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Add list of references using AMICI #659

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Add list of references using AMICI
dweindl Mar 19, 2019
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Add references.md
dweindl Mar 19, 2019
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Merge branch 'develop' into references
FFroehlich Mar 20, 2019
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Update references
dweindl Mar 20, 2019
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Merge branch 'references' of github.com:ICB-DCM/AMICI into references
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List AMICI publications by year
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2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -15,6 +15,8 @@ Online documentation is available as [github-pages](http://icb-dcm.github.io/AMI

[Fröhlich, F., Theis, F. J., Rädler, J. O., & Hasenauer, J. (2017). Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics, 33(7), 1049-1056. doi: 10.1093/bioinformatics/btw764](https://doi.org/10.1093/bioinformatics/btw764)

[Full list](documentation/references.md)

## Current build status

[![PyPI version](https://badge.fury.io/py/amici.svg)](https://badge.fury.io/py/amici)
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---
bibliography: amici_refs.bib
nocite: '@*'
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# Bibliography
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#!/bin/sh
pandoc --filter=pandoc-citeproc bib.md > references.md
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<h1 id="bibliography" class="unnumbered">Bibliography</h1>
<div id="refs" class="references">
<div id="ref-BallnusSch2018">
<p>Ballnus, Benjamin, Steffen Schaper, Fabian J Theis, and Jan Hasenauer. 2018. “Bayesian Parameter Estimation for Biochemical Reaction Networks Using Region-Based Adaptive Parallel Tempering.” <em>Bioinformatics</em> 34 (13): i494–i501. <a href="https://doi.org/10.1093/bioinformatics/bty229" class="uri">https://doi.org/10.1093/bioinformatics/bty229</a>.</p>
</div>
<div id="ref-BallnusHug2017">
<p>Ballnus, B., S. Hug, K. Hatz, L. Görlitz, J. Hasenauer, and F. J. Theis. 2017. “Comprehensive Benchmarking of Markov Chain Monte Carlo Methods for Dynamical Systems.” <em>BMC Syst. Biol.</em> 11 (63). <a href="https://doi.org/10.1186/s12918-017-0433-1" class="uri">https://doi.org/10.1186/s12918-017-0433-1</a>.</p>
</div>
<div id="ref-BastCal2018">
<p>Bast, Lisa, Filippo Calzolari, Michael Strasser, Jan Hasenauer, Fabian J. Theis, Jovica Ninkovic, and Carsten Marr. 2018. “Subtle Changes in Clonal Dynamics Underlie the Age-Related Decline in Neurogenesis.” <em>Cell Reports</em>.</p>
</div>
<div id="ref-BoigerHas2016">
<p>Boiger, R., J. Hasenauer, S. Hross, and B. Kaltenbacher. 2016. “Integration Based Profile Likelihood Calculation for PDE Constrained Parameter Estimation Problems.” <em>Inverse Prob.</em> 32 (12): 125009. <a href="https://doi.org/10.1088/0266-5611/32/12/125009" class="uri">https://doi.org/10.1088/0266-5611/32/12/125009</a>.</p>
</div>
<div id="ref-DharmarajanKal2019">
<p>Dharmarajan, Lekshmi, Hans-Michael Kaltenbach, Fabian Rudolf, and Joerg Stelling. 2019. “A Simple and Flexible Computational Framework for Inferring Sources of Heterogeneity from Single-Cell Dynamics.” <em>Cell Systems</em> 8 (1). Elsevier: 15–26.e11. <a href="https://doi.org/10.1016/j.cels.2018.12.007" class="uri">https://doi.org/10.1016/j.cels.2018.12.007</a>.</p>
