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--- documentation:publications [12:44 21.05.2016] – [Research papers] Walter
+++ documentation:publications [14:47 17.08.2021] (current) – [Education] moved to GitLab Pages Diego Jahn
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 ~~NOTOC~~
 ===== Publications =====
-=== Software ===
-| J. Starruß, W. de Back, L. Brusch and A. Deutsch. \\  [[http://dx.doi.org/10.1093/bioinformatics/btt772|Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology.]] \\ //Bioinformatics//, 30(9):1331-1332, 2014. \\ <sub>//Please use this reference when citing the software.//</sub> |
 === Research papers ===
-| O. Parvu and D. Gilbert. \\  [[http://dx.doi.org/10.1371/journal.pone.0154847|A Novel Method to Verify Multilevel Computational Models of Biological Systems Using Multiscale Spatio-Temporal Meta Model Checking]]. \\ //PLoS ONE//, 11(5): e0154847, 2016.|
+| Meyer, K., Ostrenko, O., Bourantas, G., Morales-Navarrete, H., Porat-Shliom, N., Segovia-Miranda, F., Nonaka, H., Ghaemi, A., Verbavatz, J.M., Brusch, L. and Sbalzarini, I., Kalaidzidis, Y., Weigert, R., Zerial M. \\ [[http://dx.doi.org/10.1016/j.cels.2017.02.008|A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.]] //Cell Systems// 4 (3), 277–290, 2017.|
+| K.B. Hoffmann, A. Voss-Böhme, J.C. Rink, L. Brusch. \\ [[http://dx.doi.org/10.1098/rsif.2017.0466|A dynamically diluted alignment model reveals the impact of cell turnover on the plasticity of tissue polarity patterns.]] //Journal of the Royal Society Interface// 14 (135), 20170466, 2017. |
+| O. Ostrenko, P. Incardona, R. Ramaswamy, L. Brusch, I.F. Sbalzarini. \\ [[http://dx.doi.org/10.1371/journal.pcbi.1005865|pSSAlib: The partial-propensity stochastic chemical network simulator.]] //PLoS Computational Biology// 13(12), e1005865, 2017. |
+| O. Parvu and D. Gilbert. \\  [[http://dx.doi.org/10.1371/journal.pone.0154847|A novel method to verify multilevel computational models of biological systems using multiscale spatio-temporal meta model checking]]. \\ //PLoS ONE//, 11(5): e0154847, 2016.|
 | M. Herberg, T. Zerjatke, W. de Back, I. Glauche and I. Roeder. \\ [[http://dx.doi.org/10.1002/cyto.a.22598|Image-based quantification and mathematical modeling of spatial heterogeneity in ESC colonies]]. \\ //Cytometry: Part A//, 2015.|
 | O. Parvu and D. Gilbert. \\ [[http://www.biomedcentral.com/1752-0509/8/124/abstract|Automatic validation of computational models using pseudo-3D spatio-temporal model checking.]] \\ //BMC Systems Biology//,  8:124, 2014.|
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 === Also cited in ===
+| Appleton, E., Madsen, C., Roehner, N. and Densmore, D.,\\ [[http://cshperspectives.cshlp.org/content/early/2017/02/27/cshperspect.a023978.abstract|Design Automation in Synthetic Biology.]] // Cold Spring Harbor Perspectives in Biology//, 2017. |
+| Cytowski, M., Szymańska, Z., Umiński, P., Andrejczuk, G. and Raszkowski, K. \\ [[https://www.hindawi.com/journals/sp/2017/8721612/|Implementation of an Agent-Based Parallel Tissue Modelling Framework for the Intel MIC Architecture]]. //Scientific Programming//, 2017. |
+| P. Macklin, H. Frieboes, J. Sparks, A. Ghaffarizadeh, S. Friedman, E. Juarez, E. Jonckheere, S. Mumenthaler \\ [[http://link.springer.com/chapter/10.1007/978-3-319-42023-3_12|Progress Towards Computational 3-D Multicellular Systems Biology]] \\ In: // Systems Biology of Tumor Microenvironment // (edited by: K. Rejniak), 2016. |
 |J. S. Yu, N. Bagheri. \\ [[http://dx.doi.org/10.1016/j.copbio.2016.04.002|Multi-class and multi-scale models of complex biological phenomena]] \\ // Current Opinion in Biotechnology//, 39:167–173, 2016. |
 | O. Chara, E. Tanaka, L. Brusch. \\  [[http://dx.doi.org/10.1016/B978-0-12-391498-9.00011-5|Mathematical Modeling of Regenerative Processes]]. \\ In: // Current Topics in Developmental Biology//: Mechanisms of Regeneration (edited by: B. Galliot) Volume 108, 2014. |
@@ Line 29: / Line 30: @@
 | S. Kang, S. Kahan, J. McDermott, N. Flann and I. Shmulevich. \\ [[http://bioinformatics.oxfordjournals.org/content/30/21/3101.short|Biocellion: accelerating computer simulation of multicellular biological system models]]. \\ // Bioinformatics// 30(2):3101-3108, 2014.|
-=== Education ===
+Beyond this selection, 44 sources have so far cited our paper in total (as of Dec. 2017).
