TY - JOUR AU - Li, C. AU - Donizelli, M. AU - Rodriguez, N. AU - Dharuri, H. AU - Endler, L. AU - Chelliah, V. AU - Li, L. AU - He, E. AU - Henry, A. AU - Stefan, M. I. PY - 2010 DA - 2010// TI - Biomodels database: an enhanced, curated and annotated resource for published quantitative kinetic models JO - BMC Syst Biol VL - 4 UR - https://doi.org/10.1186/1752-0509-4-92 DO - 10.1186/1752-0509-4-92 ID - Li2010 ER - TY - JOUR AU - Ashyraliyev, M. AU - Fomekong-Nanfack, Y. AU - Kaandorp, J. A. AU - Blom, J. G. PY - 2009 DA - 2009// TI - Systems biology: parameter estimation for biochemical models JO - The FEBS J VL - 276 UR - https://doi.org/10.1111/j.1742-4658.2008.06844.x DO - 10.1111/j.1742-4658.2008.06844.x ID - Ashyraliyev2009 ER - TY - JOUR AU - Boulesteix, A. -. L. AU - Binder, H. AU - Abrahamowicz, M. AU - Sauerbrei, W. PY - 2018 DA - 2018// TI - On the necessity and design of studies comparing statistical methods JO - Biom J VL - 60 UR - https://doi.org/10.1002/bimj.201700129 DO - 10.1002/bimj.201700129 ID - Boulesteix2018 ER - TY - JOUR AU - Ioannidis, J. P. PY - 2018 DA - 2018// TI - Meta-research: why research on research matters JO - PLoS Biol VL - 16 UR - https://doi.org/10.1371/journal.pbio.2005468 DO - 10.1371/journal.pbio.2005468 ID - Ioannidis2018 ER - TY - JOUR AU - Kreutz, C. PY - 2016 DA - 2016// TI - New concepts for evaluating the performance of computational methods JO - IFAC-PapersOnLine VL - 49 UR - https://doi.org/10.1016/j.ifacol.2016.12.104 DO - 10.1016/j.ifacol.2016.12.104 ID - Kreutz2016 ER - TY - STD TI - Mangul S, Martin LS, Hill BL, Lam A. K. -M., Distler MG, Zelikovsky A, Eskin E, Flint J. Systematic benchmarking of omics computational tools. Nat Commun. 2019; 10. https://doi.org/10.1038/s41467-019-09406-4. ID - ref6 ER - TY - JOUR AU - Aniba, M. R. AU - Poch, O. AU - Thompson, J. D. PY - 2010 DA - 2010// TI - Issues in bioinformatics benchmarking: the case study of multiple sequence alignment JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq625 DO - 10.1093/nar/gkq625 ID - Aniba2010 ER - TY - JOUR AU - Boulesteix, A. -. L. AU - Lauer, S. AU - Eugster, M. J. PY - 2013 DA - 2013// TI - A plea for neutral comparison studies in computational sciences JO - PloS ONE VL - 8 UR - https://doi.org/10.1371/journal.pone.0061562 DO - 10.1371/journal.pone.0061562 ID - Boulesteix2013 ER - TY - STD TI - Capella-Gutierrez S, De La Iglesia D, Haas J, Lourenco A, Gonzalez JMF, Repchevsky D, Dessimoz C, Schwede T, Notredame C, Gelpi JL, et al. Lessons learned: recommendations for establishing critical periodic scientific benchmarking. BioRxiv. 2017;181677. https://doi.org/10.1101/181677. ID - ref9 ER - TY - JOUR AU - Boulesteix, A. -. L. PY - 2015 DA - 2015// TI - Ten simple rules for reducing overoptimistic reporting in methodological computational research JO - PLoS Comput Biol VL - 11 UR - https://doi.org/10.1371/journal.pcbi.1004191 DO - 10.1371/journal.pcbi.1004191 ID - Boulesteix2015 ER - TY - JOUR AU - Peters, B. AU - Brenner, S. E. AU - Wang, E. AU - Slonim, D. AU - Kann, M. G. PY - 2018 DA - 2018// TI - Putting benchmarks in their rightful place: the heart of computational biology JO - PLoS Comput Biol VL - 14 UR - https://doi.org/10.1371/journal.pcbi.1006494 DO - 10.1371/journal.pcbi.1006494 ID - Peters2018 ER - TY - JOUR AU - Weber, L. M. AU - Saelens, W. AU - Cannoodt, R. AU - Soneson, C. AU - Hapfelmeier, A. AU - Gardner, P. P. AU - Boulesteix, A. -. L. AU - Saeys, Y. AU - Robinson, M. D. PY - 2019 DA - 2019// TI - Essential guidelines for computational method benchmarking JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1738-8 DO - 10.1186/s13059-019-1738-8 ID - Weber2019 ER - TY - JOUR AU - Fröhlich, F. AU - Theis, F. J. AU - Rädler, J. O. AU - Hasenauer, J. PY - 2016 DA - 2016// TI - Parameter estimation for dynamical systems with discrete events and logical operations JO - Bioinformatics VL - 33 ID - Fröhlich2016 ER - TY - JOUR AU - Fiedler, A. AU - Raeth, S. AU - Theis, F. J. AU - Hausser, A. AU - Hasenauer, J. PY - 2016 DA - 2016// TI - Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints JO - BMC Syst Biol VL - 10 UR - https://doi.org/10.1186/s12918-016-0319-7 DO - 10.1186/s12918-016-0319-7 ID - Fiedler2016 ER - TY - CHAP AU - Fröhlich, F. AU - Loos, C. AU - Hasenauer, J. PY - 2019 DA - 2019// TI - Scalable inference of ordinary differential equation models of biochemical processes BT - Gene Regulatory Networks PB - Springer CY - New York ID - Fröhlich2019 ER - TY - JOUR AU - Sun, J. AU - Garibaldi, J. M. AU - Hodgman, C. PY - 2012 DA - 2012// TI - Parameter estimation using metaheuristics in systems biology: a comprehensive review JO - IEEE/ACM Trans Comput Biol Bioinforma VL - 9 UR - https://doi.org/10.1109/TCBB.2011.67 DO - 10.1109/TCBB.2011.67 ID - Sun2012 ER - TY - JOUR AU - Peifer, M. AU - Timmer, J. PY - 2007 DA - 2007// TI - Parameter estimation in ordinary differential equations for biochemical processes using the method of multiple shooting JO - IET Syst Biol VL - 1 UR - https://doi.org/10.1049/iet-syb:20060067 DO - 10.1049/iet-syb:20060067 ID - Peifer2007 ER - TY - JOUR AU - Steiert, B. AU - Raue, A. AU - Timmer, J. AU - Kreutz, C. PY - 2012 DA - 2012// TI - Experimental design for parameter estimation of gene regulatory networks JO - PLoS ONE VL - 7 UR - https://doi.org/10.1371/journal.pone.0040052 DO - 10.1371/journal.pone.0040052 ID - Steiert2012 ER - TY - JOUR AU - Meyer, P. AU - Cokelaer, T. AU - Chandran, D. AU - Kim, K. H. AU - Loh, P. -. R. AU - Tucker, G. AU - Lipson, M. AU - Berger, B. AU - Kreutz, C. AU - Raue, A. PY - 2014 DA - 2014// TI - Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach JO - BMC Syst Biol VL - 8 UR - https://doi.org/10.1186/1752-0509-8-13 DO - 10.1186/1752-0509-8-13 ID - Meyer2014 ER - TY - JOUR AU - Coleman, T. F. AU - Li, Y. PY - 1996 DA - 1996// TI - An interior trust-region approach for non-linear minimization subject to bounds JO - SIAM J Optim VL - 6 UR - https://doi.org/10.1137/0806023 DO - 10.1137/0806023 ID - Coleman1996 ER - TY - JOUR AU - Raue, A. AU - Steiert, B. AU - Schelker, M. AU - Kreutz, C. AU - Maiwald, T. AU - Hass, H. AU - Vanlier, J. AU - Toensing, C. AU - Adlung, L. AU - Engesser, R. AU - Mader, W. AU - Heinemann, T. AU - Hasenauer, J. AU - Schilling, M. AU - Hoefer, T. AU - Klipp, E. AU - Theis, F. AU - Klingmueller, U. AU - Schoeberl, B. AU - Timmer, J. PY - 2015 DA - 2015// TI - Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv405 DO - 10.1093/bioinformatics/btv405 ID - Raue2015 ER - TY - JOUR AU - Raue, A. AU - Schilling, M. AU - Bachmann, J. AU - Matteson, A. AU - Schelke, M. AU - Kaschek, D. AU - Hug, S. AU - Kreutz, C. AU - Harms, B. D. AU - Theis, F. J. PY - 2013 DA - 2013// TI - Lessons learned from quantitative dynamical modeling in systems biology JO - PLoS ONE VL - 8 UR - https://doi.org/10.1371/journal.pone.0074335 DO - 10.1371/journal.pone.0074335 ID - Raue2013 ER - TY - STD TI - Wieland FG. Implementation and assessment of optimization approaches for parameter estimation in systems biology. Masters thesis, University of Freiburg. 2016. https://freidok.uni-freiburg.de/data/150319. UR - https://freidok.uni-freiburg.de/data/150319 ID - ref23 ER - TY - STD TI - Schweiger T. The performance of constrained optimization for ordinary differential equation models. Bachelor thesis, University of Freiburg. 