizon 2020 research and innovation program under grant agreement No 686282 (CanPathPro) and the German Ministry of Education and Research (BMBF) under the grant agreement No 01ZX1310B (SYS-Stomach) and No 01ZX1705A (INCOME).},
title = {A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology},
year = {2019},
issn = {2405-8963},
note = {8th Conference on Foundations of Systems Biology in Engineering FOSBE 2019},
Expand Down Expand Up @@ -711,7 +711,7 @@ @Article{Schaelte2020.01.30.927004
url = {https://www.biorxiv.org/content/early/2020/01/31/2020.01.30.927004},
}

@Article{Adlung866871,
@Article{AdlungSta2019,
author = {Adlung, Lorenz and Stapor, Paul and T{\"o}nsing, Christian and Schmiester, Leonard and Schwarzm{\"u}ller, Luisa E. and Wang, Dantong and Timmer, Jens and Klingm{\"u}ller, Ursula and Hasenauer, Jan and Schilling, Marcel},
journal = {bioRxiv},
title = {Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes define survival threshold in erythroid progenitor cells},
Expand All @@ -725,10 +725,10 @@ @Article{Adlung866871
url = {https://www.biorxiv.org/content/early/2019/12/07/866871},
}

@Article{PITT201872,
@Article{PittGom2018,
author = {Jake Alan Pitt and Lucian Gomoescu and Constantinos C. Pantelides and Benoît Chachuat and Julio R. Banga},
journal = {IFAC-PapersOnLine},
title = {Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators⁎⁎This project has received funding from the European Unions Horizon 2020 research and innovation program under grant agreement 675585 (Marie Sklodowska-Curie ITN SyMBioSys). The authors JAP and LG are Marie Sklodowska-Curie Early Stage Researchers at IIM-CSIC (Spain) and PSE Ltd (UK) respectively.},
title = {Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators},
year = {2018},
issn = {2405-8963},
note = {7th Conference on Foundation of Systems Biology in Engineering FOSBE 2018},
Expand All @@ -752,7 +752,7 @@ @MastersThesis{Watanabe2019
url = {https://hdl.handle.net/20.500.12380/256855},
}

@Article{Erdem2020.11.09.373407,
@Article{ErdemBen2020,
author = {Erdem, Cemal and Bensman, Ethan M. and Mutsuddy, Arnab and Saint-Antoine, Michael M. and Bouhaddou, Mehdi and Blake, Robert C. and Dodd, Will and Gross, Sean M. and Heiser, Laura M. and Feltus, F. Alex and Birtwistle, Marc R.},
journal = {bioRxiv},
title = {A Simple and Efficient Pipeline for Construction, Merging, Expansion, and Simulation of Large-Scale, Single-Cell Mechanistic Models},
Expand Down Expand Up @@ -811,6 +811,59 @@ @Article{RaimundezDud2021
url = {https://www.sciencedirect.com/science/article/pii/S1755436521000037},
}

@Article{vanRosmalenSmi2021,
author = {R.P. {van Rosmalen} and R.W. Smith and V.A.P. {Martins dos Santos} and C. Fleck and M. Suarez-Diez},
journal = {Metabolic Engineering},
title = {Model reduction of genome-scale metabolic models as a basis for targeted kinetic models},
year = {2021},
issn = {1096-7176},
pages = {74-84},
volume = {64},
abstract = {Constraint-based, genome-scale metabolic models are an essential tool to guide metabolic engineering. However, they lack the detail and time dimension that kinetic models with enzyme dynamics offer. Model reduction can be used to bridge the gap between the two methods and allow for the integration of kinetic models into the Design-Built-Test-Learn cycle. Here we show that these reduced size models can be representative of the dynamics of the original model and demonstrate the automated generation and parameterisation of such models. Using these minimal models of metabolism could allow for further exploration of dynamic responses in metabolic networks.},
doi = {https://doi.org/10.1016/j.ymben.2021.01.008},
keywords = {Metabolic engineering, DBTL cycle, Model reduction, Model optimisation, Model-driven design, Synthetic biology},
url = {https://www.sciencedirect.com/science/article/pii/S1096717621000161},
}

