Update references (#2691)

* JostWei2025

* PerssonFro2025

Author: dweindl

doc/amici_refs.bib

@@ -1480,6 +1480,36 @@ @Electronic{HuckJak2025
   modificationdate = {2025-03-10T08:58:09},
 }
 
+@Article{JostWei2025,
+  author           = {Jost, Paul Jonas and Weindl, Daniel and Wunderling, Klaus and Thiele, Christoph and Hasenauer, Jan},
+  journal          = {bioRxiv},
+  title            = {Pseudo-time trajectory of single-cell lipidomics: Suggestion for experimental setup and computational analysis},
+  year             = {2025},
+  abstract         = {Cellular heterogeneity is a fundamental facet of cell biology, influencing cellular signaling, metabolism, and gene regulation. Its accurate quantification requires measurements at the single-cell level. Most high-throughput single-cell technologies provide only a snapshot of cellular heterogeneity at a specific time point because the measurement is destructive. This limits our current ability to understand the dynamics of cellular behavior and quantify cell-specific parameters.We propose an experimental setup combined with a model-based analysis framework, enabling the extraction of longitudinal data from a single destructive measurement. Although broadly applicable, we focus on lipid metabolism, a domain where obtaining longitudinal single-cell data has remained elusive due to technical constraints.Our method leverages multiple labels whose measurements are linked to a shared dynamic. This allows the estimation of cell-specific parameters and the quantification of heterogeneity. This framework establishes a foundation for future investigations, providing a roadmap toward a deeper understanding of dynamic cellular processes.Competing Interest StatementThe authors have declared no competing interest.},
+  creationdate     = {2025-04-23T11:16:11},
+  doi              = {10.1101/2025.04.11.648323},
+  elocation-id     = {2025.04.11.648323},
+  eprint           = {https://www.biorxiv.org/content/early/2025/04/17/2025.04.11.648323.full.pdf},
+  modificationdate = {2025-04-23T11:16:11},
+  publisher        = {Cold Spring Harbor Laboratory},
+  url              = {https://www.biorxiv.org/content/early/2025/04/17/2025.04.11.648323},
+}
+
+@Article{PerssonFro2025,
+  author           = {Persson, Sebastian and Frohlich, Fabian and Grein, Stephan and Lomna, Torkel and Ognissanti, Damiano and Hassselgren, Viktor and Hasenauer, Jan and Cvijovic, Marija},
+  journal          = {bioRxiv},
+  title            = {PEtab.jl: Advancing the Efficiency and Utility of Dynamic Modelling},
+  year             = {2025},
+  abstract         = {Dynamic models are useful to study processes ranging from cell signalling to cell differentiation. Common modelling workflows, such as model exploration and parameter estimation, are computationally demanding. The Julia programming language is a promising tool to address these computational challenges. To evaluate it, we developed SBMLImporter.jl and PEtab.jl, a package for model fitting. SBMLImporter.jl was used to evaluate different stochastic simulators against PySB and RoadRunner, overall Julia simulators proved fastest. For Ordinary Differential Equations (ODE) models solvers, gradient methods, and parameter estimation performance were evaluated using PEtab benchmark problems. For the latter two tasks PEtab.jl was compared against pyPESTO, which employs the high-performance AMICI library. Guidelines for choosing ODE solver were produced by evaluating 31 ODE solvers for 29 models. Further, by leveraging automatic differentiation PEtab.jl proved efficient and, for up to medium-sized models, was often at least twice faster than pyPESTO, showcasing how Julia{\textquoteright}s ecosystem can accelerate modelling workflows.Competing Interest Statement.F consults for DeepOrigin, no impact on study.Swedish Research CouncilSwedish Research Council, , VR2023-04319, VR2017-05117Swedish Foundation for Strategic ResearchSwedish Foundation for Strategic Research, , FFL15-0238},
+  creationdate     = {2025-05-05T09:44:36},
+  doi              = {10.1101/2025.04.30.651378},
+  elocation-id     = {2025.04.30.651378},
+  eprint           = {https://www.biorxiv.org/content/early/2025/05/04/2025.04.30.651378.full.pdf},
+  modificationdate = {2025-05-05T09:44:36},
+  publisher        = {Cold Spring Harbor Laboratory},
+  url              = {https://www.biorxiv.org/content/early/2025/05/04/2025.04.30.651378},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping:

doc/references.md

@@ -1,6 +1,6 @@
 # References
 
-List of publications using AMICI. Total number is 97.
+List of publications using AMICI. Total number is 99.
 