2017. https://freidok.uni-freiburg.de/data/150371. UR - https://freidok.uni-freiburg.de/data/150371 ID - ref24 ER - TY - JOUR AU - Egea, J. A. AU - Balsa-Canto, E. AU - Garcia, M. -. S. G. AU - Banga, J. R. PY - 2009 DA - 2009// TI - Dynamic optimization of non-linear processes with an enhanced scatter search method JO - Ind Eng Chem Res VL - 48 UR - https://doi.org/10.1021/ie801717t DO - 10.1021/ie801717t ID - Egea2009 ER - TY - JOUR AU - Egea, J. A. AU - Marti, R. AU - Banga, J. R. PY - 2010 DA - 2010// TI - An evolutionary method for complex-process optimization JO - Comput Oper Res VL - 37 UR - https://doi.org/10.1016/j.cor.2009.05.003 DO - 10.1016/j.cor.2009.05.003 ID - Egea2010 ER - TY - JOUR AU - Gábor, A. AU - Banga, J. R. PY - 2015 DA - 2015// TI - Robust and efficient parameter estimation in dynamic models of biological systems JO - BMC Syst Biol VL - 9 UR - https://doi.org/10.1186/s12918-015-0219-2 DO - 10.1186/s12918-015-0219-2 ID - Gábor2015 ER - TY - JOUR AU - Moles, C. G. AU - Mendes, P. AU - Banga, J. R. PY - 2003 DA - 2003// TI - Parameter estimation in biochemical pathways: a comparison of global optimization methods JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1262503 DO - 10.1101/gr.1262503 ID - Moles2003 ER - TY - JOUR AU - Villaverde, A. F. AU - Fröhlich, F. AU - Weindl, D. AU - Hasenauer, J. AU - Banga, J. R. PY - 2018 DA - 2018// TI - Benchmarking optimization methods for parameter estimation in large kinetic models JO - Bioinformatics VL - 35 UR - https://doi.org/10.1093/bioinformatics/bty736 DO - 10.1093/bioinformatics/bty736 ID - Villaverde2018 ER - TY - JOUR AU - Fröhlich, F. AU - Kaltenbacher, B. AU - Theis, F. J. AU - Hasenauer, J. PY - 2017 DA - 2017// TI - Scalable parameter estimation for genome-scale biochemical reaction networks JO - PLoS Comput Biol VL - 13 UR - https://doi.org/10.1371/journal.pcbi.1005331 DO - 10.1371/journal.pcbi.1005331 ID - Fröhlich2017 ER - TY - JOUR AU - Degasperi, A. AU - Fey, D. AU - Kholodenko, B. N. PY - 2017 DA - 2017// TI - Performance of objective functions and optimisation procedures for parameter estimation in system biology models JO - NPJ Syst Biol Appl VL - 3 UR - https://doi.org/10.1038/s41540-017-0023-2 DO - 10.1038/s41540-017-0023-2 ID - Degasperi2017 ER - TY - JOUR AU - Hass, H. AU - Loos, C. AU - Raimúndez-Álvarez, E. AU - Timmer, J. AU - Hasenauer, J. AU - Kreutz, C. PY - 2019 DA - 2019// TI - Benchmark problems for dynamic modeling of intracellular processes JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/btz020 DO - 10.1093/bioinformatics/btz020 ID - Hass2019 ER - TY - JOUR AU - Raue, A. AU - Kreutz, C. AU - Maiwald, T. AU - Bachmann, J. AU - Schilling, M. AU - Klingmüller, U. AU - Timmer, J. PY - 2009 DA - 2009// TI - Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp358 DO - 10.1093/bioinformatics/btp358 ID - Raue2009 ER - TY - JOUR AU - Hengl, S. AU - Kreutz, C. AU - Timmer, J. AU - Maiwald, T. PY - 2007 DA - 2007// TI - Data-based identifiability analysis of non-linear dynamical models JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm382 DO - 10.1093/bioinformatics/btm382 ID - Hengl2007 ER - TY - JOUR AU - Kreutz, C. PY - 2018 DA - 2018// TI - An easy and efficient approach for testing identifiability JO - Bioinformatics VL - 34 UR - https://doi.org/10.1093/bioinformatics/bty035 DO - 10.1093/bioinformatics/bty035 ID - Kreutz2018 ER - TY - STD TI - Winkelmann B. Implementation and evaluation of optimization algorithms for parameter estimation in systems biology. Bachelor thesis, University of Freiburg. 2016. https://doi.org/10.6094/UNIFR/150371. ID - ref36 ER - TY - JOUR AU - Bergmann, F. T. AU - Adams, R. AU - Moodie, S. AU - Cooper, J. AU - Glont, M. AU - Golebiewski, M. AU - Hucka, M. AU - Laibe, C. AU - Miller, A. K. AU - Nickerson, D. P. PY - 2014 DA - 2014// TI - COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project JO - BMC Bioinformatics VL - 15 UR - https://doi.org/10.1186/s12859-014-0369-z DO - 10.1186/s12859-014-0369-z ID - Bergmann2014 ER - TY - JOUR AU - Villaverde, A. F. AU - Henriques, D. AU - Smallbone, K. AU - Bongard, S. AU - Schmid, J. AU - Cicin-Sain, D. AU - Crombach, A. AU - Saez-Rodriguez, J. AU - Mauch, K. AU - Balsa-Canto, E. AU - Mendes, P. AU - Jaeger, J. AU - Banga, J. R. PY - 2015 DA - 2015// TI - BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology JO - BMC Syst Biol VL - 9 UR - https://doi.org/10.1186/s12918-015-0144-4 DO - 10.1186/s12918-015-0144-4 ID - Villaverde2015 ER -