</div>
<div id="ref-FiedlerRae2016">
<p>Fiedler, A., S. Raeth, F. J. Theis, A. Hausser, and J. Hasenauer. 2016. “Tailored Parameter Optimization Methods for Ordinary Differential Equation Models with Steady-State Constraints.” <em>BMC Syst. Biol.</em> 10 (80). <a href="https://doi.org/10.1186/s12918-016-0319-7" class="uri">https://doi.org/10.1186/s12918-016-0319-7</a>.</p>
</div>
<div id="ref-FischerFie2017">
<p>Fischer, David S., Anna K. Fiedler, Eric Kernfeld, Ryan M. J. Genga, Jan Hasenauer, Rene Maehr, and Fabian J. Theis. 2017. “Beyond Pseudotime: Following T-Cell Maturation in Single-Cell RNAseq Time Series.” <em>bioRxiv</em>. Cold Spring Harbor Laboratory. <a href="https://doi.org/10.1101/219188" class="uri">https://doi.org/10.1101/219188</a>.</p>
</div>
<div id="ref-FroehlichKes2017">
<p>Fröhlich, Fabian, Thomas Kessler, Daniel Weindl, Alexey Shadrin, Leonard Schmiester, Hendrik Hache, Artur Muradyan, et al. 2017. “Efficient Parameterization of Large-Scale Mechanistic Models Enables Drug Response Prediction for Cancer Cell Lines.” <em>bioRxiv</em>. Cold Spring Harbor Labs Journals. <a href="https://doi.org/10.1101/174094" class="uri">https://doi.org/10.1101/174094</a>.</p>
</div>
<div id="ref-FroehlichRei2018">
<p>Fröhlich, Fabian, Anita Reiser, Laura Fink, Daniel Woschée, Thomas Ligon, Fabian Joachim Theis, Joachim Oskar Rädler, and Jan Hasenauer. 2018. “Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics After Transfection.” <em>Npj Systems Biology and Applications</em> 5 (1): 1. <a href="https://doi.org/10.1038/s41540-018-0079-7" class="uri">https://doi.org/10.1038/s41540-018-0079-7</a>.</p>
</div>
<div id="ref-FroehlichKal2017">
<p>Fröhlich, F., B. Kaltenbacher, F. J. Theis, and J. Hasenauer. 2017. “Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.” <em>PLoS Comput. Biol.</em> 13 (1): e1005331. <a href="https://doi.org/10.1371/journal.pcbi.1005331" class="uri">https://doi.org/10.1371/journal.pcbi.1005331</a>.</p>
</div>
<div id="ref-FroehlichThe2016">
<p>Fröhlich, F., F. J. Theis, J. O. Rädler, and J. Hasenauer. 2017. “Parameter Estimation for Dynamical Systems with Discrete Events and Logical Operations.” <em>Bioinformatics</em> 33 (7): 1049–56. <a href="https://doi.org/10.1093/bioinformatics/btw764" class="uri">https://doi.org/10.1093/bioinformatics/btw764</a>.</p>
</div>
<div id="ref-FroehlichTho2016">
<p>Fröhlich, F., P. Thomas, A. Kazeroonian, F. J. Theis, R. Grima, and J. Hasenauer. 2016. “Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion.” <em>PLoS Comput. Biol.</em> 12 (7): e1005030. <a href="https://doi.org/10.1371/journal.pcbi.1005030" class="uri">https://doi.org/10.1371/journal.pcbi.1005030</a>.</p>
</div>
<div id="ref-GreggSar2019">
<p>Gregg, Robert W, Saumendra N Sarkar, and Jason E Shoemaker. 2019. “Mathematical Modeling of the cGAS Pathway Reveals Robustness of Dna Sensing to Trex1 Feedback.” <em>Journal of Theoretical Biology</em> 462 (February): 148–57. <a href="https://doi.org/10.1016/j.jtbi.2018.11.001" class="uri">https://doi.org/10.1016/j.jtbi.2018.11.001</a>.</p>
</div>
<div id="ref-HrossFie2016">
<p>Hross, S., A. Fiedler, F. J. Theis, and J. Hasenauer. 2016. “Quantitative Comparison of Competing PDE Models for Pom1p Dynamics in Fission Yeast.” In <em>Proc. 6th IFAC Conf. Found. Syst. Biol. Eng.</em>, edited by R. Findeisen, E. Bullinger, E. Balsa-Canto, and K. Bernaerts, 49:264–69. 26. IFAC-PapersOnLine. <a href="https://doi.org/10.1016/j.ifacol.2016.12.136" class="uri">https://doi.org/10.1016/j.ifacol.2016.12.136</a>.</p>