@Article{StenPod2021,
author = {Sten, Sebastian and Pod{\'e}us, Henrik and Sundqvist, Nicolas and Elinder, Fredrik and Engstr{\"o}m, Maria and Cedersund, Gunnar},
journal = {bioRxiv},
title = {A multi-data based quantitative model for the neurovascular coupling in the brain},
year = {2021},
abstract = {The neurovascular coupling (NVC) forms the foundation for functional imaging techniques of the brain, since NVC connects neural activity with observable hemodynamic changes. Many aspects of the NVC have been studied both experimentally and with mathematical models: various combinations of blood volume and flow, electrical activity, oxygen saturation measures, blood oxygenation level-dependent (BOLD) response, and optogenetics have been measured and modeled in rodents, primates, or humans. We now present a first inter-connected mathematical model that describes all such data types simultaneously. The model can predict independent validation data not used for training. Using simulations, we show for example how complex bimodal behaviors appear upon stimulation. These simulations thus demonstrate how our new quantitative model, incorporating most of the core aspects of the NVC, can be used to mechanistically explain each of its constituent datasets.Competing Interest StatementThe authors have declared no competing interest.},
doi = {10.1101/2021.03.25.437053},
elocation-id = {2021.03.25.437053},
eprint = {https://www.biorxiv.org/content/early/2021/03/26/2021.03.25.437053.full.pdf},
publisher = {Cold Spring Harbor Laboratory},
url = {https://www.biorxiv.org/content/early/2021/03/26/2021.03.25.437053},
}

@PhdThesis{Gaspari2021,
author = {Gaspari, Erika},
school = {Wageningen University},
title = {Model-driven design of Mycoplasma as a vaccine chassis},
year = {2021},
address = {Wageningen},
comment = {WU thesis 7758 Includes bibliographical references. - With summaries in English, Italian and Spanish
10.18174/539593},
doi = {10.18174/539593},
issn = {9789463956864},
url = {https://edepot.wur.nl/539593},
}

@Article{VanhoeferMat2021,
author = {Jakob Vanhoefer and Marta R. a. Matos and Dilan Pathirana and Yannik Schälte and Jan Hasenauer},
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journal = {Journal of Open Source Software},
title = {yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML},
year = {2021},
number = {61},
pages = {3215},
volume = {6},
doi = {10.21105/joss.03215},
publisher = {The Open Journal},
url = {https://doi.org/10.21105/joss.03215},
}

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

@Comment{jabref-meta: grouping:
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24 changes: 18 additions & 6 deletions documentation/references.md
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@@ -1,11 +1,14 @@
# References

List of publications using AMICI. Total number is 51.
List of publications using AMICI. Total number is 55.

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

<h1 class="unnumbered" id="section">2021</h1>
<div id="refs" class="references hanging-indent" role="doc-bibliography">
<div id="ref-Gaspari2021">
<p>Gaspari, Erika. 2021. “Model-Driven Design of Mycoplasma as a Vaccine Chassis.” PhD thesis, Wageningen: Wageningen University. <a href="https://doi.org/10.18174/539593">https://doi.org/10.18174/539593</a>.</p>
</div>
<div id="ref-RaimundezDud2021">
<p>Raimúndez, Elba, Erika Dudkin, Jakob Vanhoefer, Emad Alamoudi, Simon Merkt, Lara Fuhrmann, Fan Bai, and Jan Hasenauer. 2021. “COVID-19 Outbreak in Wuhan Demonstrates the Limitations of Publicly Available Case Numbers for Epidemiological Modeling.” <em>Epidemics</em> 34: 100439. <a href="https://doi.org/https://doi.org/10.1016/j.epidem.2021.100439">https://doi.org/https://doi.org/10.1016/j.epidem.2021.100439</a>.</p>
</div>
Expand All @@ -15,13 +18,22 @@ If you applied AMICI in your work and your publication is missing, please let us
<div id="ref-StaedterSch2021">
<p>Städter, Philipp, Yannik Schälte, Leonard Schmiester, Jan Hasenauer, and Paul L. Stapor. 2021. “Benchmarking of Numerical Integration Methods for Ode Models of Biological Systems.” <em>Scientific Reports</em> 11 (1): 2696. <a href="https://doi.org/10.1038/s41598-021-82196-2">https://doi.org/10.1038/s41598-021-82196-2</a>.</p>
</div>
<div id="ref-StenPod2021">
<p>Sten, Sebastian, Henrik Podéus, Nicolas Sundqvist, Fredrik Elinder, Maria Engström, and Gunnar Cedersund. 2021. “A Multi-Data Based Quantitative Model for the Neurovascular Coupling in the Brain.” <em>bioRxiv</em>. <a href="https://doi.org/10.1101/2021.03.25.437053">https://doi.org/10.1101/2021.03.25.437053</a>.</p>
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Is it intentional that many publications appear to have the first author as [Last Name], [First Name] then subsequent authors as [First Name] [Last Name]?