 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).
@@ -14,19 +14,33 @@ If you applied AMICI in your work and your publication is missing, please let us
 
 <h1 class="unnumbered" id="section">2025</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-HuckJak2025" class="csl-entry" role="listitem">
 Huck, Wilhelm, Miglė Jakštaitė, Tao Zhou, Frank Nelissen, and Bob van
 Sluijs. 2025. <span>“Timed Batch Inputs Unlock Significantly Higher
 Yields for Enzymatic Cascades.”</span> 2025. <a
 href="https://doi.org/10.21203/rs.3.rs-5917349/v1">https://doi.org/10.21203/rs.3.rs-5917349/v1</a>.
 </div>
+<div id="ref-JostWei2025" class="csl-entry" role="listitem">
+Jost, Paul Jonas, Daniel Weindl, Klaus Wunderling, Christoph Thiele, and
+Jan Hasenauer. 2025. <span>“Pseudo-Time Trajectory of Single-Cell
+Lipidomics: Suggestion for Experimental Setup and Computational
+Analysis.”</span> <em>bioRxiv</em>. <a
+href="https://doi.org/10.1101/2025.04.11.648323">https://doi.org/10.1101/2025.04.11.648323</a>.
+</div>
 <div id="ref-NoordijkRei2025" class="csl-entry" role="listitem">
 Noordijk, Ben, Marcel Reinders, Aalt D. J. van Dijk, and Dick de Ridder.
 2025. <span>“<span>BADDADAN</span>: Mechanistic Modelling of Time Series
 Gene Module Expression.”</span> <em>bioRxiv</em>. <a
 href="https://doi.org/10.1101/2025.02.18.638670">https://doi.org/10.1101/2025.02.18.638670</a>.
 </div>
+<div id="ref-PerssonFro2025" class="csl-entry" role="listitem">
+Persson, Sebastian, Fabian Frohlich, Stephan Grein, Torkel Lomna,
+Damiano Ognissanti, Viktor Hassselgren, Jan Hasenauer, and Marija
+Cvijovic. 2025. <span>“PEtab.jl: Advancing the Efficiency and Utility of
+Dynamic Modelling.”</span> <em>bioRxiv</em>. <a
+href="https://doi.org/10.1101/2025.04.30.651378">https://doi.org/10.1101/2025.04.30.651378</a>.
+</div>
 <div id="ref-SmithMal2025" class="csl-entry" role="listitem">
 Smith, Lucian, Rahuman S. Malik-Sheriff, Tung V. N. Nguyen, Henning
 Hermjakob, Jonathan Karr, Bilal Shaikh, Logan Drescher, et al. 2025.
@@ -38,7 +52,7 @@ href="https://doi.org/10.1101/2025.01.16.633337">https://doi.org/10.1101/2025.01
 </div>
 <h1 class="unnumbered" id="section">2024</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-ArmisteadHoe2024" class="csl-entry" role="listitem">
 Armistead, Joy, Sebastian Höpfl, Pierre Goldhausen, Andrea
 Müller-Hartmann, Evelin Fahle, Julia Hatzold, Rainer Franzen, Susanne
@@ -146,7 +160,7 @@ href="https://doi.org/10.1038/s41467-024-45886-9">https://doi.org/10.1038/s41467
 </div>
 <h1 class="unnumbered" id="section">2023</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-BuckBas2023" class="csl-entry" role="listitem">
 Buck, Michèle C., Lisa Bast, Judith S. Hecker, Jennifer Rivière, Maja
 Rothenberg-Thurley, Luisa Vogel, Dantong Wang, et al. 2023.
@@ -231,7 +245,7 @@ href="https://doi.org/10.1113/JP284652">https://doi.org/10.1113/JP284652</a>.
 </div>
 <h1 class="unnumbered" id="section">2022</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-AlbadryHoe2022" class="csl-entry" role="listitem">