-Morpheus was used in the following courses:
-| [[http://www.gscn.org|GSCN]] workshop on [[http://tu-dresden.de/die_tu_dresden/fakultaeten/medizinische_fakultaet/inst/imb/folder_events/gscn2014|Computational Stem Cell Biology]] \\ 1-2 December 2014. |
-| [[http://www.digs-bb.de/digs-bb|DIGS-BB]] course on Spatio-temporal Pattern Formation in Cells and Tissues \\ Autumn 2012 and 2013. |
-| [[http://www.ecmi-indmath.org/|ECMI]] modeling week [[http://www.math.tu-dresden.de/essim2012|European Summer School in Industrial Mathematics and Modelling Week]] \\ (ESSIM2012) August 12-22, 2012. \\ \\ Described in this paper: \\ F. Rost, A. Quintero, M. Myllykoski, A. Igolkina, A. Rohde O’Sullivan Freltoft, N. Dixit \\ [[http://www.mafy.lut.fi/EcmiNL/issues.php?action=viewart&ID=280|Morphogenesis and Dynamics of Multicellular Systems]] \\ ECMI Newsletter, 52, October 2012. |
 === Conferences ===
 Talks and poster presentations at the following conferences and workshops:
 | W. de Back, Morpheus 2: Modeling and simulation platform for multicellular systems biology. And MorpheusML: declarative markup language for multicellular systems biology, Workshop "Towards a unified framework for benchmarking multi-cellular models and simulation software" (organized D. Drasdo and S. Hoehme et al., Leipzig, March 2016 (invited talks)|
-| W. de Back, J. Starruß, L. Brusch, A. Deutsch, Morpheus: Computational modeling for stem cell biologists, [[http://www.gscn.org/Conferences/2015|3rd International Conference of the German Stem Cell Network]] (**GSCN 2015**), Franktfurt am Main, Germany, September 2015 (talk)|
 | W. de Back, [[http://www.dagstuhl.de/wiki/index.php/14481|Spatial multiscale computational systems biology]], Schloss **Dagstuhl** - Leibniz-Zentrum für Informatik, Germany, November 2014 (talk) |
-| W. de Back, A. Köhn-Luque, A. Deutsch, Morpheus: a user-friendly modeling environment for multicellular systems, Joint Annual Meeting of the Japanese Society for Mathematical Biology and the Society for Mathematical Biology (**JSMB/SMB**), Osaka, Japan, 2014. ({{:documentation:morpheus_smb_sjmb_2014.pdf|abstract}}) (talk)|
-| W. de Back, J. Starruß, L. Brusch, A. Deutsch, Morpheus: a User-friendly Modeling Environment for Multiscale and Multicellular Systems Biology, 5th Conference on Systems Biology of Mammalian Cells (**SBMC**), Berlin, Germany, 2014. ({{:documentation:morpheus_sbmc_2014.pdf|poster}}) |
 | L. Brusch, W. de Back, J. Starruß, A. Deutsch, Morpheus: a User-friendly Modeling Environment for Multiscale and Multicellular Systems Biology,  Symposium on "//Executable cell biology for tissue engineering and regenerative medicine//", **[[http://www.termis.org/eu2014/|TERMIS-EU]]**, Genova, Italy, 2014. ({{:documentation:termiseu2014_morpheus.pdf|abstract}}) (talk)|
 | W. de Back, Integrative modeling in developmental systems biology, Institute for Medical Informatics and Biometry,  Medical Faculty „Carl Gustav Carus“, Technische Universität Dresden, 2013. (talk)|
-| A. Köhn-Luque [[http://www.cs.kyoto-u.ac.jp/wp-content/uploads/2012/11/6th-seminar-poster.pdf|Morpheus: a simulation environment for multicellular and multiscale systems biology]], High Performance Computing Center, Kyoto University, Japan, 2012. (talk)|
-| W. de Back, J. Starruß, A. Deutsch, Morpheus: a novel modeling environment  for multicellular systems biology, **BIOTEC** Forum: Bioinformatics and Computational Biology, Dresden, 2012. (poster)|
-| W. de Back, J. Starruß, A. Deutsch, Morpheus: modeling environment for multicellular systems biology, 4th Conference on Systems Biology of Mammalian Cells (**SBMC**), Leipzig, 2012. (poster)|
-| W. de Back, J. Starruß, A. Deutsch, Morpheus: a Modeling Environment for Multiscale Morphodynamics, 12th International Conference on Systems Biology (**ICSB**), Heidelberg/Mannheim, 2011. (poster)|
 | W. de Back, A. Deutsch, Morpheus: Modeling and Simulation in Multicellular System Biology, 1st Sino-German Workshop on Simulation, Changsha, China, 2011. (talk)|
-| W. de Back, J. Starruß, Multiscale Modeling of Morphodynamic Systems, 3rd Conference on Systems Biology of Mammalian Cells (**SBMC**), Freiburg, 2010. (poster)|
-| W. de Back, J. Starruß, Multiscale Modeling of Morphodynamic Systems, 4th **CRTD** Summer conference on Regenerative Medicine, Dresden, 2010. (poster)|
-| W. de Back, J. Starruß, [[http://mitpress.mit.edu/sites/default/files/titles/alife/0262290758chap72.pdf|Middle-out Modeling of Multiscale Morphodynamics]], 12th International Conference on the Synthesis and Simulation of Living Systems (**ALIFE XII**), Odense, Denmark, 2010. In: H. Fellermann et al. (Eds.) Proceedings of the Twelfth International Conference on Artificial Life (Alife XII), MIT Press, Cambridge, MA., 2010. (talk)|
-| W. de Back, J. Starruß, Multiscale Modeling of Morphodynamic Systems, [[http://cwp.embo.org/w10-25|EMBO Workshop in System Biology of Development]], Ascona, Switzerland, 2010. (**EMBO Poster award**) |