</div>
<div id="ref-KazeroonianFro2016">
<p>Kazeroonian, A., F. Fröhlich, A. Raue, F. J. Theis, and J. Hasenauer. 2016. “CERENA: Chemical REaction Network Analyzer – A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.” <em>PLoS ONE</em> 11 (1): e0146732. <a href="https://doi.org/10.1371/journal.pone.0146732" class="uri">https://doi.org/10.1371/journal.pone.0146732</a>.</p>
</div>
<div id="ref-KazeroonianThe2017">
<p>Kazeroonian, A., F. J. Theis, and J. Hasenauer. 2017. “A Scalable Moment-Closure Approximation for Large-Scale Biochemical Reaction Networks.” <em>Bioinformatics</em> 33 (14): i293–i300. <a href="https://doi.org/10.1093/bioinformatics/btx249" class="uri">https://doi.org/10.1093/bioinformatics/btx249</a>.</p>
</div>
<div id="ref-LoosKra2018">
<p>Loos, Carolin, Sabrina Krause, and Jan Hasenauer. 2018. “Hierarchical Optimization for the Efficient Parametrization of ODE Models.” <em>Bioinformatics</em> 34 (24): 4266–73. <a href="https://doi.org/10.1093/bioinformatics/bty514" class="uri">https://doi.org/10.1093/bioinformatics/bty514</a>.</p>
</div>
<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). Elsevier: 593–603. <a href="https://doi.org/10.1016/j.cels.2018.04.008" class="uri">https://doi.org/10.1016/j.cels.2018.04.008</a>.</p>
</div>
<div id="ref-LoosFie2016">
<p>Loos, C., A. Fiedler, and J. Hasenauer. 2016. “Parameter Estimation for Reaction Rate Equation Constrained Mixture Models.” In <em>Proc. 13th Int. Conf. Comp. Meth. Syst. Biol.</em>, edited by E. Bartocci, P. Lio, and N. Paoletti, 186–200. Lecture Notes in Bioinformatics. Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-45177-0" class="uri">https://doi.org/10.1007/978-3-319-45177-0</a>.</p>
</div>
<div id="ref-LoosMar2015">
<p>Loos, C., C. Marr, F. J. Theis, and J. Hasenauer. 2015. “Computational Methods in Systems Biology.” In, edited by O. Roux and J. Bourdon, 9308:52–63. Lecture Notes in Computer Science. Springer International Publishing.</p>
</div>
<div id="ref-MaierLoo2017">
<p>Maier, C., C. Loos, and J. Hasenauer. 2017. “Robust Parameter Estimation for Dynamical Systems from Outlier-Corrupted Data.” <em>Bioinformatics</em> 33 (5): 718–25. <a href="https://doi.org/10.1093/bioinformatics/btw703" class="uri">https://doi.org/10.1093/bioinformatics/btw703</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>To Appear in Proc. Of the Foundations of Syst. Biol. In Engin. (FOSBE)</em>.</p>
</div>
<div id="ref-Schmiester579045">
<p>Schmiester, Leonard, Yannik Schaelte, Fabian Froehlich, Jan Hasenauer, and Daniel Weindl. 2019. “Efficient Parameterization of Large-Scale Dynamic Models Based on Relative Measurements.” <em>bioRxiv</em>. Cold Spring Harbor Laboratory. <a href="https://doi.org/10.1101/579045" class="uri">https://doi.org/10.1101/579045</a>.</p>
</div>
<div id="ref-StaporFro2018">
<p>Stapor, Paul, Fabian Fröhlich, and Jan Hasenauer. 2018. “Optimization and Profile Calculation of ODE Models Using Second Order Adjoint Sensitivity Analysis.” <em>Bioinformatics</em> 34 (13). Oxford University Press: i151–i159.</p>
</div>
<div id="ref-VillaverdeFro2018">
<p>Villaverde, Alejandro F., Fabian Froehlich, Daniel Weindl, Jan Hasenauer, and Julio R Banga. 2018. “Benchmarking Optimization Methods for Parameter Estimation in Large Kinetic Models.” <em>Bioinformatics</em>, bty736.</p>
</div>
</div>