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Not my favorite, but that's what pandoc-citeproc does :)

</div>
<div id="ref-VanhoeferMat2021">
<p>Vanhoefer, Jakob, Marta R. a. Matos, Dilan Pathirana, Yannik Schälte, and Jan Hasenauer. 2021. “Yaml2sbml: Human-Readable and -Writable Specification of Ode Models and Their Conversion to Sbml.” <em>Journal of Open Source Software</em> 6 (61): 3215. <a href="https://doi.org/10.21105/joss.03215">https://doi.org/10.21105/joss.03215</a>.</p>
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Suggested change
<p>Vanhoefer, Jakob, Marta R. a. Matos, Dilan Pathirana, Yannik Schälte, and Jan Hasenauer. 2021. “Yaml2sbml: Human-Readable and -Writable Specification of Ode Models and Their Conversion to Sbml.” <em>Journal of Open Source Software</em> 6 (61): 3215. <a href="https://doi.org/10.21105/joss.03215">https://doi.org/10.21105/joss.03215</a>.</p>
<p>Vanhoefer, Jakob, Marta R. A. Matos, Dilan Pathirana, Yannik Schälte, and Jan Hasenauer. 2021. “yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML.” <em>Journal of Open Source Software</em> 6 (61): 3215. <a href="https://doi.org/10.21105/joss.03215">https://doi.org/10.21105/joss.03215</a>.</p>

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Is this generated automatically from the .bib? There, the title is capitalized as in the publication.

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Yes, it's auto-generated. With the current solution, it's unfortunately not easily possible to change the style. Maybe needs to be rewritten at some point.