 Albadry, Mohamed, Sebastian Höpfl, Nadia Ehteshamzad, Matthias König,
 Michael Böttcher, Jasna Neumann, Amelie Lupp, et al. 2022.
@@ -310,7 +324,7 @@ href="https://doi.org/10.1109/TCBB.2022.3213914">https://doi.org/10.1109/TCBB.20
 </div>
 <h1 class="unnumbered" id="section">2021</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-AdlungSta2021" class="csl-entry" role="listitem">
 Adlung, Lorenz, Paul Stapor, Christian Tönsing, Leonard Schmiester,
 Luisa E. Schwarzmüller, Lena Postawa, Dantong Wang, et al. 2021.
@@ -409,7 +423,7 @@ href="https://doi.org/10.1093/bib/bbab387">https://doi.org/10.1093/bib/bbab387</
 </div>
 <h1 class="unnumbered" id="section">2020</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-AlabertLoo2020" class="csl-entry" role="listitem">
 Alabert, Constance, Carolin Loos, Moritz Voelker-Albert, Simona
 Graziano, Ignasi Forné, Nazaret Reveron-Gomez, Lea Schuh, et al. 2020.
@@ -497,7 +511,7 @@ href="https://doi.org/10.1007/s00449-020-02360-2">https://doi.org/10.1007/s00449
 </div>
 <h1 class="unnumbered" id="section">2019</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-DharmarajanKal2019" class="csl-entry" role="listitem">
 Dharmarajan, Lekshmi, Hans-Michael Kaltenbach, Fabian Rudolf, and Joerg
 Stelling. 2019. <span>“A Simple and Flexible Computational Framework for
@@ -584,7 +598,7 @@ href="https://hdl.handle.net/20.500.12380/256855">https://hdl.handle.net/20.500.
 </div>
 <h1 class="unnumbered" id="section">2018</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-BallnusSch2018" class="csl-entry" role="listitem">
 Ballnus, Benjamin, Steffen Schaper, Fabian J Theis, and Jan Hasenauer.
 2018. <span>“Bayesian Parameter Estimation for Biochemical Reaction
@@ -666,7 +680,7 @@ href="https://doi.org/10.1093/bioinformatics/bty736">https://doi.org/10.1093/bio
 </div>
 <h1 class="unnumbered" id="section">2017</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-BallnusHug2017" class="csl-entry" role="listitem">
 Ballnus, B., S. Hug, K. Hatz, L. Görlitz, J. Hasenauer, and F. J. Theis.
 2017. <span>“Comprehensive Benchmarking of <span>Markov</span> Chain
@@ -703,7 +717,7 @@ href="https://doi.org/10.1093/bioinformatics/btw703">https://doi.org/10.1093/bio
 </div>
 <h1 class="unnumbered" id="section">2016</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-BoigerHas2016" class="csl-entry" role="listitem">
 Boiger, R., J. Hasenauer, S. Hross, and B. Kaltenbacher. 2016.
 <span>“Integration Based Profile Likelihood Calculation for
@@ -753,7 +767,7 @@ href="https://doi.org/10.1007/978-3-319-45177-0">https://doi.org/10.1007/978-3-3
 </div>
 <h1 class="unnumbered" id="section">2015</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
-role="list">
+data-entry-spacing="0" role="list">
 <div id="ref-LoosMar2015" class="csl-entry" role="listitem">
 Loos, C., C. Marr, F. J. Theis, and J. Hasenauer. 2015.
 <span>“Computational Methods in Systems Biology.”</span> In, edited by