</div>
<div id="ref-vanRosmalenSmi2021">
<p>van Rosmalen, R. P., R. W. Smith, V. A. P. Martins dos Santos, C. Fleck, and M. Suarez-Diez. 2021. “Model Reduction of Genome-Scale Metabolic Models as a Basis for Targeted Kinetic Models.” <em>Metabolic Engineering</em> 64: 74–84. <a href="https://doi.org/https://doi.org/10.1016/j.ymben.2021.01.008">https://doi.org/https://doi.org/10.1016/j.ymben.2021.01.008</a>.</p>
</div>
</div>
<h1 class="unnumbered" id="section">2020</h1>
<div id="refs" class="references hanging-indent" role="doc-bibliography">
<div id="ref-AlabertLoo2020">
<p>Alabert, Constance, Carolin Loos, Moritz Voelker-Albert, Simona Graziano, Ignasi Forné, Nazaret Reveron-Gomez, Lea Schuh, et al. 2020. “Domain Model Explains Propagation Dynamics and Stability of Histone H3k27 and H3k36 Methylation Landscapes.” <em>Cell Reports</em> 30 (4): 1223–1234.e8. <a href="https://doi.org/10.1016/j.celrep.2019.12.060">https://doi.org/10.1016/j.celrep.2019.12.060</a>.</p>
</div>
<div id="ref-Erdem2020.11.09.373407">
<div id="ref-ErdemBen2020">
<p>Erdem, Cemal, Ethan M. Bensman, Arnab Mutsuddy, Michael M. Saint-Antoine, Mehdi Bouhaddou, Robert C. Blake, Will Dodd, et al. 2020. “A Simple and Efficient Pipeline for Construction, Merging, Expansion, and Simulation of Large-Scale, Single-Cell Mechanistic Models.” <em>bioRxiv</em>. <a href="https://doi.org/10.1101/2020.11.09.373407">https://doi.org/10.1101/2020.11.09.373407</a>.</p>
</div>
<div id="ref-GerosaChi2020">
Expand Down Expand Up @@ -54,7 +66,7 @@ If you applied AMICI in your work and your publication is missing, please let us
</div>
<h1 class="unnumbered" id="section">2019</h1>
<div id="refs" class="references hanging-indent" role="doc-bibliography">
<div id="ref-Adlung866871">
<div id="ref-AdlungSta2019">
<p>Adlung, Lorenz, Paul Stapor, Christian Tönsing, Leonard Schmiester, Luisa E. Schwarzmüller, Dantong Wang, Jens Timmer, Ursula Klingmüller, Jan Hasenauer, and Marcel Schilling. 2019. “Cell-to-Cell Variability in Jak2/Stat5 Pathway Components and Cytoplasmic Volumes Define Survival Threshold in Erythroid Progenitor Cells.” <em>bioRxiv</em>. <a href="https://doi.org/10.1101/866871">https://doi.org/10.1101/866871</a>.</p>
</div>
<div id="ref-DharmarajanKal2019">
Expand Down Expand Up @@ -88,7 +100,7 @@ If you applied AMICI in your work and your publication is missing, please let us
<p>Terje Lines, Glenn, Łukasz Paszkowski, Leonard Schmiester, Daniel Weindl, Paul Stapor, and Jan Hasenauer. 2019. “Efficient Computation of Steady States in Large-Scale Ode Models of Biochemical Reaction Networks.” <em>IFAC-PapersOnLine</em> 52 (26): 32–37. <a href="https://doi.org/10.1016/j.ifacol.2019.12.232">https://doi.org/10.1016/j.ifacol.2019.12.232</a>.</p>
</div>
<div id="ref-VillaverdeRai2019">
<p>Villaverde, Alejandro F., Elba Raimúndez, Jan Hasenauer, and Julio R. Banga. 2019. “A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology⁎⁎This Research Has Received Funding from the European Unions Horizon 2020 Research and Innovation Program Under Grant Agreement No 686282 (Canpathpro) and the German Ministry of Education and Research (Bmbf) Under the Grant Agreement No 01ZX1310B (Sys-Stomach) and No 01ZX1705A (Income).” <em>IFAC-PapersOnLine</em> 52 (26): 45–51. <a href="https://doi.org/10.1016/j.ifacol.2019.12.234">https://doi.org/10.1016/j.ifacol.2019.12.234</a>.</p>
<p>Villaverde, Alejandro F., Elba Raimúndez, Jan Hasenauer, and Julio R. Banga. 2019. “A Comparison of Methods for Quantifying Prediction Uncertainty in Systems Biology.” <em>IFAC-PapersOnLine</em> 52 (26): 45–51. <a href="https://doi.org/10.1016/j.ifacol.2019.12.234">https://doi.org/10.1016/j.ifacol.2019.12.234</a>.</p>
</div>
<div id="ref-WangSta2019">
<p>Wang, Dantong, Paul Stapor, and Jan Hasenauer. 2019. “Dirac Mixture Distributions for the Approximation of Mixed Effects Models.” <em>IFAC-PapersOnLine</em> 52 (26): 200–206. <a href="https://doi.org/10.1016/j.ifacol.2019.12.258">https://doi.org/10.1016/j.ifacol.2019.12.258</a>.</p>
Expand Down Expand Up @@ -120,8 +132,8 @@ If you applied AMICI in your work and your publication is missing, please let us
<div id="ref-LoosMoe2018">
<p>Loos, Carolin, Katharina Moeller, Fabian Fröhlich, Tim Hucho, and Jan Hasenauer. 2018. “A Hierarchical, Data-Driven Approach to Modeling Single-Cell Populations Predicts Latent Causes of Cell-to-Cell Variability.” <em>Cell Systems</em> 6 (5): 593–603. <a href="https://doi.org/10.1016/j.cels.2018.04.008">https://doi.org/10.1016/j.cels.2018.04.008</a>.</p>
</div>
<div id="ref-PITT201872">
<p>Pitt, Jake Alan, Lucian Gomoescu, Constantinos C. Pantelides, Benoît Chachuat, and Julio R. Banga. 2018. “Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators⁎⁎This Project Has Received Funding from the European Unions Horizon 2020 Research and Innovation Program Under Grant Agreement 675585 (Marie Sklodowska-Curie Itn Symbiosys). The Authors Jap and Lg Are Marie Sklodowska-Curie Early Stage Researchers at Iim-Csic (Spain) and Pse Ltd (Uk) Respectively.” <em>IFAC-PapersOnLine</em> 51 (19): 72–75. <a href="https://doi.org/https://doi.org/10.1016/j.ifacol.2018.09.040">https://doi.org/https://doi.org/10.1016/j.ifacol.2018.09.040</a>.</p>
<div id="ref-PittGom2018">
<p>Pitt, Jake Alan, Lucian Gomoescu, Constantinos C. Pantelides, Benoît Chachuat, and Julio R. Banga. 2018. “Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators.” <em>IFAC-PapersOnLine</em> 51 (19): 72–75. <a href="https://doi.org/https://doi.org/10.1016/j.ifacol.2018.09.040">https://doi.org/https://doi.org/10.1016/j.ifacol.2018.09.040</a>.</p>
</div>
<div id="ref-SchaelteSta2018">
<p>Schälte, Y., P. Stapor, and J. Hasenauer. 2018. “Evaluation of Derivative-Free Optimizers for Parameter Estimation in Systems Biology.” <em>FAC-PapersOnLine</em> 51 (19): 98–101. <a href="https://doi.org/10.1016/j.ifacol.2018.09.025">https://doi.org/10.1016/j.ifacol.2018.09.025</a>.</p>
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